Predicted highly expressed genes of diverse prokaryotic genomes
Predicted highly expressed genes of diverse prokaryotic genomes
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DOI：
10.1128/jb.182.18.5238-5250.2000
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发表时间：
2000-09-01
影响因子：
3.2
通讯作者：
Mrázek, J
中科院分区：
文献类型：
--
作者：
Karlin, S;Mrázek, J
我们预测基因表达水平的方法与基因类别之间的密码子使用差异有关。在原核基因组中，密码子使用与平均基因强烈偏离但密码子使用与核糖体蛋白基因、翻译和转录加工因子以及分子伴侣降解蛋白足够相似的基因被预测为高度表达（PHX）。根据这些标准，大多数原核生物基因组中的PHX基因包括编码核糖体蛋白、翻译和转录加工因子、伴侣蛋白和主要能量代谢基因的基因。特别是，对于快速生长的菌种埃希氏菌、霍乱弧菌、枯草芽孢杆菌和流感嗜血杆菌，主要的糖酵解和三羧酸循环基因是PHX。在集胞藻中，光合作用的主要基因是PHX，而在产甲烷菌中，PHX基因包括那些甲烷生成所必需的基因。总的来说，三个蛋白质家族核糖体蛋白，蛋白质合成因子和伴侣复合物在生命周期的许多阶段都是必需的，显然细菌已经进化出密码子使用来维持适当的生长，稳定性和可塑性。对耐辐射奇球菌对高剂量电离辐射的抵抗能力的新解释是基于过量的PHX伴侣降解基因和解毒基因。分析了选定类别的基因的表达水平，包括鞭毛、电子传递、解毒、组氨酸激酶等。鞭毛PHX基因在螺旋体基因组中是显著的。PHX基因与强Shine-Dalgarno信号序列正相关。特异性调节蛋白，例如，双组分传感器蛋白，很少是PHX。参与维生素合成途径的基因的预测表达水平较低。几个独特的PHX基因的可用完整的原核基因组突出显示。PHX基因与化学计量，多功能性和操纵子结构的关系进行了讨论。我们的方法可用于补充实验表达分析。
Our approach in predicting gene expression levels relates to codon usage differences among gene classes. In prokaryotic genomes, genes that deviate strongly in codon usage from the average gene but are sufficiently similar in codon usage to ribosomal protein genes, to translation and transcription processing factors, and to chaperone-degradation proteins are predicted highly expressed (PHX). By these criteria, PHX genes in most prokaryotic genomes include those encoding ribosomal proteins, translation and transcription processing factors, and chaperone proteins and genes of principal energy metabolism. In particular, for the fast-growing species Escherichia call, Vibrio cholerae, Bacillus subtilis, and Haemophilus influenzae, major glycolysis and tricarboxylic acid cycle genes are PHX. In Synechocystis, prime genes of photosynthesis are PHX, and in methanogens, PHX genes include those essential for methanogenesis. Overall, the three protein families-ribosomal proteins, protein synthesis factors, and chaperone complexes-are needed at many stages of the life cycle, and apparently bacteria have evolved codon usage to maintain appropriate growth, stability, and plasticity. New interpretations of the capacity of Deinococcus radiodurans for resistance to high doses of ionizing radiation is based on an excess of PHX chaperone-degradation genes and detoxification genes. Expression levels of selected classes of genes, including those for flagella, electron transport, detoxification, histidine kinases, and others, are analyzed. Flagellar PHX genes are conspicuous among spirochete genomes. PHX genes are positively correlated with strong Shine-Dalgarno signal sequences. Specific regulatory proteins, e.g., two-component sensor proteins, are rarely PHX. Genes involved in pathways for the synthesis of vitamins record low predicted expression levels. Several distinctive PHX genes of the available complete prokaryotic genomes are highlighted. Relationships of PHX genes with stoichiometry, multifunctionality, and operon structures are discussed. Our methodology may be used complementary to experimental expression analysis.