Alejandro-Marín Catalina Maria, Bosch Rafael, Nogales Balbina
Group of Microbiology, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain.
Group of Microbiology, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain.
Mar Genomics. 2014 Oct;17:25-33. doi: 10.1016/j.margen.2014.05.008. Epub 2014 Jun 3.
The protocatechuate branch of the β-ketoadipate pathway is the most common pathway for degradation of monoaromatic compounds in the Roseobacter lineage. We analyzed 43 Roseobacter genomes in order to determine if they possessed all genetic elements for this pathway and if there were common patterns in gene organization. The eight genes of the pathway (pcaG, -H, -B, -C, -D, -I, -J, and -F), possible regulators, and genes encoding for proteins with related function (i.e. catabolism of 4-hydroxybenzoate, catechol, and meta-cleavage of protocatechuate) were predicted by sequence homology analysis. Most of the Roseobacters studied had putatively a complete protocatechuate branch of the β-ketoadipate pathway while 11 of them would probably have an incomplete pathway. Thirty-one Roseobacters would be potentially able of transforming 4-hydroxybenzoate to protocatechuate, and 13 of them might transform catechol via ortho-cleavage, the starting reaction of the catechol branch of the β-ketoadipate pathway. We observed variability in gene organization, with no clear relationship between gene order and Roseobacter taxonomy. Genes were usually organized in several gene clusters. One of the clusters (pcaRIJF) was not reported previously in Roseobacters. The presence of the putative regulator pcaR in these bacteria was also a novel finding. The conserved ORF (chp), encoding for a protein of family DUF849 whose functional role has been proven recently, was detected in 34 genomes. Sequence homology confirmed that proteins encoded by chp corresponded to putative BKACE G4 proteins, which are able to transform β-ketoadipate. Therefore, most Roseobacters seemed to possess two different enzymes for transforming β-ketoadipate. We also report two possible regulation mechanisms of gene pobA (encoding for the enzyme transforming 4-hydroxybenzoate to protocatechuate): via PcaQ, the regulator commonly found with pca genes, and via an independent regulator (PobR). The results of this study evidence the relevance of 4-hydroxybenzoate, protocatechuate and β-ketoadipate degradation pathways in Roseobacters and provide a more complex view of possible regulation mechanisms.
β-酮己二酸途径中的原儿茶酸分支是玫瑰杆菌谱系中单芳香族化合物降解的最常见途径。我们分析了43个玫瑰杆菌基因组，以确定它们是否拥有该途径的所有遗传元件，以及基因组织中是否存在共同模式。通过序列同源性分析预测了该途径的八个基因（pcaG、-H、-B、-C、-D、-I、-J和-F）、可能的调节因子以及编码相关功能蛋白质的基因（即4-羟基苯甲酸的分解代谢、儿茶酚以及原儿茶酸的间位裂解）。大多数被研究的玫瑰杆菌推测拥有β-酮己二酸途径完整的原儿茶酸分支，而其中11个可能具有不完整的途径。31个玫瑰杆菌可能能够将4-羟基苯甲酸转化为原儿茶酸，其中13个可能通过邻位裂解转化儿茶酚，这是β-酮己二酸途径中儿茶酚分支的起始反应。我们观察到基因组织存在变异性，基因顺序与玫瑰杆菌分类学之间没有明显关系。基因通常组织成几个基因簇。其中一个簇（pcaRIJF）以前在玫瑰杆菌中未被报道。这些细菌中假定调节因子pcaR的存在也是一个新发现。在34个基因组中检测到了保守的开放阅读框（chp），其编码最近已证实功能作用的DUF849家族蛋白质。序列同源性证实，chp编码的蛋白质对应于假定的BKACE G4蛋白质，其能够转化β-酮己二酸。因此，大多数玫瑰杆菌似乎拥有两种不同的用于转化β-酮己二酸的酶。我们还报道了基因pobA（编码将4-羟基苯甲酸转化为原儿茶酸的酶）的两种可能调节机制：通过通常与pca基因一起发现的调节因子PcaQ，以及通过一个独立的调节因子（PobR）。这项研究的结果证明了4-羟基苯甲酸、原儿茶酸和β-酮己二酸降解途径在玫瑰杆菌中的相关性，并提供了关于可能调节机制的更复杂观点。
