Department of Biological Sciences, University of Delaware, 341 Wolf Hall, Newark, DE, 19716, USA.
BMC Microbiol. 2019 May 27;19(1):112. doi: 10.1186/s12866-019-1487-6.
Utilizing unique carbohydrates or utilizing them more efficiently help bacteria expand and colonize new niches. Horizontal gene transfer (HGT) of catabolic systems is a powerful mechanism by which bacteria can acquire new phenotypic traits that can increase survival and fitness in different niches. In this work, we examined carbon catabolism diversity among Vibrio parahaemolyticus, a marine species that is also an important human and fish pathogen.
Phenotypic differences in carbon utilization between Vibrio parahaemolyticus strains lead us to examine genotypic differences in this species and the family Vibrionaceae in general. Bioinformatics analysis showed that the ability to utilize D-galactose was present in all V. parahaemolyticus but at least two distinct transporters were present; a major facilitator superfamily (MFS) transporter and a sodium/galactose transporter (SGLT). Growth and genetic analyses demonstrated that SGLT was a more efficient transporter of D-galactose and was the predominant type among strains. Phylogenetic analysis showed that D-galactose gene galM was acquired multiples times within the family Vibrionaceae and was transferred between distantly related species. The ability to utilize D-gluconate was universal within the species. Deletion of eda (VP0065), which encodes aldolase, a key enzyme in the Entner-Doudoroff (ED) pathway, reached a similar biomass to wild type when grown on D-gluconate as a sole carbon source. Two additional eda genes were identified, VPA1708 (eda2) associated with a D-glucuronate cluster and VPA0083 (eda3) that clustered with an oligogalacturonide (OGA) metabolism cluster. EDA2 and EDA3 were variably distributed among the species. A metabolic island was identified that contained citrate fermentation, L-rhamnose and OGA metabolism clusters as well as a CRISPR-Cas system. Phylogenetic analysis showed that CitF and RhaA had a limited distribution among V. parahaemolyticus, and RhaA was acquired at least three times. Within V. parahaemolyticus, two different regions contained the gene for L-arabinose catabolism and most strains had the ability to catabolism this sugar.
Our data suggest that horizontal transfer of metabolic systems among Vibrionaceae is an important source of metabolic diversity. This work identified four EDA homologues suggesting that the ED pathway plays a significant role in metabolism. We describe previously uncharacterized metabolism islands that were hotspots for the gain and loss of functional modules likely mediated by transposons.
利用独特的碳水化合物或更有效地利用它们，有助于细菌扩展并殖民新的小生境。分解代谢系统的水平基因转移（HGT）是细菌获得新表型特征的强大机制，这些特征可以提高在不同小生境中的生存和适应能力。在这项工作中，我们研究了副溶血弧菌（一种海洋物种，也是重要的人类和鱼类病原体）中的碳分解代谢多样性。
副溶血弧菌菌株之间在碳利用方面的表型差异促使我们检查该物种以及整个弧菌科的基因型差异。生物信息学分析表明，所有副溶血弧菌都具有利用 D-半乳糖的能力，但至少存在两种不同的转运蛋白；一种是主要易化剂超家族（MFS）转运蛋白，另一种是钠/半乳糖转运蛋白（SGLT）。生长和遗传分析表明，SGLT 是 D-半乳糖的更有效转运蛋白，并且在菌株中占主导地位。系统发育分析表明，D-半乳糖基因 galM 在弧菌科内多次获得，并在亲缘关系较远的物种之间转移。该物种内普遍具有利用 D-葡萄糖酸的能力。当仅以 D-葡萄糖酸作为碳源生长时，缺失编码关键酶醛缩酶的 eda（VP0065）的突变株与野生型达到相似的生物量。鉴定出另外两个 eda 基因，VPA1708（eda2）与 D-葡萄糖醛酸簇相关，VPA0083（eda3）与寡半乳糖醛酸（OGA）代谢簇聚类。EDA2 和 EDA3 在物种间的分布不同。鉴定出一个代谢岛，其中包含柠檬酸发酵、L-鼠李糖和 OGA 代谢簇以及 CRISPR-Cas 系统。系统发育分析表明，CitF 和 RhaA 在副溶血弧菌中的分布有限，并且 RhaA 至少获得了三次。在副溶血弧菌中，两个不同的区域包含 L-阿拉伯糖分解代谢基因，大多数菌株都具有分解这种糖的能力。
我们的数据表明，弧菌科之间代谢系统的水平转移是代谢多样性的重要来源。这项工作鉴定了四个 EDA 同源物，表明 ED 途径在代谢中起着重要作用。我们描述了以前未表征的代谢岛，这些代谢岛是功能模块获得和丧失的热点，可能由转座子介导。
