16 April 2019

Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.

DOI : 10.1186/s12864-019-5619-z

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Ernesto Pérez-Rueda, PhD.

BACKGROUND: Crl, identified for curli production, is a small transcription

factor that stimulates the association of the σS factor (RpoS) with the RNA

polymerase core through direct and specific interactions, increasing the

transcription rate of genes during the transition from exponential to stationary

phase at low temperatures, using indole as an effector molecule. The lack of a

comprehensive collection of information on the Crl regulon makes it difficult to

identify a dominant function of Crl and to generate any hypotheses concerning

its taxonomical distribution in archaeal and bacterial organisms.

RESULTS: In this work, based on a systematic literature review, we identified

the first comprehensive dataset of 86 genes under the control of Crl in the

bacterium Escherichia coli K-12; those genes correspond to 40% of the σS regulon

in this bacterium. Based on an analysis of orthologs in 18 archaeal and 69

bacterial taxonomical divisions and using E. coli K-12 as a framework, we

suggest three main events that resulted in this regulon's actual form: (i) in a

first step, rpoS, a gene widely distributed in bacteria and archaea cellular

domains, was recruited to regulate genes involved in ancient metabolic

processes, such as those associated with glycolysis and the tricarboxylic acid

cycle; (ii) in a second step, the regulon recruited those genes involved in

metabolic processes, which are mainly taxonomically constrained to

Proteobacteria, with some secondary losses, such as those genes involved in

responses to stress or starvation and cell adhesion, among others; and (iii) in

a posterior step, Crl might have been recruited in Enterobacteriaceae; because

its taxonomical pattern constrained to this bacterial order, however further

analysis are necessary.

CONCLUSIONS: Therefore, we suggest that the regulon Crl is highly flexible for

phenotypic adaptation, probably as consequence of the diverse growth

environments associated with all organisms in which members of this regulatory

network are present.

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Ernesto Pérez-Rueda

Edificio2

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