iac gene expression in the indole-3-acetic acid-degrading soil bacterium Enterobacter soli LF7Â

We show for soil bacterium Enterobacter soli LF7 (synonym Enterobacter asburiae LF7a) that possession of a iac (indole 3-acetic acid catabolic) gene cluster is causatively linked to the ability to utilize the plant hormone indole 3-acetic acid (IAA) as a carbon and energy source. Genome-wide transcriptional profiling by mRNA sequencing revealed that these iac genes chromosomally arranged as iacHABICDEFG and coding for the transformation of IAA to catechol, were the most highly induced (>29-fold) among the relatively few (<1%) differentially expressed genes in response to IAA. Also highly induced and immediately downstream of the iac cluster were genes for a Major Facilitator Superfamily protein (mfs) and enzymes of the ß-ketoadipate pathway (pcaIJD-catBCA), which channels catechol into central metabolism. This entire iacHABICDEFG-mfs-pcaIJD-catBCA gene set was constitutively expressed in a iacR deletion mutant, confirming the role of iacR, annotated as coding for a MarR-type regulator and located upstream of iacH, as a repressor of iac gene expression. The research described here was funded from grants #2010-03544 and #2013-02075 awarded to JHJL by the United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) Agriculture and Food Research Initiative (AFRI) Overall design: Orthogonal comparison of gene expression profiles generated by illumina sequencing of RNA from two bacterial strains, i.e. wildtype (wt or WT) Enterobacter soli LF7 and its iacR targeted deletion mutant ?iacR::cat (mut or DeltaR), growing on succinate, and spiked with 200uM indole-3-acetic acid (+IAA or IAA200) or not (-IAA or H2O).本研究以土壤细菌固体肠杆菌LF7（Enterobacter soli LF7，同义名：阿氏肠杆菌LF7a，Enterobacter asburiae LF7a）为研究对象，证实其携带的iac（吲哚-3-乙酸分解）基因簇与利用植物激素吲哚-3-乙酸（IAA）作为碳源与能源的能力存在因果关联。通过mRNA测序进行的全基因组转录组分析结果显示，这些以iacHABICDEFG基因顺序在染色体上排布、负责将IAA转化为儿茶酚的iac基因，在响应IAA的差异表达基因（占比<1%）中上调幅度最高（>29倍）。在iac基因簇下游紧邻区域的基因同样呈现高诱导表达，包括编码主要促进因子超家族蛋白（MFS）的基因，以及β-酮己二酸途径（pcaIJD-catBCA）相关酶编码基因，该途径可将儿茶酚导入中心代谢途径。上述完整的iacHABICDEFG-mfs-pcaIJD-catBCA基因集在iacR缺失突变体中呈组成型表达，这证实了iacR的调控功能：该基因被注释为编码MarR型调控蛋白，位于iacH上游，作为iac基因表达的阻遏蛋白。本研究由美国农业部（USDA）国家食品与农业研究所（NIFA）农业与食品研究倡议（AFRI）向JHJL拨付的编号为#2010-03544与#2013-02075的项目资助。实验设计概述：对两种细菌菌株的基因表达谱进行正交比较，所用菌株为野生型（wt/WT）固体肠杆菌LF7及其靶向iacR缺失突变体ΔiacR::cat（mut/ΔR）。菌株均培养于以琥珀酸盐为碳源的培养基中，并分别补加200μM吲哚-3-乙酸（+IAA/IAA200）或不添加（-IAA/H₂O）。