Studies on codon usage in Entamoeba histolytica
Codon usage bias of Entamoeba histolytica, a protozoan parasite, was investigated using the available DNA sequence data. Entamoeba histolytica having AT rich genome, is expected to have A and/or T at the third position of codons. Overall codon usage data analysis indicates that A and/or T ending cod...
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| Veröffentlicht in: | International journal for parasitology 2000-05, Vol.30 (6), p.715-722 |
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| container_title | International journal for parasitology |
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| creator | Ghosh, T.C. Gupta, S.K. Majumdar, S. |
| description | Codon usage bias of
Entamoeba histolytica, a protozoan parasite, was investigated using the available DNA sequence data.
Entamoeba histolytica having AT rich genome, is expected to have A and/or T at the third position of codons. Overall codon usage data analysis indicates that A and/or T ending codons are strongly biased in the coding region of this organism. However, multivariate statistical analysis suggests that there is a single major trend in codon usage variation among the genes. The genes which are supposed to be highly expressed are clustered at one end, while the majority of the putatively lowly expressed genes are clustered at the other end. The codon usage pattern is distinctly different in these two sets of genes. C ending codons are significantly higher in the putatively highly expressed genes suggesting that C ending codons are translationally optimal in this organism. In the putatively lowly expressed genes A and/or T ending codons are predominant, which suggests that compositional constraints are playing the major role in shaping codon usage variation among the lowly expressed genes. These results suggest that both mutational bias and translational selection are operational in the codon usage variation in this organism. |
| doi_str_mv | 10.1016/S0020-7519(00)00042-4 |
| format | Article |
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Entamoeba histolytica, a protozoan parasite, was investigated using the available DNA sequence data.
Entamoeba histolytica having AT rich genome, is expected to have A and/or T at the third position of codons. Overall codon usage data analysis indicates that A and/or T ending codons are strongly biased in the coding region of this organism. However, multivariate statistical analysis suggests that there is a single major trend in codon usage variation among the genes. The genes which are supposed to be highly expressed are clustered at one end, while the majority of the putatively lowly expressed genes are clustered at the other end. The codon usage pattern is distinctly different in these two sets of genes. C ending codons are significantly higher in the putatively highly expressed genes suggesting that C ending codons are translationally optimal in this organism. In the putatively lowly expressed genes A and/or T ending codons are predominant, which suggests that compositional constraints are playing the major role in shaping codon usage variation among the lowly expressed genes. These results suggest that both mutational bias and translational selection are operational in the codon usage variation in this organism.</description><identifier>ISSN: 0020-7519</identifier><identifier>EISSN: 1879-0135</identifier><identifier>DOI: 10.1016/S0020-7519(00)00042-4</identifier><identifier>PMID: 10856505</identifier><identifier>CODEN: IJPYBT</identifier><language>eng</language><publisher>Oxford: Elsevier Ltd</publisher><subject>Animals ; Biochemistry. Physiology. Immunology. Molecular biology ; Biological and medical sciences ; Codon ; Codon usage ; Compositional constraints ; Correspondence analysis ; DNA Mutational Analysis ; DNA, Protozoan - chemistry ; Effective number of codons ; Entamoeba histolytica ; Entamoeba histolytica - genetics ; Fundamental and applied biological sciences. Psychology ; Gene Library ; Genetic Variation ; Highly expressed genes ; Lowly expressed genes ; Molecular Sequence Data ; Multivariate statistical analysis ; Mutational bias ; Parasite ; Protozoa ; Structure-Activity Relationship ; Translational selection</subject><ispartof>International journal for parasitology, 2000-05, Vol.30 (6), p.715-722</ispartof><rights>2000 Australian Society for Parasitology Inc</rights><rights>2000 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c421t-3cbb4d81e494f49861c04d243a662f1286150802aaafdd508aa589939af01bb73</citedby><cites>FETCH-LOGICAL-c421t-3cbb4d81e494f49861c04d243a662f1286150802aaafdd508aa589939af01bb73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0020751900000424$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=1437491$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/10856505$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ghosh, T.C.</creatorcontrib><creatorcontrib>Gupta, S.K.</creatorcontrib><creatorcontrib>Majumdar, S.</creatorcontrib><title>Studies on codon usage in Entamoeba histolytica</title><title>International journal for parasitology</title><addtitle>Int J Parasitol</addtitle><description>Codon usage bias of
Entamoeba histolytica, a protozoan parasite, was investigated using the available DNA sequence data.
Entamoeba histolytica having AT rich genome, is expected to have A and/or T at the third position of codons. Overall codon usage data analysis indicates that A and/or T ending codons are strongly biased in the coding region of this organism. However, multivariate statistical analysis suggests that there is a single major trend in codon usage variation among the genes. The genes which are supposed to be highly expressed are clustered at one end, while the majority of the putatively lowly expressed genes are clustered at the other end. The codon usage pattern is distinctly different in these two sets of genes. C ending codons are significantly higher in the putatively highly expressed genes suggesting that C ending codons are translationally optimal in this organism. In the putatively lowly expressed genes A and/or T ending codons are predominant, which suggests that compositional constraints are playing the major role in shaping codon usage variation among the lowly expressed genes. These results suggest that both mutational bias and translational selection are operational in the codon usage variation in this organism.</description><subject>Animals</subject><subject>Biochemistry. Physiology. Immunology. Molecular biology</subject><subject>Biological and medical sciences</subject><subject>Codon</subject><subject>Codon usage</subject><subject>Compositional constraints</subject><subject>Correspondence analysis</subject><subject>DNA Mutational Analysis</subject><subject>DNA, Protozoan - chemistry</subject><subject>Effective number of codons</subject><subject>Entamoeba histolytica</subject><subject>Entamoeba histolytica - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Library</subject><subject>Genetic Variation</subject><subject>Highly expressed genes</subject><subject>Lowly expressed genes</subject><subject>Molecular Sequence Data</subject><subject>Multivariate statistical analysis</subject><subject>Mutational bias</subject><subject>Parasite</subject><subject>Protozoa</subject><subject>Structure-Activity Relationship</subject><subject>Translational selection</subject><issn>0020-7519</issn><issn>1879-0135</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2000</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkEtLw0AQgBdRbK3-BCUHET3EziS7SfYkUuoDCh6q52Wyu9GVNKnZROi_N32g3nqZGYZvHnyMnSPcImAyngNEEKYC5TXADQDwKOQHbIhZKkPAWByy4S8yYCfefwKgiDk_ZgOETCQCxJCN521nnPVBXQW6Nn3sPL3bwFXBtGppUducgg_n27pctU7TKTsqqPT2bJdH7O1h-jp5Cmcvj8-T-1moeYRtGOs85yZDyyUvuMwS1MBNxGNKkqjAqG8IyCAiosKYviQSmZSxpAIwz9N4xK62e5dN_dVZ36qF89qWJVW27rxKEbNEimgviKngQiaiB8UW1E3tfWMLtWzcgpqVQlBrpWqjVK19KQC1Uap4P3exO9DlC2v-TW0d9sDlDiCvqSwaqrTzfxyPUy6xx-62mO21fTvbKK-drbQ1rrG6VaZ2ez75AV1HkBY</recordid><startdate>20000501</startdate><enddate>20000501</enddate><creator>Ghosh, T.C.</creator><creator>Gupta, S.K.</creator><creator>Majumdar, S.</creator><general>Elsevier Ltd</general><general>Elsevier Science</general><scope>IQODW</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>7TM</scope><scope>M7N</scope><scope>7X8</scope></search><sort><creationdate>20000501</creationdate><title>Studies on codon usage in Entamoeba histolytica</title><author>Ghosh, T.C. ; Gupta, S.K. ; Majumdar, S.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c421t-3cbb4d81e494f49861c04d243a662f1286150802aaafdd508aa589939af01bb73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2000</creationdate><topic>Animals</topic><topic>Biochemistry. Physiology. Immunology. Molecular biology</topic><topic>Biological and medical sciences</topic><topic>Codon</topic><topic>Codon usage</topic><topic>Compositional constraints</topic><topic>Correspondence analysis</topic><topic>DNA Mutational Analysis</topic><topic>DNA, Protozoan - chemistry</topic><topic>Effective number of codons</topic><topic>Entamoeba histolytica</topic><topic>Entamoeba histolytica - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Library</topic><topic>Genetic Variation</topic><topic>Highly expressed genes</topic><topic>Lowly expressed genes</topic><topic>Molecular Sequence Data</topic><topic>Multivariate statistical analysis</topic><topic>Mutational bias</topic><topic>Parasite</topic><topic>Protozoa</topic><topic>Structure-Activity Relationship</topic><topic>Translational selection</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ghosh, T.C.</creatorcontrib><creatorcontrib>Gupta, S.K.</creatorcontrib><creatorcontrib>Majumdar, S.</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>MEDLINE - Academic</collection><jtitle>International journal for parasitology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ghosh, T.C.</au><au>Gupta, S.K.</au><au>Majumdar, S.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Studies on codon usage in Entamoeba histolytica</atitle><jtitle>International journal for parasitology</jtitle><addtitle>Int J Parasitol</addtitle><date>2000-05-01</date><risdate>2000</risdate><volume>30</volume><issue>6</issue><spage>715</spage><epage>722</epage><pages>715-722</pages><issn>0020-7519</issn><eissn>1879-0135</eissn><coden>IJPYBT</coden><abstract>Codon usage bias of
Entamoeba histolytica, a protozoan parasite, was investigated using the available DNA sequence data.
Entamoeba histolytica having AT rich genome, is expected to have A and/or T at the third position of codons. Overall codon usage data analysis indicates that A and/or T ending codons are strongly biased in the coding region of this organism. However, multivariate statistical analysis suggests that there is a single major trend in codon usage variation among the genes. The genes which are supposed to be highly expressed are clustered at one end, while the majority of the putatively lowly expressed genes are clustered at the other end. The codon usage pattern is distinctly different in these two sets of genes. C ending codons are significantly higher in the putatively highly expressed genes suggesting that C ending codons are translationally optimal in this organism. In the putatively lowly expressed genes A and/or T ending codons are predominant, which suggests that compositional constraints are playing the major role in shaping codon usage variation among the lowly expressed genes. These results suggest that both mutational bias and translational selection are operational in the codon usage variation in this organism.</abstract><cop>Oxford</cop><pub>Elsevier Ltd</pub><pmid>10856505</pmid><doi>10.1016/S0020-7519(00)00042-4</doi><tpages>8</tpages></addata></record> |
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| subjects | Animals Biochemistry. Physiology. Immunology. Molecular biology Biological and medical sciences Codon Codon usage Compositional constraints Correspondence analysis DNA Mutational Analysis DNA, Protozoan - chemistry Effective number of codons Entamoeba histolytica Entamoeba histolytica - genetics Fundamental and applied biological sciences. Psychology Gene Library Genetic Variation Highly expressed genes Lowly expressed genes Molecular Sequence Data Multivariate statistical analysis Mutational bias Parasite Protozoa Structure-Activity Relationship Translational selection |
| title | Studies on codon usage in Entamoeba histolytica |
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