Abstract
Bacterial physiology is regulated at different levels, from mRNA synthesis to translational regulation and protein modification. Herein, we propose a parameter, dubbed post-transcriptional variation (PTV), that allows extracting information on post-transcriptional regulation from the combined analysis of transcriptomic and proteomic data. We have applied this parameter for getting a deeper insight in the regulon of the Pseudomonas aeruginosa post-transcriptional regulator Crc. P. aeruginosa is a free-living microorganism, and part of its ecological success relies on its capability of using a large number of carbon sources. The hierarchical assimilation of these sources when present in combination is regulated by Crc that, together with Hfq (the RNA-binding chaperon in the complex), impedes their translation when catabolite repression is triggered. Most studies on Crc regulation are based either in transcriptomics or in proteomics data, which cannot provide information on post-transcriptional regulation when analysed independently. Using the PTV parameter, we present a comprehensive map of the Crc post-transcriptional regulon. In addition of controlling the use of primary and secondary carbon sources, Crc regulates as well cell respiration, c-di-GMP mediated signalling, and iron utilization. Thus, besides controlling the hyerarchical assimilation of carbon sources, Crc is an important element for keeping bacterial homeostasis and, consequently, metabolic robustness.
Highlights
P. aeruginosa is an important opportunistic pathogen able to live in different ecosystems as well as to infect immunocompromised patients
Transcriptomic is insufficient to describe the direct targets of Crc regulation, since the information is at the mRNA level and the effect of Crc is at the level of translation
While the analysis of the differential recovery of mRNAs bound to this regulator is useful for defining its potential targets, this methodology does not allow to get a direct picture of the effect of this potential binding on the actual translational regulation of the messengers, which is only formally provided when more specific assays, as the translation fusions described in the same article, are made
Summary
P. aeruginosa is an important opportunistic pathogen able to live in different ecosystems as well as to infect immunocompromised patients. To perform a global analysis of the post-transcriptional effect of Crc on P. aeruginosa physiology, we have compared the transcriptomes and proteomes of a Crc deficient mutant with those of its parental wild-type strain and have defined a novel parameter, dubbed as post-transcriptional variation parameter, to track post-transcriptional regulation at a global scale. Using this parameter, we have been able to describe more precisely the network of Crc-associated post-transcriptional regulation in P. aeruginosa. In addition to the specific application to the study of Crc, the post-transcriptional variation parameter defined in our work, is a simple tool for identifying the elements of translational regulons at a global scale
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