Microbial Phytopathology, Institute of Microbiology, Faculty of Biology and Pharmacy, Friedrich-Schiller-University, Jena, Germany.
J Basic Microbiol. 2012 Apr;52(2):195-205. doi: 10.1002/jobm.201100067. Epub 2011 Jul 21.
Every organism can be characterized by the amino acid composition of its proteome. So far it was assumed that these compositions are determined by the GC content of the DNA or, in some cases, by extreme lifestyles, like thermophily or halophily. Here, we focussed our analysis on eight amino acids, each of which is encoded by both, GC and AT rich codons, to identify finer amino acid patterns beyond the GC dominance. We investigated the conceptually translated proteomes of 1029 bacterial and archaeal strains with sequenced genomes for amino acid composition. Using correspondence analysis, we found that phylogenetic groups within bacteria and archaea generally can be discriminated from other groups due to their amino acid composition. In some cases, single organisms, e.g. Treponema pallidum strains or Mycoplasma penetrans, are characterized by extreme amino acid compositions. We assume that our data could provide a basis for a new approach to analyze evolution of bacterial and archaeal groups. Furthermore, for single organisms, the detailed knowledge of the amino acid composition of the entire proteome encoded in the genome could lead to a better understanding, important for pharmaceutical or biotechnological applications. We recommend that information about amino acid compositions should be provided in databases, comparable to the GC content of genomes.
每种生物体都可以通过其蛋白质组的氨基酸组成来描述。到目前为止，人们认为这些组成是由 DNA 的 GC 含量决定的，或者在某些情况下是由极端的生活方式决定的，如嗜热或嗜盐。在这里，我们将分析重点放在了 8 种氨基酸上，每一种氨基酸都由 GC 和 AT 丰富的密码子编码，以确定超越 GC 优势的更精细的氨基酸模式。我们研究了 1029 株具有测序基因组的细菌和古细菌的概念性翻译蛋白质组的氨基酸组成。使用对应分析，我们发现细菌和古细菌中的系统发育群通常可以根据它们的氨基酸组成与其他群区分开来。在某些情况下，单个生物体，如苍白密螺旋体菌株或支原体穿透菌，其氨基酸组成非常极端。我们假设我们的数据可以为分析细菌和古细菌群的进化提供一个新的方法。此外，对于单个生物体来说，对基因组中编码的整个蛋白质组的氨基酸组成的详细了解可能有助于更好地理解，这对于药物或生物技术应用很重要。我们建议在数据库中提供有关氨基酸组成的信息，这类似于基因组的 GC 含量。
