Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in <it>Chlamydia trachomatis </it>serovar L2 and D strains
<p>Abstract</p> <p>Background</p> <p>Chlamydia have reduced genomes that reflect their obligately parasitic lifestyle. Despite their different tissue tropisms, chlamydial strains share a large number of common genes and have few recognized pseudogenes, indicating genomi...
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| Format: | Article |
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BMC
2009-07-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/9/166 |
| _version_ | 1819350234548928512 |
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| author | Graham David E Fisher Derek J Giles Teresa N |
| author_facet | Graham David E Fisher Derek J Giles Teresa N |
| author_sort | Graham David E |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Chlamydia have reduced genomes that reflect their obligately parasitic lifestyle. Despite their different tissue tropisms, chlamydial strains share a large number of common genes and have few recognized pseudogenes, indicating genomic stability. All of the <it>Chlamydiaceae </it>have homologs of the <it>aaxABC </it>gene cluster that encodes a functional arginine:agmatine exchange system in <it>Chlamydia </it>(<it>Chlamydophila</it>)<it>pneumoniae</it>. However, <it>Chlamydia trachomatis </it>serovar L2 strains have a nonsense mutation in their <it>aaxB </it>genes, and <it>C. trachomatis </it>serovar A and B strains have frameshift mutations in their <it>aaxC </it>homologs, suggesting that relaxed selection may have enabled the evolution of <it>aax </it>pseudogenes. Biochemical experiments were performed to determine whether the <it>aaxABC </it>genes from <it>C. trachomatis </it>strains were transcribed, and mutagenesis was used to identify nucleotide substitutions that prevent protein maturation and activity. Molecular evolution techniques were applied to determine the relaxation of selection and the scope of <it>aax </it>gene inactivation in the <it>Chlamydiales</it>.</p> <p>Results</p> <p>The <it>aaxABC </it>genes were co-transcribed in <it>C. trachomatis </it>L2/434, during the mid-late stage of cellular infection. However, a stop codon in the <it>aaxB </it>gene from this strain prevented the heterologous production of an active pyruvoyl-dependent arginine decarboxylase. Replacing that ochre codon with its ancestral tryptophan codon rescued the activity of this self-cleaving enzyme. The <it>aaxB </it>gene from <it>C. trachomatis </it>D/UW-3 was heterologously expressed as a proenzyme that failed to cleave and form the catalytic pyruvoyl cofactor. This inactive protein could be rescued by replacing the arginine-115 codon with an ancestral glycine codon. The <it>aaxC </it>gene from the D/UW-3 strain encoded an active arginine:agmatine antiporter protein, while the L2/434 homolog was unexpectedly inactive. Yet the frequencies of nonsynonymous versus synonymous nucleotide substitutions show no signs of relaxed selection, consistent with the recent inactivation of these genes.</p> <p>Conclusion</p> <p>The ancestor of the <it>Chlamydiaceae </it>had a functional arginine:agmatine exchange system that is decaying through independent, parallel processes in the <it>C. trachomatis </it>lineage. Differences in arginine metabolism among <it>Chlamydiaceae </it>species may be partly associated with their tissue tropism, possibly due to the protection conferred by a functional arginine-agmatine exchange system against host nitric oxide production and innate immunity. The independent loss of AaxB activity in all sequenced <it>C. trachomatis </it>strains indicates continual gene inactivation and illustrates the difficulty of recognizing recent bacterial pseudogenes from sequence comparison, transcriptional profiling or the analysis of nucleotide substitution rates.</p> |
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| publishDate | 2009-07-01 |
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| spelling | doaj.art-f0a98bffe7ad4416bcd68ade0083fe5f2022-12-21T16:42:58ZengBMCBMC Evolutionary Biology1471-21482009-07-019116610.1186/1471-2148-9-166Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in <it>Chlamydia trachomatis </it>serovar L2 and D strainsGraham David EFisher Derek JGiles Teresa N<p>Abstract</p> <p>Background</p> <p>Chlamydia have reduced genomes that reflect their obligately parasitic lifestyle. Despite their different tissue tropisms, chlamydial strains share a large number of common genes and have few recognized pseudogenes, indicating genomic stability. All of the <it>Chlamydiaceae </it>have homologs of the <it>aaxABC </it>gene cluster that encodes a functional arginine:agmatine exchange system in <it>Chlamydia </it>(<it>Chlamydophila</it>)<it>pneumoniae</it>. However, <it>Chlamydia trachomatis </it>serovar L2 strains have a nonsense mutation in their <it>aaxB </it>genes, and <it>C. trachomatis </it>serovar A and B strains have frameshift mutations in their <it>aaxC </it>homologs, suggesting that relaxed selection may have enabled the evolution of <it>aax </it>pseudogenes. Biochemical experiments were performed to determine whether the <it>aaxABC </it>genes from <it>C. trachomatis </it>strains were transcribed, and mutagenesis was used to identify nucleotide substitutions that prevent protein maturation and activity. Molecular evolution techniques were applied to determine the relaxation of selection and the scope of <it>aax </it>gene inactivation in the <it>Chlamydiales</it>.</p> <p>Results</p> <p>The <it>aaxABC </it>genes were co-transcribed in <it>C. trachomatis </it>L2/434, during the mid-late stage of cellular infection. However, a stop codon in the <it>aaxB </it>gene from this strain prevented the heterologous production of an active pyruvoyl-dependent arginine decarboxylase. Replacing that ochre codon with its ancestral tryptophan codon rescued the activity of this self-cleaving enzyme. The <it>aaxB </it>gene from <it>C. trachomatis </it>D/UW-3 was heterologously expressed as a proenzyme that failed to cleave and form the catalytic pyruvoyl cofactor. This inactive protein could be rescued by replacing the arginine-115 codon with an ancestral glycine codon. The <it>aaxC </it>gene from the D/UW-3 strain encoded an active arginine:agmatine antiporter protein, while the L2/434 homolog was unexpectedly inactive. Yet the frequencies of nonsynonymous versus synonymous nucleotide substitutions show no signs of relaxed selection, consistent with the recent inactivation of these genes.</p> <p>Conclusion</p> <p>The ancestor of the <it>Chlamydiaceae </it>had a functional arginine:agmatine exchange system that is decaying through independent, parallel processes in the <it>C. trachomatis </it>lineage. Differences in arginine metabolism among <it>Chlamydiaceae </it>species may be partly associated with their tissue tropism, possibly due to the protection conferred by a functional arginine-agmatine exchange system against host nitric oxide production and innate immunity. The independent loss of AaxB activity in all sequenced <it>C. trachomatis </it>strains indicates continual gene inactivation and illustrates the difficulty of recognizing recent bacterial pseudogenes from sequence comparison, transcriptional profiling or the analysis of nucleotide substitution rates.</p>http://www.biomedcentral.com/1471-2148/9/166 |
| spellingShingle | Graham David E Fisher Derek J Giles Teresa N Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in <it>Chlamydia trachomatis </it>serovar L2 and D strains BMC Evolutionary Biology |
| title | Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in <it>Chlamydia trachomatis </it>serovar L2 and D strains |
| title_full | Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in <it>Chlamydia trachomatis </it>serovar L2 and D strains |
| title_fullStr | Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in <it>Chlamydia trachomatis </it>serovar L2 and D strains |
| title_full_unstemmed | Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in <it>Chlamydia trachomatis </it>serovar L2 and D strains |
| title_short | Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in <it>Chlamydia trachomatis </it>serovar L2 and D strains |
| title_sort | independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in it chlamydia trachomatis it serovar l2 and d strains |
| url | http://www.biomedcentral.com/1471-2148/9/166 |
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