Homepeptide Repeats: Implications for Protein Structure, Function and Evolution
Analysis of protein sequences from Mycobacterium tuberculosis H37Rv (Mtb H37Rv) was performed to identify homopeptide repeat-containing proteins (HRCPs). Functional annotation of the HRCPs showed that they are preferentially involved in cellular metabolism. Furthermore, these homopeptide repeats mig...
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creator | Uthayakumar, Muthukumarasamy Benazir, Bowdadu Patra, Sanjeev Vaishnavi, Marthandan Kirti Gurusaran, Manickam Sureka, Kanagarajan Jeyakanthan, Jeyaraman Sekar, Kanagaraj |
description | Analysis of protein sequences from Mycobacterium tuberculosis H37Rv (Mtb H37Rv) was performed to identify homopeptide repeat-containing proteins (HRCPs). Functional annotation of the HRCPs showed that they are preferentially involved in cellular metabolism. Furthermore, these homopeptide repeats might play some specific roles in protein–protein interaction. Repeat length differences among Bacteria, Archaea and Eukaryotes were calculated in order to identify the conservation of the repeats in these divergent kingdoms. From the results, it was evident that these repeats have a higher degree of conservation in Bacteria and Archaea than in Eukaryotes. In addition, there seems to be a direct correlation between the repeat length difference and the degree of divergence between the species. Our study supports the hypothesis that the presence of homopeptide repeats influences the rate of evolution of the protein sequences in which they are embedded. Thus, homopeptide repeat may have structural, functional and evolutionary implications on proteins. |
doi_str_mv | 10.1016/j.gpb.2012.04.001 |
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Functional annotation of the HRCPs showed that they are preferentially involved in cellular metabolism. Furthermore, these homopeptide repeats might play some specific roles in protein–protein interaction. Repeat length differences among Bacteria, Archaea and Eukaryotes were calculated in order to identify the conservation of the repeats in these divergent kingdoms. From the results, it was evident that these repeats have a higher degree of conservation in Bacteria and Archaea than in Eukaryotes. In addition, there seems to be a direct correlation between the repeat length difference and the degree of divergence between the species. Our study supports the hypothesis that the presence of homopeptide repeats influences the rate of evolution of the protein sequences in which they are embedded. Thus, homopeptide repeat may have structural, functional and evolutionary implications on proteins.</description><identifier>ISSN: 1672-0229</identifier><identifier>EISSN: 2210-3244</identifier><identifier>DOI: 10.1016/j.gpb.2012.04.001</identifier><identifier>PMID: 23084777</identifier><language>eng</language><publisher>China: Elsevier Ltd</publisher><subject>Amino Acid Sequence ; amino acid sequences ; Amino Acids - analysis ; Archaea ; Archaeal Proteins - chemistry ; bacteria ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Bioinformatics ; Biological Evolution ; Disordered regions ; Escherichia coli - chemistry ; eukaryotic cells ; evolution ; Evolution, Molecular ; Homopeptide repeats ; Humans ; Metabolism ; Models, Molecular ; Mycobacterium tuberculosis ; Mycobacterium tuberculosis - chemistry ; Mycobacterium tuberculosis - genetics ; Mycobacterium tuberculosis - metabolism ; Original Research ; Peptides - chemistry ; Peptides - genetics ; Protein Conformation ; Protein domains ; Protein structure ; Protein Structure, Tertiary ; proteins ; Proteins - chemistry ; proteomics ; Rate of evolution ; Repetitive Sequences, Amino Acid ; Replication slippage ; Sequence Analysis, Protein ; Structure-function relationships ; Sulfolobus acidocaldarius - chemistry ; 古细菌 ; 真核细胞 ; 结核分枝杆菌 ; 结核杆菌 ; 蛋白质序列 ; 蛋白质相互作用 ; 蛋白质结构 ; 进化</subject><ispartof>Genomics, proteomics & bioinformatics, 2012-08, Vol.10 (4), p.217-225</ispartof><rights>2012</rights><rights>Copyright © 2012. Published by Elsevier Ltd.</rights><rights>Copyright © Wanfang Data Co. Ltd. All Rights Reserved.</rights><rights>2012 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Published by Elsevier Ltd and Science Press. All rights reserved. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4916-ef85530980ffb2ecf15cf2e86788580bf198a6a402675bfbabae8d29ade0be083</citedby><cites>FETCH-LOGICAL-c4916-ef85530980ffb2ecf15cf2e86788580bf198a6a402675bfbabae8d29ade0be083</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://image.cqvip.com/vip1000/qk/86775X/86775X.jpg</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054710/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.gpb.2012.04.001$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,3550,27924,27925,45995,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23084777$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Uthayakumar, Muthukumarasamy</creatorcontrib><creatorcontrib>Benazir, Bowdadu</creatorcontrib><creatorcontrib>Patra, Sanjeev</creatorcontrib><creatorcontrib>Vaishnavi, Marthandan Kirti</creatorcontrib><creatorcontrib>Gurusaran, Manickam</creatorcontrib><creatorcontrib>Sureka, Kanagarajan</creatorcontrib><creatorcontrib>Jeyakanthan, Jeyaraman</creatorcontrib><creatorcontrib>Sekar, Kanagaraj</creatorcontrib><title>Homepeptide Repeats: Implications for Protein Structure, Function and Evolution</title><title>Genomics, proteomics & bioinformatics</title><addtitle>Genomics Proteomics & Bioinformatics</addtitle><description>Analysis of protein sequences from Mycobacterium tuberculosis H37Rv (Mtb H37Rv) was performed to identify homopeptide repeat-containing proteins (HRCPs). Functional annotation of the HRCPs showed that they are preferentially involved in cellular metabolism. Furthermore, these homopeptide repeats might play some specific roles in protein–protein interaction. Repeat length differences among Bacteria, Archaea and Eukaryotes were calculated in order to identify the conservation of the repeats in these divergent kingdoms. From the results, it was evident that these repeats have a higher degree of conservation in Bacteria and Archaea than in Eukaryotes. In addition, there seems to be a direct correlation between the repeat length difference and the degree of divergence between the species. Our study supports the hypothesis that the presence of homopeptide repeats influences the rate of evolution of the protein sequences in which they are embedded. Thus, homopeptide repeat may have structural, functional and evolutionary implications on proteins.</description><subject>Amino Acid Sequence</subject><subject>amino acid sequences</subject><subject>Amino Acids - analysis</subject><subject>Archaea</subject><subject>Archaeal Proteins - chemistry</subject><subject>bacteria</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Bioinformatics</subject><subject>Biological Evolution</subject><subject>Disordered regions</subject><subject>Escherichia coli - chemistry</subject><subject>eukaryotic cells</subject><subject>evolution</subject><subject>Evolution, Molecular</subject><subject>Homopeptide repeats</subject><subject>Humans</subject><subject>Metabolism</subject><subject>Models, Molecular</subject><subject>Mycobacterium tuberculosis</subject><subject>Mycobacterium tuberculosis - chemistry</subject><subject>Mycobacterium tuberculosis - genetics</subject><subject>Mycobacterium tuberculosis - metabolism</subject><subject>Original Research</subject><subject>Peptides - chemistry</subject><subject>Peptides - genetics</subject><subject>Protein Conformation</subject><subject>Protein domains</subject><subject>Protein structure</subject><subject>Protein Structure, Tertiary</subject><subject>proteins</subject><subject>Proteins - chemistry</subject><subject>proteomics</subject><subject>Rate of evolution</subject><subject>Repetitive Sequences, Amino Acid</subject><subject>Replication slippage</subject><subject>Sequence Analysis, Protein</subject><subject>Structure-function relationships</subject><subject>Sulfolobus acidocaldarius - chemistry</subject><subject>古细菌</subject><subject>真核细胞</subject><subject>结核分枝杆菌</subject><subject>结核杆菌</subject><subject>蛋白质序列</subject><subject>蛋白质相互作用</subject><subject>蛋白质结构</subject><subject>进化</subject><issn>1672-0229</issn><issn>2210-3244</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9Uc1u1DAYjBCIbgsPwAXCjQMbPjtO4lUlJFS1tFIlfkrPluN8Tr3K2qmdbHf3UfosvBOvgFe7LXDhZFvfzHzjmSR5RSAjQMoP86zt64wCoRmwDIA8SSaUEpjmlLGnyYSUFZ0CpbOD5DCEOQArGCPPkwOaA2dVVU2Sb-dugT32g2kw_R5vcgi_ft6nF4u-M0oOxtmQaufTr94NaGx6NfhRDaPH9-nZaNUWkErbpKdL143b14vkmZZdwJf78yi5Pjv9cXI-vfzy-eLk0-VUsRkpp6h5UeQw46B1TVFpUihNkZcV5wWHWpMZl6VkQMuqqHUta4m8oTPZINQIPD9KPu50-7FeYKPQDl52ovdmIf1aOGnEvxNrbkTrlqKAglUEogDZCdxJq6VtxdyN3kbLYr7eNPVmsw53q9WqFrhNGBhAGTnv9ku9ux0xDGJhgsKukxbdGAShFa0I52XxR155F4JH_WiNgNjWJ-Yi1ie24gKYiPVFzuu___TIeOgrAt7sAFo6IVtvgri-igoFxHLzuDoijncIjNkvDXoRlEGrsDEe1SAaZ_5r4O3e9I2z7a2JqTx4YHlFKec0_w20Q8Lo</recordid><startdate>201208</startdate><enddate>201208</enddate><creator>Uthayakumar, Muthukumarasamy</creator><creator>Benazir, Bowdadu</creator><creator>Patra, Sanjeev</creator><creator>Vaishnavi, Marthandan Kirti</creator><creator>Gurusaran, Manickam</creator><creator>Sureka, Kanagarajan</creator><creator>Jeyakanthan, Jeyaraman</creator><creator>Sekar, Kanagaraj</creator><general>Elsevier Ltd</general><general>Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560012, India%Department of Bioinformatics, Alagappa University, Karaikudi 630003, India</general><general>Elsevier</general><scope>2RA</scope><scope>92L</scope><scope>CQIGP</scope><scope>W94</scope><scope>WU4</scope><scope>~WA</scope><scope>6I.</scope><scope>AAFTH</scope><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>2B.</scope><scope>4A8</scope><scope>92I</scope><scope>93N</scope><scope>PSX</scope><scope>TCJ</scope><scope>5PM</scope></search><sort><creationdate>201208</creationdate><title>Homepeptide Repeats: Implications for Protein Structure, Function and Evolution</title><author>Uthayakumar, Muthukumarasamy ; 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Functional annotation of the HRCPs showed that they are preferentially involved in cellular metabolism. Furthermore, these homopeptide repeats might play some specific roles in protein–protein interaction. Repeat length differences among Bacteria, Archaea and Eukaryotes were calculated in order to identify the conservation of the repeats in these divergent kingdoms. From the results, it was evident that these repeats have a higher degree of conservation in Bacteria and Archaea than in Eukaryotes. In addition, there seems to be a direct correlation between the repeat length difference and the degree of divergence between the species. Our study supports the hypothesis that the presence of homopeptide repeats influences the rate of evolution of the protein sequences in which they are embedded. 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subjects | Amino Acid Sequence amino acid sequences Amino Acids - analysis Archaea Archaeal Proteins - chemistry bacteria Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - metabolism Bioinformatics Biological Evolution Disordered regions Escherichia coli - chemistry eukaryotic cells evolution Evolution, Molecular Homopeptide repeats Humans Metabolism Models, Molecular Mycobacterium tuberculosis Mycobacterium tuberculosis - chemistry Mycobacterium tuberculosis - genetics Mycobacterium tuberculosis - metabolism Original Research Peptides - chemistry Peptides - genetics Protein Conformation Protein domains Protein structure Protein Structure, Tertiary proteins Proteins - chemistry proteomics Rate of evolution Repetitive Sequences, Amino Acid Replication slippage Sequence Analysis, Protein Structure-function relationships Sulfolobus acidocaldarius - chemistry 古细菌 真核细胞 结核分枝杆菌 结核杆菌 蛋白质序列 蛋白质相互作用 蛋白质结构 进化 |
title | Homepeptide Repeats: Implications for Protein Structure, Function and Evolution |
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