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Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage

ABSTRACT: Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0. This analysis suggests that C8 challenge causes intracellular acidification and membrane damage.

ORGANISM(S): Escherichia coli Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE53140 | GEO | 2013/12/10

SECONDARY ACCESSION(S): PRJNA230973

REPOSITORIES: GEO

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Project description:Using microarray technology and a set of chickpea (Cicer arietinum L.) unigenes and grasspea (Lathyrus sativus L.) ESTs, chickpea responses to treatments with the defence signalling compounds salicylic acid (SA), methyl jasmonate (MeJA), and aminocyclopropane carboxylic acid (ACC) were studied in four chickpea genotypes with ranging levels of resistance to ascochyta blight (Ascochyta rabiei (Pass.) L.). The experimental system minimized environmental effects and was conducted in reference design, where samples from untreated controls acted as references against post-treatment samples. Robust data quality was achieved through the use of three biological replicates (including a dye-swap), the inclusion of negative controls, and strict selection criteria for differentially expressed genes including a fold change cut-off determined by self-to-self hybridizations, Students t test and multiple testing correction (P<0.05). Microarray observations were also validated by quantitative RT-PCR. The time-course expression patterns of 715 experimental microarray features resulted in differential expression of 425 genes in at least one condition. The A. rabiei resistant chickpea genotypes showed a more substantial range of defence-related gene induction by all treatments, indicating that they may possess stronger abilities to resist infection. Further, the involvement of SA, MeJA, and ACC signalling was identified for the regulation of some important A. rabiei responsive genes, as well as cross-talk between these pathways. This study also found evidence to suggest the involvement of A. rabiei-specific signalling mechanisms for the induction of several genes that were previously implicated in A. rabiei resistance. Overall, this study characterised the regulatory mechanisms of many chickpea genes that may be important in defence against various pathogens, as well as other cellular functions. Although the size of the microarray was limited, the results provided novel insights to the molecular control of chickpea cellular processes, which may assist the understanding of chickpea defence mechanisms and allow enhanced development of disease resistant cultivars. Keywords: time course defence-signalling teatment analysis

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Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage

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