Compositional biases of bacterial genomes and evolutionary implications
Compositional biases of bacterial genomes and evolutionary implications
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DOI：
10.1128/jb.179.12.3899-3913.1997
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发表时间：
1997-06-01
影响因子：
3.2
通讯作者：
Campbell, AM
中科院分区：
文献类型：
--
作者：
Karlin, S;Mrazek, J;Campbell, AM
我们比较和对比了15种不同的原核生物，有大量的基因组序列集合，其中包括7个完整的基因组（大肠杆菌，流感嗜血杆菌，生殖支原体，肺炎支原体，集胞藻属，菌株PCC 6803，詹氏甲烷球菌，嗜氧热杆菌）的全基因组组成的偏见和分布的短寡核苷酸。一个关键的观察结果涉及同一基因组内多个50-kb不相交重叠群上二核苷酸相对丰度谱的恒定性，（对于所有XY，分布是rho（XY）* = f（XY）*/f（X）*/f（Y）*，其中f（X）* 表示核苷酸X的频率，f（XY）* 表示二核苷酸XY的频率，两者都是从与其反向互补序列连接的序列计算的。基于这种恒定性，我们将集合{rho（XY）*}称为基因组签名。我们确定，不同基因组的50-kb样品重叠群的{rho（XY）*}载体之间的差异几乎总是超过相同基因组的那些载体之间的差异。我们发现二核苷酸CpG=CG在许多嗜热菌中代表性不足（例如，M. jannaschii，硫化叶菌属，和M. TA在原核生物和真核生物中普遍代表不足，但在硫化叶菌和嗜气假单胞菌序列中出现正常计数。流感。分枝jannschii序列在CTAG四核苷酸的极端代表性不足和CTAG位点在基因组周围的异常分布方面是前所未有的。长四核苷酸微卫星数目的比较分析区分H。流感。比较细菌序列之间的二核苷酸相对丰度差异。例如，在这些差异评估中，蓝细菌集胞藻、聚球藻和鱼腥藻不形成连贯的组，并且彼此相距远如一般革兰氏阴性序列与一般革兰氏阳性序列。来自低G +C革兰氏阳性变形菌的jannaschii是与革兰氏阴性变形菌的差异的一半。解释和假设集中在基因组签名在突出不同类别的原核物种之间的相似性和差异性中的作用，基因组签名的潜在机制，基因组组成通量的形式和水平，基因组签名作为分子生物发生的计时器的使用，以及关于真细菌、古细菌和真核生物这三个假定的生命领域以及真核生物的起源和早期进化的意义。
We compare and contrast genome-wide compositional biases and distributions of short oligonucleotides across 15 diverse prokaryotes that have substantial genomic sequence collections, These include seven complete genomes (Escherichia coli, Haemophilus influenzae, Mycoplasma genitalium, Mycoplasma pneumoniae, Synechocystis sp, strain PCC6803, Methanococcus jannaschii, and Pyrobaculum aerophilum). A key observation concerns the constancy of the dinucleotide relative abundance profiles over multiple 50-kb disjoint contigs within the same genome, (The profile is rho(XY)* = f(XY)*/f(X)*/f(Y)* for all XY, where f(X)* denotes the frequency of the nucleotide X and f(XY)* denotes the frequency of the dinucleotide XY, both computed from the sequence concatenated with its inverted complementary sequence.) On the basis of this constancy, we refer to the collection {rho(XY)*} as the genome signature, We establish that the differences between {rho(XY)*} vectors of 50-kb sample contigs of different genomes virtually always exceed the differences between those of the same genomes, Various di- and tetranucleotide biases are identified, In particular, we find that the dinucleotide CpG=CG is underrepresented in many thermophiles (e.g., M. jannaschii, Sulfolobus sp., and M. thermoautotrophicum) but overrepresented in halobacteria, TA is broadly underrepresented in prokaryotes and eukaryotes, but normal counts appear in Sulfolobus and P. aerophilum sequences, More than for any other bacterial genome, palindromic tetranucleotides are underrepresented in H. influenzae. The M. jannschii sequence is unprecedented in its extreme underrepresentation of CTAG tetranucleotides and in the anomalous distribution of CTAG sites around the genome. Comparative analysis of numbers of long tetranucleotide microsatellites distinguishes H. influenzae. Dinucleotide relative abundance differences between bacterial sequences are compared, For example, in these assessments of differences, the cyanobacteria Synechocystis, Synechococcus, and Anabaena do not form a coherent group and are as far from each other as general gram-negative sequences are from general gram-positive sequences, The difference of M. jannaschii from low-G+C gram-positive proteobacteria is one-half of the difference from gram-negative proteobacteria, Interpretations and hypotheses center on the role of the genome signature in highlighting similarities and dissimilarities across different classes of prokaryotic species, possible mechanisms underlying the genome signature, the form and level of genome compositional flux, the use of the genome signature as a chronometer of molecular phylogeny, and implications with respect to the three putative eubacterial, archaeal, and eukaryote domains of life and to the origin and early evolution of eukaryotes.