1
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Yang Y, Braga MV, Dean MD. Insertion-Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure. Genome Biol Evol 2024; 16:evae093. [PMID: 38735759 PMCID: PMC11102076 DOI: 10.1093/gbe/evae093] [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: 02/16/2024] [Revised: 04/16/2024] [Accepted: 04/21/2024] [Indexed: 05/14/2024] Open
Abstract
A fundamental goal in evolutionary biology and population genetics is to understand how selection shapes the fate of new mutations. Here, we test the null hypothesis that insertion-deletion (indel) events in protein-coding regions occur randomly with respect to secondary structures. We identified indels across 11,444 sequence alignments in mouse, rat, human, chimp, and dog genomes and then quantified their overlap with four different types of secondary structure-alpha helices, beta strands, protein bends, and protein turns-predicted by deep-learning methods of AlphaFold2. Indels overlapped secondary structures 54% as much as expected and were especially underrepresented over beta strands, which tend to form internal, stable regions of proteins. In contrast, indels were enriched by 155% over regions without any predicted secondary structures. These skews were stronger in the rodent lineages compared to the primate lineages, consistent with population genetic theory predicting that natural selection will be more efficient in species with larger effective population sizes. Nonsynonymous substitutions were also less common in regions of protein secondary structure, although not as strongly reduced as in indels. In a complementary analysis of thousands of human genomes, we showed that indels overlapping secondary structure segregated at significantly lower frequency than indels outside of secondary structure. Taken together, our study shows that indels are selected against if they overlap secondary structure, presumably because they disrupt the tertiary structure and function of a protein.
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Affiliation(s)
- Yi Yang
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew V Braga
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew D Dean
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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2
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Bowman J, Lynch VJ. Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582135. [PMID: 38463968 PMCID: PMC10925141 DOI: 10.1101/2024.02.27.582135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Elephants have emerged as a model system to study the evolution of body size and cancer resistance because, despite their immense size, they have a very low prevalence of cancer. Previous studies have found that duplication of tumor suppressors at least partly contributes to the evolution of anti-cancer cellular phenotypes in elephants. Still, many other mechanisms must have contributed to their augmented cancer resistance. Here, we use a suite of codon-based maximum-likelihood methods and a dataset of 13,310 protein-coding gene alignments from 261 Eutherian mammals to identify positively selected and rapidly evolving elephant genes. We found 496 genes (3.73% of alignments tested) with statistically significant evidence for positive selection and 660 genes (4.96% of alignments tested) that likely evolved rapidly in elephants. Positively selected and rapidly evolving genes are statistically enriched in gene ontology terms and biological pathways related to regulated cell death mechanisms, DNA damage repair, cell cycle regulation, epidermal growth factor receptor (EGFR) signaling, and immune functions, particularly neutrophil granules and degranulation. All of these biological factors are plausibly related to the evolution of cancer resistance. Thus, these positively selected and rapidly evolving genes are promising candidates for genes contributing to elephant-specific traits, including the evolution of molecular and cellular characteristics that enhance cancer resistance.
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Affiliation(s)
- Jacob Bowman
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, 14260, USA
| | - Vincent J. Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, 14260, USA
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3
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Correa Marrero M, Capdevielle S, Huang W, Al-Subhi AM, Busscher M, Busscher-Lange J, van der Wal F, de Ridder D, van Dijk ADJ, Hogenhout SA, Immink RGH. Protein interaction mapping reveals widespread targeting of development-related host transcription factors by phytoplasma effectors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1281-1297. [PMID: 37965720 DOI: 10.1111/tpj.16546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
Phytoplasmas are pathogenic bacteria that reprogram plant host development for their own benefit. Previous studies have characterized a few different phytoplasma effector proteins that destabilize specific plant transcription factors. However, these are only a small fraction of the potential effectors used by phytoplasmas; therefore, the molecular mechanisms through which phytoplasmas modulate their hosts require further investigation. To obtain further insights into the phytoplasma infection mechanisms, we generated a protein-protein interaction network between a broad set of phytoplasma effectors and a large, unbiased collection of Arabidopsis thaliana transcription factors and transcriptional regulators. We found widespread, but specific, interactions between phytoplasma effectors and host transcription factors, especially those related to host developmental processes. In particular, many unrelated effectors target specific sets of TCP transcription factors, which regulate plant development and immunity. Comparison with other host-pathogen protein interaction networks shows that phytoplasma effectors have unusual targets, indicating that phytoplasmas have evolved a unique and unusual infection strategy. This study contributes a rich and solid data source that guides further investigations of the functions of individual effectors, as demonstrated for some herein. Moreover, the dataset provides insights into the underlying molecular mechanisms of phytoplasma infection.
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Affiliation(s)
- Miguel Correa Marrero
- Bioinformatics Group, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Sylvain Capdevielle
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Weijie Huang
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Ali M Al-Subhi
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, 11 Al Khod 123, al-Seeb, Oman
| | - Marco Busscher
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Jacqueline Busscher-Lange
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Froukje van der Wal
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Richard G H Immink
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
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4
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Scheben A, Mendivil Ramos O, Kramer M, Goodwin S, Oppenheim S, Becker DJ, Schatz MC, Simmons NB, Siepel A, McCombie WR. Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biol Evol 2023; 15:evad148. [PMID: 37728212 PMCID: PMC10510315 DOI: 10.1093/gbe/evad148] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/21/2023] Open
Abstract
Bats are exceptional among mammals for their powered flight, extended lifespans, and robust immune systems and therefore have been of particular interest in comparative genomics. Using the Oxford Nanopore Technologies long-read platform, we sequenced the genomes of two bat species with key phylogenetic positions, the Jamaican fruit bat (Artibeus jamaicensis) and the Mesoamerican mustached bat (Pteronotus mesoamericanus), and carried out a comprehensive comparative genomic analysis with a diverse collection of bats and other mammals. The high-quality, long-read genome assemblies revealed a contraction of interferon (IFN)-α at the immunity-related type I IFN locus in bats, resulting in a shift in relative IFN-ω and IFN-α copy numbers. Contradicting previous hypotheses of constitutive expression of IFN-α being a feature of the bat immune system, three bat species lost all IFN-α genes. This shift to IFN-ω could contribute to the increased viral tolerance that has made bats a common reservoir for viruses that can be transmitted to humans. Antiviral genes stimulated by type I IFNs also showed evidence of rapid evolution, including a lineage-specific duplication of IFN-induced transmembrane genes and positive selection in IFIT2. In addition, 33 tumor suppressors and 6 DNA-repair genes showed signs of positive selection, perhaps contributing to increased longevity and reduced cancer rates in bats. The robust immune systems of bats rely on both bat-wide and lineage-specific evolution in the immune gene repertoire, suggesting diverse immune strategies. Our study provides new genomic resources for bats and sheds new light on the extraordinary molecular evolution in this critically important group of mammals.
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Affiliation(s)
- Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Oppenheim
- American Museum of Natural History, Institute for Comparative Genomics, New York, New York, USA
| | - Daniel J Becker
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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Gamboa M, Kitamura N, Miura K, Noda S, Kaminuma O. Evolutionary mechanisms underlying the diversification of nuclear factor of activated T cells across vertebrates. Sci Rep 2023; 13:6468. [PMID: 37156933 PMCID: PMC10167247 DOI: 10.1038/s41598-023-33751-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
The mechanisms of immunity linked to biological evolution are crucial for understanding animal morphogenesis, organogenesis, and biodiversity. The nuclear factor of activated T cells (NFAT) family consists of five members (NFATc1-c4, 5) with different functions in the immune system. However, the evolutionary dynamics of NFATs in vertebrates has not been explored. Herein, we investigated the origin and mechanisms underlying the diversification of NFATs by comparing the gene, transcript and protein sequences, and chromosome information. We defined an ancestral origin of NFATs during the bilaterian development, dated approximately 650 million years ago, where NFAT5 and NFATc1-c4 were derived independently. The conserved parallel evolution of NFATs in multiple species was probably attributed to their innate nature. Conversely, frequent gene duplications and chromosomal rearrangements in the recently evolved taxa have suggested their roles in the adaptive immune evolution. A significant correlation was observed between the chromosome rearrangements with gene duplications and the structural fixation changes in vertebrate NFATs, suggesting their role in NFAT diversification. Remarkably, a conserved gene structure around NFAT genes with vertebrate evolutionary-related breaking points indicated the inheritance of NFATs with their neighboring genes as a unit. The close relationship between NFAT diversification and vertebrate immune evolution was suggested.
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Affiliation(s)
- Maribet Gamboa
- Department of Disease Model, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan.
- Department of Ecology, Faculty of Sciences, Universidad Católica de la Santísima Concepción, 4090541, Concepción, Chile.
| | - Noriko Kitamura
- Neurovirology Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Kento Miura
- Department of Disease Model, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Satoko Noda
- Graduate School of Science and Engineering, Ibaraki University, Ibaraki, 310-8512, Japan
| | - Osamu Kaminuma
- Department of Disease Model, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan.
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6
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Choudhary P, Anyango S, Berrisford J, Tolchard J, Varadi M, Velankar S. Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data. Sci Data 2023; 10:204. [PMID: 37045837 PMCID: PMC10097656 DOI: 10.1038/s41597-023-02101-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
More than 61,000 proteins have up-to-date correspondence between their amino acid sequence (UniProtKB) and their 3D structures (PDB), enabled by the Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource. SIFTS incorporates residue-level annotations from many other biological resources. SIFTS data is available in various formats like XML, CSV and TSV format or also accessible via the PDBe REST API but always maintained separately from the structure data (PDBx/mmCIF file) in the PDB archive. Here, we extended the wwPDB PDBx/mmCIF data dictionary with additional categories to accommodate SIFTS data and added the UniProtKB, Pfam, SCOP2, and CATH residue-level annotations directly into the PDBx/mmCIF files from the PDB archive. With the integrated UniProtKB annotations, these files now provide consistent numbering of residues in different PDB entries allowing easy comparison of structure models. The extended dictionary yields a more consistent, standardised metadata description without altering the core PDB information. This development enables up-to-date cross-reference information at the residue level resulting in better data interoperability, supporting improved data analysis and visualisation.
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Grants
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- BB/V004247/1, PI:Sameer Velankar RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- DBI-2019297, PI: S.K. Burley National Science Foundation (NSF)
- DBI-2019297, PI: S.K. Burley National Science Foundation (NSF)
- DBI-2019297, PI: S.K. Burley) National Science Foundation (NSF)
- DBI-2019297, PI: S.K. Burley National Science Foundation (NSF)
- DBI-2019297, PI: S.K. Burley National Science Foundation (NSF)
- DBI-2019297, PI: S.K. Burley NSF | National Science Board (NSB)
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Affiliation(s)
- Preeti Choudhary
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Stephen Anyango
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - John Berrisford
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- AstraZeneca, Biomedical Campus, 1 Francis Crick Ave, Trumpington, Cambridge, CB2 0AA, UK
| | - James Tolchard
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Claude Bernard University, Villeurbanne, Lyon, 69100, France
| | - Mihaly Varadi
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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7
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Bricout R, Weil D, Stroebel D, Genovesio A, Roest Crollius H. Evolution is not Uniform Along Coding Sequences. Mol Biol Evol 2023; 40:7060063. [PMID: 36857092 PMCID: PMC10025431 DOI: 10.1093/molbev/msad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/02/2023] Open
Abstract
Amino acids evolve at different speeds within protein sequences, because their functional and structural roles are different. Notably, amino acids located at the surface of proteins are known to evolve more rapidly than those in the core. In particular, amino acids at the N- and C-termini of protein sequences are likely to be more exposed than those at the core of the folded protein due to their location in the peptidic chain, and they are known to be less structured. Because of these reasons, we would expect that amino acids located at protein termini would evolve faster than residues located inside the chain. Here we test this hypothesis and found that amino acids evolve almost twice as fast at protein termini compared with those in the center, hinting at a strong topological bias along the sequence length. We further show that the distribution of solvent-accessible residues and functional domains in proteins readily explain how structural and functional constraints are weaker at their termini, leading to the observed excess of amino acid substitutions. Finally, we show that the specific evolutionary rates at protein termini may have direct consequences, notably misleading in silico methods used to infer sites under positive selection within genes. These results suggest that accounting for positional information should improve evolutionary models.
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Affiliation(s)
- Raphaël Bricout
- Département de biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Paris, France
| | - Dominique Weil
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Paris, France
| | - David Stroebel
- Département de biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Paris, France
| | - Auguste Genovesio
- Département de biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Paris, France
| | - Hugues Roest Crollius
- Département de biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Paris, France
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8
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Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
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9
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Viehweger A. Faltwerk: a library for spatial exploratory data analysis of protein structures. BIOINFORMATICS ADVANCES 2023; 3:vbad007. [PMID: 36908399 PMCID: PMC9998081 DOI: 10.1093/bioadv/vbad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/10/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023]
Abstract
Summary Proteins are fundamental building blocks of life and are investigated in a broad range of scientific fields, especially in the context of recent progress using in silico structure prediction models and the surge of resulting protein structures in public databases. However, exploratory data analysis of these proteins can be slow because of the need for several methods, ranging from geometric and spatial analysis to visualization. The Python library faltwerk provides an integrated toolkit to perform explorative work with rapid feedback. This toolkit includes support for protein complexes, spatial analysis (point density or spatial autocorrelation), ligand binding site prediction and an intuitive visualization interface based on the grammar of graphics. Availability and implementation faltwerk is distributed under the permissive BSD-3 open source license. Source code and documentation, including an extensive common-use case tutorial, can be found at github.com/phiweger/faltwerk; binaries are available from the pypi repository.
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Affiliation(s)
- Adrian Viehweger
- Institute of Medical Microbiology and Virology, University of Leipzig Medical Center, Leipzig 04103, Germany.,Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
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10
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Ahmad HI, Khan FA, Khan MA, Imran S, Akhtar RW, Pandupuspitasari NS, Negara W, Chen J. Molecular Evolution of the Bactericidal/Permeability-Increasing Protein (BPIFA1) Regulating the Innate Immune Responses in Mammals. Genes (Basel) 2022; 14:genes14010015. [PMID: 36672756 PMCID: PMC9858190 DOI: 10.3390/genes14010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Bactericidal/permeability-increasing protein, a primary factor of the innate immune system of mammals, participates in natural immune protection against invading bacteria. BPIFA1 actively contributes to host defense via multiple mechanisms, such as antibacterial, surfactant, airway surface liquid control, and immunomodulatory activities. However, the evolutionary history and selection forces on the BPIFA1 gene in mammals during adaptive evolution are poorly understood. This study examined the BPIFA1 gene of humans compared with that of other mammalian species to estimate the selective pressure derived by adaptive evolution. To assess whether or not positive selection occurred, we employed several different possibility tests (M1 vs. M2 and M7 vs. M8). The proportions of positively selected sites were significant, with a likelihood log value of 93.63 for the BPIFA1 protein. The Selecton server was used on the same dataset to reconfirm positive selection for specific sites by employing the Mechanistic-Empirical Combination model, thus providing additional evidence supporting the findings of positive selection. There was convincing evidence for positive selection signals in the BPIFA1 genes of mammalian species, which was more significant for selection signs and creating signals. We performed probability tests comparing various models based on dN/dS ratios to recognize specific codons under positive selection pressure. We identified positively selected sites in the LBP-BPI domain of BPIFA1 proteins in the mammalian genome, including a lipid-binding domain with a very high degree of selectivity for DPPC. BPIFA1 activates the upper airway's innate immune system in response to numerous genetic signals in the mammalian genome. These findings highlight evolutionary advancements in immunoregulatory effects that play a significant role in the antibacterial and antiviral defenses of mammalian species.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- Correspondence: (H.I.A.); (J.C.)
| | - Faheem Ahmed Khan
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore 54000, Pakistan
- Research Center for Animal Husbandry, National Research and Innovation Agency, South Tangerang 15314, Indonesia
| | - Musarrat Abbas Khan
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Safdar Imran
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Rana Waseem Akhtar
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang 50275, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, South Tangerang 15314, Indonesia
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
- Correspondence: (H.I.A.); (J.C.)
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11
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Cellier MFM. Nramp: Deprive and conquer? Front Cell Dev Biol 2022; 10:988866. [PMID: 36313567 PMCID: PMC9606685 DOI: 10.3389/fcell.2022.988866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H+)-dependent manganese (Mn2+) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)’s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries ‘eukaryotic signature’ marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H+-dependent Mn2+ acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn2+-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn2+ sequestering defense perhaps favoring intracellular growth-competent bacteria.
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12
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Frlan R. An Evolutionary Conservation and Druggability Analysis of Enzymes Belonging to the Bacterial Shikimate Pathway. Antibiotics (Basel) 2022; 11:antibiotics11050675. [PMID: 35625318 PMCID: PMC9137983 DOI: 10.3390/antibiotics11050675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
Enzymes belonging to the shikimate pathway have long been considered promising targets for antibacterial drugs because they have no counterpart in mammals and are essential for bacterial growth and virulence. However, despite decades of research, there are currently no clinically relevant antibacterial drugs targeting any of these enzymes, and there are legitimate concerns about whether they are sufficiently druggable, i.e., whether they can be adequately modulated by small and potent drug-like molecules. In the present work, in silico analyses combining evolutionary conservation and druggability are performed to determine whether these enzymes are candidates for broad-spectrum antibacterial therapy. The results presented here indicate that the substrate-binding sites of most enzymes in this pathway are suitable drug targets because of their reasonable conservation and druggability scores. An exception was the substrate-binding site of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, which was found to be undruggable because of its high content of charged residues and extremely high overall polarity. Although the presented study was designed from the perspective of broad-spectrum antibacterial drug development, this workflow can be readily applied to any antimicrobial target analysis, whether narrow- or broad-spectrum. Moreover, this research also contributes to a deeper understanding of these enzymes and provides valuable insights into their properties.
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Affiliation(s)
- Rok Frlan
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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13
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Meyerowitz JG, Robertson MJ, Barros-Álvarez X, Panova O, Nwokonko RM, Gao Y, Skiniotis G. The oxytocin signaling complex reveals a molecular switch for cation dependence. Nat Struct Mol Biol 2022; 29:274-281. [PMID: 35241813 DOI: 10.1038/s41594-022-00728-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022]
Abstract
Oxytocin (OT) and vasopressin (AVP) are conserved peptide signaling hormones that are critical for diverse processes including osmotic homeostasis, reproduction, lactation and social interaction. OT acts through the oxytocin receptor (OTR), a magnesium-dependent G protein-coupled receptor that is a therapeutic target for treatment of postpartum hemorrhage, dysfunctional labor and autism. However, the molecular mechanisms that underlie OTR activation by OT and the dependence on magnesium remain unknown. Here we present the wild-type active-state structure of human OTR bound to OT and miniGq/i determined by cryo-EM. The structure reveals a unique activation mechanism adopted by OTR involving both the formation of a Mg2+ coordination complex between OT and the receptor, and disruption of transmembrane helix 7 (TM7) by OT. Our functional assays demonstrate the role of TM7 disruption and provide the mechanism of full agonism by OT and partial agonism by OT analogs. Furthermore, we find that the identity of a single cation-coordinating residue across vasopressin family receptors determines whether the receptor is cation-dependent. Collectively, these results demonstrate how the Mg2+-dependent OTR is activated by OT, provide essential information for structure-based drug discovery efforts and shed light on the molecular determinants of cation dependence of vasopressin family receptors throughout the animal kingdom.
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Affiliation(s)
- Justin G Meyerowitz
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Robertson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ximena Barros-Álvarez
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ouliana Panova
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert M Nwokonko
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Gao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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14
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Wise CF, Hammel SC, Herkert NJ, Ospina M, Calafat AM, Breen M, Stapleton HM. Comparative Assessment of Pesticide Exposures in Domestic Dogs and Their Owners Using Silicone Passive Samplers and Biomonitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1149-1161. [PMID: 34964617 PMCID: PMC10150270 DOI: 10.1021/acs.est.1c06819] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Pesticides are used extensively in residential settings for lawn maintenance and in homes to control household pests including application directly on pets to deter fleas and ticks. Pesticides are commonly detected in the home environment where people and pets can be subject to chronic exposure. Due to increased interest in using companion animals as sentinels for human environmental health studies, we conducted a comparative pesticide exposure assessment in 30 people and their pet dogs to determine how well silicone wristbands and silicone dog tags can predict urinary pesticide biomarkers of exposure. Using targeted gas chromatography-mass spectrometry analyses, we quantified eight pesticides in silicone samplers and used a suspect screening approach for additional pesticides. Urine samples were analyzed for 15 pesticide metabolite biomarkers. Several pesticides were detected in >70% of silicone samplers including permethrin, N,N-diethyl-meta-toluamide (DEET), and chlorpyrifos. Significant and positive correlations were observed between silicone sampler levels of permethrin and DEET with their corresponding urinary metabolites (rs = 0.50-0.96, p < 0.05) in both species. Significantly higher levels of fipronil were observed in silicone samplers from participants who reported using flea and tick products containing fipronil on their dog. This study suggests that people and their dogs have similar pesticide exposures in a home environment.
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Affiliation(s)
- Catherine F Wise
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27708, United States
| | - Stephanie C Hammel
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas J Herkert
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27708, United States
| | - Maria Ospina
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Hwy, MSS103-2, Atlanta, Georgia 30341, United States
| | - Antonia M Calafat
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Hwy, MSS103-2, Atlanta, Georgia 30341, United States
| | - Matthew Breen
- Duke Cancer Institute, Durham, North Carolina 27710, United States
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, North Carolina 27607, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27607, United States
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Heather M Stapleton
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27708, United States
- Duke Cancer Institute, Durham, North Carolina 27710, United States
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15
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Peng J, Svetec N, Zhao L. Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels. Mol Biol Evol 2021; 39:6456312. [PMID: 34878126 PMCID: PMC8789070 DOI: 10.1093/molbev/msab350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is essential in understanding the basis of function and evolution. Previous studies have shown that adaptation frequently occurs at the protein surface, such as in genes involved in host–pathogen interactions. However, it remains unclear whether adaptive sites are distributed randomly or at regions associated with particular structural or functional characteristics across the genome, since many proteins lack structural or functional annotations. Here, we seek to tackle this question by combining large-scale bioinformatic prediction, structural analysis, phylogenetic inference, and population genomic analysis of Drosophila protein-coding genes. We found that protein sequence adaptation is more relevant to function-related rather than structure-related properties. Interestingly, intermolecular interactions contribute significantly to protein adaptation. We further showed that intermolecular interactions, such as physical interactions, may play a role in the coadaptation of fast-adaptive proteins. We found that strongly differentiated amino acids across geographic regions in protein-coding genes are mostly adaptive, which may contribute to the long-term adaptive evolution. This strongly indicates that a number of adaptive sites tend to be repeatedly mutated and selected throughout evolution in the past, present, and maybe future. Our results highlight the important roles of intermolecular interactions and coadaptation in the adaptive evolution of proteins both at the species and population levels.
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Affiliation(s)
- Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
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16
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Zelek WM. Measuring Total Classical Pathway and Activities of Individual Components of the Mouse Complement Pathway. Bio Protoc 2021; 11:e4175. [PMID: 34722822 DOI: 10.21769/bioprotoc.4175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/04/2021] [Accepted: 07/09/2021] [Indexed: 01/13/2023] Open
Abstract
The complement system is a central component of innate immunity, responsible for recognition and killing of bacteria by tagging invaders through opsonisation, thereby promoting phagocytosis, and by direct lysis. Complement activity is routinely measured using functional assays that utilise erythrocytes as targets. The classical pathway haemolytic assay (CH50) with antibody sensitised sheep erythrocytes as target is used worldwide in clinical and research laboratories to measure complement activity in human and rodent sera. While there are no particular limitations in the human assay, measuring complement in mouse serum is more difficult and usually requires large amounts of serum, which is challenging to collect in experiments. In particular, it is challenging to measure the activities of individual mouse complement proteins. To overcome this hurdle, we have developed protocols that employ human sera depleted of single complement proteins as the source of the other complement proteins and test mouse serum to restore the relevant component. This simple haemolytic assay is a useful tool for confirming natural or engineered complement deficiencies and complement dysregulation in mouse models.
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Affiliation(s)
- Wioleta M Zelek
- Division of Infection and Immunity and Dementia Research Institute, School of Medicine, Cardiff University, Wales, United Kingdom
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17
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Schweininger J, Scherer M, Rothemund F, Schilling EM, Wörz S, Stamminger T, Muller YA. Cytomegalovirus immediate-early 1 proteins form a structurally distinct protein class with adaptations determining cross-species barriers. PLoS Pathog 2021; 17:e1009863. [PMID: 34370791 PMCID: PMC8376021 DOI: 10.1371/journal.ppat.1009863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/19/2021] [Accepted: 08/03/2021] [Indexed: 01/12/2023] Open
Abstract
Restriction factors are potent antiviral proteins that constitute a first line of intracellular defense by blocking viral replication and spread. During co-evolution, however, viruses have developed antagonistic proteins to modulate or degrade the restriction factors of their host. To ensure the success of lytic replication, the herpesvirus human cytomegalovirus (HCMV) expresses the immediate-early protein IE1, which acts as an antagonist of antiviral, subnuclear structures termed PML nuclear bodies (PML-NBs). IE1 interacts directly with PML, the key protein of PML-NBs, through its core domain and disrupts the dot-like multiprotein complexes thereby abrogating the antiviral effects. Here we present the crystal structures of the human and rat cytomegalovirus core domain (IE1CORE). We found that IE1CORE domains, also including the previously characterized IE1CORE of rhesus CMV, form a distinct class of proteins that are characterized by a highly similar and unique tertiary fold and quaternary assembly. This contrasts to a marked amino acid sequence diversity suggesting that strong positive selection evolved a conserved fold, while immune selection pressure may have fostered sequence divergence of IE1. At the same time, we detected specific differences in the helix arrangements of primate versus rodent IE1CORE structures. Functional characterization revealed a conserved mechanism of PML-NB disruption, however, primate and rodent IE1 proteins were only effective in cells of the natural host species but not during cross-species infection. Remarkably, we observed that expression of HCMV IE1 allows rat cytomegalovirus replication in human cells. We conclude that cytomegaloviruses have evolved a distinct protein tertiary structure of IE1 to effectively bind and inactivate an important cellular restriction factor. Furthermore, our data show that the IE1 fold has been adapted to maximize the efficacy of PML targeting in a species-specific manner and support the concept that the PML-NBs-based intrinsic defense constitutes a barrier to cross-species transmission of HCMV. Cytomegaloviruses have evolved in very close association with their hosts resulting in a highly species-specific replication. Cell-intrinsic proteins, known as restriction factors, constitute important barriers for cross-species infection of viruses. All cytomegaloviruses characterized so far express an abundant immediate-early protein, termed IE1, that binds to the cellular restriction factor promyelocytic leukemia protein (PML) and antagonizes its repressive activity on viral gene expression. Here, we present the crystal structures of the PML-binding domains of rat and human cytomegalovirus IE1. Despite low amino-acid sequence identity both proteins share a highly similar and unique fold forming a distinct protein class. Functional characterization revealed a common mechanism of PML antagonization. However, we also detected that the respective IE1 proteins only interact with PML proteins of the natural host species. Interestingly, expression of HCMV IE1 allows rat cytomegalovirus infection in human cells. This indicates that the cellular restriction factor PML forms an important barrier for cross-species infection of cytomegaloviruses that might be overcome by adaptation of IE1 protein function. Our data suggest that the cytomegalovirus IE1 structure represents an evolutionary optimized protein fold targeting PML proteins via coiled-coil interactions.
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Affiliation(s)
- Johannes Schweininger
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Myriam Scherer
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | | | | | - Sonja Wörz
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Thomas Stamminger
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
- * E-mail: (TS); (YAM)
| | - Yves A. Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- * E-mail: (TS); (YAM)
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18
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Vrtílek M, Bolnick DI. Macroevolutionary foundations of a recently evolved innate immune defense. Evolution 2021; 75:2600-2612. [PMID: 34347301 PMCID: PMC8488947 DOI: 10.1111/evo.14316] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/06/2021] [Accepted: 07/20/2021] [Indexed: 01/13/2023]
Abstract
Antagonistic interactions between hosts and parasites may drive the evolution of novel host defenses, or new parasite strategies. Host immunity is therefore one of the fastest evolving traits. But where do the novel immune traits come from? Here, we test for phylogenetic conservation in a rapidly evolving immune trait—peritoneal fibrosis. Peritoneal fibrosis is a costly defense against a specialist tapeworm, Schistocephalus solidus (Cestoda), expressed in some freshwater populations of threespine stickleback fish (Gasterosteus aculeatus, Perciformes). We asked whether stickleback fibrosis is a derived species‐specific trait or an ancestral immune response that was widely distributed across ray‐finned fish (Actinopterygii) only to be employed by threespine stickleback against the specialist parasite. We combined literature review on peritoneal fibrosis with a comparative experiment using either parasite‐specific, or nonspecific, immune challenge in deliberately selected species across fish tree of life. We show that ray‐finned fish are broadly, but not universally, able to induce peritoneal fibrosis when challenged with a generic stimulus (Alum adjuvant). The experimental species were, however, largely indifferent to the tapeworm antigen homogenate. Peritoneal fibrosis, thus, appears to be a common and deeply conserved fish immune response that was co‐opted by stickleback to adapt to a new selective challenge.
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Affiliation(s)
- Milan Vrtílek
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, 603 65, Czech Republic
| | - Daniel I Bolnick
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269
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19
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Rudolf AM, Wu Q, Li L, Wang J, Huang Y, Togo J, Liechti C, Li M, Niu C, Nie Y, Wei F, Speakman JR. A single nucleotide mutation in the dual-oxidase 2 ( DUOX2) gene causes some of the panda's unique metabolic phenotypes. Natl Sci Rev 2021; 9:nwab125. [PMID: 35251670 PMCID: PMC8890364 DOI: 10.1093/nsr/nwab125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/11/2021] [Accepted: 06/10/2021] [Indexed: 12/25/2022] Open
Abstract
The giant panda (Ailuropoda melanoleuca) is an iconic bear native to China, famous for eating almost exclusively bamboo. This unusual dietary behavior for a carnivore is enabled by several key adaptations including low physical activity, reduced organ sizes and hypothyroidism leading to lowered energy expenditure. These adaptive phenotypes have been hypothesized to arise from a panda-unique single-nucleotide mutation in the dual-oxidase 2 (DUOX2) gene, involved in thyroid hormone synthesis. To test this hypothesis, we created genome-edited mice carrying the same point mutation as the panda and investigated its effect on metabolic phenotype. Homozygous mice were 27% smaller than heterozygous and wild-type ones, had 13% lower body mass-adjusted food intake, 55% decreased physical activity, lower mass of kidneys (11%) and brain (5%), lower serum thyroxine (T4: 36%), decreased absolute (12%) and mass-adjusted (5%) daily energy expenditure, and altered gut microbiota. Supplementation with T4 reversed the effects of the mutation. This work uses a state-of-the-art genome editing approach to demonstrate the link between a single-nucleotide mutation in a key endocrine-related gene and profound adaptive changes in the metabolic phenotype, with great importance in ecology and evolution.
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Affiliation(s)
- Agata M Rudolf
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Wu
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Li
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Huang
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jacques Togo
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Christopher Liechti
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | - Min Li
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chaoqun Niu
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonggang Nie
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuwen Wei
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Centre of Excellence for Animal Ecology and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - John R Speakman
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
- Centre of Excellence for Animal Ecology and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Shenzhen Key Laboratory of Metabolic Health, Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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20
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Rodrigue N, Latrille T, Lartillot N. A Bayesian Mutation-Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes. Mol Biol Evol 2021; 38:1199-1208. [PMID: 33045094 PMCID: PMC7947879 DOI: 10.1093/molbev/msaa265] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In recent years, codon substitution models based on the mutation–selection principle have been extended for the purpose of detecting signatures of adaptive evolution in protein-coding genes. However, the approaches used to date have either focused on detecting global signals of adaptive regimes—across the entire gene—or on contexts where experimentally derived, site-specific amino acid fitness profiles are available. Here, we present a Bayesian site-heterogeneous mutation–selection framework for site-specific detection of adaptive substitution regimes given a protein-coding DNA alignment. We offer implementations, briefly present simulation results, and apply the approach on a few real data sets. Our analyses suggest that the new approach shows greater sensitivity than traditional methods. However, more study is required to assess the impact of potential model violations on the method, and gain a greater empirical sense its behavior on a broader range of real data sets. We propose an outline of such a research program.
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Affiliation(s)
- Nicolas Rodrigue
- Department of Biology, Institute of Biochemistry, and School of Mathematics and Statistics, Carleton University, Ottawa, Canada
| | - Thibault Latrille
- Université de Lyon, Université Lyon 1, CNRS; UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, Villeurbanne, F-69622, France
| | - Nicolas Lartillot
- Université de Lyon, Université Lyon 1, CNRS; UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, Villeurbanne, F-69622, France
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21
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Jovanovic VM, Sarfert M, Reyna-Blanco CS, Indrischek H, Valdivia DI, Shelest E, Nowick K. Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution. Front Genet 2021; 12:662239. [PMID: 34079582 PMCID: PMC8166252 DOI: 10.3389/fgene.2021.662239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/19/2021] [Indexed: 01/09/2023] Open
Abstract
Gene regulatory factors (GRFs), such as transcription factors, co-factors and histone-modifying enzymes, play many important roles in modifying gene expression in biological processes. They have also been proposed to underlie speciation and adaptation. To investigate potential contributions of GRFs to primate evolution, we analyzed GRF genes in 27 publicly available primate genomes. Genes coding for zinc finger (ZNF) proteins, especially ZNFs with a Krüppel-associated box (KRAB) domain were the most abundant TFs in all genomes. Gene numbers per TF family differed between all species. To detect signs of positive selection in GRF genes we investigated more than 3,000 human GRFs with their more than 70,000 orthologs in 26 non-human primates. We implemented two independent tests for positive selection, the branch-site-model of the PAML suite and aBSREL of the HyPhy suite, focusing on the human and great ape branch. Our workflow included rigorous procedures to reduce the number of false positives: excluding distantly similar orthologs, manual corrections of alignments, and considering only genes and sites detected by both tests for positive selection. Furthermore, we verified the candidate sites for selection by investigating their variation within human and non-human great ape population data. In order to approximately assign a date to positively selected sites in the human lineage, we analyzed archaic human genomes. Our work revealed with high confidence five GRFs that have been positively selected on the human lineage and one GRF that has been positively selected on the great ape lineage. These GRFs are scattered on different chromosomes and have been previously linked to diverse functions. For some of them a role in speciation and/or adaptation can be proposed based on the expression pattern or association with human diseases, but it seems that they all contributed independently to human evolution. Four of the positively selected GRFs are KRAB-ZNF proteins, that induce changes in target genes co-expression and/or through arms race with transposable elements. Since each positively selected GRF contains several sites with evidence for positive selection, we suggest that these GRFs participated pleiotropically to phenotypic adaptations in humans.
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Affiliation(s)
- Vladimir M Jovanovic
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany.,Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Melanie Sarfert
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany
| | - Carlos S Reyna-Blanco
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Henrike Indrischek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Dulce I Valdivia
- Evolutionary Genomics Laboratory and Genome Topology and Regulation Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-Irapuato), Irapuato, Mexico
| | - Ekaterina Shelest
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, United Kingdom
| | - Katja Nowick
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany
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22
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Lin HY, Song G, Lei F, Li D, Qu Y. Avian corticosteroid-binding globulin: biological function and regulatory mechanisms in physiological stress responses. Front Zool 2021; 18:22. [PMID: 33926473 PMCID: PMC8086359 DOI: 10.1186/s12983-021-00409-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/19/2021] [Indexed: 12/04/2022] Open
Abstract
Corticosteroid-binding globulin (CBG) is a high-affinity plasma protein that binds glucocorticoids (GCs) and regulates their biological activities. The structural and functional properties of CBG are crucial to understanding the biological actions of GCs in mediating stress responses and the underlying mechanisms. In response to stress, avian CBGs modulate the free and bound fractions of plasma corticosterone (CORT, the main GC), enabling them to mediate the physiological and behavioral responses that are fundamental for balancing the trade-off of energetic investment in reproduction, immunity, growth, metabolism and survival, including adaptations to extreme high-elevation or high-latitude environments. Unlike other vertebrates, avian CBGs substitute for sex hormone-binding globulin (SHBG) in transporting androgens and regulating their bioavailability, since birds lack an Shbg gene. The three-dimensional structures of avian and mammalian CBGs are highly conserved, but the steroid-binding site topographies and their modes of binding steroids differ. Given that CBG serves as the primary transporter of both GCs and reproductive hormones in birds, we aim to review the biological properties of avian CBGs in the context of steroid hormone transportation, stress responses and adaptation to harsh environments, and to provide insight into evolutionary adaptations in CBG functions occurred to accommodate physiological and endocrine changes in birds compared with mammals.
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Affiliation(s)
- Hai-Yan Lin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Dongming Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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Wallis M. Do some viruses use growth hormone, prolactin and their receptors to facilitate entry into cells?: Episodic evolution of hormones and receptors suggests host-virus arms races; related placental lactogens may provide protective viral decoys. Bioessays 2021; 43:e2000268. [PMID: 33521987 DOI: 10.1002/bies.202000268] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/30/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022]
Abstract
The molecular evolution of pituitary growth hormone and prolactin in mammals shows two unusual features: episodes of markedly accelerated evolution and, in some species, complex families of related proteins expressed in placenta and resulting from multiple gene duplications. Explanations of these phenomena in terms of physiological adaptations seem unconvincing. Here, I propose an alternative explanation, namely that these evolutionary features reflect the use of the hormones (and their receptors) as viral receptors. Episodes of rapid evolution can then be explained as due to "arms races" in which changes in the hormone lead to reduced interaction with the virus, and subsequent changes in the virus counteract this. Placental paralogues of the hormones could provide decoys that bind viruses, and protect the foetus against infection. The hypothesis implies that the extensive changes introduced into growth hormone, prolactin and their receptors during the course of mammalian evolution reflect viral interactions, not endocrine adaptations.
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Affiliation(s)
- Michael Wallis
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, UK
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Chomkatekaew C, Boonklang P, Sangphukieo A, Chewapreecha C. An Evolutionary Arms Race Between Burkholderia pseudomallei and Host Immune System: What Do We Know? Front Microbiol 2021; 11:612568. [PMID: 33552023 PMCID: PMC7858667 DOI: 10.3389/fmicb.2020.612568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
A better understanding of co-evolution between pathogens and hosts holds promise for better prevention and control strategies. This review will explore the interactions between Burkholderia pseudomallei, an environmental and opportunistic pathogen, and the human host immune system. B. pseudomallei causes "Melioidosis," a rapidly fatal tropical infectious disease predicted to affect 165,000 cases annually worldwide, of which 89,000 are fatal. Genetic heterogeneities were reported in both B. pseudomallei and human host population, some of which may, at least in part, contribute to inter-individual differences in disease susceptibility. Here, we review (i) a multi-host-pathogen characteristic of the interaction; (ii) selection pressures acting on B. pseudomallei and human genomes with the former being driven by bacterial adaptation across ranges of ecological niches while the latter are driven by human encounter of broad ranges of pathogens; (iii) the mechanisms that generate genetic diversity in bacterial and host population particularly in sequences encoding proteins functioning in host-pathogen interaction; (iv) reported genetic and structural variations of proteins or molecules observed in B. pseudomallei-human host interactions and their implications in infection outcomes. Together, these predict bacterial and host evolutionary trajectory which continues to generate genetic diversity in bacterium and operates host immune selection at the molecular level.
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Affiliation(s)
| | | | - Apiwat Sangphukieo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Wellcome Sanger Institute, Hinxton, United Kingdom
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25
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Sackton TB. Studying Natural Selection in the Era of Ubiquitous Genomes. Trends Genet 2020; 36:792-803. [DOI: 10.1016/j.tig.2020.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 01/15/2023]
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