Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?

The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies o...
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Autor*in:	Dominique Belin [verfasserIn] Pere Puigbò [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	gene genome codon usage genome hypothesis stop codons bacterial genomes

Übergeordnetes Werk:	In: Life - MDPI AG, 2012, 12(2022), 3, p 431
Übergeordnetes Werk:	volume:12 ; year:2022 ; number:3, p 431

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/life12030431

Katalog-ID:	DOAJ029877067

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allfields	10.3390/life12030431 doi (DE-627)DOAJ029877067 (DE-599)DOAJ611404d749454b6b8f174237708164a3 DE-627 ger DE-627 rakwb eng Dominique Belin verfasserin aut Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes? 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies of stop codons in a group of highly expressed genes from 196 prokaryotes under strong translational selection. The occurrence of the three translation termination codons is highly biased, with UAA (ochre) being the most prevalent in almost all bacteria. In contrast, UAG (amber) is the least frequent termination codon, e.g., only 321 occurrences (7.4%) in <i<E. coli</i< K-12 substr. W3110. Of the 253 highly expressed genes, only two end with an UAG codon. The strength of the selective bias against UAG in highly expressed genes varies among bacterial genomes, but it is not affected by the GC content of these genomes. In contrast, increased GC content results in a decrease in UAA abundance with a concomitant increase in UGA abundance. We propose that readthrough efficiency and context effects could explain the prevalence of UAA over UAG, particularly in highly expressed genes. Findings from this communication can be utilized for the optimization of gene expression. gene genome codon usage genome hypothesis stop codons bacterial genomes Science Q Pere Puigbò verfasserin aut In Life MDPI AG, 2012 12(2022), 3, p 431 (DE-627)718627156 (DE-600)2662250-6 20751729 nnns volume:12 year:2022 number:3, p 431 https://doi.org/10.3390/life12030431 kostenfrei https://doaj.org/article/611404d749454b6b8f174237708164a3 kostenfrei https://www.mdpi.com/2075-1729/12/3/431 kostenfrei https://doaj.org/toc/2075-1729 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2022 3, p 431
spelling	10.3390/life12030431 doi (DE-627)DOAJ029877067 (DE-599)DOAJ611404d749454b6b8f174237708164a3 DE-627 ger DE-627 rakwb eng Dominique Belin verfasserin aut Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes? 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies of stop codons in a group of highly expressed genes from 196 prokaryotes under strong translational selection. The occurrence of the three translation termination codons is highly biased, with UAA (ochre) being the most prevalent in almost all bacteria. In contrast, UAG (amber) is the least frequent termination codon, e.g., only 321 occurrences (7.4%) in <i<E. coli</i< K-12 substr. W3110. Of the 253 highly expressed genes, only two end with an UAG codon. The strength of the selective bias against UAG in highly expressed genes varies among bacterial genomes, but it is not affected by the GC content of these genomes. In contrast, increased GC content results in a decrease in UAA abundance with a concomitant increase in UGA abundance. We propose that readthrough efficiency and context effects could explain the prevalence of UAA over UAG, particularly in highly expressed genes. Findings from this communication can be utilized for the optimization of gene expression. gene genome codon usage genome hypothesis stop codons bacterial genomes Science Q Pere Puigbò verfasserin aut In Life MDPI AG, 2012 12(2022), 3, p 431 (DE-627)718627156 (DE-600)2662250-6 20751729 nnns volume:12 year:2022 number:3, p 431 https://doi.org/10.3390/life12030431 kostenfrei https://doaj.org/article/611404d749454b6b8f174237708164a3 kostenfrei https://www.mdpi.com/2075-1729/12/3/431 kostenfrei https://doaj.org/toc/2075-1729 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2022 3, p 431
allfields_unstemmed	10.3390/life12030431 doi (DE-627)DOAJ029877067 (DE-599)DOAJ611404d749454b6b8f174237708164a3 DE-627 ger DE-627 rakwb eng Dominique Belin verfasserin aut Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes? 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies of stop codons in a group of highly expressed genes from 196 prokaryotes under strong translational selection. The occurrence of the three translation termination codons is highly biased, with UAA (ochre) being the most prevalent in almost all bacteria. In contrast, UAG (amber) is the least frequent termination codon, e.g., only 321 occurrences (7.4%) in <i<E. coli</i< K-12 substr. W3110. Of the 253 highly expressed genes, only two end with an UAG codon. The strength of the selective bias against UAG in highly expressed genes varies among bacterial genomes, but it is not affected by the GC content of these genomes. In contrast, increased GC content results in a decrease in UAA abundance with a concomitant increase in UGA abundance. We propose that readthrough efficiency and context effects could explain the prevalence of UAA over UAG, particularly in highly expressed genes. Findings from this communication can be utilized for the optimization of gene expression. gene genome codon usage genome hypothesis stop codons bacterial genomes Science Q Pere Puigbò verfasserin aut In Life MDPI AG, 2012 12(2022), 3, p 431 (DE-627)718627156 (DE-600)2662250-6 20751729 nnns volume:12 year:2022 number:3, p 431 https://doi.org/10.3390/life12030431 kostenfrei https://doaj.org/article/611404d749454b6b8f174237708164a3 kostenfrei https://www.mdpi.com/2075-1729/12/3/431 kostenfrei https://doaj.org/toc/2075-1729 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2022 3, p 431
allfieldsGer	10.3390/life12030431 doi (DE-627)DOAJ029877067 (DE-599)DOAJ611404d749454b6b8f174237708164a3 DE-627 ger DE-627 rakwb eng Dominique Belin verfasserin aut Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes? 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies of stop codons in a group of highly expressed genes from 196 prokaryotes under strong translational selection. The occurrence of the three translation termination codons is highly biased, with UAA (ochre) being the most prevalent in almost all bacteria. In contrast, UAG (amber) is the least frequent termination codon, e.g., only 321 occurrences (7.4%) in <i<E. coli</i< K-12 substr. W3110. Of the 253 highly expressed genes, only two end with an UAG codon. The strength of the selective bias against UAG in highly expressed genes varies among bacterial genomes, but it is not affected by the GC content of these genomes. In contrast, increased GC content results in a decrease in UAA abundance with a concomitant increase in UGA abundance. We propose that readthrough efficiency and context effects could explain the prevalence of UAA over UAG, particularly in highly expressed genes. Findings from this communication can be utilized for the optimization of gene expression. gene genome codon usage genome hypothesis stop codons bacterial genomes Science Q Pere Puigbò verfasserin aut In Life MDPI AG, 2012 12(2022), 3, p 431 (DE-627)718627156 (DE-600)2662250-6 20751729 nnns volume:12 year:2022 number:3, p 431 https://doi.org/10.3390/life12030431 kostenfrei https://doaj.org/article/611404d749454b6b8f174237708164a3 kostenfrei https://www.mdpi.com/2075-1729/12/3/431 kostenfrei https://doaj.org/toc/2075-1729 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2022 3, p 431
allfieldsSound	10.3390/life12030431 doi (DE-627)DOAJ029877067 (DE-599)DOAJ611404d749454b6b8f174237708164a3 DE-627 ger DE-627 rakwb eng Dominique Belin verfasserin aut Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes? 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies of stop codons in a group of highly expressed genes from 196 prokaryotes under strong translational selection. The occurrence of the three translation termination codons is highly biased, with UAA (ochre) being the most prevalent in almost all bacteria. In contrast, UAG (amber) is the least frequent termination codon, e.g., only 321 occurrences (7.4%) in <i<E. coli</i< K-12 substr. W3110. Of the 253 highly expressed genes, only two end with an UAG codon. The strength of the selective bias against UAG in highly expressed genes varies among bacterial genomes, but it is not affected by the GC content of these genomes. In contrast, increased GC content results in a decrease in UAA abundance with a concomitant increase in UGA abundance. We propose that readthrough efficiency and context effects could explain the prevalence of UAA over UAG, particularly in highly expressed genes. Findings from this communication can be utilized for the optimization of gene expression. gene genome codon usage genome hypothesis stop codons bacterial genomes Science Q Pere Puigbò verfasserin aut In Life MDPI AG, 2012 12(2022), 3, p 431 (DE-627)718627156 (DE-600)2662250-6 20751729 nnns volume:12 year:2022 number:3, p 431 https://doi.org/10.3390/life12030431 kostenfrei https://doaj.org/article/611404d749454b6b8f174237708164a3 kostenfrei https://www.mdpi.com/2075-1729/12/3/431 kostenfrei https://doaj.org/toc/2075-1729 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2022 3, p 431
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author	Dominique Belin
spellingShingle	Dominique Belin misc gene misc genome misc codon usage misc genome hypothesis misc stop codons misc bacterial genomes misc Science misc Q Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?
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topic_title	Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes? gene genome codon usage genome hypothesis stop codons bacterial genomes
topic	misc gene misc genome misc codon usage misc genome hypothesis misc stop codons misc bacterial genomes misc Science misc Q
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title	Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?
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title_full	Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?
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title_sort	why is the uag (amber) stop codon almost absent in highly expressed bacterial genes?
title_auth	Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?
abstract	The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies of stop codons in a group of highly expressed genes from 196 prokaryotes under strong translational selection. The occurrence of the three translation termination codons is highly biased, with UAA (ochre) being the most prevalent in almost all bacteria. In contrast, UAG (amber) is the least frequent termination codon, e.g., only 321 occurrences (7.4%) in <i<E. coli</i< K-12 substr. W3110. Of the 253 highly expressed genes, only two end with an UAG codon. The strength of the selective bias against UAG in highly expressed genes varies among bacterial genomes, but it is not affected by the GC content of these genomes. In contrast, increased GC content results in a decrease in UAA abundance with a concomitant increase in UGA abundance. We propose that readthrough efficiency and context effects could explain the prevalence of UAA over UAG, particularly in highly expressed genes. Findings from this communication can be utilized for the optimization of gene expression.
abstractGer	The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies of stop codons in a group of highly expressed genes from 196 prokaryotes under strong translational selection. The occurrence of the three translation termination codons is highly biased, with UAA (ochre) being the most prevalent in almost all bacteria. In contrast, UAG (amber) is the least frequent termination codon, e.g., only 321 occurrences (7.4%) in <i<E. coli</i< K-12 substr. W3110. Of the 253 highly expressed genes, only two end with an UAG codon. The strength of the selective bias against UAG in highly expressed genes varies among bacterial genomes, but it is not affected by the GC content of these genomes. In contrast, increased GC content results in a decrease in UAA abundance with a concomitant increase in UGA abundance. We propose that readthrough efficiency and context effects could explain the prevalence of UAA over UAG, particularly in highly expressed genes. Findings from this communication can be utilized for the optimization of gene expression.
abstract_unstemmed	The genome hypothesis postulates that genes in a genome tend to conform to their species’ usage of the codon catalog and the GC content of the DNA. Thus, codon frequencies differ across organisms, including the three termination codons in the standard genetic code. Here, we analyze the frequencies of stop codons in a group of highly expressed genes from 196 prokaryotes under strong translational selection. The occurrence of the three translation termination codons is highly biased, with UAA (ochre) being the most prevalent in almost all bacteria. In contrast, UAG (amber) is the least frequent termination codon, e.g., only 321 occurrences (7.4%) in <i<E. coli</i< K-12 substr. W3110. Of the 253 highly expressed genes, only two end with an UAG codon. The strength of the selective bias against UAG in highly expressed genes varies among bacterial genomes, but it is not affected by the GC content of these genomes. In contrast, increased GC content results in a decrease in UAA abundance with a concomitant increase in UGA abundance. We propose that readthrough efficiency and context effects could explain the prevalence of UAA over UAG, particularly in highly expressed genes. Findings from this communication can be utilized for the optimization of gene expression.
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title_short	Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?
url	https://doi.org/10.3390/life12030431 https://doaj.org/article/611404d749454b6b8f174237708164a3 https://www.mdpi.com/2075-1729/12/3/431 https://doaj.org/toc/2075-1729
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