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Obligate Insect Endosymbionts Exhibit Increased Ortholog Length Variation and Loss of Large Accessory Proteins Concurrent with Genome Shrinkage
Extreme genome reduction has been observed in obligate intracellular insect mutualists and is an assumed consequence of fixed, long-term host isolation. Rapid accumulation of mutations and pseudogenization of genes no longer vital for an intracellular lifestyle, followed by deletion of many genes, a...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4007534/ https://www.ncbi.nlm.nih.gov/pubmed/24671745 http://dx.doi.org/10.1093/gbe/evu055 |
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author | Kenyon, Laura J. Sabree, Zakee L. |
author_facet | Kenyon, Laura J. Sabree, Zakee L. |
author_sort | Kenyon, Laura J. |
collection | PubMed |
description | Extreme genome reduction has been observed in obligate intracellular insect mutualists and is an assumed consequence of fixed, long-term host isolation. Rapid accumulation of mutations and pseudogenization of genes no longer vital for an intracellular lifestyle, followed by deletion of many genes, are factors that lead to genome reduction. Size reductions in individual genes due to small-scale deletions have also been implicated in contributing to overall genome shrinkage. Conserved protein functional domains are expected to exhibit low tolerance for mutations and therefore remain relatively unchanged throughout protein length reduction while nondomain regions, presumably under less selective pressures, would shorten. This hypothesis was tested using orthologous protein sets from the Flavobacteriaceae (phylum: Bacteroidetes) and Enterobacteriaceae (subphylum: Gammaproteobacteria) families, each of which includes some of the smallest known genomes. Upon examination of protein, functional domain, and nondomain region lengths, we found that proteins were not uniformly shrinking with genome reduction, but instead increased length variability and variability was observed in both the functional domain and nondomain regions. Additionally, as complete gene loss also contributes to overall genome shrinkage, we found that the largest proteins in the proteomes of nonhost-restricted bacteroidetial and gammaproteobacterial species often were inferred to be involved in secondary metabolic processes, extracellular sensing, or of unknown function. These proteins were absent in the proteomes of obligate insect endosymbionts. Therefore, loss of genes encoding large proteins not required for host-restricted lifestyles in obligate endosymbiont proteomes likely contributes to extreme genome reduction to a greater degree than gene shrinkage. |
format | Online Article Text |
id | pubmed-4007534 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-40075342014-05-02 Obligate Insect Endosymbionts Exhibit Increased Ortholog Length Variation and Loss of Large Accessory Proteins Concurrent with Genome Shrinkage Kenyon, Laura J. Sabree, Zakee L. Genome Biol Evol Research Article Extreme genome reduction has been observed in obligate intracellular insect mutualists and is an assumed consequence of fixed, long-term host isolation. Rapid accumulation of mutations and pseudogenization of genes no longer vital for an intracellular lifestyle, followed by deletion of many genes, are factors that lead to genome reduction. Size reductions in individual genes due to small-scale deletions have also been implicated in contributing to overall genome shrinkage. Conserved protein functional domains are expected to exhibit low tolerance for mutations and therefore remain relatively unchanged throughout protein length reduction while nondomain regions, presumably under less selective pressures, would shorten. This hypothesis was tested using orthologous protein sets from the Flavobacteriaceae (phylum: Bacteroidetes) and Enterobacteriaceae (subphylum: Gammaproteobacteria) families, each of which includes some of the smallest known genomes. Upon examination of protein, functional domain, and nondomain region lengths, we found that proteins were not uniformly shrinking with genome reduction, but instead increased length variability and variability was observed in both the functional domain and nondomain regions. Additionally, as complete gene loss also contributes to overall genome shrinkage, we found that the largest proteins in the proteomes of nonhost-restricted bacteroidetial and gammaproteobacterial species often were inferred to be involved in secondary metabolic processes, extracellular sensing, or of unknown function. These proteins were absent in the proteomes of obligate insect endosymbionts. Therefore, loss of genes encoding large proteins not required for host-restricted lifestyles in obligate endosymbiont proteomes likely contributes to extreme genome reduction to a greater degree than gene shrinkage. Oxford University Press 2014-03-26 /pmc/articles/PMC4007534/ /pubmed/24671745 http://dx.doi.org/10.1093/gbe/evu055 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Kenyon, Laura J. Sabree, Zakee L. Obligate Insect Endosymbionts Exhibit Increased Ortholog Length Variation and Loss of Large Accessory Proteins Concurrent with Genome Shrinkage |
title | Obligate Insect Endosymbionts Exhibit Increased Ortholog Length Variation and Loss of Large Accessory Proteins Concurrent with Genome Shrinkage |
title_full | Obligate Insect Endosymbionts Exhibit Increased Ortholog Length Variation and Loss of Large Accessory Proteins Concurrent with Genome Shrinkage |
title_fullStr | Obligate Insect Endosymbionts Exhibit Increased Ortholog Length Variation and Loss of Large Accessory Proteins Concurrent with Genome Shrinkage |
title_full_unstemmed | Obligate Insect Endosymbionts Exhibit Increased Ortholog Length Variation and Loss of Large Accessory Proteins Concurrent with Genome Shrinkage |
title_short | Obligate Insect Endosymbionts Exhibit Increased Ortholog Length Variation and Loss of Large Accessory Proteins Concurrent with Genome Shrinkage |
title_sort | obligate insect endosymbionts exhibit increased ortholog length variation and loss of large accessory proteins concurrent with genome shrinkage |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4007534/ https://www.ncbi.nlm.nih.gov/pubmed/24671745 http://dx.doi.org/10.1093/gbe/evu055 |
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