Since the late 1990’s the genome sequences for thousands of species of bacteria have been released into public databases. The release of each new genome sequence typically revealed the presence of tens to hundreds of uncharacterised genes encoding putative membrane proteins and more recently, microbial metagenomics has revealed countless more of these uncharacterised genes. Given the importance of small molecule efflux in bacteria, it is likely that a significant proportion of these genes encode for novel efflux proteins, but the elucidation of these functions is challenging. We used transcriptomics to predict that the function of a gene encoding a hypothetical membrane protein is in efflux-mediated antimicrobial resistance. We subsequently confirmed this function and the likely native substrates of the pump by using detailed biochemical and biophysical analyses. Functional studies of homologs of the protein from other bacterial species determined that the protein is a prototype for a family of multidrug efflux pumps — the Proteobacterial Antimicrobial Compound Efflux (PACE) family. The general functional genomics approach used here, and its expansion to functional metagenomics, will very likely reveal the identities of more efflux pumps and other transport proteins of scientific, clinical and commercial interest in the future.

自 1990 年代后期以来，数千种细菌的基因组序列已被发布到公共数据库中。每个新基因组序列的发布通常揭示存在数十到数百个编码假定膜蛋白的未表征基因，最近，微生物宏基因组学揭示了无数这些未表征基因。鉴于小分子外排在细菌中的重要性，这些基因的很大一部分很可能编码新的外排蛋白，但对这些功能的阐明具有挑战性。我们使用转录组学来预测编码假设膜蛋白的基因的功能是外排介导的抗菌素耐药性。我们随后通过使用详细的生化和生物物理分析证实了这种功能和泵的可能天然底物。对来自其他细菌物种的蛋白质同源物的功能研究确定，该蛋白质是多药外排泵家族的原型——变形菌抗菌复合外排 (PACE) 家族。这里使用的通用功能基因组学方法及其对功能宏基因组学的扩展，很可能会揭示更多外排泵和其他具有科学、临床和商业利益的转运蛋白的特性。