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Evolution of rhodopsin ion pumps in haloarchaea
BACKGROUND: The type 1 (microbial) rhodopsins are a diverse group of photochemically reactive proteins that display a broad yet patchy distribution among the three domains of life. Recent work indicates that this pattern is likely the result of lateral gene transfer (LGT) of rhodopsin genes between...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885257/ https://www.ncbi.nlm.nih.gov/pubmed/17511874 http://dx.doi.org/10.1186/1471-2148-7-79 |
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author | Sharma, Adrian K Walsh, David A Bapteste, Eric Rodriguez-Valera, Francisco Ford Doolittle, W Papke, R Thane |
author_facet | Sharma, Adrian K Walsh, David A Bapteste, Eric Rodriguez-Valera, Francisco Ford Doolittle, W Papke, R Thane |
author_sort | Sharma, Adrian K |
collection | PubMed |
description | BACKGROUND: The type 1 (microbial) rhodopsins are a diverse group of photochemically reactive proteins that display a broad yet patchy distribution among the three domains of life. Recent work indicates that this pattern is likely the result of lateral gene transfer (LGT) of rhodopsin genes between major lineages, and even across domain boundaries. Within the lineage in which the microbial rhodopsins were initially discovered, the haloarchaea, a similar patchy distribution is observed. In this initial study, we assess the roles of LGT and gene loss in the evolution of haloarchaeal rhodopsin ion pump genes, using phylogenetics and comparative genomics approaches. RESULTS: Mapping presence/absence of rhodopsins onto the phylogeny of the RNA polymerase B' subunit (RpoB') of the haloarchaea supports previous notions that rhodopsins are patchily distributed. The phylogeny for the bacteriorhodopsin (BR) protein revealed two discrepancies in comparison to the RpoB' marker, while the halorhodopsin (HR) tree showed incongruence to both markers. Comparative analyses of bacteriorhodopsin-linked regions of five haloarchaeal genomes supported relationships observed in the BR tree, and also identified two open reading frames (ORFs) that were more frequently linked to the bacteriorhodopsin gene than those genes previously shown to be important to the function and expression of BR. CONCLUSION: The evidence presented here reveals a complex evolutionary history for the haloarchaeal rhodopsins, with both LGT and gene loss contributing to the patchy distribution of rhodopsins within this group. Similarities between the BR and RpoB' phylogenies provide supportive evidence for the presence of bacteriorhodopsin in the last common ancestor of haloarchaea. Furthermore, two loci that we have designated bacterio-opsin associated chaperone (bac) and bacterio-opsin associated protein (bap) are inferred to have important roles in BR biogenesis based on frequent linkage and co-transfer with bacteriorhodopsin genes. |
format | Text |
id | pubmed-1885257 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-18852572007-05-31 Evolution of rhodopsin ion pumps in haloarchaea Sharma, Adrian K Walsh, David A Bapteste, Eric Rodriguez-Valera, Francisco Ford Doolittle, W Papke, R Thane BMC Evol Biol Research Article BACKGROUND: The type 1 (microbial) rhodopsins are a diverse group of photochemically reactive proteins that display a broad yet patchy distribution among the three domains of life. Recent work indicates that this pattern is likely the result of lateral gene transfer (LGT) of rhodopsin genes between major lineages, and even across domain boundaries. Within the lineage in which the microbial rhodopsins were initially discovered, the haloarchaea, a similar patchy distribution is observed. In this initial study, we assess the roles of LGT and gene loss in the evolution of haloarchaeal rhodopsin ion pump genes, using phylogenetics and comparative genomics approaches. RESULTS: Mapping presence/absence of rhodopsins onto the phylogeny of the RNA polymerase B' subunit (RpoB') of the haloarchaea supports previous notions that rhodopsins are patchily distributed. The phylogeny for the bacteriorhodopsin (BR) protein revealed two discrepancies in comparison to the RpoB' marker, while the halorhodopsin (HR) tree showed incongruence to both markers. Comparative analyses of bacteriorhodopsin-linked regions of five haloarchaeal genomes supported relationships observed in the BR tree, and also identified two open reading frames (ORFs) that were more frequently linked to the bacteriorhodopsin gene than those genes previously shown to be important to the function and expression of BR. CONCLUSION: The evidence presented here reveals a complex evolutionary history for the haloarchaeal rhodopsins, with both LGT and gene loss contributing to the patchy distribution of rhodopsins within this group. Similarities between the BR and RpoB' phylogenies provide supportive evidence for the presence of bacteriorhodopsin in the last common ancestor of haloarchaea. Furthermore, two loci that we have designated bacterio-opsin associated chaperone (bac) and bacterio-opsin associated protein (bap) are inferred to have important roles in BR biogenesis based on frequent linkage and co-transfer with bacteriorhodopsin genes. BioMed Central 2007-05-18 /pmc/articles/PMC1885257/ /pubmed/17511874 http://dx.doi.org/10.1186/1471-2148-7-79 Text en Copyright © 2007 Sharma et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Sharma, Adrian K Walsh, David A Bapteste, Eric Rodriguez-Valera, Francisco Ford Doolittle, W Papke, R Thane Evolution of rhodopsin ion pumps in haloarchaea |
title | Evolution of rhodopsin ion pumps in haloarchaea |
title_full | Evolution of rhodopsin ion pumps in haloarchaea |
title_fullStr | Evolution of rhodopsin ion pumps in haloarchaea |
title_full_unstemmed | Evolution of rhodopsin ion pumps in haloarchaea |
title_short | Evolution of rhodopsin ion pumps in haloarchaea |
title_sort | evolution of rhodopsin ion pumps in haloarchaea |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885257/ https://www.ncbi.nlm.nih.gov/pubmed/17511874 http://dx.doi.org/10.1186/1471-2148-7-79 |
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