Table_1_Genome-Wide Identification of Myxobacterial Predation Genes and Demonstration of Formaldehyde Secretion as a Potentially Predation-Resistant Trait of Pseudomonas aeruginosa.xlsx

Despite widespread use in human biology, genome-wide association studies (GWAS) of bacteria are few and have, to date, focused primarily on pathogens. Myxobacteria are predatory microbes with large patchwork genomes, with individual strains secreting unique cocktails of predatory proteins and metabolites. We investigated whether a GWAS strategy could be applied to myxobacteria to identify genes associated with predation. Deduced proteomes from 29 myxobacterial genomes (including eight Myxococcus genomes sequenced for this study), were clustered into orthologous groups, and the presence/absence of orthologues assessed in superior and inferior predators of ten prey organisms. 139 ‘predation genes’ were identified as being associated significantly with predation, including some whose annotation suggested a testable predatory mechanism. Formaldehyde dismutase (fdm) was associated with superior predation of Pseudomonas aeruginosa, and predatory activity of a strain lacking fdm could be increased by the exogenous addition of a formaldehyde detoxifying enzyme, suggesting that production of formaldehyde by P. aeruginosa acts as an anti-predation behaviour. This study establishes the utility of bacterial GWAS to investigate microbial processes beyond pathogenesis, giving plausible and verifiable associations between gene presence/absence and predatory phenotype. We propose that the slow growth rate of myxobacteria, coupled with their predatory mechanism of constitutive secretion, has rendered them relatively resistant to genome streamlining. The resultant genome expansion made possible their observed accumulation of prey-specific predatory genes, without requiring them to be selected for by frequent or recent predation on diverse prey, potentially explaining both the large pan-genome and broad prey range of myxobacteria.

尽管全基因组关联研究（genome-wide association studies, GWAS）在人类生物学中应用广泛，但针对细菌的GWAS却为数不多，且迄今为止主要集中于病原菌。黏球菌（Myxobacteria）是一类具有拼接状复杂基因组的捕食性微生物，不同菌株会分泌独特的捕食蛋白与代谢物组合。本研究探究了能否将GWAS策略应用于黏球菌，以鉴定与捕食功能相关的基因。我们对29个黏球菌基因组（包含本研究中新测序的8个黏球菌属（Myxococcus）基因组）推导得到的蛋白质组进行聚类，构建直系同源组（orthologous groups），并评估了直系同源基因在10种猎物的优势捕食者与劣势捕食者中的存在与缺失情况。最终鉴定出139个与捕食功能显著相关的“捕食相关基因”，其中部分基因的注释结果提示了可验证的捕食机制。甲醛歧化酶（formaldehyde dismutase, fdm）与铜绿假单胞菌（Pseudomonas aeruginosa）的高效捕食能力相关；缺失fdm的菌株的捕食活性可通过外源添加甲醛解毒酶得到增强，这表明铜绿假单胞菌产生的甲醛可作为一种反捕食防御行为。本研究证实了细菌GWAS可用于研究病原菌致病以外的微生物过程，为基因存在/缺失与捕食表型之间建立了合理且可验证的关联。我们提出，黏球菌缓慢的生长速率与其组成型分泌的捕食机制相结合，使其相对不易发生基因组精简。由此产生的基因组扩增使得它们能够积累猎物特异性捕食基因，而无需通过频繁或近期在多种猎物上的捕食进行选择，这或许可以解释黏球菌庞大的泛基因组（pan-genome）与宽泛的猎物范围。