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Zhang L, Leonard N, Passaro R, Luan MS, Van Tuyen P, Han LTN, Cam NH, Vogelnest L, Lynch M, Fine AE, Nga NTT, Van Long N, Rawson BM, Behie A, Van Nguyen T, Le MD, Nadler T, Walter L, Marques-Bonet T, Hofreiter M, Li M, Liu Z, Roos C. Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur. Nat Commun 2024; 15:8531. [PMID: 39358348 PMCID: PMC11447269 DOI: 10.1038/s41467-024-52811-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/23/2024] [Indexed: 10/04/2024] Open
Abstract
Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam's famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.
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Affiliation(s)
- Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- International Max Planck Research School for Genome Science (IMPRS-GS), University of Göttingen, Göttingen, Germany.
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Neahga Leonard
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Rick Passaro
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Mai Sy Luan
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Pham Van Tuyen
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Le Thi Ngoc Han
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Nguyen Huy Cam
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Larry Vogelnest
- Taronga Conservation Society Australia, Mosman, NSW, Australia
| | - Michael Lynch
- Melbourne Zoo, Zoos Victoria, Parkville, VIC, Australia
| | - Amanda E Fine
- Wildlife Conservation Society (WCS), Health Program, New York, NY, USA
| | | | - Nguyen Van Long
- Wildlife Conservation Society (WCS), Vietnam Country Program, Hanoi, Vietnam
| | - Benjamin M Rawson
- World Wildlife Fund for Nature (WWF) International, Gland, Switzerland
| | - Alison Behie
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT, Australia
| | - Truong Van Nguyen
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Department of Science, University of Potsdam, Potsdam, Germany
- Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Minh D Le
- Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
- Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Tilo Nadler
- Three Monkeys Wildlife Conservancy, Nho Quan District, Ninh Binh Province, Ninh Binh, Vietnam
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Spain
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Department of Science, University of Potsdam, Potsdam, Germany.
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, China.
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
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Chon NL, Tran S, Miller CS, Lin H, Knight JD. A Conserved Electrostatic Membrane-Binding Surface in Synaptotagmin-Like Proteins Revealed Using Molecular Phylogenetic Analysis and Homology Modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548768. [PMID: 37502952 PMCID: PMC10369986 DOI: 10.1101/2023.07.13.548768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Protein structure prediction has emerged as a core technology for understanding biomolecules and their interactions. Here, we combine homology-based structure prediction with molecular phylogenetic analysis to study the evolution of electrostatic membrane binding among vertebrate synaptotagmin-like proteins (Slps). Slp family proteins play key roles in the membrane trafficking of large dense-core secretory vesicles. Our previous experimental and computational study found that the C2A domain of Slp-4 (also called granuphilin) binds with high affinity to anionic phospholipids in the cytoplasmic leaflet of the plasma membrane through a large positively charged protein surface centered on a cluster of phosphoinositide-binding lysine residues. Because this surface contributes greatly to Slp-4 C2A domain membrane binding, we hypothesized that the net charge on the surface might be evolutionarily conserved. To test this hypothesis, the known C2A sequences of Slp-4 among vertebrates were organized by class (from mammalia to pisces) using molecular phylogenetic analysis. Consensus sequences for each class were then identified and used to generate homology structures, from which Poisson-Boltzmann electrostatic potentials were calculated. For comparison, homology structures and electrostatic potentials were also calculated for the five human Slp protein family members. The results demonstrate that the charge on the membrane-binding surface is highly conserved throughout the evolution of Slp-4, and more highly conserved than many individual residues among the human Slp family paralogs. Such molecular phylogenetic-driven computational analysis can help to describe the evolution of electrostatic interactions between proteins and membranes which are crucial for their function.
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Affiliation(s)
- Nara L. Chon
- Department of Chemistry, University of Colorado Denver
| | - Sherleen Tran
- Department of Chemistry, University of Colorado Denver
| | | | - Hai Lin
- Department of Chemistry, University of Colorado Denver
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Overduin M, Tran A, Eekels DM, Overduin F, Kervin TA. Transmembrane Membrane Readers form a Novel Class of Proteins That Include Peripheral Phosphoinositide Recognition Domains and Viral Spikes. MEMBRANES 2022; 12:1161. [PMID: 36422153 PMCID: PMC9692390 DOI: 10.3390/membranes12111161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Membrane proteins are broadly classified as transmembrane (TM) or peripheral, with functions that pertain to only a single bilayer at a given time. Here, we explicate a class of proteins that contain both transmembrane and peripheral domains, which we dub transmembrane membrane readers (TMMRs). Their transmembrane and peripheral elements anchor them to one bilayer and reversibly attach them to another section of bilayer, respectively, positioning them to tether and fuse membranes while recognizing signals such as phosphoinositides (PIs) and modifying lipid chemistries in proximity to their transmembrane domains. Here, we analyze full-length models from AlphaFold2 and Rosetta, as well as structures from nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, using the Membrane Optimal Docking Area (MODA) program to map their membrane-binding surfaces. Eukaryotic TMMRs include phospholipid-binding C1, C2, CRAL-TRIO, FYVE, GRAM, GTPase, MATH, PDZ, PH, PX, SMP, StART and WD domains within proteins including protrudin, sorting nexins and synaptotagmins. The spike proteins of SARS-CoV-2 as well as other viruses are also TMMRs, seeing as they are anchored into the viral membrane while mediating fusion with host cell membranes. As such, TMMRs have key roles in cell biology and membrane trafficking, and include drug targets for diseases such as COVID-19.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Anh Tran
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | | | - Finn Overduin
- Institute of Nutritional Science, University of Potsdam, 14476 Potsdam, Germany
| | - Troy A. Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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