Trotter Valentine V, Shatsky Maxim, Price Morgan N, Juba Thomas R, Zane Grant M, De León Kara B, Majumder Erica L-W, Gui Qin, Ali Rida, Wetmore Kelly M, Kuehl Jennifer V, Arkin Adam P, Wall Judy D, Deutschbauer Adam M, Chandonia John-Marc, Butland Gareth P
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Department of Biochemistry, University of Missouri, Columbia, MO, United States.
Front Microbiol. 2023 Mar 31;14:1095191. doi: 10.3389/fmicb.2023.1095191. eCollection 2023.
Sulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.
硫酸盐还原菌（SRB）是专性厌氧菌，能够将其生长与硫酸盐的还原相耦合。尽管SRB对全球养分循环很重要，且对石油工业造成损害，但我们对其生理学的分子理解仍然有限。为了系统地提供关于SRB生物学的新见解，我们在模式SRB希登伯勒菌（DvH）中构建了一个随机条形码转座子突变体文库，并利用这个全基因组资源来测定其基因在一系列代谢和应激条件下的重要性。除了定义DvH的必需基因集外，我们还确定了1137个非必需基因的条件表型。通过检查这些条件表型，我们能够对DvH的分子理解有一些新的认识，包括这种细菌如何合成维生素。例如，我们确定DVU0867是泛酸合成所需的非典型L-天冬氨酸脱羧酶，提供了第一个实验证据，即DvH中的生物素合成发生在一种特殊的酰基载体蛋白上且没有甲酯，并证明未表征的脱氢酶DVU0826:DVU0827是磷酸吡哆醛合成所必需的。此外，我们利用突变体适应性数据来鉴定参与多种氮源同化的基因，并深入了解氯酸盐和钼酸盐的抑制机制。我们的大规模适应性数据集和RB-TnSeq突变体文库是全社区范围的资源，可用于对这一在环境和工业上具有重要意义的细菌群体的基因功能产生进一步可检验的假设。
