Figure_3_Assimilatory_APS_PAPS_Reductase_Phylogeny

Figure 3 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea"<br>Files included:Fig3_APS_PAPS_reductase_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig3_APS_PAPS_reductase_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (172 amino acids) used for phylogeneticsFig3_APS_PAPS_Reductase_Phylogeny.png - Final Bayesian Phylogeny of Assimilatory APS/PAPS Reductases<br>Figure 3. Bayesian phylogeny of assimilatory adenyl-sulfate (APS) reductases and phosphoadenylyl-sulfate (PAPS) reductases. APS reductases and putative APS reductases are in green, PAPS reductases and putative PAPS reductases are in blue, bifunctional APS and PAPS reductase of Bacillus subtilis is in teal, and ANME proteins are bolded and in red. Archaeal and Bacterial/Eukaryal sequences formed separate clusters. Asterisks (*) indicate proteins that have been studied biochemically from Archaea (Cho, 2013; Lee et al., 2011), or Bacteria/Eukaryotes (Berndt et al., 2004; Gutierrez-Marcos et al., 1996; Kim et al., 2004; Savage et al., 1997; Suter et al., 2000; Yu et al., 2008). Length of the proteins ranged from 239 to 896 amino acids with the addition of protein domains. The protein domains, if found, are shown with filled symbols. Only 172 amino acid residues of the central shared region were used for phylogenetics. Given that two copies of APS/PAPS reductases were found in each ANME-2 lineage and clustered separately, it is likely one is for APS and the other is for PAPS reduction similar to M. jannaschii (Cho, 2013; Lee et al., 2011). Ca. Methanoperedens and four other methanogens in Methanosarcinales also contained a second putative assimilatory APS reductase more closely related to the bacterial/eukaryotic homologs, while ANME-1b contained a gene that does not cluster with assimilatory APS or PAPS reductases of known substrate. Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site.<br>

《厌氧甲烷氧化古菌同化硫酸盐还原通路的比较基因组学与蛋白质组学分析》论文中的图3<br>包含文件如下：Fig3_APS_PAPS_reductase_clustalo_alignment.faa —— 蛋白质序列的ClustalO（ClustalO）比对文件；Fig3_APS_PAPS_reductase_clustalo_alignment_filtered_for_tree.faa —— 用于系统发育分析的过滤后蛋白质序列（共172个氨基酸残基）；Fig3_APS_PAPS_Reductase_Phylogeny.png —— 同化型腺苷酰硫酸（APS，adenyl-sulfate）还原酶与磷酸腺苷酰硫酸（PAPS，phosphoadenylyl-sulfate）还原酶的最终贝叶斯系统发育图。<br><br>图3：同化型腺苷酰硫酸（APS）还原酶与磷酸腺苷酰硫酸（PAPS）还原酶的贝叶斯系统发育树。其中，APS还原酶及推定APS还原酶以绿色标注，PAPS还原酶及推定PAPS还原酶以蓝色标注，枯草芽孢杆菌（Bacillus subtilis）的双功能APS/PAPS还原酶以蓝绿色标注，厌氧甲烷氧化古菌（Anaerobic Methanotrophic Archaea，ANME）蛋白以红色加粗显示。古菌序列与细菌/真核生物序列各自形成独立聚类簇。星号（*）代表经生化实验验证的蛋白：古菌来源的验证研究对应Cho等（2013）、Lee等（2011）；细菌/真核生物来源的验证研究对应Berndt等（2004）、Gutierrez-Marcos等（1996）、Kim等（2004）、Savage等（1997）、Suter等（2000）、Yu等（2008）。<br><br>本次分析涉及的蛋白质长度介于239至896个氨基酸残基之间，部分蛋白携带额外结构域；若存在结构域，则以实心符号标注。系统发育分析仅选取核心保守区域的172个氨基酸残基进行构建。<br><br>由于每一个ANME-2演化支中均检出两份APS/PAPS还原酶拷贝且二者各自聚类，推测二者功能分别对应APS还原与PAPS还原，这与詹氏甲烷球菌（M. jannaschii）的研究结论一致（Cho等，2013；Lee等，2011）。候选甲烷被孢菌（Ca. Methanoperedens）及甲烷微菌目（Methanosarcinales）中的另外4种产甲烷古菌同样携带第二份推定同化型APS还原酶，其与细菌/真核生物的同源蛋白亲缘关系更近；而ANME-1b所携带的基因则未与已知底物特异性的同化型APS或PAPS还原酶聚类。<br><br>图中括号内标注了NCBI数据库的蛋白质登录号，或IMG数据库的基因ID。分支上的黑色圆点代表贝叶斯后验概率大于90%，标尺刻度代表每位点的氨基酸替换数目。