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Kang DY, Kim HC. Functional relation of agouti signaling proteins (ASIPs) to pigmentation and color change in the starry flounder, Platichthys stellatus. Comp Biochem Physiol A Mol Integr Physiol 2024; 291:111524. [PMID: 37981006 DOI: 10.1016/j.cbpa.2023.111524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/30/2023] [Accepted: 10/01/2023] [Indexed: 11/21/2023]
Abstract
We investigated the involvement of agouti-signaling proteins (ASIPs) in morphological pigmentation and physiological color change in flatfishes. We isolated ASIP1 and 2 mRNAs from the skin of starry flounder (Platichthys stellatus), and compared their amino acid (aa) structures to those of other animals. Then, we examined the mRNA expression levels of two ASIPs (Sf-ASIPs) in the pigmented ocular body and in the unpigmented blind body, as well as in the ordinary skin and in albino skin, in flatfishes. To investigate the role of Sf-ASIPs in physiological color change (color camouflage), we compared the expression of the two genes in two background colors (dark-green and white). Sf-ASIP1 cDNA had a 375-bp open reading frame (ORF) that encoded a protein consisting of 125 aa residues, and Sf-ASIP2 cDNA had a 402-bp ORF that encoded a protein consisting of 132 aa residues. RT-PCR revealed that the strongest Sf-ASIP1 and Sf-ASIP2 expression levels were observed in the eye and blind-skin, respectively. In Sf-ASIP1, the gene expression did not differ between the ocular-side skin and blind-side skin, nor between ordinary skin and abnormal skin of the fish. However, in Sf-ASIP2, the expression level was significantly higher in blind-side skin, compared to ocular-side skin, suggesting that the ASIP2 gene is related to the countershading body pigment pattern of the fish. In addition, the Sf-ASIP2 gene expression level was lower in the pigmented spot regions than in the unpigmented spot regions of the malpigmented pseudo-albino skins on the ocular side, implying that ASIP2 is responsible for the ocular-side pseudo-albino. Additionally, ASIP2 gene expression in the blind-side skin of ordinary fish was enhanced by a white tank, implying that a bright background color could inhibit hypermelanosis in the blind-side skin of cultured flounder by increasing the activity of the Sf-ASIP2 gene. However, we did not find any relationship of ASIPs with camouflage color changes. In conclusion, the ASIP2 gene is related to the morphological pigmentation (countershading and malpigmentation) of the skin in starry flounder, but not with physiological color changes (color camouflage) in the ocular-side skin.
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Affiliation(s)
- Duk-Young Kang
- National Institute of Fisheries Science, West Sea Fisheries Research Institute, 707 Eulwang-dong, Jung-gu, Incheon, Republic of Korea.
| | - Hyo-Chan Kim
- KMS & MC, Molecular research, Haneulbyeolbit-ro, YoungJong-1 dong, Joong-gu, Incheon, Republic of Korea
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Muyanlı EB, Yılmaz R. RT-qPCR based quantitative analysis of ARO and ADH genes in Saccharomyces cerevisiae and Metschnikowia pulcherrima strains growth white grape juice. Mol Biol Rep 2024; 51:547. [PMID: 38642187 DOI: 10.1007/s11033-024-09444-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/13/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Yeast biosynthesizes fusel alcohols in fermentation through amino acid catabolism via the Ehrlich pathway. ARO8 and ARO9 genes are involved in the first step of the Ehrlich pathway, while ADH2 and ADH5 genes are involved in the last step. In this study, we describe RT-qPCR methods to determine the gene expression level of genes (ARO8, ARO9, ADH2, ADH5) found in Saccharomyces cerevisiae (Sc) and Metschnikowia pulcherrima (Mp) strains growth pasteurized white grape juice. METHODS AND RESULTS We used RNA extraction and cDNA synthesis protocols. The RT-qPCR efficiency of primer pairs was evaluated by generating a standard curve through serial dilution of yeast-derived cDNA. Method performance criteria were determined for each RT-qPCR assay. Then, we evaluated the gene expression levels of the four genes in all samples. RNA extraction and cDNA synthesis from yeast samples demonstrated the method's capability to generate high-yield, high-purity nucleic acids, supporting further RT-qPCR analysis. The highest normalized gene expression levels of ARO8 and ARO9 were observed in SC1, SC4, and SC5 samples. No significant difference in ADH2 gene expression among Mp strains was observed during the examination of ADH2 and ADH5 genes (p < 0.05). We observed no expression of the ADH5 gene in Mp strains except MP6 strain. The expression of ADH2 and ADH5 genes was higher in Sc strains compared to Mp strains. CONCLUSIONS The results suggest that the proposed RT-qPCR methods can measure gene expression of ARO8, ARO9, ADH2, and ADH5 in Sc and Mp strains growing in pasteurized white grape juice.
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Affiliation(s)
- Elif Bircan Muyanlı
- FoodOmics Laboratory, Department of Food Engineering, Hacettepe University, Beytepe Campus, 06800, Ankara, Turkey
| | - Remziye Yılmaz
- FoodOmics Laboratory, Department of Food Engineering, Hacettepe University, Beytepe Campus, 06800, Ankara, Turkey.
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Zhang D, Tian T, Han L, Du J, Zhu T, Lei C, Song H, Li S. Expression characteristics of the cyp19a1b aromatase gene and its response to 17β-estradiol treatment in largemouth bass (Micropterus salmoides). Fish Physiol Biochem 2024; 50:575-588. [PMID: 38216846 DOI: 10.1007/s10695-023-01291-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/22/2023] [Indexed: 01/14/2024]
Abstract
To investigate the regulatory role of the cyp19a1b aromatase gene in the sexual differentiation of largemouth bass (Micropterus salmoides, LMB), we obtained the full-length cDNA sequence of cyp19a1b using rapid amplification of cDNA ends technique. Tissue expression characteristics and feedback with 17-β-estradiol (E2) were determined using quantitative real-time PCR (qRT-PCR), while gonad development was assessed through histological section observations. The cDNA sequence of LMB cyp19a1b was found to be1950 base pairs (bp) in length, including a 5' untranslated region of 145 bp, a 3' untranslated region of 278 bp, and an open reading frame encoding a protein consisting of 1527 bp that encoded 508 amino acids. The qRT-PCR results indicated that cyp19a1b abundantly expressed in the brain, followed by the gonads, and its expression in the ovaries was significantly higher than that observed in the testes (P < 0.05). After feeding fish with E2 for 30 days, the expression of cyp19a1b in the pseudo-female gonads (XY-F) was significantly higher than that in males (XY-M) (P < 0.05), whereas expression did not differ significantly between XX-F and XY-F fish (P > 0.05). Although the expression of cyp19a1b in XY-F and XX-F fish was not significantly different after 60 days (P>0.05), both exhibited significantly higher levels than that of XY-M fish (P<0.05). Histological sections analysis showed the presence of oogonia in both XY-F and XX-F fish at 30 days, while spermatogonia were observed in XY-M fish. At 60 days, primary oocytes were abundantly observed in both XY-F and XX-F fish, while a few spermatogonia were visible in XY-M fish. At 90 days, the histological sections' results showed that a large number of oocytes were visible in XY-F and XX-F fish. Additionally, the gonads of XY-M fish contained numerous spermatocytes. These results suggest that cyp19a1b plays a pivotal role in the development of ovaries and nervous system development in LMB.
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Affiliation(s)
- Dongyun Zhang
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, China Ministry of Agriculture, Guangzhou, 510380, China
- College of Life Science, Huzhou University, Huzhou, 313000, Zhejiang, China
| | - Taihang Tian
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, China Ministry of Agriculture, Guangzhou, 510380, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Linqiang Han
- Guangdong province Liangshi Aquaculture Seed Industry, Foshan, 528100, Guangdong, China
| | - Jinxing Du
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, China Ministry of Agriculture, Guangzhou, 510380, China
| | - Tao Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, China Ministry of Agriculture, Guangzhou, 510380, China
| | - Caixia Lei
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, China Ministry of Agriculture, Guangzhou, 510380, China
| | - Hongmei Song
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, China Ministry of Agriculture, Guangzhou, 510380, China.
| | - Shengjie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, China Ministry of Agriculture, Guangzhou, 510380, China.
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Jiang M, Zhou C, Wang S, Liu L, Zhang S, Wang L, Pan X. Identification of a Tetrahymena species infecting guppies, pathology, and expression of beta-tubulin during infection. Parasitol Res 2024; 123:104. [PMID: 38240890 DOI: 10.1007/s00436-024-08117-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024]
Abstract
Tetrahymenosis is caused by the ciliated protozoan Tetrahymena and is responsible for serious economic losses to the aquaculture industry worldwide. However, information regarding the molecular mechanism leading to tetrahymenosis is limited. In previous transcriptome sequencing work, it was found that one of the two β-tubulin genes in T. pyriformis was significantly expressed in infected fish, we speculated that β-tubulin is involved in T. pyriformis infecting fish. Herein, the potential biological function of the β-tubulin gene in Tetrahymena species when establishing infection in guppies was investigated by cloning the full-length cDNA of this T. pyriformis β-tubulin (BTU1) gene. The full-length cDNA of T. pyriformis BTU1 gene was 1873 bp, and the ORF occupied 1134 bp, whereas 5' UTR 434 bp, and 3' UTR 305 bp whose poly (A) tail contained 12 bases. The predicted protein encoded by T. pyriformis BTU1 gene had a calculated molecular weight of 42.26 kDa and pI of 4.48. Moreover, secondary structure analysis and tertiary structure prediction of BTU1 protein were also conducted. In addition, morphology, infraciliature, phylogeny, and histopathology of T. pyriformis isolated from guppies from a fish market in Harbin were also investigated. Furthermore, qRT-PCR analysis and experimental infection assays indicated that the expression of BTU1 gene resulted in efficient cell proliferation during infection. Collectively, our data revealed that BTU1 is a key gene involved in T. pyriformis infection in guppies, and the findings discussed herein provide valuable insights for future studies on tetrahymenosis.
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Affiliation(s)
- Mingyue Jiang
- Laboratory of Protozoology, Harbin Normal University, Harbin, 150025, China
| | - Chunyu Zhou
- Laboratory of Protozoology, Harbin Normal University, Harbin, 150025, China
| | - Sihan Wang
- Laboratory of Protozoology, Harbin Normal University, Harbin, 150025, China
| | - Lihui Liu
- Laboratory of Protozoology, Harbin Normal University, Harbin, 150025, China
| | - Shuixian Zhang
- Panzhou No.4 Primary School, Panzhou, 553599, Guizhou Province, China
| | - Li Wang
- Laboratory of Protozoology, Harbin Normal University, Harbin, 150025, China
| | - Xuming Pan
- Laboratory of Protozoology, Harbin Normal University, Harbin, 150025, China.
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Hamada S, Tsukahara T, Watanabe Y, Murata K, Mizue Y, Kubo T, Kanaseki T, Hirohashi Y, Emori M, Nakatsugawa M, Teramoto A, Yamashita T, Torigoe T. Development of T cell receptor-engineered T cells targeting the sarcoma-associated antigen papillomavirus binding factor. Cancer Sci 2024; 115:24-35. [PMID: 37879364 PMCID: PMC10823292 DOI: 10.1111/cas.15967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/17/2023] [Accepted: 08/31/2023] [Indexed: 10/27/2023] Open
Abstract
We previously identified papillomavirus binding factor (PBF) as an osteosarcoma antigen recognized by an autologous cytotoxic T lymphocyte clone. Vaccination with PBF-derived peptide presented by HLA-A24 (PBF peptide) elicited strong immune responses. In the present study, we generated T cell receptor-engineered T cells (TCR-T cells) directed against the PBF peptide (PBF TCR-T cells). PBF TCR was successfully transduced into T cells and detected using HLA-A*24:02/PBF peptide tetramer. PBF TCR-T cells generated from a healthy donor were highly expanded and recognized T2-A24 cells pulsed with PBF peptide, HLA-A24+ 293T cells transfected with PBF cDNA, and sarcoma cell lines. To establish an adoptive cell therapy model, we modified the PBF TCR by replacing both α and β constant regions with those of mice (hybrid PBF TCR). Hybrid PBF TCR-T cells also showed reactivity against T2-A24 cells pulsed with PBF peptide and to HLA-A24+ 293T cells transfected with various lengths of PBF cDNA including the PBF peptide sequence. Subsequently, we generated target cell lines highly expressing PBF (MFH03-PBF [short] epitope [+]) containing PBF peptide with in vivo tumorigenicity. Hybrid PBF TCR-T cells exhibited antitumor effects compared with mock T cells in NSG mice xenografted with MFH03-PBF (short) epitope (+) cells. CD45+ T cells significantly infiltrated xenografted tumors only in the hybrid PBF TCR T cell group and most of these cells were CD8-positive. CD8+ T cells also showed Ki-67 expression and surrounded the CD8-negative tumor cells expressing Ki-67. These findings suggest that PBF TCR-T cell therapy might be a candidate immunotherapy for sarcoma highly expressing PBF.
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Affiliation(s)
- Shuto Hamada
- Department of PathologySapporo Medical University School of MedicineSapporoJapan
- Department of Orthopaedic SurgerySapporo Medical University School of MedicineSapporoJapan
| | - Tomohide Tsukahara
- Department of PathologySapporo Medical University School of MedicineSapporoJapan
| | - Yuto Watanabe
- Department of PathologySapporo Medical University School of MedicineSapporoJapan
- Department of Orthopaedic SurgerySapporo Medical University School of MedicineSapporoJapan
| | - Kenji Murata
- Department of PathologySapporo Medical University School of MedicineSapporoJapan
- Department of Biomedical Engineering, Research Institute for Frontier MedicineSapporo Medical University School of MedicineSapporoJapan
| | - Yuka Mizue
- Department of PathologySapporo Medical University School of MedicineSapporoJapan
| | - Terufumi Kubo
- Department of PathologySapporo Medical University School of MedicineSapporoJapan
| | - Takayuki Kanaseki
- Department of PathologySapporo Medical University School of MedicineSapporoJapan
| | - Yoshihiko Hirohashi
- Department of PathologySapporo Medical University School of MedicineSapporoJapan
| | - Makoto Emori
- Department of Orthopaedic SurgerySapporo Medical University School of MedicineSapporoJapan
| | - Munehide Nakatsugawa
- Department of Diagnostic PathologyTokyo Medical University Hachioji Medical CenterHachioji, TokyoJapan
| | - Atsushi Teramoto
- Department of Orthopaedic SurgerySapporo Medical University School of MedicineSapporoJapan
| | - Toshihiko Yamashita
- Department of Orthopaedic SurgerySapporo Medical University School of MedicineSapporoJapan
| | - Toshihiko Torigoe
- Department of PathologySapporo Medical University School of MedicineSapporoJapan
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Xia R, Liu HK, Liu XF, Deng X, Qin CJ, He YF, Lin SM, Chen YJ. Molecular cloning and tissue distribution of glucokinase and glucose-6-phosphatase catalytic subunit paralogs in largemouth bass Micropterus salmoides: Regulation by dietary starch levels and a glucose load. Comp Biochem Physiol A Mol Integr Physiol 2024; 287:111523. [PMID: 37802420 DOI: 10.1016/j.cbpa.2023.111523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/25/2023] [Accepted: 10/01/2023] [Indexed: 10/10/2023]
Abstract
The dysregulation of glucose-G6P (glucose-6-phosphate) interconversion is thought to be one of the main reasons for the low glucose disposal of carnivorous fish, but is not yet well understood in largemouth bass Micropterus salmoides (LMB). In this study, the full length cDNA sequences of genes encoding glucokinase (Gck, catalyzing glucose phosphorylation) and glucose-6-phosphatase catalytic subunit (G6pc, catalyzing glucose dephosphorylation) were cloned by the RACE method from the liver of LMB. Subsequently, the distribution of g6pc and gck as well as their transcriptional regulation by dietary starch levels and a glucose load were investigated. Only one gck gene was identified, while the tandem duplication of g6pca.1 gene was named as g6pca.2 in LMB. The full cDNA sequences of g6pca.1, g6pca.2 and gck in LMB were 1585, 1813 and 2115 bp in length, encoding 478, 352 and 359 amino acids, respectively. Gck was predicted to contain two hexokinase domains, an ATP-binding domain and multiple functional sites, while G6pca.1 and G6pca.2 contained nine transmembrane helices, a PAP2 (type-2 phosphatidic acid phosphatase) domain and multiple functional amino acid sites. Both g6pca.1 and g6pca.2 were predominantly distributed in the liver and to some extent in the intraperitoneal fat, intestine and pyloric caeca, while gck was mainly transcribed in the liver and to some extent in the heart, intestine and brain. Both feeding a high starch diet and a glucose load stimulated the mRNA expression of gck in the liver of LMB. An increase of dietary starch from 9% to 14% down-regulated the transcription of g6pca.1 in the liver of LMB. However, both the mRNA levels of hepatic g6pca.1 and g6pca.2 were sharply up-regulated in LMB during 1-3 h after a glucose load. Overall, the results of this study suggested that the functions of G6pc (G6pca.1 and G6pca.2) and Gck in LMB were highly conserved in evolution. Though hepatic glucose-G6P interconversion was well regulated at the transcript level in LMB fed high starch diets, a futile cycle between glucose and G6P was induced in the liver after a glucose load.
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Affiliation(s)
- Ru Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing, China
| | - Hong-Kang Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing, China
| | - Xi-Feng Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing, China
| | - Xin Deng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing, China
| | - Chuan-Jie Qin
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang, China
| | - Yuan-Fa He
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing, China; Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, China
| | - Shi-Mei Lin
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing, China; Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, China
| | - Yong-Jun Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing, China; Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, China.
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Iben JR, Li T, Mattijssen S, Maraia RJ. Single-Molecule Poly(A) Tail Sequencing (SM-PATseq) Using the PacBio Platform. Methods Mol Biol 2024; 2723:285-301. [PMID: 37824077 DOI: 10.1007/978-1-0716-3481-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The polyadenylation of the 3' ends of messenger RNAs is an important regulator of stability and translation. We developed the single-molecule poly(A) tail sequencing method, SM-PATseq, to assay tail lengths of the whole transcriptome at nucleotide resolution using long-read sequencing. This method generates cDNA using an oligo-dT 3' splint adaptor ligation to prime first-strand cDNA synthesis, followed by random hexamer priming for second-strand synthesis. By directly sequencing the cDNA on long-read platforms, we can resolve tail lengths at nucleotide resolution, identify non-A bases within the tail, and quantify transcript abundance analogous to traditional RNAseq methods. Here, we discuss the method for generating, sequencing, and primary analysis of poly(A) tail data from total RNA using the Pacific Biosciences Sequel platform.
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Affiliation(s)
- James R Iben
- Molecular Genetics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Tianwei Li
- Molecular Genetics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sandy Mattijssen
- Section on Molecular and Cell Biology, NICHD, NIH, Bethesda, MD, USA
| | - Richard J Maraia
- Section on Molecular and Cell Biology, NICHD, NIH, Bethesda, MD, USA.
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Xu J, Guo Y, Tan Z, Ban W, Tian J, Chen K, Xu H. Molecular cloning and expression analysis of rad51 gene associated with gametogenesis in Chinese soft-shell turtle (Pelodiscus sinensis). Gene 2023; 887:147729. [PMID: 37619650 DOI: 10.1016/j.gene.2023.147729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Rad51 is a recA-like recombinase that plays a crucial role in repairing DNA double-strand breaks through homologous recombination during mitosis and meiosis in mammals and other organisms. However, its role in reptiles remains largely unclear. In this study, we aimed to investigate the physiological role of the rad51 gene in reptiles, particularly in Pelodiscus sinensis. Firstly, the cDNA of rad51 gene was cloned and analyzed in P. sinensis. The cloned cDNA contained an open reading frame (ORF) of 1020 bp and encodeed a peptide of 339 amino acids. The multiple alignments and phylogenetic tree analysis of Rad51 showed that P. sinensis shares the high identity with Chelonia mydas (97.95%) and Mus musculus (95.89%). Secondly, reverse transcription-polymerase chain reaction (RT-PCR) and real-time quantitative polymerase chain reaction (RT-qPCR) analysis showed that rad51 mRNA was highly expressed in both ovary and testis, while being weak in the somatic tissues examined in this study. Furthermore, chemical in situ hybridization (CISH) was performed to examine the expression profile of rad51 mRNA in germ cells at different stages. In the testis, rad51 mRNA expression was found to be stronger in the germ cells at early stages, specifically in spermatogonia and spermatocytes, but it was undetectable in spermatids. In the ovary, rad51 mRNA exhibited a uniform distribution in the cytoplasm of oocytes at early stages. The signal intensity of rad51 mRNA was highest in primary oocytes and gradually declined during oogenesis as the oocytes developed. These results suggest that rad51 plays a vital role in the development of germ cells, particularly during the early stages of gametogenesis in P. sinensis. The dynamic expression pattern of rad51 mRNA provides insights into the mechanisms underlying germ cell development and differentiation into gametes in turtles, even in reptiles.
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Affiliation(s)
- Jianfei Xu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Sciences of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Yonglin Guo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Sciences of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Zhimin Tan
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Sciences of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Wenzhuo Ban
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Sciences of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Jiaming Tian
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Sciences of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Kaili Chen
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Sciences of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Hongyan Xu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Sciences of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China.
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Tang Y, Zhang B, Shi H, Yan Z, Wang P, Yang Q, Huang X, Li J, Wang Z, Gun S. Cloning, expression analysis and localization of DAZL gene implicated in germ cell development of male Hezuo pig. Anim Biotechnol 2023; 34:4000-4014. [PMID: 37671929 DOI: 10.1080/10495398.2023.2249953] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Deleted in azoospermia-like (DAZL) is essential for mammalian testicular function and spermatogenesis. To explore the molecular characterization, expression patterns, and cellular localization of the DAZL in Hezuo pig testes, testicular tissue was isolated from Hezuo pig at five development stages including 30 days old (30 d), 90 days old (90 d), 120 days old (120 d), 180 days old (180 d), and 240 days old (240 d). DAZL cDNA was first cloned using the RT-PCR method, and its molecular characterization was analyzed using relevant bioinformatics software. Subsequently, the expression patterns and cellular localization of DAZL were evaluated using quantitative real-time PCR (qRT-PCR), Western blot, and immunohistochemistry. The cloning and sequence analysis showed that the Hezuo pig DAZL cDNA fragment contained 888 bp open reading frame (ORF) capable of encoding 295 amino acid residues and exhibited high identities with some other mammals. The qRT-PCR and Western blot results indicated that DAZL was specifically expressed in Hezuo pig testes, and DAZL levels of both mRNA and protein were expressed at all five reproductive stages of Hezuo pig testes, with extremely significant higher expression levels in 90 d, 120 d, 180 d, and 240 d than those in 30 d (p < 0.01). Additionally, immunohistochemistry results revealed that DAZL protein was mainly localized in gonocytes at 30 d testes, primary spermatocytes, and spermatozoon at other developmental stages, and Leydig cells throughout five development stages. Together, these results suggested that DAZL may play an important role by regulating the proliferation or differentiation of gonocytes, development of primary spermatocytes and spermatozoon, and functional maintenance of Leydig cells in testicular development and spermatogenesis of Hezuo pig. Nevertheless, the specific regulatory mechanisms underlying these phenomena still requires further investigated and verified.
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Affiliation(s)
- Yuran Tang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bo Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Haixia Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qiaoli Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiyou Li
- Gansu General Station of Animal Husbandry Technology Extension, Lanzhou, China
| | - Zike Wang
- Gansu General Station of Animal Husbandry Technology Extension, Lanzhou, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Research Center for Swine Production Engineering and Technology, Lanzhou, China
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10
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Nafchi NAM, Chilcott EM, Brown S, Fuller HR, Bowerman M, Yáñez-Muñoz RJ. Enhanced expression of the human Survival motor neuron 1 gene from a codon-optimised cDNA transgene in vitro and in vivo. Gene Ther 2023; 30:812-825. [PMID: 37322133 DOI: 10.1038/s41434-023-00406-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/14/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease particularly characterised by degeneration of ventral motor neurons. Survival motor neuron (SMN) 1 gene mutations cause SMA, and gene addition strategies to replace the faulty SMN1 copy are a therapeutic option. We have developed a novel, codon-optimised hSMN1 transgene and produced integration-proficient and integration-deficient lentiviral vectors with cytomegalovirus (CMV), human synapsin (hSYN) or human phosphoglycerate kinase (hPGK) promoters to determine the optimal expression cassette configuration. Integrating, CMV-driven and codon-optimised hSMN1 lentiviral vectors resulted in the highest production of functional SMN protein in vitro. Integration-deficient lentiviral vectors also led to significant expression of the optimised transgene and are expected to be safer than integrating vectors. Lentiviral delivery in culture led to activation of the DNA damage response, in particular elevating levels of phosphorylated ataxia telangiectasia mutated (pATM) and γH2AX, but the optimised hSMN1 transgene showed some protective effects. Neonatal delivery of adeno-associated viral vector (AAV9) vector encoding the optimised transgene to the Smn2B/- mouse model of SMA resulted in a significant increase of SMN protein levels in liver and spinal cord. This work shows the potential of a novel codon-optimised hSMN1 transgene as a therapeutic strategy for SMA.
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Affiliation(s)
- Neda A M Nafchi
- AGCTlab.org, Centre of Gene and Cell Therapy, Centre for Biomedical Sciences, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Ellie M Chilcott
- AGCTlab.org, Centre of Gene and Cell Therapy, Centre for Biomedical Sciences, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Sharon Brown
- School of Pharmacy and Bioengineering, Keele University, Staffordshire, ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, TORCH Building, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK
| | - Heidi R Fuller
- School of Pharmacy and Bioengineering, Keele University, Staffordshire, ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, TORCH Building, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK
| | - Melissa Bowerman
- Wolfson Centre for Inherited Neuromuscular Disease, TORCH Building, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK
- School of Medicine, Keele University, Staffordshire, ST5 5BG, UK
| | - Rafael J Yáñez-Muñoz
- AGCTlab.org, Centre of Gene and Cell Therapy, Centre for Biomedical Sciences, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, UK.
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11
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Morant L, Petrovic-Erfurth ML, Jordanova A. An Adapted GeneSwitch Toolkit for Comparable Cellular and Animal Models: A Proof of Concept in Modeling Charcot-Marie-Tooth Neuropathy. Int J Mol Sci 2023; 24:16138. [PMID: 38003325 PMCID: PMC10670994 DOI: 10.3390/ijms242216138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Investigating the impact of disease-causing mutations, their affected pathways, and/or potential therapeutic strategies using disease modeling often requires the generation of different in vivo and in cellulo models. To date, several approaches have been established to induce transgene expression in a controlled manner in different model systems. Several rounds of subcloning are, however, required, depending on the model organism used, thus bringing labor-intensive experiments into the technical approach and analysis comparison. The GeneSwitch™ technology is an adapted version of the classical UAS-GAL4 inducible system, allowing the spatial and temporal modulation of transgene expression. It consists of three components: a plasmid encoding for the chimeric regulatory pSwitch protein, Mifepristone as an inducer, and an inducible plasmid. While the pSwitch-containing first plasmid can be used both in vivo and in cellulo, the inducible second plasmid can only be used in cellulo. This requires a specific subcloning strategy of the inducible plasmid tailored to the model organism used. To avoid this step and unify gene expression in the transgenic models generated, we replaced the backbone vector with standard pUAS-attB plasmid for both plasmids containing either the chimeric GeneSwitch™ cDNA sequence or the transgene cDNA sequence. We optimized this adapted system to regulate transgene expression in several mammalian cell lines. Moreover, we took advantage of this new system to generate unified cellular and fruit fly models for YARS1-induced Charco-Marie-Tooth neuropathy (CMT). These new models displayed the expected CMT-like phenotypes. In the N2a neuroblastoma cells expressing YARS1 transgenes, we observed the typical "teardrop" distribution of the synthetase that was perturbed when expressing the YARS1CMT mutation. In flies, the ubiquitous expression of YARS1CMT induced dose-dependent developmental lethality and pan-neuronal expression caused locomotor deficit, while expression of the wild-type allele was harmless. Our proof-of-concept disease modeling studies support the efficacy of the adapted transgenesis system as a powerful tool allowing the design of studies with optimal data comparability.
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Affiliation(s)
- Laura Morant
- Center for Molecular Neurology, VIB, University of Antwerp, 2610 Antwerpen, Belgium; (L.M.); (M.-L.P.-E.)
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerpen, Belgium
| | - Maria-Luise Petrovic-Erfurth
- Center for Molecular Neurology, VIB, University of Antwerp, 2610 Antwerpen, Belgium; (L.M.); (M.-L.P.-E.)
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerpen, Belgium
| | - Albena Jordanova
- Center for Molecular Neurology, VIB, University of Antwerp, 2610 Antwerpen, Belgium; (L.M.); (M.-L.P.-E.)
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerpen, Belgium
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Faculty of Medicine, Medical University-Sofia, 1431 Sofia, Bulgaria
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12
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Tan MH. Identification of Bona Fide RNA Editing Sites: History, Challenges, and Opportunities. Acc Chem Res 2023; 56:3033-3044. [PMID: 37827987 DOI: 10.1021/acs.accounts.3c00462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by the adenosine deaminase acting on the RNA (ADAR) family of enzymes of which there are three members (ADAR1, ADAR2, and ADAR3), is a major gene regulatory mechanism that diversifies the transcriptome. It is widespread in many metazoans, including humans. As inosine is interpreted by cellular machineries mainly as guanosine, A-to-I editing effectively gives A-to-G nucleotide changes. Depending on its location, an editing event can generate new protein isoforms or influence other RNA processing pathways. Researchers have found that ADAR-mediated editing performs diverse functions. For example, it enables living organisms such as cephalopods to adapt rapidly to fluctuating environmental conditions such as water temperature. In development, the loss of ADAR1 is embryonically lethal partly because endogenous double-stranded RNAs (dsRNAs) are no longer marked by inosines, which signal "self", and thus cause the melanoma differentiation-associated protein 5 (MDA5) sensor to trigger a deleterious interferon response. Hence, ADAR1 plays a key role in preventing aberrant activation of the innate immune system. Furthermore, ADAR enzymes have been implicated in myriad human diseases. Intriguingly, some cancer cells are known to exploit ADAR1 activity to dodge immune responses. However, the exact identities of immunogenic RNAs in different biological contexts have remained elusive. Consequently, there is tremendous interest in identifying inosine-containing RNAs in the cell.The identification of A-to-I RNA editing sites is dependent on the sequencing of nucleic acids. Technological and algorithmic advancements over the past decades have revolutionized the way editing events are detected. At the beginning, the discovery of editing sites relies on Sanger sequencing, a first-generation technology. Both RNA, which is reverse transcribed into complementary DNA (cDNA), and genomic DNA (gDNA) from the same source are analyzed. After sequence alignment, one would require an adenosine to be present in the genome but a guanosine to be detected in the RNA sample for a position to be declared as an editing site. However, an issue with Sanger sequencing is its low throughput. Subsequently, Illumina sequencing, a second-generation technology, was invented. By permitting the simultaneous interrogation of millions of molecules, it enables many editing sites to be identified rapidly. However, a key challenge is that the Illumina platform produces short sequencing reads that can be difficult to map accurately. To tackle the challenge, we and others developed computational workflows with a series of filters to discard sites that are likely to be false positives. When Illumina sequencing data sets are properly analyzed, A-to-G variants should emerge as the most dominant mismatch type. Moreover, the quantitative nature of the data allows us to build a comprehensive atlas of editing-level measurements across different biological contexts, providing deep insights into the spatiotemporal dynamics of RNA editing. However, difficulties remain in identifying true A-to-I editing sites in short protein-coding exons or in organisms and diseases where DNA mutations and genomic polymorphisms are prevalent and mostly unknown. Nanopore sequencing, a third-generation technology, promises to address the difficulties, as it allows native RNAs to be sequenced without conversion to cDNA, preserving base modifications that can be directly detected through machine learning. We recently demonstrated that nanopore sequencing could be used to identify A-to-I editing sites in native RNA directly. Although further work is needed to enhance the detection accuracy in single molecules from fewer cells, the nanopore technology holds the potential to revolutionize epitranscriptomic studies.
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Affiliation(s)
- Meng How Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
- HP-NTU Digital Manufacturing Corporate Laboratory, Nanyang Technological University, Singapore 637460, Singapore
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13
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Lou H, Huang Y, Zhu Z, Xu Q. Cloning and Expression Analysis of Onion (Allium cepa L.) MADS-Box Genes and Regulation Mechanism of Cytoplasmic Male Sterility. Biochem Genet 2023; 61:2116-2134. [PMID: 36947296 DOI: 10.1007/s10528-023-10360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 02/27/2023] [Indexed: 03/23/2023]
Abstract
Flower organ development is one of the most important processes in plant life. However, onion CMS (cytoplasmic male sterility) shows an abnormal development of floral organs. The regulation of MADS-box transcription factors is important for flower development. To further understand the role of MADS-box transcription factors in the regulation of cytoplasmic male sterility onions. We cloned the full-length cDNA of five MADS-box transcription factors from the flowers of onion using RACE (rapid amplification of cDNA ends) technology. We used bioinformatics methods for sequence analysis and phylogenetic analysis. Real-time quantitative PCR was used to detect the expression patterns of these genes in different onion organs. The relative expression levels of five flower development genes were compared in CMS onions and wild onions. The results showed that the full-length cDNA sequences of the cloned MADS-box genes AcFUL, AcDEF, AcPI, AcAG, and AcSEP3 belonged to A, B, C, and E MADS-box genes, respectively. A phylogenetic tree construction analysis was performed on its sequence. Analysis of MADS-box gene expression in wild onion and CMS onion showed that the formation of CMS onion was caused by down-regulation of AcDEF, AcPI, and AcAG gene expression, up-regulation of AcSEP3 gene expression, and no correlation with AcFUL gene expression. This work laid the foundation for further study of the molecular mechanism of onion flower development and the molecular mechanism of CMS onion male sterility.
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Affiliation(s)
- Hu Lou
- School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yuntong Huang
- Medical Laboratory College of Youjiang Medical College for Nationalities, Baise, 533000, Guangxi, China
- Industrial College of Biomedicine and Health Industry, Youjiang Medical College for Nationalities, Baise, 533000, Guangxi, China
| | - Zhengjie Zhu
- Agriculture and Food Engineering College, Baise University, Baise, 533000, Guangxi, China
| | - Qijiang Xu
- Medical Laboratory College of Youjiang Medical College for Nationalities, Baise, 533000, Guangxi, China.
- Industrial College of Biomedicine and Health Industry, Youjiang Medical College for Nationalities, Baise, 533000, Guangxi, China.
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14
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Ye Z, Pan J, Yin Z, Wang S, Li Y, Cai X, Zheng H, Cao Z. Dendritic cells infected with recombinant adenoviral vector encoding mouse fibroblast activation protein-α and human livin α exert an antitumor effect against Lewis lung carcinoma in mice. Immun Inflamm Dis 2023; 11:e1011. [PMID: 37773704 PMCID: PMC10523997 DOI: 10.1002/iid3.1011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Fibroblast activation protein-α (FAP) and livin α are considered as cancer-associated fibroblasts (CAFs) and tumor-specific targets, respectively, for immunogenic tumor vaccines. This study is designed to decipher the antitumor effect of double-gene modified dendritic cells (DCs) on Lewis lung carcinoma (LLC). METHODS By encoding mouse FAP cDNA and human livin α (i.e., hlivin α) cDNA into recombinant adenoviral vector (rAd), rAd-FAP, rAd-hlivin α, and rAd-FAP/hlivin α were constructed, which were then transduced into mouse DCs. LLC-bearinig mice were immunized with the infected DCs (5 × 105 cells/mouse), followed by calculation of tumor volume and survival rate. The identification of CAFs from mouse LLC as well as the determination on expressions of FAP and livin α, was accomplished by western blot. Cytotoxic T lymphocyte assay was harnessed to assess the effect of the infected DCs on inducing splenic lymphocytes to lyse CAFs. RESULTS DCs were successfully transduced with rAd-FAP/hlivin α in vitro. FAP was highly expressed in CAFs. CAFs were positive for α-SMA and negative for CD45 and CD31. Livin α level was upregulated in mouse LLC. Immunization with rAd-FAP/hlivin α-transduced DCs suppressed LLC volume and improved the survival of tumor-bearing mice. Immunization with rAd-FAP/hlivin α-transduced DCs enhanced the cytotoxic effect of splenic lymphocytes on LLC tumor-derived CAFs. CONCLUSION Injection with rAd-FAP/hlivin α-transduced DCs promotes immune-enhanced tumor microenvironment by decreasing CAFs and suppresses tumor growth in LLC mouse models.
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Affiliation(s)
- Zaiting Ye
- Department of RadiologyThe Sixth Affiliated Hospital of Wenzhou Medical UniversityLishuiZhejiangChina
| | - Jiongwei Pan
- Department of RespiratoryThe Sixth Affiliated Hospital of Wenzhou Medical UniversityLishuiZhejiangChina
| | - Zhangyong Yin
- Department of RespiratoryThe Sixth Affiliated Hospital of Wenzhou Medical UniversityLishuiZhejiangChina
| | - Shuanghu Wang
- Department of MedicineLishui People's HospitalLishuiZhejiangChina
| | - Yuling Li
- Department of RespiratoryThe Sixth Affiliated Hospital of Wenzhou Medical UniversityLishuiZhejiangChina
| | - Xiaoping Cai
- Department of RespiratoryThe Sixth Affiliated Hospital of Wenzhou Medical UniversityLishuiZhejiangChina
| | - Hao Zheng
- Department of RespiratoryThe Sixth Affiliated Hospital of Wenzhou Medical UniversityLishuiZhejiangChina
| | - Zhuo Cao
- Department of RespiratoryThe Sixth Affiliated Hospital of Wenzhou Medical UniversityLishuiZhejiangChina
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15
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Keum BR, Yeo I, Koo Y, Han W, Choi SC, Kim GH, Han JK. Transmembrane protein 150b attenuates BMP signaling in the Xenopus organizer. J Cell Physiol 2023; 238:1850-1866. [PMID: 37435758 DOI: 10.1002/jcp.31059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 07/13/2023]
Abstract
The vertebrate organizer is a specified embryonic tissue that regulates dorsoventral patterning and axis formation. Although numerous cellular signaling pathways have been identified as regulators of the organizer's dynamic functions, the process remains incompletely understood, and as-yet unknown pathways remain to be explored for sophisticated mechanistic understanding of the vertebrate organizer. To identify new potential key factors of the organizer, we performed complementary DNA (cDNA) microarray screening using organizer-mimicking Xenopus laevis tissue. This analysis yielded a list of prospective organizer genes, and we determined the role of six-transmembrane domain containing transmembrane protein 150b (Tmem150b) in organizer function. Tmem150b was expressed in the organizer region and induced by Activin/Nodal signaling. In X. laevis, Tmem150b knockdown resulted in head defects and a shortened body axis. Moreover, Tmem150b negatively regulated bone morphogenetic protein (BMP) signaling, likely via physical interaction with activin receptor-like kinase 2 (ALK2). These findings demonstrated that Tmem150b functions as a novel membrane regulatory factor of BMP signaling with antagonistic effects, contributing to the understanding of regulatory molecular mechanisms of organizer axis function. Investigation of additional candidate genes identified in the cDNA microarray analysis could further delineate the genetic networks of the organizer during vertebrate embryogenesis.
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Affiliation(s)
- Byeong-Rak Keum
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
- Research Center for drug development, CYPHARMA, Daejeon, Korea
| | - Inchul Yeo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Youngmu Koo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Wonhee Han
- Department of Neurology, F. M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sun-Cheol Choi
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Gun-Hwa Kim
- Research Center for drug development, CYPHARMA, Daejeon, Korea
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Korea
| | - Jin-Kwan Han
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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16
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Reddy PH, Kshirsagar S, Bose C, Pradeepkiran JA, Hindle A, Singh SP, Reddy AP, Baig J. Rlip Reduction Induces Oxidative Stress and Mitochondrial Dysfunction in Mutant Tau-Expressed Immortalized Hippocampal Neurons: Mechanistic Insights. Cells 2023; 12:1646. [PMID: 37371116 PMCID: PMC10297078 DOI: 10.3390/cells12121646] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
RalBP1 (Rlip) is a stress-activated protein that is believed to play a large role in aging and neurodegenerative diseases such as Alzheimer's disease (AD) and other tauopathies. The purpose of our study was to understand the role of Rlip in mutant Tau-expressed immortalized hippocampal HT22 cells. In the current study, we used mutant Tau (mTau)-expressed HT22 neurons and HT22 cells transfected with Rlip-cDNA and/or silenced RNA, and studied the cell survival, mitochondrial respiration, mitochondrial function, immunoblotting, and immunofluorescence analysis of synaptic and mitophagy proteins and the colocalization of Rlip and mTau proteins. We found Rlip protein levels were reduced in mTau-HT22 cells, Rlip silenced HT22 cells, and mTau + Rlip RNA silenced HT22 cells; on the other hand, increased Rlip levels were observed in Rlip cDNA transfected HT22 cells. We found cell survival was decreased in mTau-HT22 cells and RNA-silenced HT22 cells. However, cell survival was increased in Rlip-overexpressed mTau-HT22 cells. A significantly reduced oxygen consumption rate (OCR) was found in mTau-HT22 cells and in RNA-silenced Rlip-HT22 cells, with an even greater reduction in mTau-HT22 + Rlip RNA-silenced HT22 cells. A significantly increased OCR was found in Rlip-overexpressed HT22 cells and in all groups of cells that overexpress Rlip cDNA. Mitochondrial function was defective in mTau-HT22 cells, RNA silenced Rlip in HT22 cells, and was further defective in mTau-HT22 + Rlip RNA-silenced HT22 cells; however, it was rescued in Rlip overexpressed in all groups of HT22 cells. Synaptic and mitophagy proteins were decreased in mTau-HT22 cells, and further reductions were found in RNA-silenced mTau-HT22 cells. However, these were increased in mTau + Rlip-overexpressed HT22 cells. An increased number of mitochondria and decreased mitochondrial length were found in mTau-HT22 cells. These were rescued in Rlip-overexpressed mTau-HT22 cells. These observations strongly suggest that Rlip deficiency causes oxidative stress/mitochondrial dysfunction and Rlip overexpression reverses these defects. Overall, our findings revealed that Rlip is a promising new target for aging, AD, and other tauopathies/neurological diseases.
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Affiliation(s)
- P. Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.K.); (C.B.); (J.A.P.); (A.H.); (S.P.S.); (J.B.)
- Nutritional Sciences Department, College of Human Sciences, Texas Tech University, Lubbock, TX 79409, USA;
- Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Sudhir Kshirsagar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.K.); (C.B.); (J.A.P.); (A.H.); (S.P.S.); (J.B.)
| | - Chhanda Bose
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.K.); (C.B.); (J.A.P.); (A.H.); (S.P.S.); (J.B.)
| | - Jangampalli Adi Pradeepkiran
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.K.); (C.B.); (J.A.P.); (A.H.); (S.P.S.); (J.B.)
| | - Ashly Hindle
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.K.); (C.B.); (J.A.P.); (A.H.); (S.P.S.); (J.B.)
| | - Sharda P. Singh
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.K.); (C.B.); (J.A.P.); (A.H.); (S.P.S.); (J.B.)
| | - Arubala P. Reddy
- Nutritional Sciences Department, College of Human Sciences, Texas Tech University, Lubbock, TX 79409, USA;
| | - Javaria Baig
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.K.); (C.B.); (J.A.P.); (A.H.); (S.P.S.); (J.B.)
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17
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Bian F, Lan YW, Zhao S, Deng Z, Shukla S, Acharya A, Donovan J, Le T, Milewski D, Bacchetta M, Hozain AE, Tipograf Y, Chen YW, Xu Y, Shi D, Kalinichenko VV, Kalin TV. Lung endothelial cells regulate pulmonary fibrosis through FOXF1/R-Ras signaling. Nat Commun 2023; 14:2560. [PMID: 37137915 PMCID: PMC10156846 DOI: 10.1038/s41467-023-38177-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Pulmonary fibrosis results from dysregulated lung repair and involves multiple cell types. The role of endothelial cells (EC) in lung fibrosis is poorly understood. Using single cell RNA-sequencing we identified endothelial transcription factors involved in lung fibrogenesis, including FOXF1, SMAD6, ETV6 and LEF1. Focusing on FOXF1, we found that FOXF1 is decreased in EC within human idiopathic pulmonary fibrosis (IPF) and mouse bleomycin-injured lungs. Endothelial-specific Foxf1 inhibition in mice increased collagen depositions, promoted lung inflammation, and impaired R-Ras signaling. In vitro, FOXF1-deficient EC increased proliferation, invasion and activation of human lung fibroblasts, and stimulated macrophage migration by secreting IL-6, TNFα, CCL2 and CXCL1. FOXF1 inhibited TNFα and CCL2 through direct transcriptional activation of Rras gene promoter. Transgenic overexpression or endothelial-specific nanoparticle delivery of Foxf1 cDNA decreased pulmonary fibrosis in bleomycin-injured mice. Nanoparticle delivery of FOXF1 cDNA can be considered for future therapies in IPF.
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Affiliation(s)
- Fenghua Bian
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Ying-Wei Lan
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Shuyang Zhao
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Zicheng Deng
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Center for Lung Regenerative Medicine, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- The Materials Science and Engineering Program, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH, USA
| | - Samriddhi Shukla
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Anusha Acharya
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Johnny Donovan
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Tien Le
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - David Milewski
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Matthew Bacchetta
- Departments of Thoracic and Cardiac Surgery, Department of Biomedical Engineering, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ahmed Emad Hozain
- Department of Surgery, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Yuliya Tipograf
- Department of Surgery, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Ya-Wen Chen
- Department of Cell, Developmental, and Regenerative Biology, Department of Otolaryngology, Institute for Airway Sciences, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Xu
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Donglu Shi
- The Materials Science and Engineering Program, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH, USA
| | - Vladimir V Kalinichenko
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Center for Lung Regenerative Medicine, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tanya V Kalin
- Division of Pulmonary Biology, the Perinatal Institute of Cincinnati Children's Research Foundation, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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18
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Babbar R, Tiwari LD, Mishra RC, Shimphrui R, Singh AA, Goyal I, Rana S, Kumar R, Sharma V, Tripathi G, Khungar L, Sharma J, Agrawal C, Singh G, Biswas T, Biswal AK, Sahi C, Sarkar NK, Grover A. Arabidopsis plants overexpressing additional copies of heat shock protein Hsp101 showed high heat tolerance and endo-gene silencing. Plant Sci 2023; 330:111639. [PMID: 36796649 DOI: 10.1016/j.plantsci.2023.111639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/08/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Hsp101 chaperone is vital for survival of plants under heat stress. We generated transgenic Arabidopsis thaliana (Arabidopsis) lines with extra copies of Hsp101 gene using diverse approaches. Arabidopsis plants transformed with rice Hsp101 cDNA driven by Arabidopsis Hsp101 promoter (IN lines) showed high heat tolerance while the plants transformed with rice Hsp101 cDNA driven by CaMV35S promoter (C lines) were like wild type plants in heat stress response. Transformation of Col-0 plants with 4633 bp Hsp101 genomic fragment (GF lines) from A. thaliana containing both its coding and the regulatory sequence resulted in mostly over-expressor (OX) lines and a few under-expressor (UX) lines of Hsp101. OX lines showed enhanced heat tolerance while the UX lines were overly heat sensitive. In UX lines, silencing of not only Hsp101 endo-gene was noted but also transcript of choline kinase (CK2) was silenced. Previous work established that in Arabidopsis, CK2 and Hsp101 are convergent gene pairs sharing a bidirectional promoter. The elevated AtHsp101 protein amount in most GF and IN lines was accompanied by lowered CK2 transcript levels under HS. We observed increased methylation of the promoter and gene sequence region in UX lines; however, methylation was lacking in OX lines.
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Affiliation(s)
- Richa Babbar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Lalit Dev Tiwari
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Ratnesh Chandra Mishra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Rinchuila Shimphrui
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Aditya Abha Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India; Department of Botany, University of Lucknow, Lucknow-226007, India
| | - Isha Goyal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Surbhi Rana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Ritesh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Vijyesh Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Gayatri Tripathi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Lisha Khungar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Jaydeep Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Chhavi Agrawal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Garima Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Tanya Biswas
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Anup Kumar Biswal
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, MP, India
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, MP, India
| | - Neelam K Sarkar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
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19
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Smits PJ, Sudduth CL, Konczyk DJ, Cheng YS, Vivero MP, Kozakewich HPW, Warman ML, Greene AK. Endothelial cell expression of mutant Map2k1 causes vascular malformations in mice. Angiogenesis 2023; 26:97-105. [PMID: 35972708 PMCID: PMC9918623 DOI: 10.1007/s10456-022-09853-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/29/2022] [Indexed: 11/01/2022]
Abstract
Extracranial arteriovenous malformation (AVM) is a congenital vascular anomaly causing disfigurement, bleeding, ulceration, and pain. Most lesions are associated with somatic MAP2K1 activating mutations in endothelial cells (ECs). The purpose of this study was to determine if EC expression of mutant activated MAP2K1 is sufficient to produce vascular malformations in mice. We generated mice with a ROSA26 allele containing a lox-stop-lox gene trap (GT), Map2k1 cDNA with an activating p.K57N missense mutation, an internal ribosomal entry site, and green fluorescent protein cDNA (R26GT-Map2k1-GFP). We expressed mutant MAP2K1 and GFP in ECs of fetal and newborn mice using Tg-Cdh5Cre or Tg-Cdh5CreER alleles. Tg-Cdh5Cre+/-;R26GT-Map2k1-GFP/+ animals that express mutant MAP2K1 in ECs in utero developed diffuse vascular abnormalities and died by embryonic (E) day 16.5. Tg-Cdh5CreER+/-;R26GT-Map2k1-GFP/+ animals in which mutant MAP2K1 expression was induced in ECs by tamoxifen at postnatal (P) day 1 developed vascular malformations in the brain, ear, and intestines by P23. The lesions consisted of abnormal networks of blood vessels containing recombined and non-recombined ECs. In conclusion, expression of MAP2K1 p.K57N is sufficient to cause vascular malformations in mice. This model can be used to study the malformation process and for pre-clinical pharmacologic studies.
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Affiliation(s)
- Patrick J Smits
- Department of Plastic & Oral Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA.
| | - Christopher L Sudduth
- Department of Plastic & Oral Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Dennis J Konczyk
- Department of Plastic & Oral Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Yu Sheng Cheng
- Department of Plastic & Oral Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Matthew P Vivero
- Department of Plastic & Oral Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Harry P W Kozakewich
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Matthew L Warman
- Department of Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA, 02115, USA
| | - Arin K Greene
- Department of Plastic & Oral Surgery, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
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20
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Zheng B, Wang Y, Hu J, Bao Z, Wang M. Comparative analysis of two cathepsin L genes in Asiatic hard clam (Meretrix meretrix): Similar in sequence features, different in expression profiles. Fish Shellfish Immunol 2023; 133:108527. [PMID: 36621705 DOI: 10.1016/j.fsi.2023.108527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Cathepsin L is widely found in eukaryotes and prokaryotes, and it plays important roles in innate immunity. In the present study, we cloned two cathepsin L genes (designated as MmCTSL1 and MmCTSL2, respectively) from Asiatic hard clam (Meretrix meretrix). The complete sequence of MmCTSL1 cDNA contained a 5' untranslated region (UTR) of 31 bp, a 3' UTR of 228 bp with a poly (A) tail, and an open reading frame (ORF) of 1005 bp encoding 334 amino acids with predicted molecular weight of 37.5 kDa and theoretical isoelectric point of 5.27, and contained a signal peptide (from M1 to A16), a protease inhibitor I29 family domain (from W27 to F87), and a papain family cysteine protease domain (from L118 to T333). The complete sequence of MmCTSL2 cDNA contained a 5' UTR of 50 bp, a 3' UTR of 162 bp with a poly (A) tail, and an ORF of 996 bp encoding a polypeptide of 331 amino acids with predicted molecular weight of 36.8 kDa and theoretical isoelectric point of 7.07. It contained a signal peptide (from M1 to A16), a protease inhibitor I29 family domain (from W30 to F89), and a papain family cysteine protease domain (from L115 to T330). Real-time quantitative PCR analysis demonstrated that MmCTSL1 and MmCTSL2 were widely expressed in all the tested tissues, including adductor muscle, foot, gill, hemocytes, hepatopancreas and mantle, with the highest mRNA expression level in hepatopancreas and hemocytes, respectively. After Vibrio splendidus challenge, the mRNA expression levels of MmCTSL1 and MmCTSL2 in hemocytes and hepatopancreas were both significantly up-regulated with different expression profiles. In hemocytes, the expression levels of MmCTSL1 and MmCTSL2 reached their respective peaks (3.4-fold and 13.0-fold compared with the control, respectively) at 12 h after bacterial challenge, and MmCTSL2 responds earlier than MmCTSL1. In hepatopancreas, the expression levels of MmCTSL1 and MmCTSL2 reached their respective peaks at 6 h (9.0-fold compared with the control) and 24 h (2.8-fold compared with the control) after bacterial challenge, meaning that MmCTSL1 responds earlier than MmCTSL2. At the same time, whether in hepatopancreas or hemocytes, MmCTSL1 persist for a while after the bacterial challenge peak, while MmCTSL2 would quickly return to the initial level after the bacterial challenge peak. These results indicate that cathepsin L may be involved in the immune process of hard clam against V. splendidus with different potential roles.
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Affiliation(s)
- Bo Zheng
- MOE Key Laboratory of Marine Genetics and Breeding (Qingdao 266003), and Key Laboratory of Tropical Aquatic Germplasm of Hainan Province of Sanya Oceanographic Institute (Sanya 572024), Ocean University of China, China
| | - Yan Wang
- MOE Key Laboratory of Marine Genetics and Breeding (Qingdao 266003), and Key Laboratory of Tropical Aquatic Germplasm of Hainan Province of Sanya Oceanographic Institute (Sanya 572024), Ocean University of China, China; Laboratory for Marine Fisheries Science and Food Production Processes, and Center for Marine Molecular Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding (Qingdao 266003), and Key Laboratory of Tropical Aquatic Germplasm of Hainan Province of Sanya Oceanographic Institute (Sanya 572024), Ocean University of China, China; Laboratory for Marine Fisheries Science and Food Production Processes, and Center for Marine Molecular Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding (Qingdao 266003), and Key Laboratory of Tropical Aquatic Germplasm of Hainan Province of Sanya Oceanographic Institute (Sanya 572024), Ocean University of China, China; Laboratory for Marine Fisheries Science and Food Production Processes, and Center for Marine Molecular Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Mengqiang Wang
- MOE Key Laboratory of Marine Genetics and Breeding (Qingdao 266003), and Key Laboratory of Tropical Aquatic Germplasm of Hainan Province of Sanya Oceanographic Institute (Sanya 572024), Ocean University of China, China; Laboratory for Marine Fisheries Science and Food Production Processes, and Center for Marine Molecular Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China.
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21
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Lima ER, Freire RP, Suzuki MF, Oliveira JE, Yosidaki VL, Peroni CN, Sevilhano T, Zorzeto M, Torati LS, Soares CRJ, Lima IDDM, Kronenberger T, Maltarollo VG, Bartolini P. Isolation and Characterization of the Arapaima gigas Growth Hormone (ag-GH) cDNA and Three-Dimensional Modeling of This Hormone in Comparison with the Human Hormone (hGH). Biomolecules 2023; 13:158. [PMID: 36671542 PMCID: PMC9855374 DOI: 10.3390/biom13010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/15/2022] [Accepted: 12/30/2022] [Indexed: 01/15/2023] Open
Abstract
In a previous work, the common gonadotrophic hormone α-subunit (ag-GTHα), the ag-FSH β- and ag-LH β-subunit cDNAs, were isolated and characterized by our research group from A. gigas pituitaries, while a preliminary synthesis of ag-FSH was also carried out in human embryonic kidney 293 (HEK293) cells. In the present work, the cDNA sequence encoding the ag-growth hormone (ag-GH) has also been isolated from the same giant Arapaimidae Amazonian fish. The ag-GH consists of 208 amino acids with a putative 23 amino acid signal peptide and a 185 amino acid mature peptide. The highest identity, based on the amino acid sequences, was found with the Elopiformes (82.0%), followed by Anguilliformes (79.7%) and Acipenseriformes (74.5%). The identity with the corresponding human GH (hGH) amino acid sequence is remarkable (44.8%), and the two disulfide bonds present in both sequences were perfectly conserved. Three-dimensional (3D) models of ag-GH, in comparison with hGH, were generated using the threading modeling method followed by molecular dynamics. Our simulations suggest that the two proteins have similar structural properties without major conformational changes under the simulated conditions, even though they are separated from each other by a >100 Myr evolutionary period (1 Myr = 1 million years). The sequence found will be used for the biotechnological synthesis of ag-GH while the ag-GH cDNA obtained will be utilized for preliminary Gene Therapy studies.
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Affiliation(s)
- Eliana Rosa Lima
- Instituto de Pesquisas Energéticas e Nucleares (IPEN-CNEN), Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | - Renan Passos Freire
- Instituto de Pesquisas Energéticas e Nucleares (IPEN-CNEN), Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | - Miriam Fussae Suzuki
- Instituto de Pesquisas Energéticas e Nucleares (IPEN-CNEN), Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | - João Ezequiel Oliveira
- Instituto de Pesquisas Energéticas e Nucleares (IPEN-CNEN), Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | - Vanessa Luna Yosidaki
- Instituto de Pesquisas Energéticas e Nucleares (IPEN-CNEN), Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | - Cibele Nunes Peroni
- Instituto de Pesquisas Energéticas e Nucleares (IPEN-CNEN), Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | - Thaís Sevilhano
- Instituto de Pesquisas Energéticas e Nucleares (IPEN-CNEN), Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | - Moisés Zorzeto
- Piscicultura Raça, Canabrava do Norte 78658-000, MT, Brazil
| | - Lucas Simon Torati
- EMBRAPA Pesca e Aquicultura, Loteamento Água Fria, Palmas 77008-900, TO, Brazil
| | - Carlos Roberto Jorge Soares
- Instituto de Pesquisas Energéticas e Nucleares (IPEN-CNEN), Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | - Igor Daniel de Miranda Lima
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Av. Presidente Antônio Carlos, 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, DE, 72076 Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Vinicius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Av. Presidente Antônio Carlos, 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Paolo Bartolini
- Instituto de Pesquisas Energéticas e Nucleares (IPEN-CNEN), Cidade Universitária, São Paulo 05508-000, SP, Brazil
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22
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Nouraeinejad A. The Implication of Alu cDNA in the Pathogenesis of ARMD. Curr Aging Sci 2023; 16:168-169. [PMID: 37259223 DOI: 10.2174/1874609816666230530095410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 06/02/2023]
Abstract
Age-related macular degeneration (ARMD or AMD) is a progressive, sight-threatening disease. The pathogenesis of ARMD is complex, involving many factors, such as metabolic, functional, genetic, and environmental factors. Recently, long interspersed nuclear element-1 (L1)- mediated reverse transcription (RT) of Alu RNA into cytoplasmic Alu complementary DNA (cDNA) has been associated with retinal pigment epithelium (RPE) destruction. These findings provide a strong input for a new direction in the management of ARMD, as certain human immunodeficiency virus (HIV) drugs, such as nucleoside reverse transcriptase inhibitors (NRTIs), were found to suppress inflammation and protect cells of the retina.
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Affiliation(s)
- Ali Nouraeinejad
- Department of Clinical Ophthalmology, University College London (UCL), London, United Kingdom
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23
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Li J, Yang Y, Li J, Li P, Qi H. Cell-Free Display Techniques for Protein Evolution. Adv Biochem Eng Biotechnol 2023; 185:59-90. [PMID: 37306697 DOI: 10.1007/10_2023_227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free protein synthesis (CFPS) with flexibility and controllability can provide a powerful platform for high-throughput screening of biomolecules, especially in the evolution of peptides or proteins. In this chapter, the emerging strategies for enhancing the protein expression level using different source strains, energy systems, and template designs in constructing CFPS systems are summarized and discussed in detail. In addition, we provide an overview of the ribosome display, mRNA display, cDNA display, and CIS display in vitro display technologies, which can couple genotype and phenotype by forming fusion complexes. Moreover, we point out the trend that improving the protein yields of CFPS itself can offer more favorable conditions for maintaining library diversity and display efficiency. It is hoped that the novel CFPS system can accelerate the development of protein evolution in biotechnological and medical applications.
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Affiliation(s)
- Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Youhui Yang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jinjin Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Peixian Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China.
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24
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Fan XL, Yu SS, Zhao JL, Li Y, Zhan DJ, Xu F, Lin ZH, Chen J. Brevinin-2PN, an antimicrobial peptide identified from dark-spotted frog (Pelophylax nigromaculatus), exhibits wound-healing activity. Dev Comp Immunol 2022; 137:104519. [PMID: 36041640 DOI: 10.1016/j.dci.2022.104519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Brevinins exhibit a wide range of structural features and strong biological activities. Brevinin-2, derived from several amphibians, has shown antimicrobial activities. However, little is known about the wound-healing activity of brevinin-2. In this study, brevinin-2 cDNA was identified from the skin transcriptome of the dark-spotted frog (Pelophylax nigromaculatus) and it comprises a signal peptide, a propeptide, and a mature peptide. Sequence alignment with brevinin-2 derived from other amphibians showed variability of the mature peptide, and the presence of a C-terminal cyclic heptapeptide domain (Cys-Lys-Xaa4-Cys) in the mature peptide. Dark-spotted frog brevinin-2 belonged to the brevinin-2 cluster and was closely related to brevinin-2HB1 from Pelophylax hubeiensis. Synthetic dark-spotted frog brevinin-2 mature peptide (brevinin-2PN) exhibited antibacterial activity against several pathogens by destroying cell membrane integrity and hydrolysis of genomic DNA. Brevinin-2PN exhibited significant wound-healing activity by accelerating the healing of human skin fibroblast cell scratches, influencing cell migration, and stimulating gene expression of growth factors.
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Affiliation(s)
- Xiao-Li Fan
- College of Ecology, Lishui University, Lishui, 323000, China
| | - Shui-Sheng Yu
- Ecological Forestry Development Center of Suichang County, Lishui, 323000, China
| | - Jia-Le Zhao
- College of Ecology, Lishui University, Lishui, 323000, China
| | - Yue Li
- College of Ecology, Lishui University, Lishui, 323000, China
| | - Du-Juan Zhan
- College of Ecology, Lishui University, Lishui, 323000, China
| | - Feng Xu
- Institute of Dermatology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Zhi-Hua Lin
- College of Ecology, Lishui University, Lishui, 323000, China.
| | - Jie Chen
- College of Ecology, Lishui University, Lishui, 323000, China.
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25
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Jiang J, Zhao Z, Gao S, Chen Z, Pan Y, Guan X, Jiang P, Li P, Wang B, Sun H, Dong Y, Zhou Z. Functions of lysin motif (LysM)-containing protein in antibacterial responses of sea cucumbers, Apostichopus japonicus. Fish Shellfish Immunol 2022; 131:1275-1281. [PMID: 36400371 DOI: 10.1016/j.fsi.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
The lysin motif (LysM)-containing protein is one of widespread pattern-recognition receptors in prokaryotes and eukaryotes. Numerous LysM-containing gene sequences are present in gene databases; however, few have been well characterized, especially in echinoderms. In this study, the full-length cDNA of a novel LysM-containing gene was obtained from the sea cucumber Apostichopus japonicus, named AjLysM-1, using polymerase chain reaction (PCR) combined with rapid amplification of cDNA ends. We prepared and expressed recombinant AjLysM-1 protein (rAjLysM-1) and determined its pathogen-recognition ability by enzyme-linked immunosorbent and immunofluorescence assays. We also analyzed the tissue expression pattern and response to immune challenges of AjLysM-1 using quantitative real-time reverse transcription-PCR and in situ hybridization. The AjLysM-1 protein was predicted to be an intracellular non-secreted LysM-containing protein, highly homologous to the same protein in other marine echinoderms. AjLysM-1 transcripts were highest expressed in coelomocytes and were strikingly induced by challenge with representative bacterial and fungal polysaccharides. rAjLysM-1 showed weak binding to mannan, Pseudoalteromonas nigrifaciens, and Shewanella baltica, implying that AjLysM-1 might provide inadequate defense against Gram-negative bacteria and fungi. Notably, rAjLysM-1 also interacted with tyrosine protein kinase and filamin-B, indicating that it could be involved in focal adhesion in A. japonicus. These findings improve our understanding of the functions of LysM-containing proteins in marine echinoderms.
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Affiliation(s)
- Jingwei Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Zelong Zhao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Shan Gao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Zhong Chen
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Yongjia Pan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Xiaoyan Guan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Pingzhe Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Peipei Li
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Bai Wang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Hongjuan Sun
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Ying Dong
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China.
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Shaughnessy CA, Jensen MF, Dores RM. A basal actinopterygian melanocortin receptor: Molecular and functional characterization of an Mc2r ortholog from the Senegal bichir (Polypterus senegalus). Gen Comp Endocrinol 2022; 328:114105. [PMID: 35973587 DOI: 10.1016/j.ygcen.2022.114105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022]
Abstract
In bony vertebrates, melanocortin 2 receptor (Mc2r) specifically binds adrenocorticotropic hormone (ACTH) and is responsible for mediating anterior pituitary signaling that stimulates corticosteroid production in the adrenal gland/interrenal cells. In bony fishes Mc2r requires the chaperoning of an accessory protein (Mrap1) to traffic to the membrane surface and bind ACTH. Here, we evaluated the structure and pharmacological properties of Mc2r from the Senegal bichir (Polypterus senegalus), which represents the most basal bony fish from which an Mc2r has been pharmacologically studied to date. In our experiments, cDNA constructs of the Mc2r from the Senegal bichir (sbMc2r) and various vertebrate Mrap1s were heterologously co-expressed in Chinese hamster ovary (CHO) cells, stimulated by ACTH or melanocyte-stimulating hormone (α-MSH) ligands, and assessed using a luciferase reporter gene assay. When expressed without an Mrap1, sbMc2r was not activated by ACTH. When co-expressed with Mrap1 from either chicken (Gallus gallus) or bowfin (Amia calva), sbMc2r could be activated in a dose-dependent manner by ACTH, but not α-MSH. Co-expression of sbMrap2 with sbMc2r resulted in no detectable activation of the receptor. Collectively, these results demonstrate that sbMc2r has pharmacological properties similar to those of Mc2rs of later-evolved bony fishes, such as Mrap1 dependence and ACTH selectivity, indicating that these qualities of Mc2r function are ancestral to all bony fish Mc2rs.
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Affiliation(s)
| | - Mary F Jensen
- Department of Biological Sciences, University of Denver, Denver, CO
| | - Robert M Dores
- Department of Biological Sciences, University of Denver, Denver, CO
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Ito H, Saito H, Fukui M, Tanaka A, Arakawa K. Poplar leaf abscission through induced chlorophyll breakdown by Mg-dechelatase. Plant Sci 2022; 324:111444. [PMID: 36031022 DOI: 10.1016/j.plantsci.2022.111444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/21/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Chlorophyll breakdown is observed during senescence. The first step in chlorophyll breakdown is the removal of central Mg by Mg-dechelatase. This reaction is the rate-limiting step in the chlorophyll breakdown pathway. We evaluated the effect of induced chlorophyll breakdown on abscission through the removal of Mg by Mg-dechelatase. Poplar transformants carrying the dexamethasone-inducible Mg-dechelatase gene were prepared using the Arabidopsis Stay-Green1 cDNA. When leaves were treated with dexamethasone, chlorophyll was degraded, photosynthetic capacity was reduced, and an abscission zone was formed, resulting in leaf abscission. In addition, ethylene, which plays an important role during senescence, was produced in this process. Thus, chlorophyll breakdown induces the phenotype in the same way as commonly observed during leaf senescence. This study suggests a physiological role of chlorophyll breakdown in the leaf abscission of deciduous trees. Furthermore, this study shows that the dexamethasone-inducible gene expression system is an available option for deciduous tree studies.
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Affiliation(s)
- Hisashi Ito
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo 060-0819, Japan.
| | - Hideyuki Saito
- Research Faculty of Agriculture, Hokkaido University, N9 W9, Sapporo 060-8589, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo 060-0819, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo 060-0819, Japan
| | - Keita Arakawa
- Research Faculty of Agriculture, Hokkaido University, N9 W9, Sapporo 060-8589, Japan
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Grozić A, Coker K, Dussik CM, Sabir MS, Sabir Z, Bradley A, Zhang L, Park J, Yale S, Kaneko I, Hockley M, Harris LA, Lunsford TN, Sandrin TR, Jurutka PW. Identification of putative transcriptomic biomarkers in irritable bowel syndrome (IBS): Differential gene expression and regulation of TPH1 and SERT by vitamin D. PLoS One 2022; 17:e0275683. [PMID: 36264926 PMCID: PMC9584396 DOI: 10.1371/journal.pone.0275683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
Irritable bowel syndrome (IBS) is one of the most common gastrointestinal disorders and affects approximately 4% of the global population. The diagnosis of IBS can be made based on symptoms using the validated Rome criteria and ruling out commonly occurring organic diseases. Although biomarkers exist for "IBS mimickers" such as celiac disease and inflammatory bowel disease (IBD), no such test exists for IBS. DNA microarrays of colonic tissue have been used to identify disease-associated variants in other gastrointestinal (GI) disorders. In this study, our objective was to identify biomarkers and unique gene expression patterns that may define the pathological state of IBS. Mucosal tissue samples were collected from the sigmoid colon of 29 participants (11 IBS and 18 healthy controls). DNA microarray analysis was used to assess gene expression profiling. Extraction and purification of RNA were then performed and used to synthesize cDNA. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) was employed to identify differentially expressed genes in patients diagnosed with IBS compared to healthy, non-IBS patient-derived cDNA. Additional testing probed vitamin D-mediated regulation of select genes associated with serotonergic metabolism. DNA microarray analyses led to the identification of 858 differentially expressed genes that may characterize the IBS pathological state. After screening a series of genes using a combination of gene ontological analysis and RT-qPCR, this spectrum of potential IBS biomarkers was narrowed to 23 genes, some of which are regulated by vitamin D. Seven putative IBS biomarkers, including genes involved in serotonin metabolism, were identified. This work further supports the hypothesis that IBS pathophysiology is evident within the human transcriptome and that vitamin D modulates differential expression of genes in IBS patients. This suggests that IBS pathophysiology may also involve vitamin D deficiency and/or an irregularity in serotonin metabolism.
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Affiliation(s)
- Aleksandra Grozić
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
| | - Keaton Coker
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
| | - Christopher M. Dussik
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
| | - Marya S. Sabir
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
| | - Zhela Sabir
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
| | - Arianna Bradley
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
| | - Lin Zhang
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
| | - Jin Park
- Biodesign Institute, Arizona State University, Tempe, AZ, United States of America
| | - Steven Yale
- Department of Medicine, University of Central Florida College of Medicine, Orlando, FL, United States of America
| | - Ichiro Kaneko
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, AZ, United States of America
| | - Maryam Hockley
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
| | - Lucinda A. Harris
- Mayo Clinic Division of Gastroenterology & Hepatology, Alix School of Medicine, Mayo Clinic, Scottsdale, AZ, United States of America
| | - Tisha N. Lunsford
- Mayo Clinic Division of Gastroenterology & Hepatology, Alix School of Medicine, Mayo Clinic, Scottsdale, AZ, United States of America
| | - Todd R. Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
- Julie Ann Wrigley Global Futures Laboratory, Arizona State University, Tempe, AZ, United States of America
| | - Peter W. Jurutka
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, United States of America
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, AZ, United States of America
- * E-mail:
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Chen J, Huang Y, Li J, Li Y, Zeng X, Zhao D. Overexpression of the Eucommolia ulmoides Aquaporin, EuPIP1;1, Promotes Leaf Growth, Flowering and Bolting, and Stress Tolerance in Arabidopsis. Int J Mol Sci 2022; 23:ijms231911794. [PMID: 36233096 PMCID: PMC9570377 DOI: 10.3390/ijms231911794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
Plasma membrane intrinsic protein (PIP) is one of the largest subfamilies of Aquaporins (AQPs) and plays an important role in plant growth and development, and resistance to abiotic stress. In this study, the full length of the EuPIP1;1 cDNA was cloned from Eucommia ulmoides using the rapid amplification of cDNA ends (RACE) method. The EuPIP1;1 gene was induced by drought treatment and expressed in all tested tissues, with the highest expression level in fruit. The subcellular localization showed that EuPIP1;1 was located in the plasma membrane. Constitutive overexpression of EuPIP1;1 in Arabidopsisthaliana could promote leaf growth and development, and accelerate bolting and flowering. Six genes related to growth and flowering (AtPIF4, AtTCP14, AtCRY1, AtCRY2, AtFCA and AtFT) were significantly up-regulated in transgenic lines. Further, EuPIP1;1 gene improved resistance to drought and salt stress in transgenic Arabidopsis. Under drought and salt stress treatment, the transgenic lines had a higher germination rate and accumulation of osmotic substances, lower membrane damage, and could maintain ion homeostasis. Our results suggest that EuPIP1;1 plays an essential role in plant growth and development and in the response to drought and salt stress.
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Affiliation(s)
- Jiajia Chen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China
| | - Yanhui Huang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China
| | - Jianrong Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China
| | - Yan Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China
| | - Xiaofang Zeng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China
- Correspondence: (X.Z.); (D.Z.)
| | - Degang Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, China
- Guizhou Plant Conservation Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Correspondence: (X.Z.); (D.Z.)
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Shen X, Wang Y, Hu J, Bao Z, Wang M. Molecular characterization of an LRR-only protein gene in Pacific white shrimp Litopenaeus vannamei: Sequence feature, expression pattern, and protein activity. Fish Shellfish Immunol 2022; 129:199-206. [PMID: 36058438 DOI: 10.1016/j.fsi.2022.08.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
Leucine-rich repeat (LRR)-only proteins have been proved to be involved in the innate immune responses as they could mediate protein-protein or protein-ligand interactions. In the present study, a novel LRR-only protein (LvLRRop-1) was identified and characterized from Pacific white shrimp Litopenaeus vannamei. The complete cDNA sequence of LvLRRop-1 contains an open reading frame (ORF) of 1488 bp, which encoded a polypeptide of 495 amino acids with a predicted molecular mass of 55.67 kDa and a calculated theoretical isoelectric point of 6.435. There are five LRR motifs, six LRR_TYP motifs in the protein sequence of LvLRRop-1 with consensus signature sequences of LxxLxxLxLxxNxL. The LvLRRop-1 mRNA transcripts could be detected in all the tested tissues, including eyestalk, gill, gonad, heart, hemocytes, hepatopancreas, intestine, muscle, nerve and stomach, especially highest in hemocytes and hepatopancreas. The mRNA transcripts of LvLRRop-1 increased within the first 6 h in hemocytes and hepatopancreas after Vibrio parahaemolyticus or white spot syndrome virus (WSSV) challenges. The recombinant LvLRRop-1 could bind four typical pathogen-associated molecular patterns (PAMPs), including lipopolysaccharide (LPS), peptidoglycan (PGN), glucan (GLU) and polycytidine-polycytidylic acid (poly IC), in a dose-dependent manner, and inhibit the growth of bacteria Micrococcus luteus. These data indicated that LvLRRop-1 could play a pivotal role in the innate immune response of shrimps as a kind of pattern recognition receptor (PRR).
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Affiliation(s)
- Xiaojing Shen
- MOE Key Laboratory of Marine Genetics and Breeding (Qingdao 266003), and Key Laboratory of Tropical Aquatic Germplasm of Hainan Province of Sanya Oceanographic Institution (Sanya 572024), Ocean University of China, China
| | - Yan Wang
- MOE Key Laboratory of Marine Genetics and Breeding (Qingdao 266003), and Key Laboratory of Tropical Aquatic Germplasm of Hainan Province of Sanya Oceanographic Institution (Sanya 572024), Ocean University of China, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding (Qingdao 266003), and Key Laboratory of Tropical Aquatic Germplasm of Hainan Province of Sanya Oceanographic Institution (Sanya 572024), Ocean University of China, China; Laboratory for Marine Fisheries Science and Food Production Processes, and Center for Marine Molecular Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding (Qingdao 266003), and Key Laboratory of Tropical Aquatic Germplasm of Hainan Province of Sanya Oceanographic Institution (Sanya 572024), Ocean University of China, China; Laboratory for Marine Fisheries Science and Food Production Processes, and Center for Marine Molecular Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Mengqiang Wang
- MOE Key Laboratory of Marine Genetics and Breeding (Qingdao 266003), and Key Laboratory of Tropical Aquatic Germplasm of Hainan Province of Sanya Oceanographic Institution (Sanya 572024), Ocean University of China, China; Laboratory for Marine Fisheries Science and Food Production Processes, and Center for Marine Molecular Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China.
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Qiao X, Li Y, Jin Y, Wang S, Hou L, Wang L, Song L. The involvement of an interferon-induced protein 44-like (CgIFI44L) in the antiviral immune response of Crassostrea gigas. Fish Shellfish Immunol 2022; 129:96-105. [PMID: 36055558 DOI: 10.1016/j.fsi.2022.08.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Interferon-stimulated genes (ISGs) encoding proteins are the essential executors of interferon (IFN) mediated antiviral defense. In the present study, an ISG member, interferon-induced protein 44-like (IFI44L) gene (designed as CgIFI44L-1) was identified from the Pacific oyster Crassostrea gigas. The ORF of CgIFI44L-1 cDNA was of 1437 bp encoding a polypeptide of 479 amino acids with a TLDc domain and an MMR_HSR1 domain. The mRNA transcripts of CgIFI44L-1 were detected in all the tested tissues with highest level in haemocytes, which was 15.78-fold of that in gonad (p < 0.001). Among the haemocytes, the CgIFI44L-1 protein was detected to be highly expressed in granulocytes with dominant distribution in cytoplasm. The mRNA expression level of CgIFI44L-1 in haemocytes was significantly induced by poly (I:C) stimulation, and the expression level peaked at 24 h, which was 24.24-fold (p < 0.0001) of that in control group. After the treatment with the recombinant protein of an oyster IFN-like protein (rCgIFNLP), the mRNA expression level of CgIFI44L-1 was significantly enhanced at 6 h, 12 h and 24 h, which was 2.67-fold (p < 0.001), 5.44-fold (p < 0.001) and 5.16-fold (p < 0.001) of that in control group, respectively. When the expressions of CgSTAT and CgIFNLP were knocked down by RNA interference (RNAi), the mRNA transcripts of CgIFI44L-1 were significantly down-regulated after poly (I:C) stimulation, which was 0.09-fold (p < 0.001) and 0.06-fold (p < 0.001) of those in EGFP group, respectively. These results suggested that CgIFI44L-1 was a conserved ISG in oyster, which was regulated by CgIFNLP and CgSTAT, and involved in the oyster antiviral immune response.
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Affiliation(s)
- Xue Qiao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Youjing Li
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yuhao Jin
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Sicong Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Lilin Hou
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
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Zhou J, Peng X, Ru Y, Xu J. Circ_0060077 Knockdown Alleviates High-Glucose-Induced Cell Apoptosis, Oxidative Stress, Inflammation and Fibrosis in HK-2 Cells via miR-145-5p/VASN Pathway. Inflammation 2022; 45:1911-1923. [PMID: 35729462 DOI: 10.1007/s10753-022-01649-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 01/17/2022] [Accepted: 02/09/2022] [Indexed: 12/22/2022]
Abstract
The involvement of circular RNAs (circRNAs) in the progression of diabetic nephropathy (DN) has been reported. However, the functions of circ_0060077 in DN remain unclear. HK-2 cells were treated with high glucose (HG) to establish DN cell model. Quantitative real-time polymerase chain reaction (qRT-PCR) was proceeded to determine the levels of circ_0060077, microRNA-145-5p (miR-145-5p) and vasorin (VASN). Cell counting kit-8 (CCK-8) assay, 5-ethynyl-2'-deoxyuridine (EdU) assay and colony formation assay were conducted to assess cell proliferation ability. Flow cytometry analysis was employed for cell apoptosis. The oxidative stress level was evaluated by commercial kits. Enzyme-linked immunosorbent assay (ELISA) was adopted to examine the concentrations of inflammatory factors. Western blot assay was utilized for protein levels. Dual-luciferase reporter assay and RNA pull-down assay were manipulated to analyze the relationships among circ_0060077, miR-145-5p and VASN. Circ_0060077 level was increased in DN patients and HG-stimulated HK-2 cells. Circ_0060077 knockdown ameliorated the inhibitory effect of HG on HK-2 cell proliferation and the promotional effects on cell apoptosis, oxidative stress, inflammation and fibrosis. MiR-145-5p was identified as the target for circ_0060077 and miR-145-5p inhibition ameliorated the effect of circ_0060077 silencing on HG-induced HK-2 cell injury. Moreover, miR-145-5p directly bound to VASN. Overexpression of miR-145-5p facilitated cell proliferation and repressed apoptosis, oxidative injury, inflammation and fibrosis in HG-induced HK-2 cells by targeting VASN. Circ_0060077 silencing protected HK-2 cells from HG-induced damage by regulating miR-145-5p/VASN axis.
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Affiliation(s)
- Jinjin Zhou
- Department of Nephrology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang City, Henan Province, China
| | - Xia Peng
- Department of Nephrology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang City, Henan Province, China
| | - Yanhai Ru
- Department of Nephrology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang City, Henan Province, China
| | - Jiayun Xu
- Department of Nephrology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang City, Henan Province, China.
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Huang J, Hao Y, Lai K, Lyu L, Yuan X, Yang G, Li W, Sun C. Neurosecretory protein GL in GIFT tilapia (Oreochromis niloticus): cDNA cloning, tissue distribution and effects of feeding on its expression. Gen Comp Endocrinol 2022; 327:114096. [PMID: 35841941 DOI: 10.1016/j.ygcen.2022.114096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 06/29/2022] [Accepted: 07/10/2022] [Indexed: 11/16/2022]
Abstract
Neurosecretory protein GL (NPGL), a novel neuropeptide, has been identified in the hypothalamus of chicks and rodents. NPGL plays a crucial role in monitoring energetic status via the regulation of feeding and metabolism. However, no study on NPGL has been reported in fish thus far. In the present study, the full-length cDNA of NPGL was identified from the hypothalamus of GIFT tilapia (Oreochromis niloticus). The ORF of tilapia NPGL is 471 bp and encodes a precursor peptide with a size of 156 a.a, consisting of a 26 a.a signal peptide and an 82 a.a mature peptide. Tissue distribution profiles of npgl in tilapia were acquired using semiquantitative PCR and in situ hybridization (ISH). The results showed that the highest npgl mRNA is expressed in the telencephalic-preoptic complex, which comprises both the telencephalon and the anterior preoptic area (POA) of male tilapia, and in the ovary of female tilapia. In addition, in male tilapia, the ISH results showed that the cells containing npgl mRNA were distributed exclusively in the anterior periventricular pretectal nucleus (Ppa) of the POA. FISH results demonstrated that npgl mRNA is also expressed in the lateral tuberal nucleus of the hypothalamus (NLT). Real-time PCR showed that npgl mRNA significantly increased in the telencephalic-preoptic complex of male tilapia that were fasted for 24 h and then fed a full diet for 20 min compared with the unfed group. Results of the FISH study showed that parvocellular cells containing npgl mRNA in the Ppa of fed fish were apparently more abundant than those of the unfed group. Few npgl positive signals also appeared in the NLT after full feeding, where pomc mRNA is highly expressed. These results indicate that NPGL may be a short-term satiety factor in fish and that the coexpression of NPGL and POMC may be present in the hypothalamus of male tilapia.
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Affiliation(s)
- Jinfeng Huang
- State Key Laboratory Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yuchen Hao
- State Key Laboratory Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Kingwai Lai
- State Key Laboratory Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Likang Lyu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR China
| | - Xi Yuan
- State Key Laboratory Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Guokun Yang
- State Key Laboratory Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wensheng Li
- State Key Laboratory Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Caiyun Sun
- State Key Laboratory Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China.
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Benavides M, Bonnet S, Le Moigne FAC, Armin G, Inomura K, Hallstrøm S, Riemann L, Berman-Frank I, Poletti E, Garel M, Grosso O, Leblanc K, Guigue C, Tedetti M, Dupouy C. Sinking Trichodesmium fixes nitrogen in the dark ocean. ISME J 2022; 16:2398-2405. [PMID: 35835942 PMCID: PMC9478103 DOI: 10.1038/s41396-022-01289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 01/04/2023]
Abstract
The photosynthetic cyanobacterium Trichodesmium is widely distributed in the surface low latitude ocean where it contributes significantly to N2 fixation and primary productivity. Previous studies found nifH genes and intact Trichodesmium colonies in the sunlight-deprived meso- and bathypelagic layers of the ocean (200-4000 m depth). Yet, the ability of Trichodesmium to fix N2 in the dark ocean has not been explored. We performed 15N2 incubations in sediment traps at 170, 270 and 1000 m at two locations in the South Pacific. Sinking Trichodesmium colonies fixed N2 at similar rates than previously observed in the surface ocean (36-214 fmol N cell-1 d-1). This activity accounted for 40 ± 28% of the bulk N2 fixation rates measured in the traps, indicating that other diazotrophs were also active in the mesopelagic zone. Accordingly, cDNA nifH amplicon sequencing revealed that while Trichodesmium accounted for most of the expressed nifH genes in the traps, other diazotrophs such as Chlorobium and Deltaproteobacteria were also active. Laboratory experiments simulating mesopelagic conditions confirmed that increasing hydrostatic pressure and decreasing temperature reduced but did not completely inhibit N2 fixation in Trichodesmium. Finally, using a cell metabolism model we predict that Trichodesmium uses photosynthesis-derived stored carbon to sustain N2 fixation while sinking into the mesopelagic. We conclude that sinking Trichodesmium provides ammonium, dissolved organic matter and biomass to mesopelagic prokaryotes.
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Affiliation(s)
- Mar Benavides
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
- Turing Center for Living Systems, Aix-Marseille University, 13009, Marseille, France.
| | - Sophie Bonnet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Frédéric A C Le Moigne
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
- LEMAR, Laboratoire des Sciences de l'Environnement Marin, UMR6539, CNRS, UBO, IFREMER, IRD, 29280, Plouzané, Technopôle Brest-Iroise, France
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt, Carmel, Haifa, Israel
| | - Emilie Poletti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Garel
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Olivier Grosso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Karine Leblanc
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Catherine Guigue
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Tedetti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Cécile Dupouy
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
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Xia J, Xin W, Wang F, Xie W, Liu Y, Xu J. Cloning and Characterization of Fructose-1,6-Bisphosphate Aldolase from Euphausia superba. Int J Mol Sci 2022; 23:ijms231810478. [PMID: 36142390 PMCID: PMC9499490 DOI: 10.3390/ijms231810478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) is a highly conserved enzyme that is involved in glycolysis and gluconeogenesis. In this study, we cloned the fructose-1,6-bisphosphate aldolase gene from Euphausia superba (EsFBA). The full-length cDNA sequence of EsFBA is 1098 bp long and encodes a 365-amino-acid protein. The fructose-1,6-bisphosphate aldolase gene was expressed in Escherichia coli (E. coli). A highly purified protein was obtained using HisTrap HP affinity chromatography and size-exclusion chromatography. The predicted three-dimensional structure of EsFBA showed a 65.66% homology with human aldolase, whereas it had the highest homology (84.38%) with the FBA of Penaeus vannamei. Recombinant EsFBA had the highest activity at 45 °C and pH 7.0 in phosphate buffer. By examining the activity of metal ions and EDTA, we found that the effect of metal ions and EDTA on EsFBA's enzyme activity was not significant, while the presence of borohydride severely reduced the enzymatic activity; thus, EsFBA was confirmed to be a class I aldolase. Furthermore, targeted mutations at positions 34, 147, 188, and 230 confirmed that they are key amino acid residues for EsFBA.
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Affiliation(s)
- Jikun Xia
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Wanmeng Xin
- State Key Laboratory of Biocatalysts and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Fang Wang
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
| | - Wancui Xie
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yi Liu
- State Key Laboratory of Biocatalysts and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
- Correspondence: (Y.L.); (J.X.)
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China
- Correspondence: (Y.L.); (J.X.)
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Jiang P, Gao S, Chen Z, Sun H, Li P, Yue D, Pan Y, Wang X, Mi R, Dong Y, Jiang J, Zhou Z. Cloning and characterization of a phosphomevalonate kinase gene that is involved in saponin biosynthesis in the sea cucumber Apostichopus japonicus. Fish Shellfish Immunol 2022; 128:67-73. [PMID: 35921931 DOI: 10.1016/j.fsi.2022.07.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/18/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
The sea cucumber Apostichopus japonicus is one of the most dominant and economically important aquaculture species in China. Saponin, which possesses notable biological and pharmacological properties, is a key determinant of the nutritional and health value of A. japonicus. In the present study, we amplified the full-length cDNA of a phosphomevalonate kinase (PMK) gene (named AjPMK) using rapid amplification of cDNA ends (RACE). Subsequently, we engineered a recombinant AjPMK (rAjPMK) protein and assessed its enzymatic activity by enzyme-linked immunosorbent assay (ELISA). Proteins that interact with rAjPMK were screened and identified via pull-down assay combined with liquid chromatography with tandem mass spectrometry (LC-MS/MS). We found that the full-length cDNA of AjPMK contained 1354 bp and an open reading frame (ORF) of 612 bp. The AjPMK protein was predicted not to contain a signal peptide but to contain a phosphonolate kinase domain seen in higher eukaryotes and a P-loop with a relatively conserved nucleoside triphosphate hydrolase domain. The molecular weight of the AjPMK protein was estimated to be 23.81 kDa, and its isoelectric point was predicted to be 8.72. Phylogenetic analysis showed that AjPMK had a closer evolutionary relationship with genes from starfish than with those of other selected species. Besides, we found that rAjPMK synthesized mevalonate-5-diphosphate, interacted either directly or indirectly with crucial pattern recognition receptors (PRRs) and was regulated by immune-related processes, including antioxidative reactions, stress resistance responses and enzyme hydrolysis. Moreover, AjPMK also interacted with farnesyl pyrophosphate synthase, an enzyme reported to be involved in saponin biosynthesis. Together, our findings implied that AjPMK may be directly involved in saponin biosynthesis and the regulation of various innate immune processes.
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Affiliation(s)
- Pingzhe Jiang
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Shan Gao
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Zhong Chen
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Hongjuan Sun
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Peipei Li
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Dongmei Yue
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Yongjia Pan
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Xuda Wang
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Rui Mi
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Ying Dong
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Jingwei Jiang
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China.
| | - Zunchun Zhou
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China.
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Ganapathi M, Friocourt G, Gueguen N, Friederich MW, Le Gac G, Okur V, Loaëc N, Ludwig T, Ka C, Tanji K, Marcorelles P, Theodorou E, Lignelli-Dipple A, Voisset C, Walker MA, Briere LC, Bourhis A, Blondel M, LeDuc C, Hagen J, Cooper C, Muraresku C, Ferec C, Garenne A, Lelez-Soquet S, Rogers CA, Shen Y, Strode DK, Bizargity P, Iglesias A, Goldstein A, High FA, Network UD, Sweetser DA, Ganetzky R, Van Hove JLK, Procaccio V, Le Marechal C, Chung WK. A homozygous splice variant in ATP5PO, disrupts mitochondrial complex V function and causes Leigh syndrome in two unrelated families. J Inherit Metab Dis 2022; 45:996-1012. [PMID: 35621276 PMCID: PMC9474623 DOI: 10.1002/jimd.12526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 11/10/2022]
Abstract
Mitochondrial complex V plays an important role in oxidative phosphorylation by catalyzing the generation of ATP. Most complex V subunits are nuclear encoded and not yet associated with recognized Mendelian disorders. Using exome sequencing, we identified a rare homozygous splice variant (c.87+3A>G) in ATP5PO, the complex V subunit which encodes the oligomycin sensitivity conferring protein, in three individuals from two unrelated families, with clinical suspicion of a mitochondrial disorder. These individuals had a similar, severe infantile and often lethal multi-systemic disorder that included hypotonia, developmental delay, hypertrophic cardiomyopathy, progressive epileptic encephalopathy, progressive cerebral atrophy, and white matter abnormalities on brain MRI consistent with Leigh syndrome. cDNA studies showed a predominant shortened transcript with skipping of exon 2 and low levels of the normal full-length transcript. Fibroblasts from the affected individuals demonstrated decreased ATP5PO protein, defective assembly of complex V with markedly reduced amounts of peripheral stalk proteins, and complex V hydrolytic activity. Further, expression of human ATP5PO cDNA without exon 2 (hATP5PO-∆ex2) in yeast cells deleted for yATP5 (ATP5PO homolog) was unable to rescue growth on media which requires oxidative phosphorylation when compared to the wild type construct (hATP5PO-WT), indicating that exon 2 deletion leads to a non-functional protein. Collectively, our findings support the pathogenicity of the ATP5PO c.87+3A>G variant, which significantly reduces but does not eliminate complex V activity. These data along with the recent report of an affected individual with ATP5PO variants, add to the evidence that rare biallelic variants in ATP5PO result in defective complex V assembly, function and are associated with Leigh syndrome.
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Affiliation(s)
- Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Naig Gueguen
- MitoLab, UMR CNRS 6015 - INSERM U1083, MitoVasc Institute, Angers University Hospital, Angers, France
| | - Marisa W Friederich
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Volkan Okur
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Thomas Ludwig
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Chandran Ka
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Kurenai Tanji
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Pascale Marcorelles
- CHRU de Brest, Service d'anatomie cytologie pathologie, CHU et centre de référence des maladies neuromusculaires, Brest, France
| | - Evangelos Theodorou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Medical Genetics & Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Angela Lignelli-Dipple
- Department of Radiology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Melissa A Walker
- Division of Neurogenetics, Child Neurology, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Amélie Bourhis
- CHRU de Brest, Service d'anatomie cytologie pathologie, CHU et centre de référence des maladies neuromusculaires, Brest, France
| | | | - Charles LeDuc
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Jacob Hagen
- Department of Biomedical Sciences, Columbia University Irving Medical Center, New York, New York, USA
| | - Cathleen Cooper
- Department of Radiology, Columbia University Irving Medical Center, New York, New York, USA
| | - Colleen Muraresku
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Cassandra A Rogers
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yufeng Shen
- Department of Biomedical Sciences, Columbia University Irving Medical Center, New York, New York, USA
| | - Dana K Strode
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
| | - Peyman Bizargity
- Division of Medical Genetics, Cohen Children's Medical Center, New York, New York, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, New York, USA
| | - Alejandro Iglesias
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Amy Goldstein
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frances A High
- Division of Medical Genetics & Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Medical Genetics & Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rebecca Ganetzky
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Johan L K Van Hove
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015 - INSERM U1083, MitoVasc Institute, Angers University Hospital, Angers, France
| | - Cedric Le Marechal
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
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Zhang R, Liu Y, Wang W, Xu Y, Wang Z, Zhong H, Tang C, Wang J, Sun H, Mao H, Yan J. A novel interleukin-1 receptor-associated kinase 4 from blunt snout bream (Megalobrama amblycephala) is involved in inflammatory response via MyD88-mediated NF-κB signal pathway. Fish Shellfish Immunol 2022; 127:23-34. [PMID: 35661767 DOI: 10.1016/j.fsi.2022.05.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/22/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Interleukin-1 receptor-associated kinase 4 (IRAK4) plays a crucial role in the Toll-like receptor/IL-1R signal pathway, which mediates the downstream signal transduction involved in innate and adaptive immunity. In the present study, an IRAK4 homologue (named as MaIRAK4) from blunt snout bream (Megalobrama amblycephala) was cloned and characterized. The open reading frame (ORF) of MaIRAK4 contains 1422 nucleotides, encoding a putative protein of 473 amino acids. Protein structural analysis revealed that MaIRAK4 has an N-terminal death domain (DD) and a central kinase domain (S_TKc), similar to those of mammals and other fishes. Multiple sequence alignment demonstrated that MaIRAK4 is highly homologous with that of grass carp (97.67%). The qRT-PCR analysis showed that MaIRAK4 expressed widely in all examined tissues, including heart, liver, spleen, kidney, head-kidney, gill, intestine and muscle, with the highest expression in the liver and spleen. After stimulation with LPS, MaIRAK4 expression upregulated significantly and reached a peak at 6 h and 12 h post LPS stimulation in the spleen and head-kidney, respectively. After challenge with Aeromonas hydrophila, MaIRAK4 expression peaked at 48 h and 72 h in spleen/head-kidney and liver, respectively. These results implied that MaIRAK4 is involved in the host defense against bacterial infection. Subcellular localization analysis indicated that MaIRAK4 distributed in the cytoplasm. Co-immunoprecipitation and subcellular co-localization assay revealed that MaIRAK4 can combine with MaMyD88 through DD domain. MaIRAK4 overexpression can induce slightly the NF-κB promoter activity in HEK 293 cells. However, the activity of NF-κB promoter was dramatically enhanced after co-transfection with MaIRAK4 and MaMyD88 plasmids. The results showed that MaIRAK4 was involved in NF-κB signal pathway mediated by maMyD88. The expression level of pro-inflammatory cytokines (IL-1β, IL-6, IL-8 and TNF-α) decreased significantly after the siRNA-mediated knockdown of MaIRAK4. Together, these results suggest that MaIRAK4 plays an important function in the innate immunity of M. amblycephala by inducing cytokines expression.
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Affiliation(s)
- Ru Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Yang Liu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Wenjun Wang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Yandong Xu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Zuzhen Wang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Huan Zhong
- College of Animal Science and Technology, Hunan Agriculture University, Changsha, 410128, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Jing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
| | - Hongyang Sun
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Haibin Mao
- Department of Biology Education, ZhouNan High School, Changsha, 410008, China
| | - Jinpeng Yan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China.
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Cai WH, Zheng XQ, Liang YR. High-Light-Induced Degradation of Photosystem II Subunits’ Involvement in the Albino Phenotype in Tea Plants. Int J Mol Sci 2022; 23:ijms23158522. [PMID: 35955658 PMCID: PMC9369412 DOI: 10.3390/ijms23158522] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The light-sensitive (LS) albino tea plant grows albinic shoots lacking chlorophylls (Chls) under high-light (HL) conditions, and the albinic shoots re-green under low light (LL) conditions. The albinic shoots contain a high level of amino acids and are preferential materials for processing quality green tea. The young plants of the albino tea cultivars are difficult to be cultivated owing to lacking Chls. The mechanisms of the tea leaf bleaching and re-greening are unknown. We detected the activity and composition of photosystem II (PSII) subunits in LS albino tea cultivar “Huangjinya” (HJY), with a normal green-leaf cultivar “Jinxuan” (JX) as control so as to find the relationship of PSII impairment to the albino phenotype in tea. The PSII of HJY is more vulnerable to HL-stress than JX. HL-induced degradation of PSII subunits CP43, CP47, PsbP, PsbR. and light-harvest chlorophyll–protein complexes led to the exposure and degradation of D1 and D2, in which partial fragments of the degraded subunits were crosslinked to form larger aggregates. Two copies of subunits PsbO, psbN, and Lhcb1 were expressed in response to HL stress. The cDNA sequencing of CP43 shows that there is no difference in sequences of PsbC cDNA and putative amino acids of CP43 between HJY and JX. The de novo synthesis and/or repair of PSII subunits is considered to be involved in the impairment of PSII complexes, and the latter played a predominant role in the albino phenotype in the LS albino tea plant.
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Zhang F, Isak AN, Yang S, Song Y, Ren L, Feng C, Chen G. Smartly responsive DNA-miRNA hybrids packaged in exosomes for synergistic enhancement of cancer cell apoptosis. Nanoscale 2022; 14:6612-6619. [PMID: 35421879 DOI: 10.1039/d1nr08539e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Endogenous and exogenous tumor-related microRNAs (miRNAs) are considered promising tumor biomarkers and tumor therapeutic agents. In this work, we propose a miRNA self-responsive drug delivery system (miR-SR DDS), which enables the association between endogenous and exogenous miRNAs, so as to achieve a smart responsive and synergistic drug delivery. The miR-SR DDS consists of DNA-miRNA hybrids of let-7a and the complementary DNA of miR-155, which was packaged in exosomes. In response to the overexpressed miR-155 in breast cancer cells, the hybrids disintegrate and release let-7a and the complementary DNA of miR-155 to inhibit the expression of HMGA1 and relieve the inhibition of SOX1, respectively. Under the dual-targeted gene regulation, results show that the growth, migration and invasion of breast cancer cells can be synergistically inhibited through the Wnt/β-catenin signaling pathway. The concept and successful practice of the miR-SR DDS can be used as a reference for the development of miRNA drugs.
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Affiliation(s)
- Fan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Albertina N Isak
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Shiqi Yang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Yuchen Song
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Lingjie Ren
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
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Liu Y, Li S, Yang H, Chen Y, Fan D. Decreased carboxylesterase expression associated with increased susceptibility to insecticide in Mythimna separata. Arch Insect Biochem Physiol 2022; 109:e21859. [PMID: 34881457 DOI: 10.1002/arch.21859] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/26/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
Carboxylesterases are one of the three major types of detoxification enzyme in insects. In this study, we screened 12 full-length carboxylesterase cDNA sequences from the oriental armyworm Mythimna separata; they were named MsCarE1-MsCarE12 and registered in GenBank with accession numbers MK440541-MK440552. Treatment of fourth instar larvae of M. separata with the LD50 of the insecticide chlorantraniliprole increased the expression levels of MsCarE3 and MsCarE4, while treatment with the LD50 of lambda-cyhalothrin significantly increased the expression levels of MsCarE5 and MsCarE10. Spatiotemporal expression detection showed that MsCarE3, MsCarE4, MsCarE5, and MsCarE10 were expressed at different developmental stages and in different tissues of M. separata and their expression levels were different. Induction using a high dose of chlorantraniliprole resulted in lower expression of MsCarE3 and MsCarE4. LD50 of lambda-cyhalothrin induced higher expression of MsCarE5 and MsCarE10, while LD70 induced higher MsCarE10 expression at 3, 6, and 12 h after treatment. RNA interference successfully inhibited the expression of MsCarE3, MsCarE4, MsCarE5, and MsCarE10, to different degrees at different time points. Silencing of MsCarE5, or MsCarE5 and MsCarE10 simultaneously changed carboxylesterase activity and increased the susceptibility of M. separata larvae to lambda-cyhalothrin. This study provides a new method to increase the insect susceptibility to insecticide.
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Affiliation(s)
- Yan Liu
- Department of Plant Protection, College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Shuangyu Li
- Department of Plant Protection, College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Hongjia Yang
- Department of Plant Protection, College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Yaru Chen
- Department of Plant Protection, College of Agronomy, Northeast Agricultural University, Harbin, China
| | - Dong Fan
- Department of Plant Protection, College of Agronomy, Northeast Agricultural University, Harbin, China
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Su Z, Xuan X, Sheng Z, Wang F, Zhang X, Ye D, Wang X, Dong T, Pei D, Zhang P, Fang J, Wang C. Characterization and regulatory mechanism analysis of VvmiR156a-VvAGL80 pair during grapevine flowering and parthenocarpy process induced by gibberellin. Plant Genome 2022; 15:e20181. [PMID: 34882981 DOI: 10.1002/tpg2.20181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
MicroRNA156 (miR156) is an important conserved miRNA family in plants. Recently, we revealed VvmiR156a could involve in the modulation of gibberellin (GA)-mediated flower and berry development process of grapevine (Vitis vinifera L.). However, how to manipulate this process is unclear. For this, we used the GA-induced grapevine parthenocarpy system to investigate the regulatory roles of VvmiR156a during this process. Here, we cloned the mature and precursor sequences of VvmiR156a in Wink grape and identified its potential target gene VvAGL80, which belongs to the MADS-box gene family. Moreover, using RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-RACE) and poly(A)polymerase-mediated 3' rapid amplification of cDNA (PPM-RACE) technologies, it confirmed that VvAGL80 was the true target gene of VvmiR159a. Analysis of promoter cis-elements and β-glucuronidase (GUS) staining showed that both VvmiR156a and VvAGL80 contained GA-responsive elements and could respond to GA treatments. Quantitative real-time-polymerase chain reaction (qRT-PCR) analysis exhibited the VvmiR156a and VvAGL80 showed opposite expression trends during grapevine flower and berry development, indicating that VvmiR156a negatively regulated the expression of VvAGL80 during this process. After GA treatment, the expression of miR156 in flowers was downregulated significantly, while that of VvAGL80 was upregulated, thereby accelerating grapevine flowering. Furthermore, GA treatment enhanced the negative regulation of VvmiR156a on VvAGL80 in seed, especially at the seed-coat hardening stage, which was the key period of seed growth and development. Our findings enriched the knowledge of the regulatory mechanism of the miRNA-mediated grapevine parthenocarpy process.
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Affiliation(s)
- Ziwen Su
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xuxian Xuan
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Zilu Sheng
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Fei Wang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Xiaowen Zhang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Dongdong Ye
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Xicheng Wang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Tianyu Dong
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Dan Pei
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Peian Zhang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural Univ., Nanjing, 210095, China
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Challal D, Colin J, Villa T, Libri D. A Modified Cross-Linking Analysis of cDNAs (CRAC ) Protocol for Detecting RNA-Protein Interactions and Transcription at Single-Nucleotide Resolution. Methods Mol Biol 2022; 2477:35-55. [PMID: 35524110 DOI: 10.1007/978-1-0716-2257-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Detecting protein-RNA interactions in vivo is essential for deciphering many important cellular pathways. Several methods have been described for this purpose, among which cross-linking analysis of cDNA, CRAC. This method relies on a first step of UV cross-linking of living yeast cells and several subsequent steps of purification of the protein-RNA complexes, some of which under denaturing condition. Without altering the general principle of the method, we have modified and improved the protocol, with the specific aim of sequencing the nascent RNA isolated from transcription complexes and generate high-resolution and directional transcription maps.
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Affiliation(s)
- Drice Challal
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
- Institut Curie, PSL Research University, CNRS UMR 3348, Orsay, France
| | - Jessie Colin
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
- Ecole Pratique des Hautes Etudes - PSL Research university, Paris, France
- Unité Biologie des ARN des Pathogènes Fongiques, Institut Pasteur, Paris, France
| | - Tommaso Villa
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Domenico Libri
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France.
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Yasuno R, Mitani Y, Ohmiya Y. Gene Cloning and Functional Analysis of the Luciferase from Luminous Syllids of the Genus Odontosyllis. Methods Mol Biol 2022; 2524:3-15. [PMID: 35821459 DOI: 10.1007/978-1-0716-2453-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The marine fireworm Odontosyllis spp. produce the bluish-green bioluminescence (BL). Despite years of research, molecular mechanisms of this unique luciferin-luciferase reaction have not been elucidated. Recently, the genes encoding luciferases of O. undecimdonta and O. enopla have been identified. Here, we describe gene cloning techniques for the luciferase of Odontosyllis spp. from a small number of specimens using highly sensitive mass spectrometry analysis in combination with RNA-sequencing. The luciferase activities of the cloned cDNAs are confirmed by BL assay in vitro using recombinant protein expressed in mammalian cells.
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Affiliation(s)
- Rie Yasuno
- Cellular and Molecular Biotechnology Research Institute, Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yasuo Mitani
- Bioproduction Research Institute, AIST, Sapporo, Japan.
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, AIST, Osaka, Japan
- Osaka Institute of Technology (OIT), Osaka, Japan
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Sliadovskii D, Ponomareva T, Molchanov M, Pozdnyakova-Filatova I, Timchenko M, Marchenkov V, Gusev O, Sogorin E. β-elimination of hyaluronate by red king crab hyaluronidase. Sci Rep 2021; 11:22600. [PMID: 34799594 PMCID: PMC8604925 DOI: 10.1038/s41598-021-01890-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/03/2021] [Indexed: 11/09/2022] Open
Abstract
Crustacean hyaluronidases are poorly understood both in terms of their enzymatic properties and in terms of their structural features. In this work, we show that the hepatopancreas homogenate of the red king crab has a hyaluronidase activity that is an order of magnitude higher than its commercial counterpart. Zymography revealed that the molecular weight of a protein with hyalorunidase activity is 40-50 kDa. Analysis of the hepatopancreas transcriptome and results of cloning and sequencing of cDNA revealed a hyaluronidase sequence with an expected molecular weight of 42.5 kDa. Further analysis showed that hyaluronat enzymatic cleavage follows the [Formula: see text]-elimination mechanism, which is well known for bacterial hyaluronidases. The results of ion-exchange chromatography showed that the final product of hyaluronate degradation is unsaturated tetrasaccharide. Thus, we identified a new hyaluronidase of higher eukaryotes, which is not integrated into the modern classification of hyaluronidases.
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Affiliation(s)
- Dmitrii Sliadovskii
- Federal Research Center "Pushchino Scientific Center for Biological Research of the RAS", Pushchino, Russia, 142290
| | - Tatyana Ponomareva
- Federal Research Center "Pushchino Scientific Center for Biological Research of the RAS", Pushchino, Russia, 142290
| | - Maxim Molchanov
- Institute of Theoretical and Experimental Biophysics of the RAS, Pushchino, Russia, 142290
| | - Irina Pozdnyakova-Filatova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the RAS", G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russia, 142290
| | - Maria Timchenko
- Federal Research Center "Pushchino Scientific Center for Biological Research of the RAS", Pushchino, Russia, 142290
| | | | - Oleg Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia, 420012
- Graduate School of Medicine, Juntendo University, Tokyo , 113-8421, Japan
| | - Evgeny Sogorin
- Federal Research Center "Pushchino Scientific Center for Biological Research of the RAS", Pushchino, Russia, 142290.
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Diao P, Sun H, Bao Z, Li W, Niu N, Li W, Wuriyanghan H. Expression of an Antiviral Gene GmRUN1 from Soybean Is Regulated via Intron-Mediated Enhancement (IME). Viruses 2021; 13:2032. [PMID: 34696462 PMCID: PMC8539222 DOI: 10.3390/v13102032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/18/2022] Open
Abstract
Most of R (resistance) genes encode the protein containing NBS-LRR (nucleotide binding site and leucine-rich repeat) domains. Here, N. benthamiana plants were used for transient expression assays at 3-4 weeks of age. We identified a TNL (TIR-NBS-LRR) encoding gene GmRUN1 that was resistant to both soybean mosaic virus (SMV) and tobacco mosaic virus (TMV). Truncation analysis indicated the importance of all three canonical domains for GmRUN1-mediated antiviral activity. Promoter-GUS analysis showed that GmRUN1 expression is inducible by both salicylic acid (SA) and a transcription factor GmDREB3 via the cis-elements as-1 and ERE (ethylene response element), which are present in its promoter region. Interestingly, GmRUN1 gDNA (genomic DNA) shows higher viral resistance than its cDNA (complementary DNA), indicating the existence of intron-mediated enhancement (IME) for GmRUN1 regulation. We provided evidence that intron2 of GmRUN1 increased the mRNA level of native gene GmRUN1, a soybean antiviral gene SRC7 and also a reporter gene Luciferase, indicating the general transcriptional enhancement of intron2 in different genes. In summary, we identified an antiviral TNL type soybean gene GmRUN1, expression of which was regulated at different layers. The investigation of GmRUN1 gene regulatory network would help to explore the mechanism underlying soybean-SMV interactions.
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Affiliation(s)
- Pengfei Diao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Hongyu Sun
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Zhuo Bao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Wenxia Li
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Niu Niu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. PLoS One 2021; 16:e0244468. [PMID: 34432798 PMCID: PMC8386831 DOI: 10.1371/journal.pone.0244468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/09/2021] [Indexed: 02/06/2023] Open
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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S Alotaibi S, El-Shehawi AM, M Elseehy M. Heat Shock Proteins Expression Is Regulated by Promoter CpG Methylation/demethylation under Heat Stress in Wheat Varieties. Pak J Biol Sci 2021; 23:1310-1320. [PMID: 32981265 DOI: 10.3923/pjbs.2020.1310.1320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Heat shock proteins are induced by high temperature and other environmental stimuli to protect cellular proteins. Despite extensive research on the molecular response to heat stress, the effect of high temperatures on genes and pathways remains unclear. This study investigated the expression of the HSP17 gene in nine Egyptian wheat varieties and the role of HSP17 promoter CpG methylation in the regulation of HSP17 under high temperature. MATERIALS AND METHODS The HSP17 expression was investigated by using semi-quantitative PCR analysis. Methylation at the HSP17 promoter proximal region was analyzed using bisulphite sequencing and CpG viewer software. RESULTS Under normal conditions, HSP17 and methyltransferase 3 (MET3) exhibited similar expression levels in the 9 studied varieties. After exposure to high temperature, the expression level of HSP17 in Giza155 was barely detected. Among the nine varieties, the expression level of HSP17 was highest in Giza168 (11.3 folds of Giza155). Analysis of methylation of 14 CpG islands at the HSP17 proximal promoter sequence showed that methylation of 10 CpG islands differed only by 10-20%, whereas methylation at the other 4 CpGs differed by 56.7-60%. The high expression of HSP17 in Giza168 in response to high temperature was associated with low methylation of four CpGs and low MET3 expression, whereas low expression of HSP17 in Giza155 was associated with high methylation and high MET3 expression. CONCLUSION The results can aid the development of next-generation approaches to the evaluation of commercial wheat varieties and the development of next-generation approaches to plant breeding employing epiallele integration.
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Yang XQ, Zhao XL, Yu H, Zhang J, Han LX, Liu D. Speckled 100 kDa gene in pigs: Alternative splicing, subcellular localization, and response to interferon-α stimulation. Gene 2021; 791:145710. [PMID: 33984443 DOI: 10.1016/j.gene.2021.145710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/27/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
Speckled 100 kDa (Sp100) plays an important role in the antiviral immune response, however, little is known about porcine Sp100. In this study, porcine Sp100 was cloned and its response to interferon (IFN) α was identified. We obtained the cDNA (V1) of the gene, SP100, and seven alternative splicing variants (V2-8). Isoform V1 encoded a 386 amino acid protein and contained a homogeneously-staining region (HSR) domain. Isoforms V3, 4, 6 and 7 were deletion/insertion variants and contained HSR domain as V1. The splicing of porcine SP100 was very complicated and many transcripts existed as revealed by cloning and minigene analyses. Using GFP-fusion constructs isoforms V1, 3, 4, 6 and 7 were localized to nucleus and the nuclear localization signal was identified as PSNRKRR at positions 331-337 of V1. Porcine SP100 was unevenly distributed in all tissues studied and differentially expressed between pigs with different disease-resistance/susceptibilities. Porcine SP100 was strongly increased by IFNα due to the existence of an IFN-stimulated response element in the promoter. A single nucleotide - 70A > C polymorphism enhanced promoter activity. The results provided the basis for determining the role of Sp100 in antiviral responses and may assist in breeding pigs with high disease-resistance.
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Affiliation(s)
- Xiu-Qin Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China.
| | - Xue-Lian Zhao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Hao Yu
- Jilin University, Changchun 130012, China
| | - Jiao Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Li-Xin Han
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
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50
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Bednarz-Misa I, Fleszar MG, Fortuna P, Lewandowski Ł, Mierzchała-Pasierb M, Diakowska D, Krzystek-Korpacka M. Altered L-Arginine Metabolic Pathways in Gastric Cancer: Potential Therapeutic Targets and Biomarkers. Biomolecules 2021; 11:biom11081086. [PMID: 34439753 PMCID: PMC8395015 DOI: 10.3390/biom11081086] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022] Open
Abstract
There is a pressing need for molecular targets and biomarkers in gastric cancer (GC). We aimed at identifying aberrations in L-arginine metabolism with therapeutic and diagnostic potential. Systemic metabolites were quantified using mass spectrometry in 293 individuals and enzymes’ gene expression was quantified in 29 paired tumor-normal samples using qPCR and referred to cancer pathology and molecular landscape. Patients with cancer or benign disorders had reduced systemic arginine, citrulline, and ornithine and elevated symmetric dimethylarginine and dimethylamine. Citrulline and ornithine depletion was accentuated in metastasizing cancers. Metabolite diagnostic panel had 91% accuracy in detecting cancer and 70% accuracy in differentiating cancer from benign disorders. Gastric tumors had upregulated NOS2 and downregulated ASL, PRMT2, ORNT1, and DDAH1 expression. NOS2 upregulation was less and ASL downregulation was more pronounced in metastatic cancers. Tumor ASL and PRMT2 expression was inversely related to local advancement. Enzyme up- or downregulation was greater or significant solely in cardia subtype. Metabolic reprogramming in GC includes aberrant L-arginine metabolism, reflecting GC subtype and pathology, and is manifested by altered interplay of its intermediates and enzymes. Exploiting L-arginine metabolic pathways for diagnostic and therapeutic purposes is warranted. Functional studies on ASL, PRMT2, and ORNT1 in GC are needed.
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Affiliation(s)
- Iwona Bednarz-Misa
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, 50-368 Wroclaw, Poland; (I.B.-M.); (M.G.F.); (P.F.); (Ł.L.); (M.M.-P.)
| | - Mariusz G. Fleszar
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, 50-368 Wroclaw, Poland; (I.B.-M.); (M.G.F.); (P.F.); (Ł.L.); (M.M.-P.)
| | - Paulina Fortuna
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, 50-368 Wroclaw, Poland; (I.B.-M.); (M.G.F.); (P.F.); (Ł.L.); (M.M.-P.)
| | - Łukasz Lewandowski
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, 50-368 Wroclaw, Poland; (I.B.-M.); (M.G.F.); (P.F.); (Ł.L.); (M.M.-P.)
| | - Magdalena Mierzchała-Pasierb
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, 50-368 Wroclaw, Poland; (I.B.-M.); (M.G.F.); (P.F.); (Ł.L.); (M.M.-P.)
| | - Dorota Diakowska
- Department of Gastrointestinal and General Surgery, Wroclaw Medical University, 50-368 Wroclaw, Poland;
- Department of Nervous System Diseases, Wroclaw Medical University, 51-618 Wroclaw, Poland
| | - Małgorzata Krzystek-Korpacka
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, 50-368 Wroclaw, Poland; (I.B.-M.); (M.G.F.); (P.F.); (Ł.L.); (M.M.-P.)
- Correspondence:
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