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Wang H, Zhang Y, Feng X, Hong J, Aamir Manzoor M, Zhou X, Zhou Q, Cai Y. Transcription factor PbMYB80 regulates lignification of stone cells and undergoes RING finger protein PbRHY1-mediated degradation in pear fruit. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:883-900. [PMID: 37944017 DOI: 10.1093/jxb/erad434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
The Chinese white pear (Pyrus bretschneideri) fruit carries a high proportion of stone cells, adversely affecting fruit quality. Lignin is a main component of stone cells in pear fruit. In this study, we discovered that a pear MYB transcription factor, PbMYB80, binds to the promoters of key lignin biosynthesis genes and inhibits their expression. Stable overexpression of PbMYB80 in Arabidopsis showed that lignin deposition and secondary wall thickening were inhibited, and the expression of the lignin biosynthesis genes in transgenic Arabidopsis was decreased. Transient overexpression of PbMYB80 in pear fruit inhibited lignin metabolism and stone cell development, and the expression of some genes in the lignin metabolism pathway was reduced. In contrast, silencing PbMYB80 with VIGS increased the lignin and stone cell content in pear fruit, and increased expression of genes in the lignin metabolism pathway. By screening a pear fruit cDNA library in yeast, we found that PbMYB80 binds to a RING finger (PbRHY1) protein. We also showed that PbRHY1 exhibits E3 ubiquitin ligase activity and degrades ubiquitinated PbMYB80 in vivo and in vitro. This investigation contributes to a better understanding of the regulation of lignin biosynthesis in pear fruit, and provides a theoretical foundation for increasing pear fruit quality at the molecular level.
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Affiliation(s)
- Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yingjie Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaofeng Feng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Jiayi Hong
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Muhammad Aamir Manzoor
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xinyue Zhou
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qifang Zhou
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
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2
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Singh G, Kaur N, Khanna R, Kaur R, Gudi S, Kaur R, Sidhu N, Vikal Y, Mangat GS. 2Gs and plant architecture: breaking grain yield ceiling through breeding approaches for next wave of revolution in rice ( Oryza sativa L.). Crit Rev Biotechnol 2024; 44:139-162. [PMID: 36176065 DOI: 10.1080/07388551.2022.2112648] [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: 11/28/2021] [Revised: 07/10/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022]
Abstract
Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of GW7 (for grain weight) and DEP2 (for grain number) genes present on chromosome 7 revealed the possibility of simultaneous introgression of these two genes, if desirable allelic variants were found in the single donor parent. This review article will reveal the genetic nature of 2Gs traits and use this knowledge to break the yield ceiling by using different breeding and biotechnological tools, which will sustain the world's food requirements.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Renu Khanna
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rupinder Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navjot Sidhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - G S Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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3
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Malik AH, Khurshaid N, Shabir N, Ashraf N. Transcriptome wide identification, characterization and expression analysis of PHD gene family in Crocus sativus. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:81-91. [PMID: 38435850 PMCID: PMC10902251 DOI: 10.1007/s12298-024-01410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 03/05/2024]
Abstract
Crocus sativus L., of the Iridaceae family, yields world's most prized spice, saffron. Saffron is well known for its distinctive aroma, odour and colour, which are imputed to the presence of some specific glycosylated apocarotenoids. Even though the main biosynthetic pathway and most of the enzymes leading to apocarotenoid production have been identified, the regulatory mechanisms that govern the developmental stage and tissue specific production of apocarotenoids in Crocus remain comparatively unravelled. Towards this, we report identification, and characterization of plant homeodomain (PHD) finger transcription factor family in Crocus sativus. We also report cloning and characterisation of CstPHD27 from C. sativus. CstPHD27 recorded highest expression in stigma throughout flower development. CstPHD27 exhibited expression pattern which corresponded to the apocarotenoid accumulation in Crocus stigmas. CstPHD27 is nuclear localized and transcriptionally active in yeast Y187 strain. Over-expression of CstPHD27 in Crocus stigmas enhanced apocarotenoid content by upregulating the biosynthetic pathway genes. This report on PHD finger transcription factor family from C. sativus may offer a basis for elucidating role of this gene family in this traditionally and industrially prized crop. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01410-3.
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Affiliation(s)
- Aubid Hussain Malik
- Plant Molecular Biology and Biotechnology Division, CSIR—Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, Jammu and Kashmir 190005 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Nargis Khurshaid
- Plant Molecular Biology and Biotechnology Division, CSIR—Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, Jammu and Kashmir 190005 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Najwa Shabir
- Plant Molecular Biology and Biotechnology Division, CSIR—Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, Jammu and Kashmir 190005 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Nasheeman Ashraf
- Plant Molecular Biology and Biotechnology Division, CSIR—Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, Jammu and Kashmir 190005 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
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4
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Wen J, Deng M, Zhao K, Zhou H, Wu R, Li M, Cheng H, Li P, Zhang R, Lv J. Characterization of Plant Homeodomain Transcription Factor Genes Involved in Flower Development and Multiple Abiotic Stress Response in Pepper. Genes (Basel) 2023; 14:1737. [PMID: 37761877 PMCID: PMC10531376 DOI: 10.3390/genes14091737] [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: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Plant homeodomain (PHD) transcription factor genes are involved in plant development and in a plant's response to stress. However, there are few reports about this gene family in peppers (Capsicum annuum L.). In this study, the pepper inbred line "Zunla-1" was used as the reference genome, and a total of 43 PHD genes were identified, and systematic analysis was performed to study the chromosomal location, evolutionary relationship, gene structure, domains, and upstream cis-regulatory elements of the CaPHD genes. The fewest CaPHD genes were located on chromosome 4, while the most were on chromosome 3. Genes with similar gene structures and domains were clustered together. Expression analysis showed that the expression of CaPHD genes was quite different in different tissues and in response to various stress treatments. The expression of CaPHD17 was different in the early stage of flower bud development in the near-isogenic cytoplasmic male-sterile inbred and the maintainer inbred lines. It is speculated that this gene is involved in the development of male sterility in pepper. CaPHD37 was significantly upregulated in leaves and roots after heat stress, and it is speculated that CaPHD37 plays an important role in tolerating heat stress in pepper; in addition, CaPHD9, CaPHD10, CaPHD11, CaPHD17, CaPHD19, CaPHD20, and CaPHD43 were not sensitive to abiotic stress or hormonal factors. This study will provide the basis for further research into the function of CaPHD genes in plant development and responses to abiotic stresses and hormones.
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Affiliation(s)
- Jinfen Wen
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650500, China;
| | - Minghua Deng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Kai Zhao
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Huidan Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Rui Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Mengjuan Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Hong Cheng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Pingping Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Ruihao Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Junheng Lv
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
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Jeong SY, Choi JH, Kim J, Woo JS, Lee EH. Tripartite Motif-Containing Protein 32 (TRIM32): What Does It Do for Skeletal Muscle? Cells 2023; 12:2104. [PMID: 37626915 PMCID: PMC10453674 DOI: 10.3390/cells12162104] [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: 07/19/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Tripartite motif-containing protein 32 (TRIM32) is a member of the tripartite motif family and is highly conserved from flies to humans. Via its E3 ubiquitin ligase activity, TRIM32 mediates and regulates many physiological and pathophysiological processes, such as growth, differentiation, muscle regeneration, immunity, and carcinogenesis. TRIM32 plays multifunctional roles in the maintenance of skeletal muscle. Genetic variations in the TRIM32 gene are associated with skeletal muscular dystrophies in humans, including limb-girdle muscular dystrophy type 2H (LGMD2H). LGMD2H-causing genetic variations of TRIM32 occur most frequently in the C-terminal NHL (ncl-1, HT2A, and lin-41) repeats of TRIM32. LGMD2H is characterized by skeletal muscle dystrophy, myopathy, and atrophy. Surprisingly, most patients with LGMD2H show minimal or no dysfunction in other tissues or organs, despite the broad expression of TRIM32 in various tissues. This suggests more prominent roles for TRIM32 in skeletal muscle than in other tissues or organs. This review is focused on understanding the physiological roles of TRIM32 in skeletal muscle, the pathophysiological mechanisms mediated by TRIM32 genetic variants in LGMD2H patients, and the correlations between TRIM32 and Duchenne muscular dystrophy (DMD).
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Affiliation(s)
- Seung Yeon Jeong
- Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jun Hee Choi
- Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jooho Kim
- Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jin Seok Woo
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 10833, USA
| | - Eun Hui Lee
- Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
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6
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Splan KE, Choi SR, Claycomb RE, Eckart-Frank IK, Nagdev S, Rodemeier ME. Disruption of zinc (II) binding and dimeric protein structure of the XIAP-RING domain by copper (I) ions. J Biol Inorg Chem 2023:10.1007/s00775-023-02002-4. [PMID: 37268744 DOI: 10.1007/s00775-023-02002-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/15/2023] [Indexed: 06/04/2023]
Abstract
Modulation of metalloprotein structure and function via metal ion substitution may constitute a molecular basis for metal ion toxicity and/or metal-mediated functional control. The X-linked Inhibitor of Apoptosis Protein (XIAP) is a metalloprotein that requires zinc for proper structure and function. In addition to its role as a modulator of apoptosis, XIAP has been implicated in copper homeostasis. Given the similar coordination preferences of copper and zinc, investigation of XIAP structure and function upon interaction with copper is relevant. The Really Interesting New Gene (RING) domain of XIAP is representative of a class of zinc finger proteins that utilize a bi-nuclear zinc-binding motif to maintain proper structure and ubiquitin ligase function. Herein, we report the characterization of copper (I) binding to the Zn2-RING domain of XIAP. Electronic absorption studies that monitor copper-thiolate interactions demonstrate that the RING domain of XIAP binds 5-6 Cu(I) ions and that copper is thermodynamically preferred relative to zinc. Repetition of the experiments in the presence of the Zn(II)-specific dye Mag-Fura2 shows that Cu(I) addition results in Zn(II) ejection from the protein, even in the presence of glutathione. Loss of dimeric structure of the RING domain, which is a requirement for its ubiquitin ligase activity, upon copper substitution at the zinc-binding sites, was readily observed via size exclusion chromatography. These results provide a molecular basis for the modulation of RING function by copper and add to the growing body of literature that describe the impact of Cu(I) on zinc metalloprotein structure and function.
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Affiliation(s)
- Kathryn E Splan
- Department of Chemistry, Macalester College, 1600 Grand Avenue, Saint Paul, MN, 55105, USA.
| | - Sylvia R Choi
- Department of Chemistry, Macalester College, 1600 Grand Avenue, Saint Paul, MN, 55105, USA
| | - Ruth E Claycomb
- Department of Chemistry, Macalester College, 1600 Grand Avenue, Saint Paul, MN, 55105, USA
| | - Isaiah K Eckart-Frank
- Department of Chemistry, Macalester College, 1600 Grand Avenue, Saint Paul, MN, 55105, USA
| | - Shreya Nagdev
- Department of Chemistry, Macalester College, 1600 Grand Avenue, Saint Paul, MN, 55105, USA
| | - Madeline E Rodemeier
- Department of Chemistry, Macalester College, 1600 Grand Avenue, Saint Paul, MN, 55105, USA
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7
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Pang F, Niu J, Solanki MK, Nosheen S, Liu Z, Wang Z. PHD-finger family genes in wheat ( Triticum aestivum L.): Evolutionary conservatism, functional diversification, and active expression in abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1016831. [PMID: 36578331 PMCID: PMC9791960 DOI: 10.3389/fpls.2022.1016831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Plant homeodomain (PHD) transcription factors (TFs) are a class of proteins with conserved Cys4-His-Cys3 domains that play important roles in plant growth and development and in response to abiotic stresses. Although characterization of PHDs has been performed in plants, little is known about their function in wheat (Triticum aestivum L.), especially under stress conditions. In the present study, 244 TaPHDs were identified in wheat using comparative genomics. We renamed them TaPHD1-244 based on their chromosomal distribution, and almost all PHD proteins were predicted to be located in the nucleus. According to the unrooted neighbor-joining phylogenetic tree, gene structure, and motif analyses, PHD genes were divided into four clades. A total of 149 TaPHD genes were assigned to arise from duplication events. Furthermore, 230 gene pairs came from wheat itself, and 119, 186, 168, 7, 2, and 6 gene pairs came from six other species (Hordeum vulgareto, Zea mays, Oryza sativa, Arabidopsis thaliana, Brassica rapa, and Gossypium raimondii, respectively). A total of 548 interacting protein branches were identified to be involved in the protein interaction network. Tissue-specific expression pattern analysis showed that TaPHDs were highly expressed in the stigma and ovary during flowering, suggesting that the TaPHD gene plays an active role in the reproductive growth of wheat. In addition, the qRT-PCR results further confirmed that these TaPHD genes are involved in the abiotic stress response of wheat. In conclusion, our study provides a theoretical basis for deciphering the molecular functions of TaPHDs, particularly in response to abiotic stress.
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Affiliation(s)
- Fei Pang
- College of Agriculture, Yulin Normal University, Yulin, China
| | - Junqi Niu
- College of Agriculture, Yulin Normal University, Yulin, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Shaista Nosheen
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Zhaoliang Liu
- College of Agriculture, Yulin Normal University, Yulin, China
| | - Zhen Wang
- College of Agriculture, Yulin Normal University, Yulin, China
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8
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Mulenga A, Radulovic Z, Porter L, Britten TH, Kim TK, Tirloni L, Gaithuma AK, Adeniyi-Ipadeola GO, Dietrich JK, Moresco JJ, Yates JR. Identification and characterization of proteins that form the inner core Ixodes scapularis tick attachment cement layer. Sci Rep 2022; 12:21300. [PMID: 36494396 PMCID: PMC9734129 DOI: 10.1038/s41598-022-24881-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Ixodes scapularis long-term blood feeding behavior is facilitated by a tick secreted bio adhesive (tick cement) that attaches tick mouthparts to skin tissue and prevents the host from dislodging the attached tick. Understanding tick cement formation is highly sought after as its disruption will prevent tick feeding. This study describes proteins that form the inner core layer of I. scapularis tick cement as disrupting these proteins will likely stop formation of the outer cortical layer. The inner core cement layer completes formation by 24 h of tick attachment. Thus, we used laser-capture microdissection to isolate cement from cryosections of 6 h and 24 h tick attachment sites and to distinguish between early and late inner core cement proteins. LC-MS/MS analysis identified 138 tick cement proteins (TCPs) of which 37 and 35 were unique in cement of 6 and 24 h attached ticks respectively. We grouped TCPs in 14 functional categories: cuticular protein (16%), tick specific proteins of unknown function, cytoskeletal proteins, and enzymes (13% each), enzymes (10%), antioxidant, glycine rich, scaffolding, heat shock, histone, histamine binding, proteases and protease inhibitors, and miscellaneous (3-6% each). Gene ontology analysis confirm that TCPs are enriched for bio adhesive properties. Our data offer insights into tick cement bonding patterns and set the foundation for understanding the molecular basis of I. scapularis tick cement formation.
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Affiliation(s)
- Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA.
| | - Zeljko Radulovic
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
- Department of Biology, Stephen F. Austin State University, Nacogdoches, TX, USA
| | - Lindsay Porter
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
- Department of Biology, Stephen F. Austin State University, Nacogdoches, TX, USA
| | - Taylor Hollman Britten
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
| | - Tae Kwon Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Lucas Tirloni
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Alex Kiarie Gaithuma
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
| | - Grace O Adeniyi-Ipadeola
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jolene K Dietrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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9
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Zhang Z, Xiang S, Cui R, Peng H, Mridul R, Xiang M. ILP-2: A New Bane and Therapeutic Target for Human Cancers. Front Oncol 2022; 12:922596. [PMID: 35814477 PMCID: PMC9260022 DOI: 10.3389/fonc.2022.922596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Inhibitor of apoptosis protein-related-like protein-2 (ILP-2), also known as BIRC-8, is a member of the inhibitor of apoptosis protein (IAPs) family, which mainly encodes the negative regulator of apoptosis. It is selectively overexpressed in a variety of human tumors and can help tumor cells evade apoptosis, promote tumor cell growth, increase tumor cell aggressiveness, and appears to be involved in tumor cell resistance to chemotherapeutic drugs. Several studies have shown that downregulation of ILP-2 expression increases apoptosis, inhibits metastasis, reduces cell growth potential, and sensitizes tumor cells to chemotherapeutic drugs. In addition, ILP-2 inhibits apoptosis in a unique manner; it does not directly inhibit the activity of caspases but induces apoptosis by cooperating with other apoptosis-related proteins. Here, we review the current understanding of the various roles of ILP-2 in the apoptotic cascade and explore the use of interfering ILP-2, and the combination of related anti-tumor agents, as a novel strategy for cancer therapy.
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Affiliation(s)
- Zhiliang Zhang
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Siqi Xiang
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Ruxia Cui
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Hang Peng
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Roy Mridul
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
| | - Mingjun Xiang
- Department of Biochemistry and Immunology, Medical Research Center, Institute of Medicine, Jishou University, Jishou, China
- The State Ethnic Committee's Key Laboratory of Clinical Engineering Laboratory of Xiangxi Miao Pediatric Tuina, Jishou University, Jishou, China
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10
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Guk JY, Jang MJ, Kim S. Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses. BMC PLANT BIOLOGY 2022; 22:206. [PMID: 35443608 PMCID: PMC9020097 DOI: 10.1186/s12870-022-03580-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/06/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays an important role in epigenetics by regulating gene expression in eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies. RESULTS We performed genome-wide re-annotation in Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice), Capsicum annuum (pepper), Solanum tuberosum (potato), and Solanum lycopersicum (tomato) to better understand the role of PHD-finger genes in these species. Our investigation identified 875 PHD-finger genes, of which 225 (26% of total) were newly identified, including 57 (54%) novel PHD-finger genes in pepper. The PHD-finger genes of the five plant species have various integrated domains that may be responsible for the diversification of structures and functions of these genes. Evolutionary analyses suggest that PHD-finger genes were expanded recently by lineage-specific duplication, especially in pepper and potato, resulting in diverse repertoires of PHD-finger genes among the species. We validated the expression of six newly identified PHD-finger genes in pepper with qRT-PCR. Transcriptome analyses suggest potential functions of PHD-finger genes in response to various abiotic stresses in pepper. CONCLUSIONS Our data, including the updated annotation of PHD-finger genes, provide useful information for further evolutionary and functional analyses to better understand the roles of the PHD-finger gene family in pepper.
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Affiliation(s)
- Ji-Yoon Guk
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Min-Jeong Jang
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea.
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11
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Niu X, Cui H, Gu X, Wu T, Sun M, Zhou C, Ma M. Nuclear Receptor PXR Confers Irradiation Resistance by Promoting DNA Damage Response Through Stabilization of ATF3. Front Oncol 2022; 12:837980. [PMID: 35372071 PMCID: PMC8965888 DOI: 10.3389/fonc.2022.837980] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/10/2022] [Indexed: 12/26/2022] Open
Abstract
Low response rate to radiotherapy remains a problem for liver and colorectal cancer patients due to inappropriate DNA damage response in tumors. Here, we report that pregnane X receptor (PXR) contributes to irradiation (IR) resistance by promoting activating transcription factor 3 (ATF3)-mediated ataxia-telangiectasia-mutated protein (ATM) activation. PXR stabilized ATF3 protein by blocking its ubiquitination. PXR–ATF3 interaction is required for regulating ATF3, as one mutant of lysine (K) 42R of ATF3 lost binding with PXR and abolished PXR-reduced ubiquitination of ATF3. On the other hand, threonine (T) 432A of PXR lost binding with ATF3 and further compromised ATM activation. Moreover, the PXR–ATF3 interaction increases ATF3 stabilization through disrupting ATF3–murine double minute 2 (MDM2) interaction and negatively regulating MDM2 protein expression. PXR enhanced MDM2 auto-ubiquitination and shortened its half-life, therefore compromising the MDM2-mediated degradation of ATF3 protein. Structurally, both ATF3 and PXR bind to the RING domain of MDM2, and on the other hand, MDM2 binds with PXR on the DNA-binding domain (DBD), which contains zinc finger sequence. Zinc finger sequence is well known for nuclear receptor peroxisome proliferator-activated receptor-γ (PPARγ) playing E3 ligase activity to degrade nuclear factor κB (NFκB)/p65. However, whether zinc-RING sequence grants E3 ligase activity to PXR remains elusive. Taken together, these results provide a novel mechanism that PXR contributes to IR resistance by promoting ATF3-mediated ATM activation through stabilization of ATF3. Our result suggests that targeting PXR may sensitize liver and colon cancer cells to IR therapy.
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Affiliation(s)
- Xiaxia Niu
- Institute of Toxicology, School of Public Health, Lanzhou University, Lanzhou, China
| | - Hongmei Cui
- Institute of Toxicology, School of Public Health, Lanzhou University, Lanzhou, China
| | - Xinsheng Gu
- College of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Ting Wu
- Institute of Toxicology, School of Public Health, Lanzhou University, Lanzhou, China
| | - Min Sun
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Changlong Zhou
- Institute of Toxicology, School of Public Health, Lanzhou University, Lanzhou, China
| | - Mei Ma
- Institute of Toxicology, School of Public Health, Lanzhou University, Lanzhou, China
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12
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Randolph K, Hyder U, D’Orso I. KAP1/TRIM28: Transcriptional Activator and/or Repressor of Viral and Cellular Programs? Front Cell Infect Microbiol 2022; 12:834636. [PMID: 35281453 PMCID: PMC8904932 DOI: 10.3389/fcimb.2022.834636] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 01/01/2023] Open
Abstract
Several transcriptional and epigenetic regulators have been functionally linked to the control of viral and cellular gene expression programs. One such regulator is Krüppel-associated box (KRAB)-associated protein 1 (KAP1: also named TRIM28 or TIF1β), which has been extensively studied in the past three decades. Here we offer an up-to date review of its various functions in a diversity of contexts. We first summarize the discovery of KAP1 repression of endogenous retroviruses during development. We then deliberate evidence in the literature suggesting KAP1 is both an activator and repressor of HIV-1 transcription and discuss experimental differences and limitations of previous studies. Finally, we discuss KAP1 regulation of DNA and RNA viruses, and then expand on KAP1 control of cellular responses and immune functions. While KAP1 positive and negative regulation of viral and cellular transcriptional programs is vastly documented, our mechanistic understanding remains narrow. We thus propose that precision genetic tools to reveal direct KAP1 functions in gene regulation will be required to not only illuminate new biology but also provide the foundation to translate the basic discoveries from the bench to the clinics.
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13
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Wang Y, Hu H, Yuan S, LI Y, Cao K, Sun H, Liu Y. Cuprous Ions can Disrupt Structure and Functions of the RING Finger Domain of RNF11. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00631f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Copper is an essential element that plays crucial roles in a variety of biological processes, while excessive copper is harmful to cells. RNF11 is a RING finger protein associated with...
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14
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Poetz F, Corbo J, Levdansky Y, Spiegelhalter A, Lindner D, Magg V, Lebedeva S, Schweiggert J, Schott J, Valkov E, Stoecklin G. RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation. Nat Commun 2021; 12:7175. [PMID: 34887419 PMCID: PMC8660800 DOI: 10.1038/s41467-021-27471-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
The CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated mRNA degradation upon HDAC inhibition. Here, we explored acetylation-induced changes in the composition of the CCR4-NOT complex by purification of the endogenously tagged scaffold subunit NOT1 and identified RNF219 as an acetylation-regulated cofactor. We demonstrate that RNF219 is an active RING-type E3 ligase which stably associates with CCR4-NOT via NOT9 through a short linear motif (SLiM) embedded within the C-terminal low-complexity region of RNF219. By using a reconstituted six-subunit human CCR4-NOT complex, we demonstrate that RNF219 inhibits deadenylation through the direct interaction of the α-helical SLiM with the NOT9 module. Transcriptome-wide mRNA half-life measurements reveal that RNF219 attenuates global mRNA turnover in cells, with differential requirement of its RING domain. Our results establish RNF219 as an inhibitor of CCR4-NOT-mediated deadenylation, whose loss upon HDAC inhibition contributes to accelerated mRNA turnover.
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Affiliation(s)
- Fabian Poetz
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Joshua Corbo
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, 21702-1201, USA
| | - Yevgen Levdansky
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, 21702-1201, USA
| | - Alexander Spiegelhalter
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Doris Lindner
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Vera Magg
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, 69120, Heidelberg, Germany
| | - Svetlana Lebedeva
- Berlin Institute for Molecular Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, 10115, Berlin, Germany
| | - Jörg Schweiggert
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Johanna Schott
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, 21702-1201, USA.
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany.
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, 69120, Heidelberg, Germany.
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15
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Kim MS, Kang KK, Cho YG. Molecular and Functional Analysis of U-box E3 Ubiquitin Ligase Gene Family in Rice ( Oryzasativa). Int J Mol Sci 2021; 22:ijms222112088. [PMID: 34769518 PMCID: PMC8584879 DOI: 10.3390/ijms222112088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/21/2021] [Accepted: 11/05/2021] [Indexed: 02/03/2023] Open
Abstract
Proteins encoded by U-box type ubiquitin ligase (PUB) genes in rice are known to play an important role in plant responses to abiotic and biotic stresses. Functional analysis has revealed a detailed molecular mechanism involving PUB proteins in relation to abiotic and biotic stresses. In this study, characteristics of 77 OsPUB genes in rice were identified. Systematic and comprehensive analyses of the OsPUB gene family were then performed, including analysis of conserved domains, phylogenetic relationships, gene structure, chromosome location, cis-acting elements, and expression patterns. Through transcriptome analysis, we confirmed that 16 OsPUB genes show similar expression patterns in drought stress and blast infection response pathways. Numerous cis-acting elements were found in promoter sequences of 16 OsPUB genes, indicating that the OsPUB genes might be involved in complex regulatory networks to control hormones, stress responses, and cellular development. We performed qRT-PCR on 16 OsPUB genes under drought stress and blast infection to further identify the reliability of transcriptome and cis-element analysis data. It was confirmed that the expression pattern was similar to RNA-sequencing analysis results. The transcription of OsPUB under various stress conditions indicates that the PUB gene might have various functions in the responses of rice to abiotic and biotic stresses. Taken together, these results indicate that the genome-wide analysis of OsPUB genes can provide a solid basis for the functional analysis of U-box E3 ubiquitin ligase genes. The molecular information of the U-box E3 ubiquitin ligase gene family in rice, including gene expression patterns and cis-acting regulatory elements, could be useful for future crop breeding programs by genome editing.
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Affiliation(s)
- Me-Sun Kim
- Department of Crop Science, College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea;
| | - Kwon-Kyoo Kang
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea;
| | - Yong-Gu Cho
- Department of Crop Science, College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea;
- Correspondence:
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16
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Zheng W, Sun L, Yang L, Xu T. The circular RNA circBCL2L1 regulates innate immune responses via microRNA-mediated downregulation of TRAF6 in teleost fish. J Biol Chem 2021; 297:101199. [PMID: 34536420 PMCID: PMC8487061 DOI: 10.1016/j.jbc.2021.101199] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022] Open
Abstract
Growing numbers of studies have shown that circular RNAs (circRNAs) can function as regulatory factors to regulate the innate immune response, cell proliferation, cell migration, and other important processes in mammals. However, the function and regulatory mechanism of circRNAs in lower vertebrates are still unclear. Here, we discovered a novel circRNA derived from the gene encoding Bcl-2-like protein 1 (BCL2L1) gene, named circBCL2L1, which was related to the innate immune responses in teleost fish. Results indicated that circBCL2L1 played essential roles in host antiviral immunity and antibacterial immunity. Our study also identified a microRNA, miR-30c-3-3p, which could inhibit the innate immune response by targeting inflammatory mediator TRAF6. And TRAF6 is a key signal transduction factor in innate immune response mediated by TLRs. Moreover, we also found that the antiviral and antibacterial effects inhibited by miR-30c-3-3p could be reversed with the expression of circBCL2L1. Our data revealed that circBCL2L1 functioned as a competing endogenous RNA (ceRNA) of TRAF6 by competing for binding with miR-30c-3-3p, leading to activation of the NF-κB/IRF3 inflammatory pathway and then enhancing the innate immune responses. Our results suggest that circRNAs can play an important role in the innate immune response of teleost fish.
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Affiliation(s)
- Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Lingping Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Liyuan Yang
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China.
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17
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Zhou J, Tang ZY, Sun XL. RNF38 inhibits osteosarcoma cell proliferation by binding to CRY1. Biochem Cell Biol 2021; 99:629-635. [PMID: 34460347 DOI: 10.1139/bcb-2021-0093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The PI3K/AKT pathway plays an important role in the development of osteosarcoma. RNF38 interferes with activation of the AKT pathway. Cryptochrome1 (CRY1) inhibits osteosarcoma proliferation through the AKT pathway. We aimed to clarify whether RNF38 affects the proliferation of osteosarcoma cells by regulating the PI3K/AKT pathway through its interaction with CRY1. The mRNA levels of RNF38 were determined using qRT-PCR. Protein levels of RNF38, p-p70S6, p70S6, +p-AKT, AKT, p-mTOR, mTOR, and CRY1 were detected by western blotting. The proliferation of osteosarcoma cells was detected using CCK-8 and colony formation assays. The interaction between CRY1 and RNF38 was detected by co-immunoprecipitation and GST pull-down assays. RNF38 expression was higher in Saos-2 and U20S cells than in hFOB cells. Overexpression of RNF38 promoted the proliferation of osteosarcoma cells, the number of colonies, and p-AKT and p-mTOR levels, suggesting that overexpression of RNF38 activated the PI3K/AKT pathway. In addition, RNF38 directly binds to the N-terminal of CRY1. The simultaneous knockdown of RNF38 and CRY1 restored the level of p-AKT, which was reduced by RNF38 knockdown alone. RNF38 affects the proliferation of osteosarcoma cells by regulating the PI3K/AKT pathway through its interaction with CRY1.
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Affiliation(s)
- Jian Zhou
- Articular Orthopaedics, The Third Affiliated Hospital of Soochow University, Changzhou 213000, Jiangsu Province, China.,Articular Orthopaedics, The Third Affiliated Hospital of Soochow University, Changzhou 213000, Jiangsu Province, China
| | - Zhen-Yu Tang
- Articular Orthopaedics, The Third Affiliated Hospital of Soochow University, Changzhou 213000, Jiangsu Province, China.,Articular Orthopaedics, The Third Affiliated Hospital of Soochow University, Changzhou 213000, Jiangsu Province, China
| | - Xiao-Liang Sun
- Articular Orthopaedics, The Third Affiliated Hospital of Soochow University, Changzhou 213000, Jiangsu Province, China.,Articular Orthopaedics, The Third Affiliated Hospital of Soochow University, Changzhou 213000, Jiangsu Province, China
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18
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The Role of Metal Ions in Fungal Organic Acid Accumulation. Microorganisms 2021; 9:microorganisms9061267. [PMID: 34200938 PMCID: PMC8230503 DOI: 10.3390/microorganisms9061267] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/22/2022] Open
Abstract
Organic acid accumulation is probably the best-known example of primary metabolic overflow. Both bacteria and fungi are capable of producing various organic acids in large amounts under certain conditions, but in terms of productivity-and consequently, of commercial importance-fungal platforms are unparalleled. For high product yield, chemical composition of the growth medium is crucial in providing the necessary conditions, of which the concentrations of four of the first-row transition metal elements, manganese (Mn2+), iron (Fe2+), copper (Cu2+) and zinc (Zn2+) stand out. In this paper we critically review the biological roles of these ions, the possible biochemical and physiological consequences of their influence on the accumulation of the most important mono-, di- and tricarboxylic as well as sugar acids by fungi, and the metal ion-related aspects of submerged organic acid fermentations, including the necessary instrumental analytics. Since producing conditions are associated with a cell physiology that differs strongly to what is observed under “standard” growth conditions, here we consider papers and patents only in which organic acid accumulation levels achieved at least 60% of the theoretical maximum yield, and the actual trace metal ion concentrations were verified.
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19
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Soni P, Shivhare R, Kaur A, Bansal S, Sonah H, Deshmukh R, Giri J, Lata C, Ram H. Reference gene identification for gene expression analysis in rice under different metal stress. J Biotechnol 2021; 332:83-93. [PMID: 33794279 DOI: 10.1016/j.jbiotec.2021.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Real-time quantitative polymerase chain reaction (RT-qPCR) is the most common approach to quantify changes in gene expression. Appropriate internal reference genes are essential for normalization of data of RT-qPCR. In the present study, we identified suitable reference genes for analysis of gene expression in rice seedlings subjected to different heavy metal stresses such as deficiencies of iron and zinc and toxicities of cobalt, cadmium and nickel. First, from publically available RNA-Seq data we identified 10 candidate genes having stable expression. We also included commonly used house-keeping gene OsUBQ5 (Ubiquitin 5) in our analysis. Expression stability of all the 11 genes was determined by two independent tools, NormFinder and geNorm. Our results show that selected candidate reference genes have higher stability in their expression compared to that of OsUBQ5. Genes with locus ID LOC_Os03g16690, encoding an oxysterol-binding protein (OsOBP) and LOC_Os01g56580, encoding Casein Kinase_1a.3 (OsCK1a.3) were identified to be the most stably expressed reference genes under most of the conditions tested. Finally, the study reveals that it is better to use a specific reference gene for a specific heavy metal stress condition rather than using a common reference gene for multiple heavy metal stress conditions. The reference genes identified here would be very useful for gene expression studies under heavy metal stresses in rice.
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Affiliation(s)
- Praveen Soni
- Department of Botany, University of Rajasthan, Jaipur, 302004, India
| | - Radha Shivhare
- CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Amandeep Kaur
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Sakshi Bansal
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Mohali, 140308, India
| | - Jitender Giri
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Charu Lata
- CSIR-National Institute of Science Communication and Information Resources, New Delhi, 110067, India.
| | - Hasthi Ram
- National Agri-Food Biotechnology Institute, Mohali, 140308, India; National Institute of Plant Genome Research, New Delhi, 110067, India.
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20
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Bawa S, Piccirillo R, Geisbrecht ER. TRIM32: A Multifunctional Protein Involved in Muscle Homeostasis, Glucose Metabolism, and Tumorigenesis. Biomolecules 2021; 11:biom11030408. [PMID: 33802079 PMCID: PMC7999776 DOI: 10.3390/biom11030408] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/13/2022] Open
Abstract
Human tripartite motif family of proteins 32 (TRIM32) is a ubiquitous multifunctional protein that has demonstrated roles in differentiation, muscle physiology and regeneration, and tumor suppression. Mutations in TRIM32 result in two clinically diverse diseases. A mutation in the B-box domain gives rise to Bardet–Biedl syndrome (BBS), a disease whose clinical presentation shares no muscle pathology, while mutations in the NHL (NCL-1, HT2A, LIN-41) repeats of TRIM32 causes limb-girdle muscular dystrophy type 2H (LGMD2H). TRIM32 also functions as a tumor suppressor, but paradoxically is overexpressed in certain types of cancer. Recent evidence supports a role for TRIM32 in glycolytic-mediated cell growth, thus providing a possible mechanism for TRIM32 in the accumulation of cellular biomass during regeneration and tumorigenesis, including in vitro and in vivo approaches, to understand the broad spectrum of TRIM32 functions. A special emphasis is placed on the utility of the Drosophila model, a unique system to study glycolysis and anabolic pathways that contribute to the growth and homeostasis of both normal and tumor tissues.
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Affiliation(s)
- Simranjot Bawa
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA;
| | - Rosanna Piccirillo
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy;
| | - Erika R. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA;
- Correspondence: ; Tel.: +1-(785)-532-3105
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21
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Kim JH, Khan IU, Lee CW, Kim DY, Jang CS, Lim SD, Park YC, Kim JH, Seo YW. Identification and analysis of a differentially expressed wheat RING-type E3 ligase in spike primordia development during post-vernalization. PLANT CELL REPORTS 2021; 40:543-558. [PMID: 33423075 DOI: 10.1007/s00299-020-02651-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
We identified a RING-type E3 ligase (TaBAH1) protein in winter wheat that targets TaSAHH1 for degradation and might be involved in primordia development by regulating targeted protein degradation. Grain yield per spike in wheat (Triticum aestivum), is mainly determined prior to flowering during mature primordia development; however, the genes involved in primordia development have yet to be characterized. In this study, we demonstrated that, after vernalization for 50 days at 4 °C, there was a rapid acceleration in primordia development to the mature stages in the winter wheat cultivars Keumgang and Yeongkwang compared with the Chinese Spring cultivar. Although Yeongkwang flowers later than Keumgang under normal condition, it has the same heading time and reaches the WS9 stage of floral development after vernalization for 50 days. Using RNA sequencing, we identified candidate genes associated with primordia development in cvs. Keumgang and Yeongkwang, that are differentially expressed during wheat reproductive stages. Among these, the RING-type E3 ligase TaBAH1 (TraesCS5B01G373000) was transcriptionally upregulated between the double-ridge (WS2.5) stage and later stages of floret primordia development (WS10) after vernalization. Transient expression analysis indicated that TaBAH1 was localized to the plasma membrane and nucleus and was characterized by self-ubiquitination activity. Furthermore, we found that TaBAH1 interacts with TaSAHH1 to mediate its polyubiquitination and degradation through a 26S proteasomal pathway. Collectively, the findings of this study indicate that TaBAH1 might play a prominent role in post-vernalization floret primordia development.
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Affiliation(s)
- Jae Ho Kim
- Department of Plant Biotechnology, Korea University, Seongbuk-Gu, Seoul, 02841, Republic of Korea
| | - Irfan Ullah Khan
- Department of Plant Biotechnology, Korea University, Seongbuk-Gu, Seoul, 02841, Republic of Korea
| | - Cheol Won Lee
- Department of Plant Biotechnology, Korea University, Seongbuk-Gu, Seoul, 02841, Republic of Korea
| | - Dae Yeon Kim
- Department of Plant Biotechnology, Korea University, Seongbuk-Gu, Seoul, 02841, Republic of Korea
| | - Cheol Seong Jang
- Plant Genomics Laboratory, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Sung Don Lim
- Plant Genomics Laboratory, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Yong Chan Park
- Plant Genomics Laboratory, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Ju Hee Kim
- Plant Genomics Laboratory, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, Republic of Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seongbuk-Gu, Seoul, 02841, Republic of Korea.
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Yusuf AP, Abubakar MB, Malami I, Ibrahim KG, Abubakar B, Bello MB, Qusty N, Elazab ST, Imam MU, Alexiou A, Batiha GES. Zinc Metalloproteins in Epigenetics and Their Crosstalk. Life (Basel) 2021; 11:life11030186. [PMID: 33652690 PMCID: PMC7996840 DOI: 10.3390/life11030186] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
More than half a century ago, zinc was established as an essential micronutrient for normal human physiology. In silico data suggest that about 10% of the human proteome potentially binds zinc. Many proteins with zinc-binding domains (ZBDs) are involved in epigenetic modifications such as DNA methylation and histone modifications, which regulate transcription in physiological and pathological conditions. Zinc metalloproteins in epigenetics are mainly zinc metalloenzymes and zinc finger proteins (ZFPs), which are classified into writers, erasers, readers, editors, and feeders. Altogether, these classes of proteins engage in crosstalk that fundamentally maintains the epigenome's modus operandi. Changes in the expression or function of these proteins induced by zinc deficiency or loss of function mutations in their ZBDs may lead to aberrant epigenetic reprogramming, which may worsen the risk of non-communicable chronic diseases. This review attempts to address zinc's role and its proteins in natural epigenetic programming and artificial reprogramming and briefly discusses how the ZBDs in these proteins interact with the chromatin.
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Affiliation(s)
- Abdurrahman Pharmacy Yusuf
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
| | - Murtala Bello Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
- Correspondence: (M.B.A.); (A.A.); (G.E.-S.B.)
| | - Ibrahim Malami
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Kasimu Ghandi Ibrahim
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Bilyaminu Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Naeem Qusty
- Medical Laboratories Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Mecca 21955, Saudi Arabia;
| | - Sara T. Elazab
- Department of Pharmacology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Dakahlia 35516, Egypt;
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
- AFNP Med, Haidingergasse 29, 1030 Vienna, Austria
- Correspondence: (M.B.A.); (A.A.); (G.E.-S.B.)
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, AlBeheira 22511, Egypt
- Correspondence: (M.B.A.); (A.A.); (G.E.-S.B.)
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Butt BG, Scourfield EJ, Graham SC. Non-native fold of the putative VPS39 zinc finger domain. Wellcome Open Res 2020; 5:154. [PMID: 32724865 PMCID: PMC7384125 DOI: 10.12688/wellcomeopenres.16078.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2020] [Indexed: 01/15/2023] Open
Abstract
Background: The multi-subunit homotypic fusion and vacuole protein sorting (HOPS) membrane-tethering complex is involved in regulating the fusion of late endosomes and autophagosomes with lysosomes in eukaryotes. The C-terminal regions of several HOPS components have been shown to be required for correct complex assembly, including the C-terminal really interesting new gene (RING) zinc finger domains of HOPS components VPS18 and VPS41. We sought to structurally characterise the putative C-terminal zinc finger domain of VPS39, which we hypothesised may be important for binding of VPS39 to cellular partners or to other HOPS components. Methods: We recombinantly expressed, purified and solved the crystal structure of the proposed zinc-binding region of VPS39. Results: In the structure, this region forms an anti-parallel β-hairpin that is incorporated into a homotetrameric eight-stranded β-barrel. However, the fold is stabilised by coordination of zinc ions by residues from the purification tag and an intramolecular disulphide bond between two predicted zinc ligands. Conclusions: We solved the structure of the VPS39 C-terminal domain adopting a non-native fold. Our work highlights the risk of non-native folds when purifying small zinc-containing domains with hexahistidine tags. However, the non-native structure we observe may have implications for rational protein design.
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Affiliation(s)
- Benjamin G Butt
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | | | - Stephen C Graham
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
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24
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Park YC, Jang CS. Molecular dissection of two homoeologous wheat genes encoding RING H2-type E3 ligases: TaSIRFP-3A and TaSIRFP-3B. PLANTA 2020; 252:26. [PMID: 32696139 DOI: 10.1007/s00425-020-03431-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
Two homoeologous wheat genes, TaSIRFP-3A and TaSIRFP-3B, encode the RING-HC-type E3 ligases that play an inhibitory role in sucrose metabolism in response to cold stress. In higher plants, the attachment of ubiquitin (Ub) and the subsequent recognition and degradation by the 26S proteasome affects a variety of cellular functions that are essential for survival. Here, we characterized the two homoeologous wheat genes encoding the really interesting new gene (RING) HC-type E3 ligases: TaSIRFP-3A and TaSIRFP-3B (Triticum aestivum SINA domain including RING finger protein 1 and 2), which regulate target proteins via the Ub/26S proteasome system. The TaSIRFP-3A gene was highly expressed under cold stress. In contrast, its homoeologous gene, TaSIRFP-3B, showed only a slight increase in expression levels in shoots. Despite these differences, both the proteins exhibited E3 ligase activity with the cytosol- and nucleus-targeted localization, demonstrating their conserved molecular function. Heterogeneous overexpression of TaSIRFP-3A or TaSIRFP-3B in Arabidopsis showed delayed plant growth causing a reduction in sucrose synthase enzymatic activity and photosynthetic sucrose synthesis, by regulating sucrose synthase proteins. TaSIRFP-3A- or TaSIRFP-3B-overexpressing plants showed higher hypersensitivity under cold stress than WT plants with an accumulation of reactive oxygen species (ROS). These results suggest that the negative regulation of TaSIRFP-3A and TaSIRFP-3B in response to cold stress is involved in sucrose metabolism.
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Affiliation(s)
- Yong Chan Park
- Plant Genomics Lab, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Cheol Seong Jang
- Plant Genomics Lab, Department of Bio-Resources Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Transcriptomic and Ultrastructural Signatures of K +-Induced Aggregation in Phytophthora parasitica Zoospores. Microorganisms 2020; 8:microorganisms8071012. [PMID: 32645882 PMCID: PMC7409359 DOI: 10.3390/microorganisms8071012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 11/17/2022] Open
Abstract
Most pathogenic oomycetes of the genus Phytophthora spread in water films as flagellated zoospores. Zoospores perceive and produce signals attracting other zoospores, resulting in autoaggregation in vitro or biofilm formation on plant surface. The mechanisms underlying intercellular communication and consequent attraction, adhesion and aggregation are largely unknown. In Phytophthora parasitica, the perception of a K+ gradient induces coordinated motion and aggregation. To define cellular and molecular events associated with oomycete aggregation, we combined transcriptomic and ultrastructural analyses. Results indicate involvement of electroception in K+ sensing. They establish that the transcriptome repertoire required for swimming and aggregation is already fully functional at zoospore release. At the time points analyzed, aggregates are mainly constituted of zoospores. They produce vesicular and fibrillary material discharged at cell-to-cell contacts. Consistently, the signature of transcriptome dynamics during transition to aggregates is an upregulation of genes potentially related to vesicular trafficking. Moreover, transcriptomic and functional analyses show a strong enhancement of carbonic anhydrase activity, indicating that pH homeostasis may contribute to aggregation by acting on both zoospore movement and adhesion. This study poses the molecular and cellular bases of aggregative behavior within oomycetes and expands the current knowledge of ion perception-mediated dissemination of propagules in the rhizosphere.
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26
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Butt BG, Scourfield EJ, Graham SC. Non-native fold of the putative VPS39 zinc finger domain. Wellcome Open Res 2020; 5:154. [DOI: 10.12688/wellcomeopenres.16078.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 11/20/2022] Open
Abstract
Background: The multi-subunit homotypic fusion and vacuole protein sorting (HOPS) membrane-tethering complex is involved in regulating the fusion of late endosomes and autophagosomes with lysosomes in eukaryotes. The C-terminal regions of several HOPS components have been shown to be required for correct complex assembly, including the C-terminal really interesting new gene (RING) zinc finger domains of HOPS components VPS18 and VPS41. We sought to structurally characterise the putative C-terminal zinc finger domain of VPS39, which we hypothesised may be important for binding of VPS39 to cellular partners or to other HOPS components. Methods: We recombinantly expressed, purified and solved the crystal structure of the proposed zinc-binding region of VPS39. Results: In the structure, this region forms an anti-parallel β-hairpin that is incorporated into a homotetrameric eight-stranded β-barrel. However, the fold is stabilised by coordination of zinc ions by residues from the purification tag and an intramolecular disulphide bond between two predicted zinc ligands. Conclusions: We solved the structure of the VPS39 C-terminal domain adopting a non-native fold. Our work highlights the risk of non-native folds when purifying small zinc-containing domains with hexahistidine tags. However, the non-native structure we observe may have implications for rational protein design.
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27
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Fu Q, Zhao S, Yang N, Tian M, Cai X, Zhang L, Hu J, Cao M, Xue T, Li C. Genome-wide identification, expression signature and immune functional analysis of two cathepsin S (CTSS) genes in turbot (Scophthalmus maximus L.). FISH & SHELLFISH IMMUNOLOGY 2020; 102:243-256. [PMID: 32315741 DOI: 10.1016/j.fsi.2020.04.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
Cathepsins, a superfamily of hydrolytic enzymes produced and enclosed within lysosomes, play multiple roles at physiological and pathological states. Cathepsin S is a lysosomal cysteine endopeptidase of the papain family, and exerts critical roles in the regulation of MHC class II immune responses. In the present study, we captured two Cathepsin S genes in turbot (SmCTSS1 and SmCTSS2.1), characterized their expression patterns following V. anguillarum and S. iniae infections, and explored their binding ability and agglutination capability. Firstly, the SmCTSS1 contained a 990 bp ORF encoding 329 amino acids, while SmCTSS2.1 contained a 1,014 bp ORF encoding 337 amino acids. The phylogenetic analysis revealed that both genes showed the closest relationship to their counterparts of Japanese flounder (Paralichthys olivaceus). In addition, both genes were ubiquitously expressed in all examined healthy tissues, with the highest expression level observed in spleen and intestine, respectively, while the lowest expression level both observed in liver. Both SmCTSS1 and SmCTSS2.1 were significantly differentially expressed, and exhibited general down-regulations at most time points in skin and intestine after two bacterial infections. Finally, both rSmCTSS1 and rSmCTSS2.1 showed significant binding ability to three examined microbial ligands (LPS, PGN and LTA), and strong agglutination effect to different bacteria (E. tarda, S. agalactiae, S. aureus and V. anguillarum). Collectively, this study provided valuable data for understanding the roles of CTSS in the host defense against bacterial infections in turbot, and indicated the potential vital roles of CTSS in innate immune responses of teleost species.
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Affiliation(s)
- Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shoucong Zhao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Mengyu Tian
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lu Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Hu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ting Xue
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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28
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Sharma B, Taganna J. Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato. Sci Rep 2020; 10:9581. [PMID: 32533036 PMCID: PMC7293263 DOI: 10.1038/s41598-020-66553-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
E3 ubiquitin ligases are a central modifier of plant signaling pathways that act through targeting proteins to the degradation pathway. U-box E3 ubiquitin ligases are a distinct class of E3 ligases that utilize intramolecular interactions for its scaffold stabilization. U-box E3 ubiquitin ligases are prevalent in plants in comparison to animals. However, the evolutionary aspects, genetic organizations, and functional fate of the U-box E3 gene family in plant development, especially in tomato is not well understood. In the present study, we have performed in-silico genome-wide analysis of the U-box E3 ubiquitin ligase gene family in Solanum lycopersicum. We have identified 62 U-box genes with U-box/Ub Fusion Degradation 2 (UFD2) domain. The chromosomal localization, phylogenetic analysis, gene structure, motifs, gene duplication, syntenic regions, promoter, physicochemical properties, and ontology were investigated. The U-box gene family showed significant conservation of the U-box domain throughout the gene family. Duplicated genes discerned noticeable functional transitions among duplicated genes. The gene expression profiles of U-box E3 family members show involvement in abiotic and biotic stress signaling as well as hormonal pathways. We found remarkable participation of the U-box gene family in the vegetative and reproductive tissue development. It is predicted to be actively regulating flowering time and endosperm formation. Our study provides a comprehensive picture of distribution, structural features, promoter elements, evolutionary relationship, and gene expression of the U-box gene family in the tomato. We predict the crucial participation of the U-box gene family in tomato plant development and stress responses.
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Affiliation(s)
- Bhaskar Sharma
- TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India.
- School of Life and Environmental Sciences, Faculty of Science, Engineering, and Built Environment, Deakin University, Geelong, VIC-3220, Australia.
| | - Joemar Taganna
- SciBiz Informatics, 2/F Unit 3 CFI Building, Maharlika Highway, Brgy. Guindapunan, Palo, Leyte, 6501, Philippines
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29
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Feng X, Lu T, Li J, Yang R, Hu L, Ye Y, Mao F, He L, Xu J, Wang Z, Liu Y, Zhang Y, Ji H, Zhao Y, Cheng S, Tian W, Zhang L. The Tumor Suppressor Interferon Regulatory Factor 2 Binding Protein 2 Regulates Hippo Pathway in Liver Cancer by a Feedback Loop in Mice. Hepatology 2020; 71:1988-2004. [PMID: 31538665 DOI: 10.1002/hep.30961] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/14/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIMS The conserved Hippo pathway regulates organ size, tissue homeostasis, and tumorigenesis. Interferon regulatory factor 2 binding protein 2 (IRF2BP2) was originally identified as a transcriptional corepressor. However, the association between IRF2BP2 and the Hippo pathway remains largely unknown. In addition, the biological function and regulation mechanism of IRF2BP2 in liver cancer are poorly understood. APPROACH AND RESULTS In this study, we uncovered the clinical significance of IRF2BP2 in suppressing hepatocellular carcinogenesis. We showed that IRF2BP2, a direct target repressed by the Yes-associated protein (YAP)/TEA domain transcription factor 4 (TEAD4) transcriptional complex, inhibited YAP activity through a feedback loop. IRF2BP2 stabilized vestigial-like family member 4 (VGLL4) and further enhanced VGLL4's inhibitory function on YAP. Moreover, liver-specific IRF2BP2 overexpression suppressed tumor formation induced by Hippo pathway inactivation. CONCLUSIONS These results revealed the important role of IRF2BP2 in repressing liver cancer progression and highlighted a feedback loop underlying the Hippo pathway in organ-size control and tumorigenesis.
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Affiliation(s)
- Xue Feng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Tiantian Lu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinhui Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ruizeng Yang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Liqiao Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Ye
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Feifei Mao
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Lingli He
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinjin Xu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Zuoyun Wang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yingbin Liu
- Department of General Surgery, Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yonglong Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yun Zhao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shuqun Cheng
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Wei Tian
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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Asmamaw MD, Liu Y, Zheng YC, Shi XJ, Liu HM. Skp2 in the ubiquitin-proteasome system: A comprehensive review. Med Res Rev 2020; 40:1920-1949. [PMID: 32391596 DOI: 10.1002/med.21675] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/26/2020] [Accepted: 04/27/2020] [Indexed: 12/19/2022]
Abstract
The ubiquitin-proteasome system (UPS) is a complex process that regulates protein stability and activity by the sequential actions of E1, E2 and E3 enzymes to influence diverse aspects of eukaryotic cells. However, due to the diversity of proteins in cells, substrate selection is a highly critical part of the process. As a key player in UPS, E3 ubiquitin ligases recruit substrates for ubiquitination specifically. Among them, RING E3 ubiquitin ligases which are the most abundant E3 ubiquitin ligases contribute to diverse cellular processes. The multisubunit cullin-RING ligases (CRLs) are the largest family of RING E3 ubiquitin ligases with tremendous plasticity in substrate specificity and regulate a vast array of cellular functions. The F-box protein Skp2 is a component of CRL1 (the prototype of CRLs) which is expressed in many tissues and participates in multiple cellular functions such as cell proliferation, metabolism, and tumorigenesis by contributing to the ubiquitination and subsequent degradation of several specific tumor suppressors. Most importantly, Skp2 plays a pivotal role in a plethora of cancer-associated signaling pathways. It enhances cell growth, accelerates cell cycle progression, promotes migration and invasion, and inhibits cell apoptosis among others. Hence, targeting Skp2 may represent a novel and attractive strategy for the treatment of different human cancers overexpressing this oncogene. In this review article, we summarized the known roles of Skp2 both in health and disease states in relation to the UPS.
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Affiliation(s)
- Moges Dessale Asmamaw
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Ministry of Education of China, Zhengzhou, Henan, China
| | - Ying Liu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Ministry of Education of China, Zhengzhou, Henan, China
| | - Yi-Chao Zheng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Ministry of Education of China, Zhengzhou, Henan, China
| | - Xiao-Jing Shi
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Ministry of Education of China, Zhengzhou, Henan, China
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Henan Key Laboratory of Drug Quality Control & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Ministry of Education of China, Zhengzhou, Henan, China
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31
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Li YH, Liu TB. Zinc Finger Proteins in the Human Fungal Pathogen Cryptococcus neoformans. Int J Mol Sci 2020; 21:ijms21041361. [PMID: 32085473 PMCID: PMC7072944 DOI: 10.3390/ijms21041361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 12/17/2022] Open
Abstract
Zinc is one of the essential trace elements in eukaryotes and it is a critical structural component of a large number of proteins. Zinc finger proteins (ZNFs) are zinc-finger domain-containing proteins stabilized by bound zinc ions and they form the most abundant proteins, serving extraordinarily diverse biological functions. In recent years, many ZNFs have been identified and characterized in the human fungal pathogen Cryptococcus neoformans, a fungal pathogen causing fatal meningitis mainly in immunocompromised individuals. It has been shown that ZNFs play important roles in the morphological development, differentiation, and virulence of C. neoformans. In this review, we, first, briefly introduce the ZNFs and their classification. Then, we explain the identification and classification of the ZNFs in C. neoformans. Next, we focus on the biological role of the ZNFs functionally characterized so far in the sexual reproduction, virulence factor production, ion homeostasis, pathogenesis, and stress resistance in C. neoformans. We also discuss the perspectives on future function studies of ZNFs in C. neoformans.
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Affiliation(s)
- Yuan-Hong Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Tong-Bao Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
- Correspondence: ; Tel.: +86-23-6825-1088
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32
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Tong Y, Lear TB, Evankovich J, Chen Y, Londino JD, Myerburg MM, Zhang Y, Popescu ID, McDyer JF, McVerry BJ, Lockwood KC, Jurczak MJ, Liu Y, Chen BB. The RNFT2/IL-3Rα axis regulates IL-3 signaling and innate immunity. JCI Insight 2020; 5:133652. [PMID: 31990690 DOI: 10.1172/jci.insight.133652] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/09/2020] [Indexed: 01/01/2023] Open
Abstract
Interleukin-3 (IL-3) receptor α (IL-3Rα) is the α subunit of the ligand-specific IL-3R and initiates intracellular signaling in response to IL-3. IL-3 amplifies proinflammatory signaling and cytokine storm in murine sepsis models. Here we found that RNFT2 (RING finger transmembrane-domain containing protein 2, also TMEM118), a previously uncharacterized RING finger ubiquitin E3 ligase, negatively regulated IL-3-dependent cellular responses through IL-3Rα ubiquitination and degradation in the proteasome. In vitro, IL-3 stimulation promoted IL-3Rα proteasomal degradation dependent on RNFT2, and we identified IL-3Rα lysine 357 as a ubiquitin acceptor site. We determined that LPS priming reduces RNFT2 abundance, extends IL-3Rα half-life, and sensitizes cells to the effects of IL-3, acting synergistically to increase proinflammatory signaling. In vivo, IL-3 synergized with LPS to exacerbate lung inflammation in LPS and Pseudomonas aeruginosa-challenged mice; conversely, IL-3 neutralization reduced LPS-induced lung injury. Further, RNFT2 overexpression reduced lung inflammation and injury, whereas Rnft2 knockdown exacerbated inflammatory responses in LPS-induced murine lung injury. Last, we examined RNFT2 and IL-3Rα in human lung explants from patients with cystic fibrosis and also showed that IL-3 is elevated in mechanically ventilated critically ill humans at risk for acute respiratory distress syndrome. These results identify RNFT2 as a negative regulator of IL-3Rα and show a potential role for the RNFT2/IL-3Rα/IL-3 axis in regulating innate immune responses in the lung.
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Affiliation(s)
- Yao Tong
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Anesthesiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Travis B Lear
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Environmental and Occupational Health, School of Public Health, and.,Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John Evankovich
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yanwen Chen
- Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Gastroenterology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - James D Londino
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Michael M Myerburg
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yingze Zhang
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Iulia D Popescu
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John F McDyer
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bryan J McVerry
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Environmental and Occupational Health, School of Public Health, and
| | - Karina C Lockwood
- Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michael J Jurczak
- Division of Endocrinology and Metabolism, Department of Medicine, School of Medicine
| | - Yuan Liu
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,McGowan Institute for Regenerative Medicine, and
| | - Bill B Chen
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Chen J, Zhang L, Yang N, Cao M, Tian M, Fu Q, Su B, Li C. Characterization of the immune roles of cathepsin L in turbot (Scophthalmus maximus L.) mucosal immunity. FISH & SHELLFISH IMMUNOLOGY 2020; 97:322-335. [PMID: 31805413 DOI: 10.1016/j.fsi.2019.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/25/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Cathepsin L (CTSL) is one of the crucial enzymes in cathepsin family, which has been widely known for its involvement in the innate immunity. However, it still remains poorly understood how CTSL modulates the immune system of teleosts. In this study, we captured three cathepsin L genes (SmCTSL, SmCTSL.1 and SmCTSL1) from turbot (Scophthalmus maximus). The coding sequences of SmCTSL, SmCTSL.1 and SmCTSL1 are 1,026 bp, 1,005 bp and 1,017 bp in length and encode 341, 334 and 338 amino acids, respectively. In details, transcripts of CTSL genes share same domains as other CTSL genes, one signal peptide, one propeptide and one papain family cysteine protease domain. Protein interaction network analysis indicated that turbot CTSL genes may play important roles in apoptotic signaling and involve in innate immune response. Evidence from subcellular localization demonstrated that the three Cathepsin L proteins were ubiquitous in nucleus and cytoplasm. The cathepsin L genes were widely expressed in all the tested tissues with the highest expression level of SmCTSL in spleen, and SmCTSL.1 and SmCTSL1 in intestine. Following Vibrio anguillarum, Edwardsiella tarda and Streptococcus iniae challenge, these cathepsin L genes were significantly regulated in mucosal tissues in all the challenges, especially significant down-regulation occurred rapidly in intestine in all the three challenges. In addition, the three cathepsin L genes showed strong binding ability to all the examined microbial ligands (LPS, PGN and LTA). Further studies should be used to analyze the specific function of these three cathepsin L genes. By then, we can use their function to maintain the integrity of the mucosal barrier, thereby promoting the disease resistance line and family selection in turbot.
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Affiliation(s)
- Jinghua Chen
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Lu Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Mengyu Tian
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China.
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Research Progress on Plant RING-Finger Proteins. Genes (Basel) 2019; 10:genes10120973. [PMID: 31779262 PMCID: PMC6969932 DOI: 10.3390/genes10120973] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 12/17/2022] Open
Abstract
E3 ubiquitin ligases are the most expanded components of the ubiquitin proteasome system (UPS). They mediate the recognition of substrates and later transfer the ubiquitin (Ub) of the system. Really Interesting New Gene (RING) finger proteins characterized by the RING domain, which contains 40–60 residues, are thought to be E3 ubiquitin ligase. RING-finger proteins play significant roles in plant growth, stress resistance, and signal transduction. In this study, we mainly describe the structural characteristics, classifications, and subcellular localizations of RING-finger proteins, as well the physiological processes of RING-finger proteins in plant growth and development. We also summarize the functions of plant RING-finger proteins in plant stress resistance. Finally, further research on plant RING-finger proteins is suggested, thereby establishing a strong foundation for the future study of plant RING-finger proteins.
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35
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Li B, Li S, He Q, Du S. Generation of MuRF-GFP transgenic zebrafish models for investigating murf gene expression and protein localization in Smyd1b and Hsp90α1 knockdown embryos. Comp Biochem Physiol B Biochem Mol Biol 2019; 240:110368. [PMID: 31669374 DOI: 10.1016/j.cbpb.2019.110368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 12/18/2022]
Abstract
Muscle-specific RING-finger proteins (MuRFs) are E3 ubiquitin ligases that play important roles in protein quality control in skeletal and cardiac muscles. Here we characterized murf gene expression and protein localization in zebrafish embryos. We found that the zebrafish genome contains six murf genes, including murf1a, murf1b, murf2a, murf2b, murf3 and a murf2-like gene that are specifically expressed in skeletal and cardiac muscles of zebrafish embryos. To analyze the subcellular localization, we generated transgenic zebrafish models expressing MurF1a-GFP or MuRF2a-GFP fusion proteins. MuRF1a-GFP and MuRF2a-GFP showed distinct patterns of subcellular localization. MuRF1a-GFP displayed a striated pattern of localization in myofibers, whereas MuRF2a-GFP mainly exhibited a random pattern of punctate distribution. The MuRF1a-GFP signal appeared as small dots aligned along the M-lines of the sarcomeres in skeletal myofibers. To determine whether knockdown of smyd1b or hsp90α1 that increased myosin protein degradation could alter murf gene expression or MuRF protein localization, we knocked down smyd1b or hsp90α1 in wild type, Tg(ef1a:MurF1a-GFP) and Tg(ef1a:MuRF2a-GFP) transgenic zebrafish embryos. Knockdown of smyd1b or hsp90α1 had no effect on murf gene expression. However, the sarcomeric distribution of MuRF1a-GFP was abolished in the knockdown embryos. This was accompanied by an increased random punctate distribution of MuRF1a-GFP in muscle cells of zebrafish embryos. Collectively, these studies demonstrate that MuRFs are specifically expressed in developing muscles of zebrafish embryos. The M-line localization MuRF1a is altered by sarcomere disruption in smyd1b or hsp90α1 knockdown embryos.
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Affiliation(s)
- Baojun Li
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, Shanxi, China; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 701 East Pratt Street, Baltimore, MD 21202, USA
| | - Siping Li
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 701 East Pratt Street, Baltimore, MD 21202, USA
| | - Qiuxia He
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 701 East Pratt Street, Baltimore, MD 21202, USA
| | - Shaojun Du
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 701 East Pratt Street, Baltimore, MD 21202, USA.
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36
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Tagua VG, Navarro E, Gutiérrez G, Garre V, Corrochano LM. Light regulates a Phycomyces blakesleeanus gene family similar to the carotenogenic repressor gene of Mucor circinelloides. Fungal Biol 2019; 124:338-351. [PMID: 32389296 DOI: 10.1016/j.funbio.2019.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/15/2022]
Abstract
The transcription of about 5-10 % of the genes in Phycomyces blakesleeanus is regulated by light. Among the most up-regulated, we have identified four genes, crgA-D, with similarity to crgA of Mucor circinelloides, a gene encoding a repressor of light-inducible carotenogenesis. The four proteins have the same structure with two RING RING Finger domains and a LON domain, suggesting that they could act as ubiquitin ligases, as their M. circinelloides homolog. The expression of these genes is induced by light with different thresholds as in other Mucoromycotina fungi like Blakeslea trispora and M. circinelloides. Only the P. blakesleeanus crgD gene could restore the wild type phenotype in a M. circinelloides null crgA mutant suggesting that P. blakesleeanus crgD is the functional homolog of crgA in M. circinelloides. Despite their sequence similarity it is possible that the P. blakesleeanus Crg proteins do not participate in the regulation of beta-carotene biosynthesis since none of the carotene-overproducing mutants of P. blakesleeanus had mutations in any of the crg genes. Our results provide further support of the differences in the regulation of the biosynthesis of beta-carotene in these two Mucoromycotina fungi.
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Affiliation(s)
- Víctor G Tagua
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Spain; Present address: Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.
| | - Eusebio Navarro
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Spain
| | - Gabriel Gutiérrez
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Spain
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Spain
| | - Luis M Corrochano
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Spain.
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37
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Wu LX, Wei CC, Yang SB, Zhao T, Luo Z. Effects of Fat and Fatty Acids on the Formation of Autolysosomes in the Livers from Yellow Catfish Pelteobagrus Fulvidraco. Genes (Basel) 2019; 10:E751. [PMID: 31557940 PMCID: PMC6826758 DOI: 10.3390/genes10100751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/14/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023] Open
Abstract
The autophagy-lysosome pathway, which involves many crucial genes and proteins, plays crucial roles in the maintenance of intracellular homeostasis by the degradation of damaged components. At present, some of these genes and proteins have been identified but their specific functions are largely unknown. This study was performed to clone and characterize the full-length cDNA sequences of nine key autolysosome-related genes (vps11, vps16, vps18, vps33b, vps41, lamp1, mcoln1, ctsd1 and tfeb) from yellow catfish Pelteobagrus fulvidraco. The expression of these genes and the transcriptional responses to a high-fat diet and fatty acids (FAs) (palmitic acid (PA) and oleic acid (OA)) were investigated. The mRNAs of these genes could be detected in heart, liver, muscle, spleen, brain, mesenteric adipose tissue, intestine, kidney and ovary, but varied with the tissues. In the liver, the mRNA levels of the nine autolysosome-related genes were lower in fish fed a high-fat diet than those fed the control, indicating that a high-fat diet inhibited formation of autolysosomes. Palmitic acid (a saturated FA) significantly inhibited the formation of autolysosomes at 12 h, 24 h and 48 h incubation. In contrast, oleic acid (an unsaturated FA) significantly induced the formation of autolysosomes at 12 h, but inhibited them at 24 h. At 48 h, the effects of OA incubation on autolysosomes were OA concentration-dependent in primary hepatocytes of P. fulvidraco. The results of flow cytometry and laser confocal observations confirmed these results. PA and OA incubation also increased intracellular non-esterified fatty acid (NEFA) concentration at 12 h, 24 h and 48 h, and influenced mRNA levels of fatty acid binding protein (fabp) and fatty acid transport protein 4 (fatp4) which facilitate FA transport in primary hepatocytes of P. fulvidraco. The present study demonstrated the molecular characterization of the nine autolysosome-related genes and their transcriptional responses to fat and FAs in fish, which provides the basis for further exploring their regulatory mechanism in vertebrates.
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Affiliation(s)
- Li-Xiang Wu
- Laboratory of Molecular Nutrition for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chuan-Chuan Wei
- Laboratory of Molecular Nutrition for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shui-Bo Yang
- Laboratory of Molecular Nutrition for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan 430070, China.
| | - Tao Zhao
- Laboratory of Molecular Nutrition for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan 430070, China.
| | - Zhi Luo
- Laboratory of Molecular Nutrition for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan 430070, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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38
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Gu Z, Men S, Zhu J, Hao Q, Tong N, Liu ZA, Zhang H, Shu Q, Wang L. Chalcone synthase is ubiquitinated and degraded via interactions with a RING-H2 protein in petals of Paeonia 'He Xie'. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4749-4762. [PMID: 31106836 PMCID: PMC6760318 DOI: 10.1093/jxb/erz245] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/12/2019] [Indexed: 05/07/2023]
Abstract
Flavonoids are secondary metabolites widely distributed among angiosperms, where they play diverse roles in plant growth, development, and evolution. The regulation of flavonoid biosynthesis in plants has been extensively studied at the transcriptional level, but post-transcriptional, translational, and post-translational control of flavonoid biosynthesis remain poorly understood. In this study, we analysed post-translational regulation of flavonoid biosynthesis in the ornamental plant Paeonia, using proteome and ubiquitylome profiling, in conjunction with transcriptome data. Three enzymes involved in flavonoid biosynthesis were identified as being putative targets of ubiquitin-mediated degradation. Among these, chalcone synthase (PhCHS) was shown to have the greatest number of ubiquitination sites. We examined PhCHS abundance in petals using PhCHS-specific antibody and found that its accumulation decreased at later developmental stages, resulting from 26S proteasome-mediated degradation. We further identified a ring domain-containing protein (PhRING-H2) that physically interacts with PhCHS and demonstrated that PhRING-H2 is required for PhCHS ubiquitination. Taken together, our results suggest that PhRING-H2-mediates PhCHS ubiquitination and degradation is an important mechanism of post-translational regulation of flavonoid biosynthesis in Paeonia, providing a theoretical basis for the manipulation of flavonoid biosynthesis in plants.
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Affiliation(s)
- Zhaoyu Gu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Siqi Men
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jin Zhu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qing Hao
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ningning Tong
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Zheng-An Liu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hechen Zhang
- Horticulture Institute of He’nan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qingyan Shu
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Correspondence: or
| | - Liangsheng Wang
- Key Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
- Correspondence: or
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Ganz J, Melancon E, Wilson C, Amores A, Batzel P, Strader M, Braasch I, Diba P, Kuhlman JA, Postlethwait JH, Eisen JS. Epigenetic factors Dnmt1 and Uhrf1 coordinate intestinal development. Dev Biol 2019; 455:473-484. [PMID: 31394080 DOI: 10.1016/j.ydbio.2019.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/05/2019] [Accepted: 08/01/2019] [Indexed: 12/15/2022]
Abstract
Intestinal tract development is a coordinated process involving signaling among the progenitors and developing cells from all three germ layers. Development of endoderm-derived intestinal epithelium has been shown to depend on epigenetic modifications, but whether that is also the case for intestinal tract cell types from other germ layers remains unclear. We found that functional loss of a DNA methylation machinery component, ubiquitin-like protein containing PHD and RING finger domains 1 (uhrf1), leads to reduced numbers of ectoderm-derived enteric neurons and severe disruption of mesoderm-derived intestinal smooth muscle. Genetic chimeras revealed that Uhrf1 functions both cell-autonomously in enteric neuron precursors and cell-non-autonomously in surrounding intestinal cells, consistent with what is known about signaling interactions between these cell types that promote one another's development. Uhrf1 recruits the DNA methyltransferase Dnmt1 to unmethylated DNA during replication. Dnmt1 is also expressed in enteric neurons and smooth muscle progenitors. dnmt1 mutants have fewer enteric neurons and disrupted intestinal smooth muscle compared to wildtypes. Because dnmt1;uhrf1 double mutants have a similar phenotype to dnmt1 and uhrf1 single mutants, Dnmt1 and Uhrf1 must function together during enteric neuron and intestinal muscle development. This work shows that genes controlling epigenetic modifications are important to coordinate intestinal tract development, provides the first demonstration that these genes influence development of the ENS, and advances uhrf1 and dnmt1 as potential new Hirschsprung disease candidates.
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Affiliation(s)
- Julia Ganz
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Ellie Melancon
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Catherine Wilson
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Angel Amores
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Peter Batzel
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Marie Strader
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Ingo Braasch
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Parham Diba
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Julie A Kuhlman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - John H Postlethwait
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Judith S Eisen
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA.
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40
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Seaborne RA, Hughes DC, Turner DC, Owens DJ, Baehr LM, Gorski P, Semenova EA, Borisov OV, Larin AK, Popov DV, Generozov EV, Sutherland H, Ahmetov II, Jarvis JC, Bodine SC, Sharples AP. UBR5 is a novel E3 ubiquitin ligase involved in skeletal muscle hypertrophy and recovery from atrophy. J Physiol 2019; 597:3727-3749. [PMID: 31093990 DOI: 10.1113/jp278073] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/10/2019] [Indexed: 01/03/2023] Open
Abstract
KEY POINTS We have recently identified that a HECT domain E3 ubiquitin ligase, named UBR5, is altered epigenetically (via DNA methylation) after human skeletal muscle hypertrophy, where its gene expression is positively correlated with increasing lean leg mass after training and retraining. In the present study we extensively investigate this novel and uncharacterised E3 ubiquitin ligase (UBR5) in skeletal muscle atrophy, recovery from atrophy and injury, anabolism and hypertrophy. We demonstrated that UBR5 was epigenetically altered via DNA methylation during recovery from atrophy. We also determined that UBR5 was alternatively regulated versus well characterised E3 ligases, MuRF1/MAFbx, at the gene expression level during atrophy, recovery from atrophy and hypertrophy. UBR5 also increased at the protein level during recovery from atrophy and injury, hypertrophy and during human muscle cell differentiation. Finally, in humans, genetic variations of the UBR5 gene were strongly associated with larger fast-twitch muscle fibres and strength/power performance versus endurance/untrained phenotypes. ABSTRACT We aimed to investigate a novel and uncharacterized E3 ubiquitin ligase in skeletal muscle atrophy, recovery from atrophy/injury, anabolism and hypertrophy. We demonstrated an alternate gene expression profile for UBR5 vs. well characterized E3-ligases, MuRF1/MAFbx, where, after atrophy evoked by continuous-low-frequency electrical-stimulation in rats, MuRF1/MAFbx were both elevated, yet UBR5 was unchanged. Furthermore, after recovery of muscle mass post TTX-induced atrophy in rats, UBR5 was hypomethylated and increased at the gene expression level, whereas a suppression of MuRF1/MAFbx was observed. At the protein level, we also demonstrated a significant increase in UBR5 after recovery of muscle mass from hindlimb unloading in both adult and aged rats, as well as after recovery from atrophy evoked by nerve crush injury in mice. During anabolism and hypertrophy, UBR5 gene expression increased following acute loading in three-dimensional bioengineered mouse muscle in vitro, and after chronic electrical stimulation-induced hypertrophy in rats in vivo, without increases in MuRF1/MAFbx. Additionally, UBR5 protein abundance increased following functional overload-induced hypertrophy of the plantaris muscle in mice and during differentiation of primary human muscle cells. Finally, in humans, genetic association studies (>700,000 single nucleotide polymorphisms) demonstrated that the A alleles of rs10505025 and rs4734621 single nucleotide polymorphisms in the UBR5 gene were strongly associated with larger cross-sectional area of fast-twitch muscle fibres and favoured strength/power vs. endurance/untrained phenotypes. Overall, we suggest that: (i) UBR5 comprises a novel E3 ubiquitin ligase that is inversely regulated to MuRF1/MAFbx; (ii) UBR5 is epigenetically regulated; and (iii) UBR5 is elevated at both the gene expression and protein level during recovery from skeletal muscle atrophy and hypertrophy.
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Affiliation(s)
- Robert A Seaborne
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Institute for Science and Technology in Medicine (ISTM), School of Medicine, Keele University, Keele, UK.,Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David C Hughes
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Daniel C Turner
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Institute for Science and Technology in Medicine (ISTM), School of Medicine, Keele University, Keele, UK
| | - Daniel J Owens
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - Leslie M Baehr
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Piotr Gorski
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Institute for Science and Technology in Medicine (ISTM), School of Medicine, Keele University, Keele, UK
| | - Ekaterina A Semenova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Oleg V Borisov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.,Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Andrey K Larin
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daniil V Popov
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Edward V Generozov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Hazel Sutherland
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - Ildus I Ahmetov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.,Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia.,Department of Physical Education, Plekhanov Russian University of Economics, Moscow, Russia.,Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - Jonathan C Jarvis
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - Sue C Bodine
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Adam P Sharples
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Institute for Science and Technology in Medicine (ISTM), School of Medicine, Keele University, Keele, UK
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Mishra R, Upadhyay A, Prajapati VK, Dhiman R, Poluri KM, Jana NR, Mishra A. LRSAM1 E3 ubiquitin ligase: molecular neurobiological perspectives linked with brain diseases. Cell Mol Life Sci 2019; 76:2093-2110. [PMID: 30826859 PMCID: PMC11105512 DOI: 10.1007/s00018-019-03055-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 02/13/2019] [Accepted: 02/21/2019] [Indexed: 01/01/2023]
Abstract
Cellular protein quality control (PQC) plays a significant role in the maintenance of cellular homeostasis. Failure of PQC mechanism may lead to various neurodegenerative diseases due to accumulation of aberrant proteins. To avoid such fatal neuronal conditions PQC employs autophagy and ubiquitin proteasome system (UPS) to degrade misfolded proteins. Few quality control (QC) E3 ubiquitin ligases interplay an important role to specifically recognize misfolded proteins for their intracellular degradation. Leucine-rich repeat and sterile alpha motif-containing 1 (LRSAM1) is a really interesting new gene (RING) class protein that possesses E3 ubiquitin ligase activity with promising applications in PQC. LRSAM1 is also known as RING finger leucine repeat rich (RIFLE) or TSG 101-associated ligase (TAL). LRSAM1 has various cellular functions as it modulates the protein aggregation, endosomal sorting machinery and virus egress from the cells. Thus, this makes LRSAM1 interesting to study not only in protein conformational disorders such as neurodegeneration but also in immunological and other cancerous disorders. Furthermore, LRSAM1 interacts with both cellular protein degradation machineries and hence it can participate in maintenance of overall cellular proteostasis. Still, more research work on the quality control molecular functions of LRSAM1 is needed to comprehend its roles in various protein aggregatory diseases. Earlier findings suggest that in a mouse model of Charcot-Marie-Tooth (CMT) disease, lack of LRSAM1 functions sensitizes peripheral axons to degeneration. It has been observed that in CMT the patients retain dominant and recessive mutations of LRSAM1 gene, which encodes most likely a defective protein. However, still the comprehensive molecular pathomechanism of LRSAM1 in neuronal functions and neurodegenerative diseases is not known. The current article systematically represents the molecular functions, nature and detailed characterization of LRSAM1 E3 ubiquitin ligase. Here, we review emerging molecular mechanisms of LRSAM1 linked with neurobiological functions, with a clear focus on the mechanism of neurodegeneration and also on other diseases. Better understanding of LRSAM1 neurobiological and intracellular functions may contribute to develop promising novel therapeutic approaches, which can also propose new lines of molecular beneficial targets for various neurodegenerative diseases.
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Affiliation(s)
- Ribhav Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, 342037, India
| | - Arun Upadhyay
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, 342037, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8 Bandarsindri, Ajmer, Rajasthan, 305817, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Nihar Ranjan Jana
- School of Bioscience, Indian Institute of Technology, Kharagpur, Kharagpur, 721302, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, 342037, India.
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Zhang Y, Li Z, Kholodkevich S, Sharov A, Feng Y, Ren N, Sun K. Cadmium-induced oxidative stress, histopathology, and transcriptome changes in the hepatopancreas of freshwater crayfish (Procambarus clarkii). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:944-955. [PMID: 30970501 DOI: 10.1016/j.scitotenv.2019.02.159] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/01/2019] [Accepted: 02/10/2019] [Indexed: 05/06/2023]
Abstract
Cadmium (Cd) is a common contaminant in environment. Crayfish are considered suitable for indicating the impact of heavy metals on the environment. However, there is limited information on the mechanisms causing damage to the hepatopancreas of Procambarus clarkii exposed to Cd. We exposed adult male P. clarkii to 2.0, 5.0, and 10.0 mg/L Cd for 24, 48, and 72 h to explore Cd toxicity. Afterwards, we measured bioaccumulations in the hepatopancreas and determined malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST). Additionally, the hepatopancreas histopathology was analyzed and the transcriptome analysis of the P. clarkii hepatopancreas under Cd stress was conducted. The results revealed that hepatopancreas could accumulate Cd in a time- and dose-dependent manner. Cd induced significant changes in MDA content and antioxidant enzyme activity. Severe histological alterations were observed in crayfish hepatopancreas. After 72 h exposure to 2.0, 5.0, and 10.0 mg/L Cd, transcriptome analysis identified 1061, 747, and 1086 differentially expressed genes (DEGs), respectively. Exposure to 5.0 mg/L Cd inhibited heme binding, tetrapyrrole binding, iron ion binding and activity of oxidoreductase and sulfotransferase, while exposure to 10.0 mg/L Cd enhanced the export of matters from nucleus. In the hepatopancreas treated with 10.0 mg/L Cd, pathways related to diseases and immune system were significantly enriched. Meanwhile, 31, 31, 24, 7, and 12 identified DEGs were associated with the oxidation-reduction process, immune system, ion homeostasis, digestion and absorption, and ATPases, respectively. Our study provides comprehensive information for exploring the toxic mechanisms of Cd and candidate biomarkers for aquatic Cd risk evaluation.
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Affiliation(s)
- Yu Zhang
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zheyu Li
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Sergey Kholodkevich
- Institute of Earth Sciences, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Andrey Sharov
- Institute of Earth Sciences, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Yujie Feng
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kai Sun
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Miyamoto K, Fujiwara Y, Saito K. Zinc finger domain of the human DTX protein adopts a unique RING fold. Protein Sci 2019; 28:1151-1156. [PMID: 30927328 DOI: 10.1002/pro.3610] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/27/2019] [Indexed: 12/24/2022]
Abstract
The Deltex (DTX) family is involved in ubiquitination and acts as Notch signaling modifiers for controlling cell fate determination. DTX promotes the development of the ubiquitin chain via its RING finger (DTX_RING). In this study, the solution structure of DTX_RING was determined using nuclear magnetic resonance (NMR). Moreover, by experiments with a metallochromic indicator, we spectrophotometrically estimated the stoichiometry of zinc ions and found that DTX_RING possesses zinc-binding capabilities. The Simple Modular Architecture Research Tool database predicted the structure of DTX_RING as a typical RING finger. However, the actual DTX_RING structure adopts a novel RING fold with a unique topology distinct from other RING fingers. We unveiled the position and the range of the DTX_RING active site at the atomic level. Artificial RING fingers (ARFs) are made by grafting active sites of the RING fingers onto cross-brace structure motifs. Therefore, the present structural analysis could be useful for designing a novel ARF.
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Affiliation(s)
- Kazuhide Miyamoto
- Department of Pharmaceutical Health Care, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo, Japan
| | - Yuma Fujiwara
- Department of Pharmaceutical Health Care, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo, Japan
| | - Kazuki Saito
- Department of Pharmaceutical Health Care, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo, Japan
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Adhikary S, Chakravarti D, Terranova C, Sengupta I, Maitituoheti M, Dasgupta A, Srivastava DK, Ma J, Raman AT, Tarco E, Sahin AA, Bassett R, Yang F, Tapia C, Roy S, Rai K, Das C. Atypical plant homeodomain of UBR7 functions as an H2BK120Ub ligase and breast tumor suppressor. Nat Commun 2019; 10:1398. [PMID: 30923315 PMCID: PMC6438984 DOI: 10.1038/s41467-019-08986-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/09/2019] [Indexed: 12/17/2022] Open
Abstract
The roles of Plant Homeodomain (PHD) fingers in catalysis of histone modifications are unknown. We demonstrated that the PHD finger of Ubiquitin Protein Ligase E3 Component N-Recognin7 (UBR7) harbors E3 ubiquitin ligase activity toward monoubiquitination of histone H2B at lysine120 (H2BK120Ub). Purified PHD finger or full-length UBR7 monoubiquitinated H2BK120 in vitro, and loss of UBR7 drastically reduced H2BK120Ub genome-wide binding sites in MCF10A cells. Low UBR7 expression was correlated with occurrence of triple-negative breast cancer and metastatic tumors. Consistently, UBR7 knockdown enhanced the invasiveness, induced epithelial-to-mesenchymal transition and promoted metastasis. Conversely, ectopic expression of UBR7 restored these cellular phenotypes and reduced tumor growth. Mechanistically, UBR7 loss reduced H2BK120Ub levels on cell adhesion genes, including CDH4, and upregulated the Wnt/β-Catenin signaling pathway. CDH4 overexpression could partially revert UBR7-dependent cellular phenotypes. Collectively, our results established UBR7 as a histone H2B monoubiquitin ligase that suppresses tumorigenesis and metastasis of triple-negative breast cancer.
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Affiliation(s)
- Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata, 700064, India
- Structural Biology and Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Deepavali Chakravarti
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Christopher Terranova
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Isha Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata, 700064, India
| | - Mayinuer Maitituoheti
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Anirban Dasgupta
- Structural Biology and Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Dushyant Kumar Srivastava
- Structural Biology and Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Junsheng Ma
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ayush T Raman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Emily Tarco
- Department of Translational Molecular Pathology and Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Aysegul A Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Roland Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Fei Yang
- Department of Translational Molecular Pathology and Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Coya Tapia
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Siddhartha Roy
- Structural Biology and Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India.
| | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata, 700064, India.
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Peng R, Zhang PF, Yang X, Wei CY, Huang XY, Cai JB, Lu JC, Gao C, Sun HX, Gao Q, Bai DS, Shi GM, Ke AW, Fan J. Overexpression of RNF38 facilitates TGF-β signaling by Ubiquitinating and degrading AHNAK in hepatocellular carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:113. [PMID: 30836988 PMCID: PMC6402116 DOI: 10.1186/s13046-019-1113-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/18/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND RING finger protein 38 (RNF38), a member of the RNF protein family, has just emerged as a vital driver of cancer progression. However, the oncogenic mechanisms of RNF38 remain unexplored. METHODS Using frozen tumor tissue and tissue microarray from hepatocellular carcinoma (HCC) patients, we tried to probe the expression of RNF38 in HCC and its clinical value. Then the biological functions of RNF38 were analyzed in vivo and vitro. Stable isotope labeling with amino acids (SILAC) in cell culture and co-immunoprecipitation proteomic analyses were combined to reveal the potential mechanism of RNF38 in HCC progression. RESULTS We report that RNF38 expression was markedly higher in HCC tissues than in peritumor tissues. Correspondingly, RNF38 overexpression promoted the HCC cell migration and invasion and inhibited apoptosis both in vitro and in vivo. And elevated RNF38 expression induced HCC cell epithelial-mesenchymal transition by facilitating transforming growth factor-β (TGF-β) signaling via ubiquitinating and degrading neuroblast differentiation-associated protein (AHNAK), a well-established inhibitor of TGF-β signaling. Furthermore, AHNAK interference restored the HCC cell invasion and metastasis deprived by RNF38 downregulation. Clinically, elevated RNF38 and transforming growth factor beta receptor 1 (TGFBR1) expression was related to short overall survival (OS) and high cumulative recurrence rates in HCC patients. CONCLUSIONS High levels of RNF38 promote HCC by facilitating TGF-β signaling and are a novel marker for predicting the prognosis of HCC patients and a potential therapeutic target in HCC.
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Affiliation(s)
- Rui Peng
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China.,Clinical Medical College, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Peng-Fei Zhang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China.,Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200031, China
| | - Xuan Yang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Chuan-Yuan Wei
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Xiao-Yong Huang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Jia-Bin Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Jia-Cheng Lu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Chao Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Hai-Xiang Sun
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Qiang Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Dou-Sheng Bai
- Clinical Medical College, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Guo-Ming Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China.
| | - Ai-Wu Ke
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China.
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China. .,Cancer Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200031, People's Republic of China.
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Identification and characterization of novel double zinc fingers encoded by putative proteins in genome of white spot syndrome virus. Arch Virol 2019; 164:961-969. [PMID: 30690656 DOI: 10.1007/s00705-019-04150-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/24/2018] [Indexed: 12/27/2022]
Abstract
White spot syndrome virus (WSSV), is a major viral pathogen affecting the shrimp culture industry worldwide. Studies in understanding the mechanisms of WSSV pathogenicity has led to the identification of The Really Interesting New Gene (RING) finger domains in WSSV encoded proteins that have been shown to function as E3 ligase modulating the host-ubiquitin pathway. In this study, we report two proteins encoded by the WSSV genome to harbor a double zinc finger domain, one each in its N- and C-terminal region. Sequence and structural analysis of the two domains showed the N- and C-terminal domains to be similar to known RING1 and RING2 domains of eukaryotic RBR (RING-between-RING) ligases respectively. This is the first report wherein genes within WSSV are shown to encode for double RING domains, which could pave way in understanding further, the function of these proteins and their role in the pathogenic mechanisms of the virus.
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47
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Yang M, Han R, Ni LY, Luo XC, Li AX, Dan XM, Li YW. Molecular characteristics and functional study of tumor necrosis factor receptor-associated factor 2 from the orange-spotted grouper (Epinephelus coioides). FISH & SHELLFISH IMMUNOLOGY 2019; 84:726-732. [PMID: 30393173 DOI: 10.1016/j.fsi.2018.10.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/09/2018] [Accepted: 10/26/2018] [Indexed: 06/08/2023]
Abstract
In mammals, tumor necrosis factor receptor-associated factor 2 (TRAF2) is a crucial intracellular adaptor protein, which performs a vital role in numerous signaling pathways that activate NF-κB, MAPKs, and IRFs. In the present study, three TRAF2 sequences were identified from the orange-spotted grouper (Epinephelus coioides), and named EcTRAF2-1, EcTRAF2-2, and EcTRAF2-3. These sequences contained conserved structure features that were similar to those of mammals. EcTRAF2-1 shared relatively low sequence identity with the other two EcTRAF2s. In healthy E. coioides, EcTRAF2s were widely expressed in all tissues tested, but with distinct expression profiles. After infection with Cryptocaryon irritans, EcTRAF2s was markedly upregulated in the gill and head kidney at most time points, implying that EcTRAF2s may be involved in host defense against C. irritans infection. In HEK293T cells, EcTRAF2s were scattered in the cytoplasm. EcTRAF2-1 and EcTRAF2-2 increased the activity of NF-κB, while EcTRAF2-3 reduced NF-κB activation mediated by EcTRAF2-1 implying that EcTRAF2-3 might be a negative regulator of EcTRAF2-1.
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Affiliation(s)
- Man Yang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China, Agricultural University, Guangzhou, 510642, China
| | - Rui Han
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China, Agricultural University, Guangzhou, 510642, China
| | - Lu-Yun Ni
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China, Agricultural University, Guangzhou, 510642, China
| | - Xiao-Chun Luo
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - An-Xing Li
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Lab for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong Province, PR China
| | - Xue-Ming Dan
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China, Agricultural University, Guangzhou, 510642, China.
| | - Yan-Wei Li
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China, Agricultural University, Guangzhou, 510642, China.
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48
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Pi B, He X, Ruan Y, Jang JC, Huang Y. Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa. BMC PLANT BIOLOGY 2018; 18:373. [PMID: 30587139 PMCID: PMC6307296 DOI: 10.1186/s12870-018-1608-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/17/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ubiquitous CCCH nucleic acid-binding motif is found in a wide-variety of organisms. CCCH genes are involved in plant developmental processes and biotic and abiotic stress responses. Brassica rapa is a vital economic crop and classical model plant of polyploidy evolution, but the functions of CCCH genes in B. rapa are unclear. RESULTS In this study, 103 CCCH genes in B. rapa were identified. A comparative analysis of the chromosomal position, gene structure, domain organization and duplication event between B. rapa and Arabidopsis thaliana were performed. Results showed that CCCH genes could be divided into 18 subfamilies, and segmental duplication might mainly contribute to this family expansion. C-X7/8-C-X5-C3-H was the most commonly found motif, but some novel CCCH motifs were also found, along with some loses of typical CCCH motifs widespread in other plant species. The multifarious gene structures and domain organizations implicated functional diversity of CCCH genes in B. rapa. Evidence also suggested functional redundancy in at least one subfamily due to high conservation between members. Finally, the expression profiles of subfamily-IX genes indicated that they are likely involved in various stress responses. CONCLUSION This study provides the first genome-wide characterization of the CCCH genes in B. rapa. The results suggest that B. rapa CCCH genes are likely functionally divergent, but mostly involved in plant development and stress response. These results are expected to facilitate future functional characterization of this potential RNA-binding protein family in Brassica crops.
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Affiliation(s)
- Boyi Pi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Xinghui He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Ying Ruan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, Molecular Genetics, and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - Yong Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128 China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, 410128 China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, 410128 China
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A comparative analysis of KMT2D missense variants in Kabuki syndrome, cancers and the general population. J Hum Genet 2018; 64:161-170. [PMID: 30459467 DOI: 10.1038/s10038-018-0536-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/10/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022]
Abstract
Determining the clinical significance of germline and somatic KMT2D missense variants (MVs) in Kabuki syndrome (KS) and cancers can be challenging. We analysed 1920 distinct KMT2D MVs that included 1535 germline MVs in controls (Control-MVs), 584 somatic MVs in cancers (Cancer-MVs) and 201 MV in individuals with KS (KS-MVs). The proportion of MVs likely to affect splicing was significantly higher for Cancer-MVs and KS-MVs than in Control-MVs (p = 0.000018). Our analysis identified significant clustering of Cancer-MVs and KS-MVs in the PHD#3 and #4, RING#4 and SET domains. Areas of enrichment restricted to just Cancer-MVs (FYR-C and between amino acids 3043-3248) or KS-MVs (coiled-coil#5, FYR-N and between amino acids 4995-5090) were also found. Cancer-MVs and KS-MVs tended to affect more conserved residues (lower BLOSUM scores, p < 0.001 and p = 0.007). KS-MVs are more likely to increase the energy for protein folding (higher ELASPIC ∆∆G scores, p = 0.03). Cancer-MVs are more likely to disrupt protein interactions (higher StructMAn scores, p = 0.019). We reclassify several presumed pathogenic MVs as benign or as variants of uncertain significance. We raise the possibility of as yet unrecognised 'non-KS' phenotype(s) associated with some germline pathogenic KMT2D MVs. Overall, this work provides insights into the disease mechanism of KMT2D variants and can be extended to other genes, mutations in which also cause developmental syndromes and cancer.
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Liu H, Wang J, Liu Y, Hu L, Zhang C, Xing B, Du X. Human U3 protein14a is a novel type ubiquitin ligase that binds RB and promotes RB degradation depending on a leucine-rich region. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1611-1620. [DOI: 10.1016/j.bbamcr.2018.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 11/16/2022]
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