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Sloan DB, Broz AK, Kuster SA, Muthye V, Peñafiel-Ayala A, Marron JR, Lavrov DV, Brieba LG. Expansion of the MutS Gene Family in Plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603841. [PMID: 39071318 PMCID: PMC11275761 DOI: 10.1101/2024.07.17.603841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1" is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6/MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Shady A Kuster
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Viraj Muthye
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Alejandro Peñafiel-Ayala
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, México
| | - Jennifer R Marron
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Luis G Brieba
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, México
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Sengupta S, Azad RK. Reconstructing horizontal gene flow network to understand prokaryotic evolution. Open Biol 2022; 12:220169. [PMID: 36446404 PMCID: PMC9708380 DOI: 10.1098/rsob.220169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major source of phenotypic innovation and a mechanism of niche adaptation in prokaryotes. Quantification of HGT is critical to decipher its myriad roles in microbial evolution and adaptation. Advances in genome sequencing and bioinformatics have augmented our ability to understand the microbial world, particularly the direct or indirect influence of HGT on diverse life forms. Methods for detecting HGT can be classified into phylogenetic-based and parametric or composition-based approaches. Here, we exploited the complementary strengths of both the approaches to construct a high confidence horizontal gene flow network. Our network is unique in its ability to detect the transfer of native genes of a genome to genomes from other taxa, thus establishing donor and recipient organisms (taxa), rather than through a post hoc analysis as is the practice with several other approaches. The scale-free horizontal gene flow network presented here provides new insights into modes of transfer for the exchange of genetic information and also illuminates differential gene flow across phyla.
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Affiliation(s)
- Soham Sengupta
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA
| | - Rajeev K. Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA,Department of Mathematics, University of North Texas, Denton, TX 76203, USA
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Sengupta S, Azad RK. Reconstructing horizontal gene flow network to understand prokaryotic evolution. Open Biol 2022. [PMID: 36446404 DOI: 10.6084/m9.figshare.c.6307519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major source of phenotypic innovation and a mechanism of niche adaptation in prokaryotes. Quantification of HGT is critical to decipher its myriad roles in microbial evolution and adaptation. Advances in genome sequencing and bioinformatics have augmented our ability to understand the microbial world, particularly the direct or indirect influence of HGT on diverse life forms. Methods for detecting HGT can be classified into phylogenetic-based and parametric or composition-based approaches. Here, we exploited the complementary strengths of both the approaches to construct a high confidence horizontal gene flow network. Our network is unique in its ability to detect the transfer of native genes of a genome to genomes from other taxa, thus establishing donor and recipient organisms (taxa), rather than through a post hoc analysis as is the practice with several other approaches. The scale-free horizontal gene flow network presented here provides new insights into modes of transfer for the exchange of genetic information and also illuminates differential gene flow across phyla.
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Affiliation(s)
- Soham Sengupta
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA.,Department of Mathematics, University of North Texas, Denton, TX 76203, USA
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Pandey RS, Azad RK. A Protocol for Horizontally Acquired Metabolic Gene Detection in Algae. Methods Mol Biol 2022; 2396:61-69. [PMID: 34786676 DOI: 10.1007/978-1-0716-1822-6_6] [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: 06/13/2023]
Abstract
Horizontal gene transfer (HGT) or lateral gene transfer (LGT), the exchange of genetic materials among organisms by means of other than parent-to-offspring (vertical) inheritance, plays a major role in prokaryotic genome evolution, facilitating adaptation of prokaryotes to changes in the environment. Phylogenetic methods have been frequently invoked to catalog horizontally acquired genes; however, these methods are often constrained by the paucity of sequenced genomes of close relatives (and even distant relatives) for a robust analysis and reliable inference. In this chapter, we describe a HGT quantification protocol that exploits the complementary strengths of the integrative segmentation and clustering method and the comparative genomics approach to identify foreign genes. Users can use this pipeline in combination with phylogenetic tree reconstruction to identify foreign genes that are supported by multiple lines of evidence, that is, atypical composition, atypical distribution in close relatives, and aberrant phylogenetic pattern.
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Affiliation(s)
- Ravi S Pandey
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.
- Department of Mathematics, University of North Texas, Denton, TX, USA.
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Biomolecules from extremophile microalgae: From genetics to bioprocessing of a new candidate for large-scale production. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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