Gupta Radhey S
Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
Int J Syst Evol Microbiol. 2009 Oct;59(Pt 10):2510-26. doi: 10.1099/ijs.0.005678-0. Epub 2009 Jul 21.
A combination of phylogenomic and signature sequence-based (or phenetic) approaches was used to understand the evolutionary relationships among cyanobacteria. Phylogenetic trees were constructed for 34 cyanobacteria whose genomes have been sequenced, based on concatenated sequences for 45 conserved proteins and also the 16S rRNA gene. In parallel, sequence alignments of various proteins were examined to identify conserved indels (i.e. molecular signatures or synapomorphies) that are specific for either all cyanobacteria or their various clades in the phylogenetic trees. Of the >40 molecular signatures described in this work, 15 are specific for all cyanobacteria. The other cyanobacterial clades that can now be identified and circumscribed in molecular terms by using these signatures include a deep-branching clade (clade A, corresponding to the subclass Gloeobacterophycidae), consisting of Gloeobacter violaceus and two diazotrophic Synechococcus strains (JA-3-3Ab and JA2-3-B'a) (15 aa insert in EF-G); a clade comprising all other cyanobacteria except those from clade A [18 aa insert in DNA polymerase I (Pol I), 2 aa insert in the DnaX protein, 4 aa insert in TrpRS and 4-5 aa insert in tryptophan synthase beta subunit]; a clade (clade C, corresponding to the subclass Synechococcophycidae) of various marine unicellular Synechococcus and Prochlorococcus cyanobacteria (12 aa insert in Pol I, 3 aa insert in RpoB, 2 aa insert in KgsA, 6 aa insert in TyrRS, 2 aa insert in tRNA-mG1 transferase and 1 aa deletion in the RpoC protein); a clade of the low-B/A ecotype Prochlorococcus strains (5 aa deletion in LeuRS and 1 aa insert in the Ffh protein); a clade consisting of the Nostocales species/strains (subclass Nostocophycidae; 4 aa insert in the PetA protein and 5 aa insert in the ribosomal protein S3); a clade of the order Chroococcales (1 aa insert in RecA); a clade comprising the orders Nostocales, Oscillatoriales and Chroococcales [19 aa insert in DnaE, 13 aa insert in GDP-mannose pyrophosphorylase and 22-27 aa insert in NADP(H)-quinone oxidoreductase subunit D]. Two additional conserved indels in the translation-initiation factor IF-2 and riboflavin synthase alpha subunit suggest an intermediate placement of the Oscillatoriales in between the orders Nostocales and Chroococcales. The unique presence of these molecular signatures in all available sequences from the indicated groups of cyanobacteria, but not in any other cyanobacteria (or bacteria), indicates that these synapomorphies provide novel and potentially useful means for circumscription of several important taxonomic clades of cyanobacteria in more definitive terms. The species-distribution patterns of these synapomorphies also indicate that the plant/plastid homologues are not derived from the clade A or C cyanobacteria.
结合系统基因组学和基于特征序列（或表型）的方法来理解蓝藻细菌之间的进化关系。基于45种保守蛋白的串联序列以及16S rRNA基因，为34种已测序基因组的蓝藻细菌构建了系统发育树。同时，检查了各种蛋白质的序列比对，以识别特定于所有蓝藻细菌或其在系统发育树中的各个进化枝的保守插入缺失（即分子特征或共衍征）。在这项工作中描述的40多种分子特征中，有15种是所有蓝藻细菌特有的。现在可以通过使用这些特征在分子层面识别和界定的其他蓝藻细菌进化枝包括一个深分支进化枝（进化枝A，对应于蓝菌藻亚纲），由紫球藻和两种固氮的聚球藻菌株（JA-3-3Ab和JA2-3-B'a）组成（EF-G中有15个氨基酸插入）；一个进化枝，包含除进化枝A以外的所有其他蓝藻细菌[DNA聚合酶I（Pol I）中有18个氨基酸插入，DnaX蛋白中有2个氨基酸插入，色氨酸-tRNA合成酶（TrpRS）中有4个氨基酸插入，色氨酸合酶β亚基中有4 - 5个氨基酸插入]；一个由各种海洋单细胞聚球藻和原绿球藻蓝藻细菌组成的进化枝（进化枝C，对应于聚球藻亚纲）（Pol I中有12个氨基酸插入，RNA聚合酶B（RpoB）中有3个氨基酸插入，酮戊二酸合酶A（KgsA）中有2个氨基酸插入，酪氨酸-tRNA合成酶（TyrRS）中有6个氨基酸插入，tRNA-甲基鸟苷1转移酶中有2个氨基酸插入，RNA聚合酶C（RpoC）蛋白中有1个氨基酸缺失）；低B/A生态型原绿球藻菌株的进化枝（亮氨酸-tRNA合成酶（LeuRS）中有5个氨基酸缺失，信号识别颗粒蛋白Ffh中有1个氨基酸插入）；一个由念珠藻目物种/菌株组成的进化枝（念珠藻亚纲；细胞色素f（PetA）蛋白中有4个氨基酸插入，核糖体蛋白S3中有5个氨基酸插入）；色球藻目的进化枝（重组酶A（RecA）中有1个氨基酸插入）；一个包含念珠藻目、颤藻目和色球藻目的进化枝[DNA聚合酶III亚基E（DnaE）中有19个氨基酸插入，GDP-甘露糖焦磷酸化酶中有13个氨基酸插入，NADP（H）-醌氧化还原酶亚基D中有22 - 27个氨基酸插入]。翻译起始因子IF-2和核黄素合酶α亚基中的另外两个保守插入缺失表明颤藻目在念珠藻目和色球藻目之间处于中间位置。这些分子特征在所示蓝藻细菌组的所有可用序列中独特存在，但在任何其他蓝藻细菌（或细菌）中不存在，这表明这些共衍征为以更明确的术语界定蓝藻细菌的几个重要分类进化枝提供了新的且可能有用的手段。这些共衍征的物种分布模式还表明植物/质体同源物并非源自进化枝A或C的蓝藻细菌。
