Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains
Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains
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DOI：
10.1186/1471-2148-9-166
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发表时间：
2009-07-16
影响因子：
3.4
通讯作者：
Graham, David E.
中科院分区：
文献类型：
--
作者：
Giles, Teresa N.;Fisher, Derek J.;Graham, David E.
背景：衣原体的基因组减少，反映了他们专性寄生的生活方式。尽管它们的组织嗜性不同，衣原体菌株共享大量的共同基因，并有几个公认的假基因，表明基因组的稳定性。所有的衣原体科都有aaxABC基因簇的同源物，该基因簇编码肺炎衣原体（嗜衣原体）中的功能性精氨酸：胍丁胺交换系统。然而，沙眼衣原体血清型L2株在其aaxB基因中存在无义突变，而C.沙眼血清型A和B菌株在它们的aaxC同源物中具有移码突变，这表明宽松的选择可能使aax假基因得以进化。通过生化实验来确定来自C.将沙眼病毒株转录，并使用诱变来鉴定阻止蛋白质成熟和活性的核苷酸取代。结果：aaxABC基因在衣原体中共转录;沙眼衣原体L2/434，细胞感染中晚期。然而，终止密码子在aaxB基因从这个菌株阻止了异源生产的一个积极的异戊酰依赖性精氨酸脱羧酶。用它的祖先色氨酸密码子取代赭石密码子拯救了这种自我切割酶的活性。aaxB基因来自C.沙眼衣原体D/UW-3异源表达为不能切割和形成催化性异戊酰辅因子的酶原。这种无活性的蛋白质可以通过用祖先甘氨酸密码子替换精氨酸-115密码子来拯救。来自D/UW-3菌株的aaxC基因编码活性精氨酸：胍丁胺反向转运蛋白，而L2/434同源物出乎意料地无活性。然而，频率的非同义与同义的核苷酸取代显示没有迹象表明放松选择，与最近失活的这些基因。结论：衣原体科的祖先有一个功能性的精氨酸：胍丁胺交换系统，是通过独立的，平行的过程在C。沙眼谱系。衣原体属物种之间精氨酸代谢的差异可能部分与其组织嗜性，可能是由于保护功能性精氨酸胍丁胺交换系统对宿主一氧化氮的产生和先天免疫。所有测序的C.沙眼衣原体菌株表明持续的基因失活，并说明了从序列比较、转录谱或核苷酸取代率分析识别最近的细菌假基因的困难。
Background: 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 Chlamydiaceae have homologs of the aaxABC gene cluster that encodes a functional arginine: agmatine exchange system in Chlamydia (Chlamydophila) pneumoniae. However, Chlamydia trachomatis serovar L2 strains have a nonsense mutation in their aaxB genes, and C. trachomatis serovar A and B strains have frameshift mutations in their aaxC homologs, suggesting that relaxed selection may have enabled the evolution of aax pseudogenes. Biochemical experiments were performed to determine whether the aaxABC genes from C. trachomatis 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 aax gene inactivation in the Chlamydiales.Results: The aaxABC genes were co-transcribed in C. trachomatis L2/434, during the mid-late stage of cellular infection. However, a stop codon in the aaxB 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 aaxB gene from C. trachomatis 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 aaxC 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.Conclusion: The ancestor of the Chlamydiaceae had a functional arginine: agmatine exchange system that is decaying through independent, parallel processes in the C. trachomatis lineage. Differences in arginine metabolism among Chlamydiaceae 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 C. trachomatis 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.