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Zhao Y, Ma H, Wang Q, He X, Xing X, Wu X, Quan G, Bao S. Mycoplasma synoviae elongation factor thermo stable is an adhesion-associated protein that enters cells by endocytosis and stimulates DF-1 cell proliferation. BMC Vet Res 2024; 20:522. [PMID: 39558348 PMCID: PMC11575130 DOI: 10.1186/s12917-024-04374-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 11/07/2024] [Indexed: 11/20/2024] Open
Abstract
Mycoplasma synoviae is an important avian pathogen that causes respiratory infections and arthritis symptoms in chickens and turkeys, resulting in significant economic damage to the poultry farming industry worldwide. Cell adhesion is a vital stage of Mycoplasma infection, and the proteins associated with this process play an important role in its pathogenesis. Elongation factor thermo stable (EF-Ts) is an important factor in prokaryotic biosynthesis that serves as a guanosine exchange factor for elongation factor thermo unstable (EF-Tu). To date, little is known about the role of EF-Ts in Mycoplasma infection. In this study, we identified EF-Ts as an immunogenic protein in M. synoviae through liquid chromatography with tandem mass spectrometry (LC-MS/MS) screening. We constructed an E. coli recombinant expression vector and prepared a highly efficient rabbit antiserum. Immunoblot analysis and suspension immunofluorescence revealed that the EF-Ts is located in both the cell membrane and cytoplasm. The prepared rabbit EF-Ts antiserum exhibited complement-dependent Mycoplasma-killing activity and inhibited the adhesion of rEF-Ts and M. synoviae to DF-1 cells. An in-vitro binding assay showed that EF-Ts could bind to fibronectin (Fn) and chicken plasminogen (cPlg) in a dose-dependent manner. In addition, EF-Ts could internalize into cells through lipid rafts and clathrin-dependent endocytosis and induce DF-1 cell proliferation. In conclusion, our studies demonstrated that MS EF-Ts is a potentially immunogenic, novel adhesion protein that acts as a critical virulence factor in M. synoviae adhesion to host cells during infection. These studies further deepen our understanding of the pathogenic mechanism of M. synoviae.
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Affiliation(s)
- Yunhai Zhao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Haiyun Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Qing Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Xiaoxiao He
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Xiaoyong Xing
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Xiaochun Wu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Guomei Quan
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Shijun Bao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
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2
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Wu Y, Wu Z, Gao Y, Fan Y, Dong Y, Zhang Y, Gai Z, Gu S. Comprehensive genomic analysis and evaluation of in vivo and in vitro safety of Heyndrickxia coagulans BC99. Sci Rep 2024; 14:26602. [PMID: 39496841 PMCID: PMC11535476 DOI: 10.1038/s41598-024-78202-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 10/29/2024] [Indexed: 11/06/2024] Open
Abstract
This study aimed to evaluate the safety profile and beneficial effects of Heyndrickxia coagulans strain BC99 (BC99) for potential use in functional foods and pharmaceuticals. We began with whole genome sequencing of BC99, followed by a comprehensive safety assessment comprising genome analysis, hemolysis, cytotoxicity, antibiotic susceptibility tests, and cell adhesion and tolerance studies, along with acute and subacute oral toxicity studies in animal models. BC99 was isolated from a well-characterized collection originating from the feces of a healthy infant. Our results indicated no hemolytic activity on Columbia blood agar plates and broad antibiotic sensitivity, including to gentamicin, ampicillin, chloramphenicol, ciprofloxacin, and others. Cytotoxicity testing confirmed no adverse effects on HT-29 cells and significant adhesive properties to intestinal epithelial cells. Tolerance tests demonstrated over 90% viability of BC99 under simulated gastrointestinal conditions. In vivo studies in mice and rats confirmed the absence of adverse effects following oral administration. Collectively, these findings support BC99's robust tolerance to gastrointestinal environments, strong adhesion capabilities, and a broad spectrum of antibiotic resistance, underlining its potential as a safe and effective agent for gut microbiota modulation and host health enhancement.
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Affiliation(s)
- Ying Wu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, P.R. China
| | - Zhiyi Wu
- Department of Research and Development, Henan Animic Biotechnology Co., Ltd, Henan, China
| | - Yinyin Gao
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, P.R. China
| | - Yixuan Fan
- Department of Research and Development, Henan Animic Biotechnology Co., Ltd, Henan, China
| | - Yao Dong
- Germline Stem Cells and Microenvironment Lab, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yinan Zhang
- Shanghai Institute of Quality Inspection and Technical Research, Shanghai, 200233, China
| | - Zhonghui Gai
- Department of Research and Development, Henan Animic Biotechnology Co., Ltd, Henan, China.
| | - Shaobin Gu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, P.R. China.
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3
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Boccardi V, Cari L, Bastiani P, Scamosci M, Cecchetti R, Nocentini G, Mecocci P. Aberrant telomeric structures and serum markers of telomere dysfunction in healthy aging: a preliminary study. Biogerontology 2024; 25:1069-1077. [PMID: 39001954 DOI: 10.1007/s10522-024-10120-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 07/06/2024] [Indexed: 07/15/2024]
Abstract
Telomeres undergo a progressive shortening process as individuals age, and it has been proposed that severely shortened and dysfunctional telomeres play a role in the aging process and the onset of age-related diseases in human beings. An emerging body of evidence indicates that the shortening of telomeres in cultured human cells is also influenced by other replication defects occurring within telomeric repeats. These abnormalities can be detected on metaphase chromosomes. Recent studies have also identified a set of serological markers for telomere dysfunction and DNA damage (elongation factor 1α [EF-1α], stathmin, and N-acetyl-glucosaminidase). With this study, the correlation between telomere abnormalities (by FISH) and these biomarkers as measured in blood serum (by ELISA) from a cohort of 22 healthy subjects at different ages (range 26-101 years) was analyzed. A strong positive correlation between aging and the presence of aberrant telomere structures, sister telomere loss (STL), and sister telomere chromatid fusions (STCF) was detected. When serum markers of telomere dysfunction were correlated with telomere abnormalities, we found that stathmin correlated with total aberrant telomeres structures (r = 0.431, p = 0.0453) and STCF (r = 0.533, p = 0.0107). These findings suggest that serum stathmin can be considered an easy-to-get marker of telomere dysfunction and may serve as valuable indicators of aging.
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Affiliation(s)
- Virginia Boccardi
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Santa Maria Della Misericordia Hospital, Perugia, Italy.
- Department of Medicine and Surgery, Institute of Gerontology and Geriatrics, University of Perugia, Piazzale Gambuli 1, 06132, Perugia, Italy.
| | - Luigi Cari
- Department of Medicine and Surgery, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - Patrizia Bastiani
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Santa Maria Della Misericordia Hospital, Perugia, Italy
| | - Michela Scamosci
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Santa Maria Della Misericordia Hospital, Perugia, Italy
| | - Roberta Cecchetti
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Santa Maria Della Misericordia Hospital, Perugia, Italy
| | - Giuseppe Nocentini
- Department of Medicine and Surgery, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - Patrizia Mecocci
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Santa Maria Della Misericordia Hospital, Perugia, Italy
- Division of Clinical Geriatrics, NVS Department, Karolinska Institutet, Stockholm, Sweden
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4
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Sassù F, Vomáčková Kykalová B, Vieira CS, Volf P, Loza Telleria E. Stability and suitability of housekeeping genes in phlebotomine sand flies. Sci Rep 2024; 14:23353. [PMID: 39375431 PMCID: PMC11458623 DOI: 10.1038/s41598-024-74776-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024] Open
Abstract
We investigated gene expression patterns in Lutzomyia and Phlebotomus sand fly vectors of leishmaniases. Using quantitative PCR, we assessed the expression stability of potential endogenous control genes commonly used in dipterans. We analyzed Lutzomyia longipalpis and Phlebotomus papatasi samples from L3 and L4 larval stages, adult sand flies of different sexes, diets, dsRNA injection, and Leishmania infection. Six genes were evaluated: actin, α-tubulin, GAPDH, 60 S ribosomal proteins L8 and L32 (RiboL8 and RiboL32), and elongation factor 1-α (EF1-α). EF1-α was among the most stably expressed along with RiboL8 in L. longipalpis larvae and RiboL32 in adults. In P. papatasi, EF1-α and RiboL32 were the top in larvae, while EF1-α and actin were the most stable in adults. RiboL8 and actin were the most stable genes in dissected tissues and infected guts. Additionally, five primer pairs designed for L. longipalpis or P. papatasi were effective in PCR with Lutzomyia migonei, Phlebotomus duboscqi, Phlebotomus perniciosus, and Sergentomyia schwetzi cDNA. Furthermore, L. longipalpis RiboL32 and P. papatasi α-tubulin primers were suitable for qPCR with cDNA from the other four species. Our research provides tools to enhance relative gene expression studies in sand flies, facilitating the selection of endogenous control for qPCR.
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Affiliation(s)
- Fabiana Sassù
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, 128 00, Czech Republic
| | - Barbora Vomáčková Kykalová
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, 128 00, Czech Republic
| | - Cecilia Stahl Vieira
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, 128 00, Czech Republic
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, 128 00, Czech Republic
| | - Erich Loza Telleria
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, 128 00, Czech Republic.
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Li M, Lou L, Ren L, Li C, Han R, Jiang J, Qi L, Jiang Y. EIF4G2 Promotes Hepatocellular Carcinoma Progression via IRES-dependent PLEKHA1 Translation Regulation. J Proteome Res 2024; 23:4553-4566. [PMID: 39213495 DOI: 10.1021/acs.jproteome.4c00457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Hepatocellular carcinoma (HCC) is a highly lethal cancer, and proteomic studies have shown increased protein diversity and abundance in HCC tissues, whereas the role of protein translation has not been extensively explored in HCC. Our research focused on key molecules in the translation process to identify a potential contributor in HCC. We discovered that EIF4G2, a crucial translation initiation factor, is significantly upregulated in HCC tissues and associated with poor prognosis. This study uniquely highlights the impact of EIF4G2 deletion, which suppresses tumor growth and metastasis both in vitro and in vivo. Furthermore, polysome analysis and nascent protein synthesis assays revealed EIF4G2's role in regulating protein translation, specifically identifying PLEKHA1 as a key translational product. This represents a novel mechanistic insight into HCC malignancy. RNA immunoprecipitation (RIP) and Dual-luciferase reporter assays further revealed that EIF4G2 facilitates PLEKHA1 translation via an IRES-dependent manner. Importantly, the synergistic effects of EIF4G2 depletion and PLEKHA1 reduction in inhibiting cell migration and invasion underscore the therapeutic potential of targeting this axis. This study not only advances our understanding of translational regulation in HCC but also identifies the EIF4G2-PLEKHA1 axis as a promising therapeutic target, offering new avenues for intervention in HCC treatment.
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Affiliation(s)
- Manman Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lijuan Lou
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Liangliang Ren
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chaoying Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Rui Han
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Junyi Jiang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lihui Qi
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ying Jiang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
- Anhui Medical University, Hefei 230032, China
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6
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Takada H, Fujiwara K, Atkinson GC, Chiba S, Hauryliuk V. Resolution of ribosomal stalling by EF-P and ABCF ATPases YfmR and YkpA/YbiT. Nucleic Acids Res 2024; 52:9854-9866. [PMID: 38943426 PMCID: PMC11381351 DOI: 10.1093/nar/gkae556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024] Open
Abstract
Efficiency of protein synthesis on the ribosome is strongly affected by the amino acid composition of the assembled amino acid chain. Challenging sequences include proline-rich motifs as well as highly positively and negatively charged amino acid stretches. Members of the F subfamily of ABC ATPases (ABCFs) have been long hypothesised to promote translation of such problematic motifs. In this study we have applied genetics and reporter-based assays to characterise the four housekeeping ABCF ATPases of Bacillus subtilis: YdiF, YfmM, YfmR/Uup and YkpA/YbiT. We show that YfmR cooperates with the translation factor EF-P that promotes translation of Pro-rich motifs. Simultaneous loss of both YfmR and EF-P results in a dramatic growth defect. Surprisingly, this growth defect can be largely suppressed though overexpression of an EF-P variant lacking the otherwise crucial 5-amino-pentanolylated residue K32. Using in vivo reporter assays, we show that overexpression of YfmR can alleviate ribosomal stalling on Asp-Pro motifs. Finally, we demonstrate that YkpA/YbiT promotes translation of positively and negatively charged motifs but is inactive in resolving ribosomal stalls on proline-rich stretches. Collectively, our results provide insights into the function of ABCF translation factors in modulating protein synthesis in B. subtilis.
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Affiliation(s)
- Hiraku Takada
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
- Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Keigo Fujiwara
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Virus Centre, Lund University, Lund, Sweden
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Virus Centre, Lund University, Lund, Sweden
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
- Science for Life Laboratory, Lund, Sweden
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7
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Luan H, Song D, Huang K, Li S, Xu H, Kachroo P, Kachroo A, Zhao L. Genome-wide analysis of the soybean eEF gene family and its involvement in virus resistance. FRONTIERS IN PLANT SCIENCE 2024; 15:1421221. [PMID: 39224853 PMCID: PMC11366645 DOI: 10.3389/fpls.2024.1421221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
Eukaryotic elongation factors (eEFs) are protein factors that mediate the extension of peptide chain, among which eukaryotic elongation factor 1 alpha (eEF1A) is one of the most abundant protein synthesis factors. Previously we showed that the P3 protein of Soybean mosaic virus (SMV), one of the most destructive and successful viral pathogens of soybean, targets a component of the soybean translation elongation complex to facilitate its pathogenesis. Here, we conducted a systematic analyses of the soybean eEF (GmeEF) gene family in soybean and examinedits role in virus resistance. In this study, GmeEF family members were identified and characterized based on sequence analysis. The 42 members, which were unevenly distributed across the 15 chromosomes, were renamed according to their chromosomal locations. The GmeEF members were further divided into 12 subgroups based on conserved motif, gene structure, and phylogenetic analyses. Analysis of the promoter regions showed conspicuous presence of myelocytomatosis (MYC) and ethylene-responsive (ERE) cis-acting elements, which are typically involved in drought and phytohormone response, respectively, and thereby in plant stress response signaling. Transcriptome data showed that the expression of 15 GmeEF gene family members changed significantly in response to SMV infection. To further examine EF1A function in pathogen response, three different Arabidopsis mutants carrying T-DNA insertions in orthologous genes were analyzed for their response to Turnip crinkle virus (TCV) and Cucumber mosaic virus (CMV). Results showed that there was no difference in viral response between the mutants and the wild type plants. This study provides a systematic analysis of the GmeEF gene family through analysis of expression patterns and predicted protein features. Our results lay a foundation for understanding the role of eEF gene in soybean anti-viral response.
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Affiliation(s)
- Hexiang Luan
- Institute of Plant Genetic Engineering, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Daiqiao Song
- Institute of Plant Genetic Engineering, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Kai Huang
- Institute of Plant Genetic Engineering, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Shuxin Li
- Institute of Plant Genetic Engineering, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hao Xu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Pradeep Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States
| | - Aardra Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States
| | - Longgang Zhao
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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Wimmer B, Schernthaner J, Edobor G, Friedrich A, Poeltner K, Temaj G, Wimmer M, Kronsteiner E, Pichler M, Gercke H, Huber R, Kaefer N, Rinnerthaler M, Karl T, Krauß J, Mohr T, Gerner C, Hintner H, Breitenbach M, Bauer JW, Rakers C, Kuhn D, von Hagen J, Müller N, Rathner A, Breitenbach-Koller H. RiboScreen TM Technology Delivers a Ribosomal Target and a Small-Molecule Ligand for Ribosome Editing to Boost the Production Levels of Tropoelastin, the Monomeric Unit of Elastin. Int J Mol Sci 2024; 25:8430. [PMID: 39125999 PMCID: PMC11312584 DOI: 10.3390/ijms25158430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Elastin, a key structural protein essential for the elasticity of the skin and elastogenic tissues, degrades with age. Replenishing elastin holds promise for anti-aging cosmetics and the supplementation of elastic activities of the cardiovascular system. We employed RiboScreenTM, a technology for identifying molecules that enhance the production of specific proteins, to target the production of tropoelastin. We make use of RiboScreenTM in two crucial steps: first, to pinpoint a target ribosomal protein (TRP), which acts as a switch to increase the production of the protein of interest (POI), and second, to identify small molecules that activate this ribosomal protein switch. Using RiboScreenTM, we identified ribosomal protein L40, henceforth eL40, as a TRP switch to boost tropoelastin production. Drug discovery identified a small-molecule hit that binds to eL40. In-cell treatment demonstrated activity of the eL40 ligand and delivered increased tropoelastin production levels in a dose-dependent manner. Thus, we demonstrate that RiboScreenTM can successfully identify a small-molecule hit capable of selectively enhancing tropoelastin production. This compound has the potential to be developed for topical or systemic applications to promote skin rejuvenation and to supplement elastic functionality within the cardiovascular system.
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Affiliation(s)
- Bjoern Wimmer
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Jan Schernthaner
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Genevieve Edobor
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Andreas Friedrich
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Katharina Poeltner
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Gazmend Temaj
- Human Genetics, Faculty of Pharmacy, College UBT, 10000 Pristina, Kosovo;
| | - Marlies Wimmer
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Elli Kronsteiner
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Mara Pichler
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Hanna Gercke
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Ronald Huber
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Niklas Kaefer
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Mark Rinnerthaler
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Thomas Karl
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Jan Krauß
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Thomas Mohr
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; (T.M.); (C.G.)
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; (T.M.); (C.G.)
- Join Metabolome Facility, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
| | - Helmut Hintner
- Department of Dermatology and Allergology, University Hospital Salzburg, Muellner Hauptstraße 48, 5020 Salzburg, Austria; (H.H.); (J.W.B.)
| | - Michael Breitenbach
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
| | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital Salzburg, Muellner Hauptstraße 48, 5020 Salzburg, Austria; (H.H.); (J.W.B.)
| | - Christin Rakers
- Merck KGaA, Discovery & Development Technologies, Frankfurter Staße 250, 64293 Darmstadt, Germany (D.K.)
| | - Daniel Kuhn
- Merck KGaA, Discovery & Development Technologies, Frankfurter Staße 250, 64293 Darmstadt, Germany (D.K.)
| | - Joerg von Hagen
- Merck KGaA Healthcare, Frankfurter Straße 250, 64293 Darmstadt, Germany;
- ryon-Greentech Accelerator, Mainzer Straße 41, 64579 Gernsheim, Germany
| | - Norbert Müller
- Institute of Biochemistry, Johannes Kepler University, Altenbergerstraße 69, 4040 Linz, Austria;
- Department of Chemistry, Faculty of Science, University of South Bohemia in Českých Budějovicích, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Adriana Rathner
- Institute of Biochemistry, Johannes Kepler University, Altenbergerstraße 69, 4040 Linz, Austria;
| | - Hannelore Breitenbach-Koller
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; (B.W.); (J.S.); (G.E.); (A.F.); (K.P.); (M.W.); (E.K.); (M.P.); (H.G.); (R.H.); (M.R.); (T.K.); (J.K.); (M.B.)
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9
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Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024; 15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Transfer RNAs have been extensively explored as the molecules that translate the genetic code into proteins. At this interface of genetics and biochemistry, tRNAs direct the efficiency of every major step of translation by interacting with a multitude of binding partners. However, due to the variability of tRNA sequences and the abundance of diverse post-transcriptional modifications, a guidebook linking tRNA sequences to specific translational outcomes has yet to be elucidated. Here, we review substantial efforts that have collectively uncovered tRNA engineering principles that can be used as a guide for the tuning of translation fidelity. These principles have allowed for the development of basic research, expansion of the genetic code with non-canonical amino acids, and tRNA therapeutics.
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Affiliation(s)
- Joshua L Weiss
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - J C Decker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Ariadna Bolano
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Natalie Krahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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10
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Zhang W, Wang J, Shan C. The eEF1A protein in cancer: Clinical significance, oncogenic mechanisms, and targeted therapeutic strategies. Pharmacol Res 2024; 204:107195. [PMID: 38677532 DOI: 10.1016/j.phrs.2024.107195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
Eukaryotic elongation factor 1A (eEF1A) is among the most abundant proteins in eukaryotic cells. Evolutionarily conserved across species, eEF1A is in charge of translation elongation for protein biosynthesis as well as a plethora of non-translational moonlighting functions for cellular homeostasis. In malignant cells, however, eEF1A becomes a pleiotropic driver of cancer progression via a broad diversity of pathways, which are not limited to hyperactive translational output. In the past decades, mounting studies have demonstrated the causal link between eEF1A and carcinogenesis, gaining deeper insights into its multifaceted mechanisms and corroborating its value as a prognostic marker in various cancers. On the other hand, an increasing number of natural and synthetic compounds were discovered as anticancer eEF1A-targeting inhibitors. Among them, plitidepsin was approved for the treatment of multiple myeloma whereas metarrestin was currently under clinical development. Despite significant achievements in these two interrelated fields, hitherto there lacks a systematic examination of the eEF1A protein in the context of cancer research. Therefore, the present work aims to delineate its clinical implications, molecular oncogenic mechanisms, and targeted therapeutic strategies as reflected in the ever expanding body of literature, so as to deepen mechanistic understanding of eEF1A-involved tumorigenesis and inspire the development of eEF1A-targeted chemotherapeutics and biologics.
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Affiliation(s)
- Weicheng Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China.
| | - Jiyan Wang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China
| | - Changliang Shan
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China.
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11
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McLellan JL, Hanson KK. Differential effects of translation inhibitors on Plasmodium berghei liver stage parasites. Life Sci Alliance 2024; 7:e202302540. [PMID: 38575357 PMCID: PMC10994859 DOI: 10.26508/lsa.202302540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024] Open
Abstract
Increasing numbers of antimalarial compounds are being identified that converge mechanistically at inhibition of cytoplasmic translation, regardless of the molecular target or mechanism. A deeper understanding of how their effectiveness as liver stage translation inhibitors relates to their chemoprotective potential could prove useful. Here, we probed that relationship using the Plasmodium berghei-HepG2 liver stage infection model. After determining translation inhibition EC50s for five compounds, we tested them at equivalent effective concentrations to compare the parasite response to, and recovery from, a brief period of translation inhibition in early schizogony, followed by parasites to 120 h post-infection to assess antiplasmodial effects of the treatment. We show compound-specific heterogeneity in single parasite and population responses to translation inhibitor treatment, with no single metric strongly correlated to the release of hepatic merozoites for all compounds. We also demonstrate that DDD107498 is capable of exerting antiplasmodial effects on translationally arrested liver stage parasites and uncover unexpected growth dynamics during the liver stage. Our results demonstrate that translation inhibition efficacy does not determine antiplasmodial efficacy for these compounds.
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Affiliation(s)
- James L McLellan
- Department of Molecular Microbiology and Immunology and STCEID, University of Texas at San Antonio, San Antonio, TX, USA
| | - Kirsten K Hanson
- Department of Molecular Microbiology and Immunology and STCEID, University of Texas at San Antonio, San Antonio, TX, USA
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12
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Qi H, Yu M, Fan X, Zhou Y, Zhang M, Gao X. Methionine and Leucine Promote mTOR Gene Transcription and Milk Synthesis in Mammary Epithelial Cells through the eEF1Bα-UBR5-ARID1A Signaling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11733-11745. [PMID: 38725145 DOI: 10.1021/acs.jafc.4c00973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Amino acids are essential for the activation of the mechanistic target of rapamycin (mTOR), but the corresponding molecular mechanism is not yet fully understood. We previously found that Met stimulated eukaryotic elongation factor α (eEF1Bα) nuclear localization in bovine mammary epithelial cells (MECs). Herein, we explored the role and molecular mechanism of eEF1Bα in methionine (Met)- and leucine (Leu)-stimulated mTOR gene transcription and milk synthesis in MECs. eEF1Bα knockdown decreased milk protein and fat synthesis, cell proliferation, and mTOR mRNA expression and phosphorylation, whereas eEF1Bα overexpression had the opposite effects. QE-MS analysis detected that eEF1Bα was phosphorylated at Ser106 in the nucleus and Met and Leu stimulated p-eEF1Bα nuclear localization. eEF1Bα knockdown abrogated the stimulation of Met and Leu by mTOR mRNA expression and phosphorylation, and this regulatory role was dependent on its phosphorylation. Akt knockdown blocked the stimulation of Met and Leu by eEF1Bα and p-eEF1Bα expression. ChIP-PCR detected that p-eEF1Bα bound only to the -548 to -793 nt site in the mTOR promoter, and ChIP-qPCR further detected that Met and Leu stimulated this binding. eEF1Bα mediated Met and Leu' stimulation on mTOR mRNA expression and phosphorylation through inducing AT-rich interaction domain 1A (ARID1A) ubiquitination degradation, and this process depended on eEF1Bα phosphorylation. p-eEF1Bα interacted with ARID1A and ubiquitin protein ligase E3 module N-recognition 5 (UBR5), and UBR5 knockdown rescued the decrease of the ARID1A protein level by eEF1Bα overexpression. Both eEF1Bα and p-eEF1Bα were highly expressed in mouse mammary gland tissues during the lactating period. In summary, we reveal that Met and Leu stimulate mTOR transcriptional activation and milk protein and fat synthesis in MECs through eEF1Bα-UBR5-ARID1A signaling.
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Affiliation(s)
- Hao Qi
- College of Animal Science and Technology, Yangtze University, Jingzhou 434025, China
| | - Mengmemg Yu
- College of Animal Science and Technology, Yangtze University, Jingzhou 434025, China
| | - Xiuqiang Fan
- College of Animal Science and Technology, Yangtze University, Jingzhou 434025, China
| | - Yuwen Zhou
- College of Animal Science and Technology, Yangtze University, Jingzhou 434025, China
| | - Minghui Zhang
- College of Animal Science and Technology, Yangtze University, Jingzhou 434025, China
| | - Xuejun Gao
- College of Animal Science and Technology, Yangtze University, Jingzhou 434025, China
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13
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Ma Q, Shen Y, Guo W, Feng K, Huang T, Cai Y. Machine Learning Reveals Impacts of Smoking on Gene Profiles of Different Cell Types in Lung. Life (Basel) 2024; 14:502. [PMID: 38672772 PMCID: PMC11051039 DOI: 10.3390/life14040502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Smoking significantly elevates the risk of lung diseases such as chronic obstructive pulmonary disease (COPD) and lung cancer. This risk is attributed to the harmful chemicals in tobacco smoke that damage lung tissue and impair lung function. Current research on the impact of smoking on gene expression in specific lung cells is limited. This study addresses this gap by analyzing gene expression profiles at the single-cell level from 43,539 lung endothelial cells, 234,349 lung epithelial cells, 189,843 lung immune cells, and 16,031 lung stromal cells using advanced machine learning techniques. The data, categorized by different lung cell types, were classified into three smoking states: active smoker, former smoker, and never smoker. Each cell sample encompassed 28,024 feature genes. Employing an incremental feature selection method within a computational framework, several specific genes have been identified as potential markers of smoking status in different lung cell types. These include B2M, EEF1A1, and TPT1 in lung endothelial cells; FTL and MT-ATP8 in lung epithelial cells; HLA-B and HLA-C in lung immune cells; and HSP90B1 and LCN2 in lung stroma cells. Additionally, this study developed quantitative rules for representing the gene expression patterns related to smoking. This research highlights the potential of machine learning in oncology, enhancing our molecular understanding of smoking's harm and laying the groundwork for future mechanism-based studies.
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Affiliation(s)
- Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Yulong Shen
- Department of Radiotherapy, Strategic Support Force Medical Center, Beijing 100101, China;
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China;
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China;
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yudong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
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14
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Zhao X, Wang J, Li D, Ma F, Fang Y, Lu J, Hou N. Investigation of non-classical secretion of oxalate decarboxylase in Bacillus mojavensis XH1 mediated by exopeptide YydF: Mechanism and application. Int J Biol Macromol 2024; 264:130662. [PMID: 38453118 DOI: 10.1016/j.ijbiomac.2024.130662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/20/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Non-classical secretory proteins are widely found in bacteria and have been extensively studied due to their important physiological roles. However, the relevant non-classical secretory mechanisms remain unclear. In this study, we found that oxalate decarboxylase (Bacm OxDC) from Bacillus mojavensis XH1 belongs to non-classical secretory proteins. Its N-terminus showed high hydrophilicity, which was different from the conventional signal peptide. The truncation test revealed that the deletion of the N-terminus affects the structure resulting in its inability to cross the cell membrane. Further studies verified that the exported peptide YydF played an important role in the secretion process of Bacm OxDC. Experimental results on the secretion mechanism indicated that Bacm OxDC bound to the exported peptide YydF and they are translocated to the cell membrane together, after which Bacm OxDC caused cell membrane relaxation for transmembrane secretion. Thereafter, three recombinant proteins were successfully secreted with certain enzymatic activity by fusing Bacm OxDC as a guide protein with various target proteins. To the best of our knowledge, this was the first time that non-classical secretion mechanism in bacteria has been analyzed. The novel discovery may provide a reference and broaden the horizons of the secretion pathway and expression regulation of proteins.
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Affiliation(s)
- Xin Zhao
- College of Resources and Environment, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, Heilongjiang 150030, PR China
| | - Jian Wang
- College of Resources and Environment, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, Heilongjiang 150030, PR China
| | - Dapeng Li
- College of Resources and Environment, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, Heilongjiang 150030, PR China.
| | - Fang Ma
- College of Environment, Harbin Institute of Technology, No. 73 Yellow River Street, Harbin, Heilongjiang 150090, PR China
| | - Yongping Fang
- College of Resources and Environment, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, Heilongjiang 150030, PR China
| | - Jia Lu
- College of Resources and Environment, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, Heilongjiang 150030, PR China
| | - Ning Hou
- College of Resources and Environment, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, Heilongjiang 150030, PR China.
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15
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Nouraei S, Mia MS, Liu H, Turner NC, Yan G. Genome-wide association study of drought tolerance in wheat (Triticum aestivum L.) identifies SNP markers and candidate genes. Mol Genet Genomics 2024; 299:22. [PMID: 38430317 PMCID: PMC10908643 DOI: 10.1007/s00438-024-02104-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 01/11/2024] [Indexed: 03/03/2024]
Abstract
Drought stress poses a severe threat to global wheat production, necessitating an in-depth exploration of the genetic basis for drought tolerance associated traits. This study employed a 90 K SNP array to conduct a genome-wide association analysis, unravelling genetic determinants of key traits related to drought tolerance in wheat, namely plant height, root length, and root and shoot dry weight. Using the mixed linear model (MLM) method on 125 wheat accessions subjected to both well-watered and drought stress treatments, we identified 53 SNPs significantly associated with stress susceptibility (SSI) and tolerance indices (STI) for the targeted traits. Notably, chromosomes 2A and 3B stood out with ten and nine associated markers, respectively. Across 17 chromosomes, 44 unique candidate genes were pinpointed, predominantly located on the distal ends of 1A, 1B, 1D, 2A, 3A, 3B, 4A, 6A, 6B, 7A, 7B, and 7D chromosomes. These genes, implicated in diverse functions related to plant growth, development, and stress responses, offer a rich resource for future investigation. A clustering pattern emerged, notably with seven genes associated with SSI for plant height and four genes linked to both STI of plant height and shoot dry weight, converging on specific regions of chromosome arms of 2AS and 3BL. Additionally, shared genes encoding polygalacturonase, auxilin-related protein 1, peptide deformylase, and receptor-like kinase underscored the interconnectedness between plant height and shoot dry weight. In conclusion, our findings provide insights into the molecular mechanisms governing wheat drought tolerance, identifying promising genomic loci for further exploration and crop improvement strategies.
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Affiliation(s)
- Sina Nouraei
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Md Sultan Mia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Neil C Turner
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
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16
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Popper B, Bürkle M, Ciccopiedi G, Marchioretto M, Forné I, Imhof A, Straub T, Viero G, Götz M, Schieweck R. Ribosome inactivation regulates translation elongation in neurons. J Biol Chem 2024; 300:105648. [PMID: 38219816 PMCID: PMC10869266 DOI: 10.1016/j.jbc.2024.105648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/10/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
Cellular plasticity is crucial for adapting to ever-changing stimuli. As a result, cells consistently reshape their translatome, and, consequently, their proteome. The control of translational activity has been thoroughly examined at the stage of translation initiation. However, the regulation of ribosome speed in cells is widely unknown. In this study, we utilized a timed ribosome runoff approach, along with proteomics and transmission electron microscopy, to investigate global translation kinetics in cells. We found that ribosome speeds vary among various cell types, such as astrocytes, induced pluripotent human stem cells, human neural stem cells, and human and rat neurons. Of all cell types studied, mature cortical neurons exhibit the highest rate of translation. This finding is particularly remarkable because mature cortical neurons express the eukaryotic elongation factor 2 (eEF2) at lower levels than other cell types. Neurons solve this conundrum by inactivating a fraction of their ribosomes. As a result, the increase in eEF2 levels leads to a reduction of inactive ribosomes and an enhancement of active ones. Processes that alter the demand for active ribosomes, like neuronal excitation, cause increased inactivation of redundant ribosomes in an eEF2-dependent manner. Our data suggest a novel regulatory mechanism in which neurons dynamically inactivate ribosomes to facilitate translational remodeling. These findings have important implications for developmental brain disorders characterized by, among other things, aberrant translation.
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Affiliation(s)
- Bastian Popper
- Core Facility Animal Models, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Martina Bürkle
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Giuliana Ciccopiedi
- Department for Cell Biology & Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany; Graduate School of Systemic Neurosciences, LMU Munich, Munich, Germany
| | - Marta Marchioretto
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy
| | - Ignasi Forné
- Protein Analysis Unit, Department for Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Axel Imhof
- Protein Analysis Unit, Department for Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Tobias Straub
- Bioinformatics Core Facility, Department of Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Gabriella Viero
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy
| | - Magdalena Götz
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany; Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany; SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Rico Schieweck
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany; Department for Cell Biology & Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany; Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy.
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17
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McLellan JL, Hanson KK. Translation inhibition efficacy does not determine the Plasmodium berghei liver stage antiplasmodial efficacy of protein synthesis inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570699. [PMID: 38106175 PMCID: PMC10723475 DOI: 10.1101/2023.12.07.570699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Protein synthesis is a core cellular process, necessary throughout the complex lifecycle of Plasmodium parasites, thus specific translation inhibitors would be a valuable class of antimalarial drugs, capable of both treating symptomatic infections in the blood and providing chemoprotection by targeting the initial parasite population in the liver, preventing both human disease and parasite transmission back to the mosquito host. As increasing numbers of antiplasmodial compounds are identified that converge mechanistically at inhibition of cytoplasmic translation, regardless of molecular target or mechanism, it would be useful to gain deeper understanding of how their effectiveness as liver stage translation inhibitors relates to their chemoprotective potential. Here, we probed that relationship using the P. berghei-HepG2 liver stage infection model. Using o-propargyl puromycin-based labeling of the nascent proteome in P. berghei-infected HepG2 monolayers coupled with automated confocal feedback microscopy to generate unbiased, single parasite image sets of P. berghei liver stage translation, we determined translation inhibition EC50s for five compounds, encompassing parasite-specific aminoacyl tRNA synthetase inhibitors, compounds targeting the ribosome in both host and parasite, as well as DDD107498, which targets Plasmodium eEF2, and is a leading antimalarial candidate compound being clinically developed as cabamiquine. Compounds were then tested at equivalent effective concentrations to compare the parasite response to, and recovery from, a brief period of translation inhibition in early schizogony, with parasites followed up to 120 hours post-infection to assess liver stage antiplasmodial effects of the treatment. Our data conclusively show that translation inhibition efficacy per se does not determine a translation inhibitor's antiplasmodial efficacy. DDD107498 was the least effective translation inhibitor, yet exerted the strongest antimalarial effects at both 5x- and 10x EC50 concentrations. We show compound-specific heterogeneity in single parasite and population responses to translation inhibitor treatment, with no single metric strongly correlated to release of hepatic merozoites for all compound, demonstrate that DDD107498 is capable of exerting antiplasmodial effects on translationally arrested liver stage parasites, and uncover unexpected growth dynamics during the liver stage. Our results demonstrate that translation inhibition efficacy cannot function as a proxy for antiplasmodial effectiveness, and highlight the importance of exploring the ultimate, as well as proximate, mechanisms of action of these compounds on liver stage parasites.
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Affiliation(s)
- James L. McLellan
- University of Texas at San Antonio, Department of Molecular Microbiology and Immunology and STCEID, San Antonio TX, USA
| | - Kirsten K. Hanson
- University of Texas at San Antonio, Department of Molecular Microbiology and Immunology and STCEID, San Antonio TX, USA
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18
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Meng XY, Jiang QQ, Yu XD, Zhang QY, Ke F. Eukaryotic translation elongation factor 1 alpha (eEF1A) inhibits Siniperca chuatsi rhabdovirus (SCRV) infection through two distinct mechanisms. J Virol 2023; 97:e0122623. [PMID: 37861337 PMCID: PMC10688370 DOI: 10.1128/jvi.01226-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE Although a virus can regulate many cellular responses to facilitate its replication by interacting with host proteins, the host can also restrict virus infection through these interactions. In the present study, we showed that the host eukaryotic translation elongation factor 1 alpha (eEF1A), an essential protein in the translation machinery, interacted with two proteins of a fish rhabdovirus, Siniperca chuatsi rhabdovirus (SCRV), and inhibited virus infection via two different mechanisms: (i) inhibiting the formation of crucial viral protein complexes required for virus transcription and replication and (ii) promoting the ubiquitin-proteasome degradation of viral protein. We also revealed the functional regions of eEF1A that are involved in the two processes. Such a host protein inhibiting a rhabdovirus infection in two ways is rarely reported. These findings provided new information for the interactions between host and fish rhabdovirus.
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Affiliation(s)
- Xian-Yu Meng
- Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, China
| | - Qi-Qi Jiang
- Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, China
| | - Xue-Dong Yu
- Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, China
| | - Qi-Ya Zhang
- Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Fei Ke
- Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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19
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Zong B, Xiao Y, Li R, Li H, Wang P, Yang X, Zhang Y. Transcriptome and metabolome profiling to elucidate the mechanism underlying the poor growth of Streptococcus suis serotype 2 after orphan response regulator CovR deletion. Front Vet Sci 2023; 10:1280161. [PMID: 38026618 PMCID: PMC10661955 DOI: 10.3389/fvets.2023.1280161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
The deletion of orphan response regulator CovR reduces the growth rate of Streptococcus suis serotype 2 (S. suis 2). In this study, metabolome and transcriptome profiling were performed to study the mechanisms underlying the poor growth of S. suis 2 caused by the deletion of orphan response regulator CovR. By comparing S. suis 2 (ΔcovR) and S. suis 2 (SC19), 146 differentially accumulated metabolites (upregulated: 83 and downregulated: 63) and 141 differentially expressed genes (upregulated: 86 and downregulated: 55) were identified. Metabolome and functional annotation analysis revealed that the growth of ΔcovR was inhibited by the imbalance aminoacyl tRNA biosynthesis (the low contents of L-lysine, L-aspartic acid, L-glutamine, and L-glutamic acid, and the high content of L-methionine). These results provide a new insight into the underlying poor growth of S. suis 2 caused by the deletion of orphan response regulator CovR. Metabolites and candidate genes regulated by the orphan response regulator CovR and involved in the growth of S. suis 2 were reported in this study.
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Affiliation(s)
- Bingbing Zong
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Engineering Research Center of Feed Protein Resources on Agricultural By-Products, Ministry of Education, Wuhan Polytechnic University, Wuhan, China
| | - Yong Xiao
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Engineering Research Center of Feed Protein Resources on Agricultural By-Products, Ministry of Education, Wuhan Polytechnic University, Wuhan, China
| | - Rui Li
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Engineering Research Center of Feed Protein Resources on Agricultural By-Products, Ministry of Education, Wuhan Polytechnic University, Wuhan, China
| | - Huanhuan Li
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Engineering Research Center of Feed Protein Resources on Agricultural By-Products, Ministry of Education, Wuhan Polytechnic University, Wuhan, China
| | - Peiyi Wang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Engineering Research Center of Feed Protein Resources on Agricultural By-Products, Ministry of Education, Wuhan Polytechnic University, Wuhan, China
| | - Xiaopei Yang
- Wuhan Animal Disease Control Center, Wuhan, Hubei, China
| | - Yanyan Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Engineering Research Center of Feed Protein Resources on Agricultural By-Products, Ministry of Education, Wuhan Polytechnic University, Wuhan, China
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Alcalde MA, Hidalgo-Martinez D, Bru Martínez R, Sellés-Marchart S, Bonfill M, Palazon J. Insights into enhancing Centella asiatica organ cell biofactories via hairy root protein profiling. FRONTIERS IN PLANT SCIENCE 2023; 14:1274767. [PMID: 37965024 PMCID: PMC10642384 DOI: 10.3389/fpls.2023.1274767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023]
Abstract
Recent advancements in plant biotechnology have highlighted the potential of hairy roots as a biotechnological platform, primarily due to their rapid growth and ability to produce specialized metabolites. This study aimed to delve deeper into hairy root development in C. asiatica and explore the optimization of genetic transformation for enhanced bioactive compound production. Previously established hairy root lines of C. asiatica were categorized based on their centelloside production capacity into HIGH, MID, or LOW groups. These lines were then subjected to a meticulous label-free proteomic analysis to identify and quantify proteins. Subsequent multivariate and protein network analyses were conducted to discern proteome differences and commonalities. Additionally, the quantification of rol gene copy numbers was undertaken using qPCR, followed by gene expression measurements. From the proteomic analysis, 213 proteins were identified. Distinct proteome differences, especially between the LOW line and other lines, were observed. Key proteins related to essential processes like photosynthesis and specialized metabolism were identified. Notably, potential biomarkers, such as the Tr-type G domain-containing protein and alcohol dehydrogenase, were found in the HIGH group. The presence of ornithine cyclodeaminase in the hairy roots emerged as a significant biomarker linked with centelloside production capacity lines, indicating successful Rhizobium-mediated genetic transformation. However, qPCR results showed an inconsistency with rol gene expression levels, with the HIGH line displaying notably higher expression, particularly of the rolD gene. The study unveiled the importance of ornithine cyclodeaminase as a traceable biomarker for centelloside production capacity. The strong correlation between this biomarker and the rolD gene emphasizes its potential role in optimizing genetic transformation processes in C. asiatica.
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Affiliation(s)
- Miguel Angel Alcalde
- Biotechnology, Health and Education Research Group, Posgraduate School, Cesar Vallejo University, Trujillo, Peru
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Diego Hidalgo-Martinez
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Roque Bru Martínez
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology, Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Susana Sellés-Marchart
- Plant Proteomics and Functional Genomics Group, Department of Biochemistry and Molecular Biology, Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Mercedes Bonfill
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Javier Palazon
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
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21
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Kumara PM, Varun E, Sanjay JR, Madhushree AH, Thimmappa R. De novo transcriptome analysis of Dysoxylum binectariferum to unravel the biosynthesis of pharmaceutically relevant specialized metabolites. FRONTIERS IN PLANT SCIENCE 2023; 14:1098987. [PMID: 37636089 PMCID: PMC10450223 DOI: 10.3389/fpls.2023.1098987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/05/2023] [Indexed: 08/29/2023]
Abstract
The tropical tree, D. binectariferum, is a prominent source of chromone alkaloid rohitukine, which is used in the semi-syntheses of anticancer molecules such as flavopiridol and P-276-00. The biosynthetic pathway of rohitukine or its derivatives is currently unknown in plants. Here, we explored chromone alkaloid biosynthesis in D. binectariferum through targeted transcriptome sequencing. Illumina sequencing of leaves and roots of a year-old D. binectariferum seedling generated, 42.43 and 38.74 million paired-end short reads, respectively. Quality filtering and de novo assembly of the transcriptome generated 274,970 contigs and 126,788 unigenes with an N50 contig length of 1560 bp. The assembly generated 117,619 translated unigene protein sequences and 51,598 non-redundant sequences. Nearly 80% of these non-redundant sequences were annotated to publicly available protein and nucleotide databases, suggesting the completeness and effectiveness of the transcriptome assembly. Using the assembly, we identified a chalcone synthase (CHS) and three type III polyketide synthases (PKS-III; non-CHS type) that are likely to be involved in the biosynthesis of chromone ring/noreugenin moiety of rohitukine. We also identified key enzymes like lysine decarboxylase in the piperidine pathway that make the piperidine moiety of rohitukine. Besides these, the upstream enzymes in flavonoid biosynthesis like phenylalanine ammonia-lyase (PAL), trans-cinnamate 4-hydroxylase (C4H),4-coumarate-CoA ligase (4CL), and chalcone isomerase (CHI) have also been identified. Also, terpene synthases that are likely to be involved in the biosynthesis of various terpenoid scaffolds have been identified. Together, the D. binectariferum transcriptome resource forms a basis for further exploration of biosynthetic pathways of these valuable compounds through functional validation of the candidate genes and metabolic engineering in heterologous hosts. Additionally, the transcriptome dataset generated will serve as an important resource for research on functional genomics and enzyme discovery in D. binectariferum and comparative analysis with other Meliaceae family members.
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Affiliation(s)
- Patel Mohana Kumara
- Department of Biotechnology and Crop Improvement, Kittur Rani Chennamma College of Horticulture, Arabhavi, University of Horticultural Sciences, Bagalkot, Karnataka, India
- Center for Ayurveda Biology and Holistic Nutrition, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka, India
| | - Eranna Varun
- Center for Ayurveda Biology and Holistic Nutrition, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka, India
| | - Joshi Renuka Sanjay
- Center for Ayurveda Biology and Holistic Nutrition, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka, India
| | - Anchedoddi Hanumegowda Madhushree
- Center for Ayurveda Biology and Holistic Nutrition, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka, India
| | - Ramesha Thimmappa
- Amity Institute of Genome Engineering, Amity University Uttar Pradesh, Noida, India
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22
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Gangwal A, Kumar N, Sangwan N, Dhasmana N, Dhawan U, Sajid A, Arora G, Singh Y. Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages. FEMS Microbiol Rev 2023; 47:fuad044. [PMID: 37533212 PMCID: PMC10465088 DOI: 10.1093/femsre/fuad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023] Open
Abstract
Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.
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Affiliation(s)
- Aakriti Gangwal
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nitika Sangwan
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Neha Dhasmana
- School of Medicine, New York University, 550 First Avenue New York-10016, New York, United States
| | - Uma Dhawan
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Andaleeb Sajid
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Gunjan Arora
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi-110007, India
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23
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Hollinger J, Wu J, Awayda KM, O’Connell MR, Yao P. Expression and purification of the mitochondrial transmembrane protein FAM210A in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.27.542570. [PMID: 37292620 PMCID: PMC10245961 DOI: 10.1101/2023.05.27.542570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The protein Family with sequence similarity 210 member A (FAM210A) is a mitochondrial inner membrane protein that regulates the protein synthesis of mitochondrial DNA encoded genes. However, how it functions in this process is not well understood. Developing and optimizing a protein purification strategy will facilitate biochemical and structural studies of FAM210A. Here, we developed a method to purify human FAM210A with deleted mitochondrial targeting signal sequence using the MBP-His 10 fusion in Escherichia coli . The recombinant FAM210A protein was inserted into the E. coli cell membrane and purified from isolated bacterial cell membranes, followed by a two-step process using Ni-NTA resin-based immobilized-metal affinity chromatography (IMAC) and ion exchange purification. A pulldown assay validated the functionality of purified FAM210A protein interacting with human mitochondrial elongation factor EF-Tu in HEK293T cell lysates. Taken together, this study developed a method for purification of the mitochondrial transmembrane protein FAM210A partially complexed with E.coli derived EF-Tu and provides an opportunity for future potential biochemical and structural studies of recombinant FAM210A protein.
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Affiliation(s)
- Jared Hollinger
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York
| | - Kamel M. Awayda
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York
- Current Address: School of Medicine, University of California, San Francisco, California
| | - Mitchell R. O’Connell
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, New York
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24
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Ghouili E, Sassi K, Hidri Y, M’Hamed HC, Somenahally A, Xue Q, Jebara M, Nefissi Ouertani R, Riahi J, de Oliveira AC, Abid G, Muhovski Y. Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley ( Hordeum vulgare L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:526. [PMID: 36771612 PMCID: PMC9921465 DOI: 10.3390/plants12030526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in barley roots during the tillering stage. Bioinformatic tools were used to interpret the biological function, the pathway analysis and the visualisation of the network amongst the identified proteins. A total of 72 DAPs (33 upregulated and 39 downregulated) among a total of 2580 proteins were identified in response to compost treatment, suggesting multiple pathways of primary and secondary metabolism, such as carbohydrates and energy metabolism, phenylpropanoid pathway, glycolysis pathway, protein synthesis and degradation, redox homeostasis, RNA processing, stress response, cytoskeleton organisation, and phytohormone metabolic pathways. The expression of DAPs was further validated by qRT-PCR. The effects on barley plant development, such as the promotion of root growth and biomass increase, were associated with a change in energy metabolism and protein synthesis. The activation of enzymes involved in redox homeostasis and the regulation of stress response proteins suggest a protective effect of compost, consequently improving barley growth and stress acclimation through the reduction of the environmental impact of productive agriculture. Overall, these results may facilitate a better understanding of the molecular mechanism of compost-promoted plant growth and provide valuable information for the identification of critical genes/proteins in barley as potential targets of compost.
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Affiliation(s)
- Emna Ghouili
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Khaled Sassi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Yassine Hidri
- Laboratory of Integrated Olive Production in the Humid, Sub-humid and Semi-arid Region (LR16IO3), Olive Tree Institute, Cité Mahragène, P.O. Box 208, Tunis 1082, Tunisia
| | - Hatem Cheikh M’Hamed
- Agronomy Laboratory, National Institute of Agronomic Research of Tunis (INRAT), Carthage University, Hedi Karray Street, Ariana 2049, Tunisia
| | - Anil Somenahally
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843-2474, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX 79403-6603, USA
| | - Moez Jebara
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Jouhaina Riahi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Ana Caroline de Oliveira
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Yordan Muhovski
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
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25
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Tang H, Luo H, Zhang Z, Yang D. Mesenchymal Stem Cell-Derived Apoptotic Bodies: Biological Functions and Therapeutic Potential. Cells 2022; 11:cells11233879. [PMID: 36497136 PMCID: PMC9737101 DOI: 10.3390/cells11233879] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are non-hematopoietic progenitor cells with self-renewal ability and multipotency of osteogenic, chondrogenic, and adipogenic differentiation. MSCs have appeared as a promising approach for tissue regeneration and immune therapies, which are attributable not only to their differentiation into the desired cells but also to their paracrine secretion. MSC-sourced secretome consists of soluble components including growth factors, chemokines, cytokines, and encapsulated extracellular vesicles (EVs). Apoptotic bodies (ABs) are large EVs (diameter 500𠀓2000 nm) harboring a variety of cellular components including microRNA, mRNA, DNA, protein, and lipids related to the characteristics of the originating cell, which are generated during apoptosis. The released ABs as well as the genetic information they carry are engulfed by target cells such as macrophages, dendritic cells, epithelial cells, and fibroblasts, and subsequently internalized and degraded in the lysosomes, suggesting their ability to facilitate intercellular communication. In this review, we discuss the current understanding of the biological functions and therapeutic potential of MSC-derived ABs, including immunomodulation, tissue regeneration, regulation of inflammatory response, and drug delivery system.
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Affiliation(s)
| | | | | | - Di Yang
- Correspondence: ; Tel.: +86-24-31927705
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26
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Liu P, Li Y, Ye Y, Chen J, Li R, Zhang Q, Li Y, Wang W, Meng Q, Ou J, Yang Z, Sun W, Gu W. The genome and antigen proteome analysis of Spiroplasma mirum. Front Microbiol 2022; 13:996938. [PMID: 36406404 PMCID: PMC9666726 DOI: 10.3389/fmicb.2022.996938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023] Open
Abstract
Spiroplasma mirum, small motile wall-less bacteria, was originally isolated from a rabbit tick and had the ability to infect newborn mice and caused cataracts. In this study, the whole genome and antigen proteins of S. mirum were comparative analyzed and investigated. Glycolysis, pentose phosphate pathway, arginine metabolism, nucleotide biosynthesis, and citrate fermentation were found in S. mirum, while trichloroacetic acid, fatty acids metabolism, phospholipid biosynthesis, terpenoid biosynthesis, lactose-specific PTS, and cofactors synthesis were completely absent. The Sec systems of S. mirum consist of SecA, SecE, SecDF, SecG, SecY, and YidC. Signal peptidase II was identified in S. mirum, but no signal peptidase I. The relative gene order in S. mirum is largely conserved. Genome analysis of available species in Mollicutes revealed that they shared only 84 proteins. S. mirum genome has 381 pseudogenes, accounting for 31.6% of total protein-coding genes. This is the evidence that spiroplasma genome is under an ongoing genome reduction. Immunoproteomics, a new scientific technique combining proteomics and immunological analytical methods, provided the direction of our research on S. mirum. We identified 49 proteins and 11 proteins (9 proteins in common) in S. mirum by anti-S. mirum serum and negative serum, respectively. Forty proteins in S. mirum were identified in relation to the virulence. All these proteins may play key roles in the pathogeny and can be used in the future for diagnoses and prevention.
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Affiliation(s)
- Peng Liu
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Yuxin Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Youyuan Ye
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Jiaxin Chen
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Rong Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Qinyi Zhang
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Yuan Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Wen Wang
- Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - Qingguo Meng
- Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - Jingyu Ou
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Zhujun Yang
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Wei Sun
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Wei Gu
- Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
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27
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Fatkhullin B, Golubev A, Garaeva N, Validov S, Gabdulkhakov A, Yusupov M. Y98 Mutation Leads to the Loss of RsfS Anti-Association Activity in Staphylococcus aureus. Int J Mol Sci 2022; 23:ijms231810931. [PMID: 36142845 PMCID: PMC9503621 DOI: 10.3390/ijms231810931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
Ribosomal silencing factor S (RsfS) is a conserved protein that plays a role in the mechanisms of ribosome shutdown and cell survival during starvation. Recent studies demonstrated the involvement of RsfS in the biogenesis of the large ribosomal subunit. RsfS binds to the uL14 ribosomal protein on the large ribosomal subunit and prevents its association with the small subunit. Here, we estimated the contribution of RsfS amino acid side chains at the interface between RsfS and uL14 to RsfS anti-association function in Staphylococcus aureus through in vitro experiments: centrifugation in sucrose gradient profiles and an S. aureus cell-free system assay. The detected critical Y98 amino acid on the RsfS surface might become a new potential target for pharmacological drug development and treatment of S. aureus infections.
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Affiliation(s)
- Bulat Fatkhullin
- Institute of Protein Research, Russian Academy of Science, 142290 Pushchino, Russia
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964, CNRS, UMR7104, University of Strasbourg, 67400 Illkirch Graffenstaden, France
| | - Alexander Golubev
- Laboratory for Structural Analysis of Biomacromolecules, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
| | - Natalia Garaeva
- Laboratory for Structural Analysis of Biomacromolecules, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
| | - Shamil Validov
- Laboratory for Structural Analysis of Biomacromolecules, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Science, 142290 Pushchino, Russia
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964, CNRS, UMR7104, University of Strasbourg, 67400 Illkirch Graffenstaden, France
- Laboratory for Structural Analysis of Biomacromolecules, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia
- Correspondence:
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28
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Zhao S, Mai RM, Zhang T, Feng XZ, Li WT, Wang WX, Luo XM, Feng JX. Simultaneous manipulation of transcriptional regulator CxrC and translational elongation factor eEF1A enhances the production of plant-biomass-degrading enzymes of Penicillium oxalicum. BIORESOURCE TECHNOLOGY 2022; 351:127058. [PMID: 35339654 DOI: 10.1016/j.biortech.2022.127058] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Genetic engineering is an efficient approach to improve fungal bioproducts, but the specific targets are limited. In this study, it was found that the key transcription repressor CxrC of Penicillium oxalicum could physically interact with the translational elongation factor eEF1A that positively regulated the production of plant-biomass-degrading enzymes by the fungus under Avicel induction. Simultaneously deletion of the cxrC and overexpression of the eEF1A in the strain Δku70 resulted in 55.4%-314.6% higher production of cellulase, xylanase and raw-starch-degrading enzymes than that of the start strain Δku70. Transcript abundance of the genes encoding predominant cellulases, xylanases and raw-starch-degrading enzymes were significantly upregulated in the mutant ΔcxrC::eEF1A. The ΔcxrC::eEF1A enhanced saccharification efficiency of raw cassava flour by 9.3%-15.5% at early-middle stage of hydrolysis in comparison with Δku70. The obtained knowledges expanded the sources used as effective targets for increased production of plant-biomass-degrading enzymes by fungi.
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Affiliation(s)
- Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Rong-Ming Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xiang-Zhao Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Wen-Tong Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Wen-Xuan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China.
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Regulation of Leaderless mRNA Translation in Bacteria. Microorganisms 2022; 10:microorganisms10040723. [PMID: 35456773 PMCID: PMC9031893 DOI: 10.3390/microorganisms10040723] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
In bacteria, the translation of genetic information can begin through at least three different mechanisms: canonical or Shine-Dalgarno-led initiation, readthrough or 70S scanning initiation, or leaderless initiation. Here, we discuss the main features and regulation of the last, which is characterized mainly by the ability of 70S ribosomal particles to bind to AUG located at or near the 5′ end of mRNAs to initiate translation. These leaderless mRNAs (lmRNAs) are rare in enterobacteria, such as Escherichia coli, but are common in other bacteria, such as Mycobacterium tuberculosis and Deinococcus deserti, where they may represent more than 20% and even up to 60% of the genes. Given that lmRNAs are devoid of a 5′ untranslated region and the Shine-Dalgarno sequence located within it, the mechanism of translation regulation must depend on molecular strategies that are different from what has been observed in the Shine-Dalgarno-led translation. Diverse regulatory mechanisms have been proposed, including the processing of ribosomal RNA and changes in the abundance of translation factors, but all of them produce global changes in the initiation of lmRNA translation. Thus, further research will be required to understand how the initiation of the translation of particular lmRNA genes is regulated.
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