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Kou X, Cao P, Zhao Z, Zhang X, Dai Y, Wang K, Wu J, Zhang S. Comparative genomic analysis of the RabGAP gene family in seven Rosaceae species, and functional identification of PbrRabGAP10 in controlling pollen tube growth by mediating cellulose deposition in pear. Int J Biol Macromol 2024; 256:128498. [PMID: 38042315 DOI: 10.1016/j.ijbiomac.2023.128498] [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: 08/12/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
Rab GTPase-activating proteins (RabGAPs), serving as crucial signaling switches, play essential roles in several physiological processes related to plant growth and development. However, despite their importance, information regarding the RabGAP gene family and their biological functions remains unknown in the Rosaceae. In this study, we identified a total of 127 RabGAP genes in seven Rosaceae species, which were divided into five subfamilies. Our findings indicate that whole genome duplication (WGD) events or dispersed duplication events largely contributed to the expansion of RabGAP family members within Rosaceae species. Through tissue-specific expression analyses, we revealed that the PbrRabGAP genes exhibited distinct expression patterns in different pear tissues. Furthermore, by examining the expression pattern during pollen development and employing an antisense oligonucleotide approach, we demonstrated that PbrRabGAP10, located in the cytoplasm, mediates the imbalance of cellulose distribution, thus regulating pollen tube elongation. In conclusion, the present study offers an overview of the RabGAP family in Rosaceae genomes and serves as the basis for further functional studies.
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Affiliation(s)
- Xiaobing Kou
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, People's Republic of China.
| | - Peng Cao
- College of Faculty of Applied Technology, Huaiyin Institute of Technology, Huai'an 223003, China
| | - Zhen Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Zhang
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, People's Republic of China
| | - Yan Dai
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, People's Republic of China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, People's Republic of China
| | - Juyou Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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2
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Joyce W, Warwicker J, Shiels HA, Perry SF. Evolution and divergence of teleost adrenergic receptors: why sometimes 'the drugs don't work' in fish. J Exp Biol 2023; 226:jeb245859. [PMID: 37823524 DOI: 10.1242/jeb.245859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Adrenaline and noradrenaline, released as hormones and/or neurotransmitters, exert diverse physiological functions in vertebrates, and teleost fishes are widely used as model organisms to study adrenergic regulation; however, such investigations often rely on receptor subtype-specific pharmacological agents (agonists and antagonists; see Glossary) developed and validated in mammals. Meanwhile, evolutionary (phylogenetic and comparative genomic) studies have begun to unravel the diversification of adrenergic receptors (ARs) and reveal that whole-genome duplications and pseudogenization events in fishes results in notable distinctions from mammals in their genomic repertoire of ARs, while lineage-specific gene losses within teleosts have generated significant interspecific variability. In this Review, we visit the evolutionary history of ARs (including α1-, α2- and β-ARs) to highlight the prominent interspecific differences in teleosts, as well as between teleosts and other vertebrates. We also show that structural modelling of teleost ARs predicts differences in ligand binding affinity compared with mammalian orthologs. To emphasize the difficulty of studying the roles of different AR subtypes in fish, we collate examples from the literature of fish ARs behaving atypically compared with standard mammalian pharmacology. Thereafter, we focus on specific case studies of the liver, heart and red blood cells, where our understanding of AR expression has benefited from combining pharmacological approaches with molecular genetics. Finally, we briefly discuss the ongoing advances in 'omics' technologies that, alongside classical pharmacology, will provide abundant opportunities to further explore adrenergic signalling in teleosts.
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Affiliation(s)
- William Joyce
- Department of Biology - Zoophysiology, Aarhus University, 8000 Aarhus C, Denmark
| | - Jim Warwicker
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Holly A Shiels
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Steve F Perry
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada, K1N 6N5
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3
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Dimitrakopoulou D, Khwatenge CN, James-Zorn C, Paiola M, Bellin EW, Tian Y, Sundararaj N, Polak EJ, Grayfer L, Barnard D, Ohta Y, Horb M, Sang Y, Robert J. Advances in the Xenopus immunome: Diversification, expansion, and contraction. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 145:104734. [PMID: 37172665 PMCID: PMC10230362 DOI: 10.1016/j.dci.2023.104734] [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: 08/03/2022] [Revised: 03/18/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Xenopus is a genus of African clawed frogs including two species, X. tropicalis and X. laevis that are extensively used in experimental biology, immunology, and biomedical studies. The availability of fully sequenced and annotated Xenopus genomes is strengthening genome-wide analyses of gene families and transgenesis to model human diseases. However, inaccuracies in genome annotation for genes involved in the immune system (i.e., immunome) hamper immunogenetic studies. Furthermore, advanced genome technologies (e.g., single-cell and RNA-Seq) rely on well-annotated genomes. The annotation problems of Xenopus immunome include a lack of established orthology across taxa, merged gene models, poor representation in gene pages on Xenbase, misannotated genes and missing gene IDs. The Xenopus Research Resource for Immunobiology in collaboration with Xenbase and a group of investigators are working to resolve these issues in the latest versions of genome browsers. In this review, we summarize the current problems of previously misannotated gene families that we have recently resolved. We also highlight the expansion, contraction, and diversification of previously misannotated gene families.
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Affiliation(s)
- Dionysia Dimitrakopoulou
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Collins N Khwatenge
- Department of Agriculture and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, USA
| | - Christina James-Zorn
- Xenbase, Division of Developmental Biology, Cincinnti Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Matthieu Paiola
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Eleanor Wise Bellin
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Yun Tian
- Department of Agriculture and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, USA
| | - Nivitha Sundararaj
- Xenbase, Division of Developmental Biology, Cincinnti Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Emma J Polak
- Biology Department, Worcester State University, MA, USA
| | - Leon Grayfer
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Daron Barnard
- Biology Department, Worcester State University, MA, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marko Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Yongming Sang
- Department of Agriculture and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, USA.
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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4
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Huang Z, Xu L, Cai C, Zhou Y, Liu J, Xu Z, Zhu Z, Kang W, Cen W, Pei S, Chen D, Shi C, Wu X, Huang Y, Xu C, Yan Y, Yang Y, Xue T, He W, Hu X, Zhang Y, Chen Y, Bi C, He C, Xue L, Xiao S, Yue Z, Jiang Y, Yu JK, Jarvis E, Li G, Lin G, Zhang Q, Zhou Q. Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. Proc Natl Acad Sci U S A 2023; 120:e2201504120. [PMID: 36867684 PMCID: PMC10013865 DOI: 10.1073/pnas.2201504120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/18/2023] [Indexed: 03/05/2023] Open
Abstract
The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding of the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole-genome duplications, which gave rise to the extant microchromosomes likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its three-dimensional chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the Hox gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.
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Affiliation(s)
- Zhen Huang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian350108, China
| | - Luohao Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing400715, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Chongqing400715, China
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna1090, Austria
| | - Cheng Cai
- The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Yitao Zhou
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Jing Liu
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna1090, Austria
| | - Zaoxu Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing400715, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Chongqing400715, China
| | - Zexian Zhu
- The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Wen Kang
- The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Wan Cen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Surui Pei
- Annoroad Gene Technology Co., Ltd, Beijing100180, China
| | - Duo Chen
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Xiaotong Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Yongji Huang
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian350108, China
| | - Chaohua Xu
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Yanan Yan
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Ying Yang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Ting Xue
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Wenjin He
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Xuefeng Hu
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Yanding Zhang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Youqiang Chen
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Changwei Bi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu210096, China
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu210096, China
| | - Lingzhan Xue
- Aquaculture and Genetic breeding laboratory, Freshwater Fisheries Research Institute of Fujian, Fuzhou, Fujian350002, China
| | - Shijun Xiao
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin130118, China
| | - Zhicao Yue
- Department of Cell Biology and Medical Genetics, Carson International Cancer Center, and Guangdong Key Laboratory for Genome Stability and Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
| | - Yu Jiang
- Annoroad Gene Technology Co., Ltd, Beijing100180, China
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei11529, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan26242, Taiwan
| | - Erich D. Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY10065
- HHMI, Chevy Chase, MD20815
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Gang Lin
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Annoroad Gene Technology Co., Ltd, Beijing100180, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Qiujin Zhang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Annoroad Gene Technology Co., Ltd, Beijing100180, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Qi Zhou
- The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Hangzhou, Zhejiang310052, China
- Evolutionary and Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou, Zhejiang310058, China
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5
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Gamble MC, Williams BR, Singh N, Posa L, Freyberg Z, Logan RW, Puig S. Mu-opioid receptor and receptor tyrosine kinase crosstalk: Implications in mechanisms of opioid tolerance, reduced analgesia to neuropathic pain, dependence, and reward. Front Syst Neurosci 2022; 16:1059089. [PMID: 36532632 PMCID: PMC9751598 DOI: 10.3389/fnsys.2022.1059089] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 07/30/2023] Open
Abstract
Despite the prevalence of opioid misuse, opioids remain the frontline treatment regimen for severe pain. However, opioid safety is hampered by side-effects such as analgesic tolerance, reduced analgesia to neuropathic pain, physical dependence, or reward. These side effects promote development of opioid use disorders and ultimately cause overdose deaths due to opioid-induced respiratory depression. The intertwined nature of signaling via μ-opioid receptors (MOR), the primary target of prescription opioids, with signaling pathways responsible for opioid side-effects presents important challenges. Therefore, a critical objective is to uncouple cellular and molecular mechanisms that selectively modulate analgesia from those that mediate side-effects. One such mechanism could be the transactivation of receptor tyrosine kinases (RTKs) via MOR. Notably, MOR-mediated side-effects can be uncoupled from analgesia signaling via targeting RTK family receptors, highlighting physiological relevance of MOR-RTKs crosstalk. This review focuses on the current state of knowledge surrounding the basic pharmacology of RTKs and bidirectional regulation of MOR signaling, as well as how MOR-RTK signaling may modulate undesirable effects of chronic opioid use, including opioid analgesic tolerance, reduced analgesia to neuropathic pain, physical dependence, and reward. Further research is needed to better understand RTK-MOR transactivation signaling pathways, and to determine if RTKs are a plausible therapeutic target for mitigating opioid side effects.
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Affiliation(s)
- Mackenzie C. Gamble
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
- Molecular and Translational Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Benjamin R. Williams
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
| | - Navsharan Singh
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
| | - Luca Posa
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Ryan W. Logan
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
- Center for Systems Neuroscience, Boston University, Boston, MA, United States
| | - Stephanie Puig
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
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6
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Paiola M, Ma S, Robert J. Evolution and Potential Subfunctionalization of Duplicated fms-Related Class III Receptor Tyrosine Kinase flt3s and Their Ligands in the Allotetraploid Xenopus laevis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:960-969. [PMID: 36130129 PMCID: PMC9512362 DOI: 10.4049/jimmunol.2200201] [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: 03/15/2022] [Accepted: 06/29/2022] [Indexed: 11/06/2022]
Abstract
The fms-related tyrosine kinase 3 (Flt3) and its ligand (Flt3lg) are important regulators of hematopoiesis and dendritic cell (DC) homeostasis with unsettled coevolution. Gene synteny and deduced amino acid sequence analyses identified conserved flt3 gene orthologs across all jawed vertebrates. In contrast, flt3lg orthologs were not retrieved in ray-finned fish, and the gene locus exhibited more variability among species. Interestingly, duplicated flt3/flt3lg genes were maintained in the allotetraploid Xenopus laevis Comparison of modeled structures of X. laevis Flt3 and Flt3lg homoeologs with the related diploid Xenopus tropicalis and with humans indicated a higher conformational divergence between the homoeologous pairs than their respective counterparts. The distinctive developmental and tissue expression patterns of Flt3 and Flt3lg homoeologs in tadpoles and adult frogs suggest a subfunctionalization of these homoeologs. To characterize Flt3 cell surface expression, X. laevis-tagged rFlt3lg.S and rFlt3lg.L were produced. Both rFlt3lg.S and rFlt3lg.L bind in vitro Flt3.S and Flt3.L and can trigger Erk1/2 signaling, which is consistent with a partial overlapping function between homoeologs. In spleen, Flt3.S/L cell surface expression was detected on a fraction of B cells and a population of MHC class IIhigh/CD8+ leukocytes phenotypically similar to the recently described dual follicular/conventional DC-like XL cells. Our result suggests that 1) Flt3lg.S and Flt3lg.L are both involved in XL cell homeostasis and that 2) XL cells have hematopoietic origin. Furthermore, we detected surface expression of the macrophage/monocyte marker Csf1r.S on XL cells as in mammalian and chicken DCs, which points to a common evolutionary origin in vertebrate DCs.
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Affiliation(s)
- Matthieu Paiola
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Siyuan Ma
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
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7
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Bakopoulos D, Whisstock JC, Warr CG, Johnson TK. Macrophage self‐renewal is regulated by transient expression of
PDGF‐ and VEGF‐related factor 2. FEBS J 2022; 289:3735-3751. [DOI: 10.1111/febs.16364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/24/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Daniel Bakopoulos
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - James C. Whisstock
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University Clayton Vic. Australia
- Department of Biochemistry and Molecular Biology Monash University Clayton Vic. Australia
| | - Coral G. Warr
- School of Biological Sciences Monash University Clayton Vic. Australia
- School of Molecular Sciences La Trobe University Bundoora Vic. Australia
| | - Travis K. Johnson
- School of Biological Sciences Monash University Clayton Vic. Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University Clayton Vic. Australia
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8
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Yeung W, Kwon A, Taujale R, Bunn C, Venkat A, Kannan N. Evolution of functional diversity in the holozoan tyrosine kinome. Mol Biol Evol 2021; 38:5625-5639. [PMID: 34515793 PMCID: PMC8662651 DOI: 10.1093/molbev/msab272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The emergence of multicellularity is strongly correlated with the expansion of tyrosine kinases, a conserved family of signaling enzymes that regulates pathways essential for cell-to-cell communication. Although tyrosine kinases have been classified from several model organisms, a molecular-level understanding of tyrosine kinase evolution across all holozoans is currently lacking. Using a hierarchical sequence constraint-based classification of diverse holozoan tyrosine kinases, we construct a new phylogenetic tree that identifies two ancient clades of cytoplasmic and receptor tyrosine kinases separated by the presence of an extended insert segment in the kinase domain connecting the D and E-helices. Present in nearly all receptor tyrosine kinases, this fast-evolving insertion imparts diverse functionalities, such as post-translational modification sites and regulatory interactions. Eph and EGFR receptor tyrosine kinases are two exceptions which lack this insert, each forming an independent lineage characterized by unique functional features. We also identify common constraints shared across multiple tyrosine kinase families which warrant the designation of three new subgroups: Src module (SrcM), insulin receptor kinase-like (IRKL), and fibroblast, platelet-derived, vascular, and growth factor receptors (FPVR). Subgroup-specific constraints reflect shared autoinhibitory interactions involved in kinase conformational regulation. Conservation analyses describe how diverse tyrosine kinase signaling functions arose through the addition of family-specific motifs upon subgroup-specific features and coevolving protein domains. We propose the oldest tyrosine kinases, IRKL, SrcM, and Csk, originated from unicellular premetazoans and were coopted for complex multicellular functions. The increased frequency of oncogenic variants in more recent tyrosine kinases suggests that lineage-specific functionalities are selectively altered in human cancers.
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Affiliation(s)
- Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Annie Kwon
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Rahil Taujale
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Claire Bunn
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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9
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Bayazeid O, Rahman T. Correlation Analysis of Target Selectivity and Side Effects of FDA‐Approved Kinase Inhibitors**. ChemistrySelect 2021. [DOI: 10.1002/slct.202101367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Omer Bayazeid
- Department of Pharmacognosy Faculty of Pharmacy Hacettepe University, Sihhiye 06100 Ankara Turkey
| | - Taufiq Rahman
- Department of Pharmacology University of Cambridge Tennis Court Road Cambridge CB2 1PD UK
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10
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Arcas A, Wilkinson DG, Nieto MÁ. The Evolutionary History of Ephs and Ephrins: Toward Multicellular Organisms. Mol Biol Evol 2020; 37:379-394. [PMID: 31589243 PMCID: PMC6993872 DOI: 10.1093/molbev/msz222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Eph receptor (Eph) and ephrin signaling regulate fundamental developmental processes through both forward and reverse signaling triggered upon cell–cell contact. In vertebrates, they are both classified into classes A and B, and some representatives have been identified in many metazoan groups, where their expression and functions have been well studied. We have extended previous phylogenetic analyses and examined the presence of Eph and ephrins in the tree of life to determine their origin and evolution. We have found that 1) premetazoan choanoflagellates may already have rudimental Eph/ephrin signaling as they have an Eph-/ephrin-like pair and homologs of downstream-signaling genes; 2) both forward- and reverse-downstream signaling might already occur in Porifera since sponges have most genes involved in these types of signaling; 3) the nonvertebrate metazoan Eph is a type-B receptor that can bind ephrins regardless of their membrane-anchoring structure, glycosylphosphatidylinositol, or transmembrane; 4) Eph/ephrin cross-class binding is specific to Gnathostomata; and 5) kinase-dead Eph receptors can be traced back to Gnathostomata. We conclude that Eph/ephrin signaling is of older origin than previously believed. We also examined the presence of protein domains associated with functional characteristics and the appearance and conservation of downstream-signaling pathways to understand the original and derived functions of Ephs and ephrins. We find that the evolutionary history of these gene families points to an ancestral function in cell–cell interactions that could contribute to the emergence of multicellularity and, in particular, to the required segregation of cell populations.
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Affiliation(s)
- Aida Arcas
- Instituto de Neurociencias (CSIC-UMH), Avda, San Juan de Alicante, Spain
| | - David G Wilkinson
- Neural Development Laboratory, The Francis Crick Institute, London, United Kingdom
| | - M Ángela Nieto
- Instituto de Neurociencias (CSIC-UMH), Avda, San Juan de Alicante, Spain
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11
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Lei Y, Yang L, Jiang H, Chen J, Sun N, Lv W, He S. Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae. SCIENCE CHINA-LIFE SCIENCES 2020; 64:1149-1164. [PMID: 33051703 DOI: 10.1007/s11427-020-1809-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
Abstract
Whole-genome duplications (WGDs) are an important contributor to phenotypic innovations in evolutionary history. The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates. In this study, the evolutionary changes of hemoglobin (Hb) repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish, including eight diploid and four tetraploid species. Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species. Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes. Data were integrated with the expression profiles of the genes during ontogeny. Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family; each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications. This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression. Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems.
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Affiliation(s)
- Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Sun
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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12
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Li L, Liu D, Liu A, Li J, Wang H, Zhou J. Genomic Survey of Tyrosine Kinases Repertoire in Electrophorus electricus With an Emphasis on Evolutionary Conservation and Diversification. Evol Bioinform Online 2020; 16:1176934320922519. [PMID: 32546936 PMCID: PMC7249569 DOI: 10.1177/1176934320922519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/07/2020] [Indexed: 12/05/2022] Open
Abstract
Tyrosine kinases (TKs) play key roles in the regulation of multicellularity in
organisms and involved primarily in cell growth, differentiation, and
cell-to-cell communication. Genome-wide characterization of TKs has been
conducted in many metazoans; however, systematic information regarding this
superfamily in Electrophorus electricus (electric eel) is still
lacking. In this study, we identified 114 TK genes in the E
electricus genome and investigated their evolution, molecular
features, and domain architecture using phylogenetic profiling to gain a better
understanding of their similarities and specificity. Our results suggested that
the electric eel TK (EeTK) repertoire was shaped by whole-genome duplications
(WGDs) and tandem duplication events. Compared with other vertebrate TKs, gene
members in Jak, Src, and EGFR subfamily duplicated specifically, but with
members lost in Eph, Axl, and Ack subfamily in electric eel. We also conducted
an exhaustive survey of TK genes in genomic databases, identifying 1674 TK
proteins in 31 representative species covering all the main metazoan lineages.
Extensive evolutionary analysis indicated that TK repertoire in vertebrates
tended to be remarkably conserved, but the gene members in each subfamily were
very variable. Comparative expression profile analysis showed that electric
organ tissues and muscle shared a similar pattern with specific highly expressed
TKs (ie, epha7, musk, jak1, and pdgfra), suggesting that regulation of TKs might
play an important role in specifying an electric organ identity from its muscle
precursor. We further identified TK genes exhibiting tissue-specific expression
patterns, indicating that members in TKs participated in subfunctionalization
representing an evolutionary divergence required for the performance of
different tissues. This work generates valuable information for further gene
function analysis and identifying candidate TK genes reflecting their unique
tissue-function specializations in electric eel.
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Affiliation(s)
- Ling Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Dangyun Liu
- Department of Central Laboratory, The Affiliated Huaian No.1 People's Hospital, Nanjing Medical University, Huai'an, P.R. China
| | - Ake Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, P.R. China
| | - Jingquan Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
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13
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Singh PP, Isambert H. OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates. Nucleic Acids Res 2020; 48:D724-D730. [PMID: 31612943 PMCID: PMC7145513 DOI: 10.1093/nar/gkz909] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/20/2019] [Accepted: 10/10/2019] [Indexed: 12/12/2022] Open
Abstract
All vertebrates including human have evolved from an ancestor that underwent two rounds of whole genome duplication (2R-WGD). In addition, teleost fish underwent an additional third round of genome duplication (3R-WGD). The genes retained from these genome duplications, so-called ohnologs, have been instrumental in the evolution of vertebrate complexity, development and susceptibility to genetic diseases. However, the identification of vertebrate ohnologs has been challenging, due to lineage specific genome rearrangements since 2R- and 3R-WGD. We previously identified vertebrate ohnologs using a novel synteny comparison across multiple genomes. Here, we refine and apply this approach on 27 vertebrate genomes to identify ohnologs from both 2R- and 3R-WGD, while taking into account the phylogenetically biased sampling of available species. We assemble vertebrate ohnolog pairs and families in an expanded OHNOLOGS v2 database. We find that teleost fish have retained more 2R-WGD ohnologs than mammals and sauropsids, and that these 2R-ohnologs have retained significantly more ohnologs from the subsequent 3R-WGD than genes without 2R-ohnologs. Interestingly, species with fewer extant genes, such as sauropsids, have retained similar or higher proportions of ohnologs. OHNOLOGS v2 should allow deeper evolutionary genomic analysis of the impact of WGD on vertebrates and can be freely accessed at http://ohnologs.curie.fr.
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Affiliation(s)
- Param Priya Singh
- Institut Curie, Research Center, CNRS UMR168, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Hervé Isambert
- Institut Curie, Research Center, CNRS UMR168, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
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14
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EGFR Signaling Causes Morphine Tolerance and Mechanical Sensitization in Rats. eNeuro 2020; 7:ENEURO.0460-18.2020. [PMID: 32111605 PMCID: PMC7218007 DOI: 10.1523/eneuro.0460-18.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/29/2018] [Accepted: 02/17/2020] [Indexed: 01/18/2023] Open
Abstract
The safety and efficacy of opioids are compromised as analgesic tolerance develops. Opioids are also ineffective against neuropathic pain. Recent reports have suggested that inhibitors of the epidermal growth factor receptor (EGFR), a receptor tyrosine kinase (RTK), may have analgesic effects in cancer patients suffering from neuropathic pain. It has been shown that the platelet-derived growth factor receptor-β (PDGFR-β), an RTK that has been shown to interact with the EGFR, mediates opioid tolerance but does not induce analgesia. Therefore, we sought to determine whether EGFR signaling was involved in opioid tolerance and whether EGFR and PDGFR signaling could induce pain in rats. We found that gefitinib, an EGFR antagonist, eliminated morphine tolerance. In addition, repeated EGF administration rendered animals unresponsive to subsequent analgesic doses of morphine, a phenomenon we call "pre-tolerance." Using a nerve injury model, we found that gefitinib alone was not analgesic. Rather, it reversed insensitivity to morphine analgesia (pre-tolerance) caused by the release of EGF by injured nerves. We also showed that repeated, but not acute EGF or PDGF-BB administration induced mechanical hypersensitivity in rats. EGFR and PDGFR-β signaling interacted to produce this sensitization. EGFR was widely expressed in primary sensory afferent cell bodies, demonstrating a neuroanatomical substrate for our findings. Taken together, our results suggest a direct mechanistic link between opioid tolerance and mechanical sensitization. EGFR antagonism could eventually play an important clinical role in the treatment of opioid tolerance and neuropathic pain that is refractory to opioid treatment.
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15
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Nye DMR, Albertson RM, Weiner AT, Hertzler JI, Shorey M, Goberdhan DCI, Wilson C, Janes KA, Rolls MM. The receptor tyrosine kinase Ror is required for dendrite regeneration in Drosophila neurons. PLoS Biol 2020; 18:e3000657. [PMID: 32163406 PMCID: PMC7067388 DOI: 10.1371/journal.pbio.3000657] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022] Open
Abstract
While many regulators of axon regeneration have been identified, very little is known about mechanisms that allow dendrites to regenerate after injury. Using a Drosophila model of dendrite regeneration, we performed a candidate screen of receptor tyrosine kinases (RTKs) and found a requirement for RTK-like orphan receptor (Ror). We confirmed that Ror was required for regeneration in two different neuron types using RNA interference (RNAi) and mutants. Ror was not required for axon regeneration or normal dendrite development, suggesting a specific role in dendrite regeneration. Ror can act as a Wnt coreceptor with frizzleds (fzs) in other contexts, so we tested the involvement of Wnt signaling proteins in dendrite regeneration. We found that knockdown of fz, dishevelled (dsh), Axin, and gilgamesh (gish) also reduced dendrite regeneration. Moreover, Ror was required to position dsh and Axin in dendrites. We recently found that Wnt signaling proteins, including dsh and Axin, localize microtubule nucleation machinery in dendrites. We therefore hypothesized that Ror may act by regulating microtubule nucleation at baseline and during dendrite regeneration. Consistent with this hypothesis, localization of the core nucleation protein γTubulin was reduced in Ror RNAi neurons, and this effect was strongest during dendrite regeneration. In addition, dendrite regeneration was sensitive to partial reduction of γTubulin. We conclude that Ror promotes dendrite regeneration as part of a Wnt signaling pathway that regulates dendritic microtubule nucleation.
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Affiliation(s)
- Derek M. R. Nye
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- MSTP Program, Milton S. Hershey College of Medicine, Hershey, Pennsylvania, United States of America
| | - Richard M. Albertson
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- MSTP Program, Milton S. Hershey College of Medicine, Hershey, Pennsylvania, United States of America
| | - Alexis T. Weiner
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - J. Ian Hertzler
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Matthew Shorey
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | | | - Clive Wilson
- Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Kevin A. Janes
- Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Melissa M. Rolls
- Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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16
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Hahn N, Büschgens L, Schwedhelm-Domeyer N, Bank S, Geurten BRH, Neugebauer P, Massih B, Göpfert MC, Heinrich R. The Orphan Cytokine Receptor CRLF3 Emerged With the Origin of the Nervous System and Is a Neuroprotective Erythropoietin Receptor in Locusts. Front Mol Neurosci 2019; 12:251. [PMID: 31680856 PMCID: PMC6797617 DOI: 10.3389/fnmol.2019.00251] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/27/2019] [Indexed: 12/19/2022] Open
Abstract
The orphan cytokine receptor-like factor 3 (CRLF3) was identified as a neuroprotective erythropoietin receptor in locust neurons and emerged with the evolution of the eumetazoan nervous system. Human CRLF3 belongs to class I helical cytokine receptors that mediate pleiotropic cellular reactions to injury and diverse physiological challenges. It is expressed in various tissues including the central nervous system but its ligand remains unidentified. A CRLF3 ortholog in the holometabolous beetle Tribolium castaneum was recently shown to induce anti-apoptotic mechanisms upon stimulation with human recombinant erythropoietin. To test the hypothesis that CRLF3 represents an ancient cell-protective receptor for erythropoietin-like cytokines, we investigated its presence across metazoan species. Furthermore, we examined CRLF3 expression and function in the hemimetabolous insect Locusta migratoria. Phylogenetic analysis of CRLF3 sequences indicated that CRLF3 is absent in Porifera, Placozoa and Ctenophora, all lacking the traditional nervous system. However, it is present in all major eumetazoan groups ranging from cnidarians over protostomians to mammals. The CRLF3 sequence is highly conserved and abundant amongst vertebrates. In contrast, relatively few invertebrates express CRLF3 and these sequences show greater variability, suggesting frequent loss due to low functional importance. In L. migratoria, we identified the transcript Lm-crlf3 by RACE-PCR and detected its expression in locust brain, skeletal muscle and hemocytes. These findings correspond to the ubiquitous expression of crlf3 in mammalian tissues. We demonstrate that the sole addition of double-stranded RNA to the culture medium (called soaking RNA interference) specifically interferes with protein expression in locust primary brain cell cultures. This technique was used to knock down Lm-crlf3 expression and to abolish its physiological function. We confirmed that recombinant human erythropoietin rescues locust brain neurons from hypoxia-induced apoptosis and showed that this neuroprotective effect is absent after knocking down Lm-crlf3. Our results affirm the erythropoietin-induced neuroprotective function of CRLF3 in a second insect species from a different taxonomic group. They suggest that the phylogenetically conserved CRLF3 receptor may function as a cell protective receptor for erythropoietin or a structurally related cytokine also in other animals including vertebrate and mammalian species.
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Affiliation(s)
- Nina Hahn
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Luca Büschgens
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Nicola Schwedhelm-Domeyer
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Sarah Bank
- Department of Animal Evolution and Biodiversity, Institute for Zoology & Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Bart R H Geurten
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Pia Neugebauer
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Bita Massih
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Martin C Göpfert
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
| | - Ralf Heinrich
- Department of Cellular Neurobiology, Institute for Zoology and Anthropology, Georg-August University of Göttingen, Göttingen, Germany
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17
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Rodríguez-Fdez S, Bustelo XR. The Vav GEF Family: An Evolutionary and Functional Perspective. Cells 2019; 8:E465. [PMID: 31100928 PMCID: PMC6562523 DOI: 10.3390/cells8050465] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/10/2019] [Accepted: 05/15/2019] [Indexed: 02/07/2023] Open
Abstract
Vav proteins play roles as guanosine nucleotide exchange factors for Rho GTPases and signaling adaptors downstream of protein tyrosine kinases. The recent sequencing of the genomes of many species has revealed that this protein family originated in choanozoans, a group of unicellular organisms from which animal metazoans are believed to have originated from. Since then, the Vav family underwent expansions and reductions in its members during the evolutionary transitions that originated the agnates, chondrichthyes, some teleost fish, and some neoaves. Exotic members of the family harboring atypical structural domains can be also found in some invertebrate species. In this review, we will provide a phylogenetic perspective of the evolution of the Vav family. We will also pay attention to the structure, signaling properties, regulatory layers, and functions of Vav proteins in both invertebrate and vertebrate species.
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Affiliation(s)
- Sonia Rodríguez-Fdez
- Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Campus Unamuno, E37007 Salamanca, Spain.
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18
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Gu L, Xia C. Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes. BMC Evol Biol 2019; 19:9. [PMID: 30621595 PMCID: PMC6325677 DOI: 10.1186/s12862-018-1323-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attention considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the apolipoprotein D (ApoD) ligand-transporter genes in a cluster manner specific to teleost fishes. RESULTS Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, positive selection detection and breakpoints detection, the single ApoD gene in the ancestor expanded into two clusters following a dynamic evolutionary pattern in teleost fishes. Orthologous genes show conserved expression patterns, whereas lineage-specific duplicated genes show tissue-specific expression patterns and even evolve new gene expression profiles. Positive selection occurred in branches before and after gene duplication, especially for lineage-specific duplicated genes. Cluster analyses based on protein 3D structure comparisons, especially comparisons of the four loops at the opening side, show gene duplication-segregating patterns. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes. ApoD clusters are located next to the breakpoints of genome rearrangements. CONCLUSIONS Here, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both the protein and expression levels after duplication. Evidence from different aspects-i.e., abnormal expression-induced disease in humans, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes under positive selection and their location next to the breakpoints of genome rearrangements-suggests the potentially advantageous roles of ApoD genes in teleost fishes. The cluster expansion of ApoD genes specific to teleost fishes provides thus an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.
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Affiliation(s)
- Langyu Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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19
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Teleost Fish-Specific Preferential Retention of Pigmentation Gene-Containing Families After Whole Genome Duplications in Vertebrates. G3-GENES GENOMES GENETICS 2018; 8:1795-1806. [PMID: 29599177 PMCID: PMC5940169 DOI: 10.1534/g3.118.200201] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vertebrate pigmentation is a highly diverse trait mainly determined by neural crest cell derivatives. It has been suggested that two rounds (1R/2R) of whole-genome duplications (WGDs) at the basis of vertebrates allowed changes in gene regulation associated with neural crest evolution. Subsequently, the teleost fish lineage experienced other WGDs, including the teleost-specific Ts3R before teleost radiation and the more recent Ss4R at the basis of salmonids. As the teleost lineage harbors the highest number of pigment cell types and pigmentation diversity in vertebrates, WGDs might have contributed to the evolution and diversification of the pigmentation gene repertoire in teleosts. We have compared the impact of the basal vertebrate 1R/2R duplications with that of the teleost-specific Ts3R and salmonid-specific Ss4R WGDs on 181 gene families containing genes involved in pigmentation. We show that pigmentation genes (PGs) have been globally more frequently retained as duplicates than other genes after Ts3R and Ss4R but not after the early 1R/2R. This is also true for non-pigmentary paralogs of PGs, suggesting that the function in pigmentation is not the sole key driver of gene retention after WGDs. On the long-term, specific categories of PGs have been repeatedly preferentially retained after ancient 1R/2R and Ts3R WGDs, possibly linked to the molecular nature of their proteins (e.g., DNA binding transcriptional regulators) and their central position in protein-protein interaction networks. Taken together, our results support a major role of WGDs in the diversification of the pigmentation gene repertoire in the teleost lineage, with a possible link with the diversity of pigment cell lineages observed in these animals compared to other vertebrates.
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20
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He S, Tong X, Han M, Bai Y, Dai F. Genome-Wide Identification and Characterization of Tyrosine Kinases in the Silkworm, Bombyx mori. Int J Mol Sci 2018; 19:E934. [PMID: 29561793 PMCID: PMC5979338 DOI: 10.3390/ijms19040934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 12/19/2022] Open
Abstract
The tyrosine kinases (TKs) are important parts of metazoan signaling pathways and play significant roles in cell growth, development, apoptosis and disease. Genome-wide characterization of TKs has been conducted in many metazoans, however, systematic information about this family in Lepidoptera is still lacking. We retrieved 33 TK-encoding genes in silkworm and classified them into 25 subfamilies by sequence analysis, without members in AXL, FRK, PDGFR, STYK1 and TIE subfamilies. Although domain sequences in each subfamily are conserved, TKs in vertebrates tend to be remarkably conserved and stable. Our results of phylogenetic analysis supported the previous conclusion for the second major expansion of TK family. Gene-Ontology (GO) analysis revealed that a higher proportion of BmTKs played roles in binding, catalysis, signal transduction, metabolism, biological regulation and response to stimulus, compared to all silkworm genes annotated in GO. Moreover, the expression profile analysis of BmTKs among multiple tissues and developmental stages demonstrated that many genes exhibited stage-specific and/or sex-related expression during embryogenesis, molting and metamorphosis, and that 8 BmTKs presented tissue-specific high expression. Our study provides systematic description of silkworm tyrosine kinases, and may also provide further insights into metazoan TKs and assist future studies addressing their functions.
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Affiliation(s)
- Songzhen He
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
| | - Minjin Han
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
| | - Yanmin Bai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing 400715, China.
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21
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Kwon A, John M, Ruan Z, Kannan N. Coupled regulation by the juxtamembrane and sterile α motif (SAM) linker is a hallmark of ephrin tyrosine kinase evolution. J Biol Chem 2018; 293:5102-5116. [PMID: 29432127 DOI: 10.1074/jbc.ra117.001296] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/18/2018] [Indexed: 11/06/2022] Open
Abstract
Ephrin (Eph) receptor tyrosine kinases have evolutionarily diverged from other tyrosine kinases to respond to specific activation and regulatory signals that require close coupling of kinase catalytic and regulatory functions. However, the evolutionary basis for such functional coupling is not fully understood. We employed an evolutionary systems approach involving statistical mining of large sequence and structural data sets to define the hallmarks of Eph kinase evolution and functional specialization. We found that some of the most distinguishing Eph-specific residues structurally tether the flanking juxtamembrane and sterile α motif (SAM) linker regions to the kinase domain, and substitutions of these residues in EphA3 resulted in faster kinase activation. We report for the first time that the SAM domain linker is functionally coupled to the juxtamembrane through co-conserved residues in the kinase domain and that together these residues provide a structural framework for coupling catalytic and regulatory functions. The unique organization of Eph-specific tethering networks and the identification of other Eph-specific sequence features of unknown functions provide new hypotheses for future functional studies and new clues to disease mutations altering Eph kinase-specific functions.
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Affiliation(s)
- Annie Kwon
- From the Institute of Bioinformatics and
| | - Mihir John
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Zheng Ruan
- From the Institute of Bioinformatics and
| | - Natarajan Kannan
- From the Institute of Bioinformatics and .,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
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22
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Evans AL, Blackburn JWD, Taruc K, Kipp A, Dirk BS, Hunt NR, Barr SD, Dikeakos JD, Heit B. Antagonistic Coevolution of MER Tyrosine Kinase Expression and Function. Mol Biol Evol 2017; 34:1613-1628. [PMID: 28369510 DOI: 10.1093/molbev/msx102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TYRO3, AXL, and MERTK (TAM) receptors are a family of receptor tyrosine kinases that maintain homeostasis through the clearance of apoptotic cells, and when defective, contribute to chronic inflammatory and autoimmune diseases such as atherosclerosis, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and Crohn's disease. In addition, certain enveloped viruses utilize TAM receptors for immune evasion and entry into host cells, with several viruses preferentially hijacking MERTK for these purposes. Despite the biological importance of TAM receptors, little is understood of their recent evolution and its impact on their function. Using evolutionary analysis of primate TAM receptor sequences, we identified strong, recent positive selection in MERTK's signal peptide and transmembrane domain that was absent from TYRO3 and AXL. Reconstruction of hominid and primate ancestral MERTK sequences revealed three nonsynonymous single nucleotide polymorphisms in the human MERTK signal peptide, with a G14C mutation resulting in a predicted non-B DNA cruciform motif, producing a significant decrease in MERTK expression with no significant effect on MERTK trafficking or half-life. Reconstruction of MERTK's transmembrane domain identified three amino acid substitutions and four amino acid insertions in humans, which led to significantly higher levels of self-clustering through the creation of a new interaction motif. This clustering counteracted the effect of the signal peptide mutations through enhancing MERTK avidity, whereas the lower MERTK expression led to reduced binding of Ebola virus-like particles. The decreased MERTK expression counterbalanced by increased avidity is consistent with antagonistic coevolution to evade viral hijacking of MERTK.
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Affiliation(s)
- Amanda L Evans
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Jack W D Blackburn
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Kyle Taruc
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Angela Kipp
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Brennan S Dirk
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Nina R Hunt
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Stephen D Barr
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology and the Centre for Human Immunology, The University of Western Ontario, London, Canada
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23
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Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates. Mol Genet Genomics 2017; 292:1405-1418. [PMID: 28819830 DOI: 10.1007/s00438-017-1356-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
Abstract
The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified. Although TK domain sequences and domain organization in each subfamily were conserved, the total number of TKs in different species was much variable. In addition, extensive evolutionary analysis in metazoans indicated that TK repertoire in vertebrates tends to be remarkably stable. Phylogenetic analysis of Eph subfamily indicated that the divergence of EphA and EphB occurred prior to the whole genome duplication (WGD) but after the split of Urochordates and vertebrates. Moreover, the expression pattern analysis of lizard TK genes among 9 different tissues showed that 14 TK genes exhibited tissue-specific expression and 6 TK genes were widely expressed. Comparative analysis of TK expression suggested that the tissue specifically expressed genes showed different expression pattern but the widely expressed genes showed similar pattern between anole lizard and human. These results may provide insights into the evolutionary diversification of animal TK genes and would aid future studies on TK protein regulation of key growth and developmental processes.
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24
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Lu XJ, Chen Q, Rong YJ, Chen F, Chen J. CXCR3.1 and CXCR3.2 Differentially Contribute to Macrophage Polarization in Teleost Fish. THE JOURNAL OF IMMUNOLOGY 2017; 198:4692-4706. [PMID: 28500070 DOI: 10.4049/jimmunol.1700101] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/18/2017] [Indexed: 12/29/2022]
Abstract
The study of multiple copies of chemokine receptor genes in various teleosts has long appealed to investigators seeking to understand the evolution of the immune system. The CXCR CXCR3 gene has two isoforms, CXCR3.1 and CXCR3.2, which are both expressed in macrophages. The distinct roles of teleost CXCR3s have not been identified previously. In this article, we found that CXCR3.1 and CXCR3.2 differentially contributed to macrophage polarization in the teleosts: ayu (Plecoglossus altivelis), grass carp (Ctenopharyngodon idella), and spotted green pufferfish (Tetraodon nigroviridis). In ayu macrophages, the P. altivelis CXCR3.1 (PaCXCR3.1) gene was constitutively expressed, whereas the P. altivelis CXCR3.2 (PaCXCR3.2) gene was induced postinfection with Escherichia coli Upon E. coli infection, PaCXCR3.1+ and PaCXCR3.2+ macrophages showed an M1 and an M2 phenotype, respectively. CXCL9-11-like proteins mediated M1 and M2 polarization by interacting with the PaCXCR3.1 and PaCXCR3.2 proteins on macrophages, respectively. The transcription factors P. altivelis STAT1 and P. altivelis STAT3 were activated in PaCXCR3.1+ and PaCXCR3.2+ macrophages, respectively. Furthermore, the prognosis of septic ayu adoptively transferred with PaCXCR3.2+ macrophages was improved. Our data reveal a previously unknown mechanism for macrophage polarization, suggesting that redundant genes may regulate crucial functions in the teleost immune system.
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Affiliation(s)
- Xin-Jiang Lu
- Laboratory of Biochemistry and Molecular Biology, Ningbo University, Ningbo 315211, People's Republic of China
| | - Qiang Chen
- Laboratory of Biochemistry and Molecular Biology, Ningbo University, Ningbo 315211, People's Republic of China
| | - Ye-Jing Rong
- Laboratory of Biochemistry and Molecular Biology, Ningbo University, Ningbo 315211, People's Republic of China
| | - Feng Chen
- Laboratory of Biochemistry and Molecular Biology, Ningbo University, Ningbo 315211, People's Republic of China
| | - Jiong Chen
- Laboratory of Biochemistry and Molecular Biology, Ningbo University, Ningbo 315211, People's Republic of China
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25
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Vlasschaert C, Cook D, Xia X, Gray DA. The evolution and functional diversification of the deubiquitinating enzyme superfamily. Genome Biol Evol 2017; 9:558-573. [PMID: 28177072 PMCID: PMC5381560 DOI: 10.1093/gbe/evx020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/18/2017] [Accepted: 02/04/2017] [Indexed: 12/16/2022] Open
Abstract
Ubiquitin and ubiquitin-like molecules are attached to and removed from cellular proteins in a dynamic and highly regulated manner. Deubiquitinating enzymes are critical to this process, and the genetic catalogue of deubiquitinating enzymes expanded greatly over the course of evolution. Extensive functional redundancy has been noted among the 93 members of the human deubiquitinating enzyme (DUB) superfamily. This is especially true of genes that were generated by duplication (termed paralogs) as they often retain considerable sequence similarity. Because complete redundancy in systems should be eliminated by selective pressure, we theorized that many overlapping DUBs must have significant and unique spatiotemporal roles that can be evaluated in an evolutionary context. We have determined the evolutionary history of the entire class of deubiquitinating enzymes, including the sequence and means of duplication for all paralogous pairs. To establish their uniqueness, we have investigated cell-type specificity in developmental and adult contexts, and have investigated the coemergence of substrates from the same duplication events. Our analysis has revealed examples of DUB gene subfunctionalization, neofunctionalization, and nonfunctionalization.
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Affiliation(s)
- Caitlyn Vlasschaert
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ontario, Canada
- The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Biology, University of Ottawa, Ontario, Canada
| | - David Cook
- The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ontario, Canada
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Douglas A. Gray
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ontario, Canada
- The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
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