Characterizations of highly expressed genes of four fast-growing bacteria
Characterizations of highly expressed genes of four fast-growing bacteria
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DOI：
10.1128/jb.183.17.5025-5040.2001
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发表时间：
2001-09-01
影响因子：
3.2
通讯作者：
Kaiser, D
中科院分区：
文献类型：
--
作者：
Karlin, S;Mr치zek, J;Kaiser, D
预测的高表达（PHX）基因是针对四种快速生长的细菌大肠杆菌，流感嗜血杆菌，弧菌霍乱和枯草芽孢杆菌的完全测序基因组的特征。我们确定基因表达水平的方法与某些基因类别之间的密码子使用差异有关：所有基因的收集（平均基因），核糖体蛋白基因的合奏，主要的翻译/转录处理因子以及伴侣/降解复合物多肽的基因。如果其密码子频率接近核糖体蛋白，主要的翻译/转录处理因子和伴侣/降解标准标准，则预测高表达基因（PHX），但与平均基因密码子频率相差很大。原核生物基因组中通常的密码子使用频率鉴定的PHX基因通常包括核糖体蛋白，主要转录/翻译处理因子（多个副本中有几种）以及主要的伴侣/降解蛋白。同样，PHX基因通常包括糖酵解，丙酮酸氧化和呼吸（有氧和厌氧），脂肪酸生物合成基因以及氨基酸和核苷酸生物合成基因的基因的糖酵解，丙酮酸氧化和呼吸（有氧和厌氧）的编码酶。基因类别通常不是PHX包括大多数修复蛋白基因，几乎所有维生素生物合成基因，两分量传感器系统的基因，大多数调节基因以及大多数在固定期或饥饿期间表达的基因。基因组之间的PHX氨基酰基-TRNA合成酶基因基因的成员对比。大肠杆菌和枯草芽孢杆菌之间的PHX能代谢基因之间也存在细微的差异，特别是在三羧酸周期的基因方面。通过二维凝胶测定评估，大肠杆菌和枯草芽孢杆菌具有高蛋白质丰度的PHX基因的良好一致。还检查了PHX基因与化学计量，多功能性和操纵子结构的关系。每个基因组中PHX基因的空间分布揭示了簇和没有PHX基因的较长区域。
Predicted highly expressed (PHX) genes are characterized for the completely sequenced genomes of the four fast-growing bacteria Escherichia coli, Haemophilus influenzae, Vibrio cholerae, and Bacillus subtilis. Our approach to ascertaining gene expression levels relates to codon usage differences among certain gene classes: the collection of all genes (average gene), the ensemble of ribosomal protein genes, major translation/transcription processing factors, and genes for polypeptides of chaperone/degradation complexes. A gene is predicted highly expressed (PHX) if its codon frequencies are close to those of the ribosomal proteins, major translation/transcription processing factor, and chaperone/degradation standards but strongly deviant from the average gene codon frequencies. PHX genes identified by their codon usage frequencies among prokaryotic genomes commonly include those for ribosomal proteins, major transcription/translation processing factors (several occurring in multiple copies), and major chaperone/degradation proteins. Also PHX genes generally include those encoding enzymes of essential energy metabolism pathways of glycolysis, pyruvate oxidation, and respiration (aerobic and anaerobic), genes of fatty acid biosynthesis, and the principal genes of amino acid and nucleotide biosyntheses. Gene classes generally not PHX include most repair protein genes, virtually all vitamin biosynthesis genes, genes of two-component sensor systems, most regulatory genes, and most genes expressed in stationary phase or during starvation. Members of the set of PHX aminoacyl-tRNA synthetase genes contrast sharply between genomes. There are also subtle differences among the PHX energy metabolism genes between E. coli and B. subtilis, particularly with respect to genes of the tricarboxylic acid cycle. The good agreement of PHX genes of E. coli and B. subtilis with high protein abundances, as assessed by two-dimensional gel determination, is verified. Relationships of PHX genes with stoichiometry, multifunctionality, and operon structures are also examined. The spatial distribution of PHX genes within each genome reveals clusters and significantly long regions without PHX genes.