The essential activities of the bacterial sigma factor

Davis, Maria C.; Kesthely, Christopher A.; Franklin, Emily A.; MacLellan, Shawn R.

doi:10.1139/cjm-2016-0576

Cited by 62 publications

(50 citation statements)

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“…To initiate transcription, a sigma factor directs binding of RNA polymerase to DNA within 50 nt upstream of a TSS ( 35 ). We determined the consensus promoter structure upstream of the 3731 TSS using unbiased motif searching to detect TSS-proximal and TSS-distal motifs corresponding to the −10 and −35 locations of sigma factor binding sites.…”

Section: Resultsmentioning

confidence: 99%

The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978

Kröger

MacKenzie

Alshabib

et al. 2018

Nucleic Acids Research

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We present the first high-resolution determination of transcriptome architecture in the priority pathogen Acinetobacter baumannii. Pooled RNA from 16 laboratory conditions was used for differential RNA-seq (dRNA-seq) to identify 3731 transcriptional start sites (TSS) and 110 small RNAs, including the first identification in A. baumannii of sRNAs encoded at the 3′ end of coding genes. Most sRNAs were conserved among sequenced A. baumannii genomes, but were only weakly conserved or absent in other Acinetobacter species. Single nucleotide mapping of TSS enabled prediction of −10 and −35 RNA polymerase binding sites and revealed an unprecedented base preference at position +2 that hints at an unrecognized transcriptional regulatory mechanism. To apply functional genomics to the problem of antimicrobial resistance, we dissected the transcriptional regulation of the drug efflux pump responsible for chloramphenicol resistance, craA. The two craA promoters were both down-regulated >1000-fold when cells were shifted to nutrient limited medium. This conditional down-regulation of craA expression renders cells sensitive to chloramphenicol, a highly effective antibiotic for the treatment of multidrug resistant infections. An online interface that facilitates open data access and visualization is provided as ‘AcinetoCom’ (http://bioinf.gen.tcd.ie/acinetocom/).

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Section: Resultsmentioning

confidence: 99%

The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978

Kröger

MacKenzie

Alshabib

et al. 2018

Nucleic Acids Research

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“…Sigma factors are essential dissociable subunits of prokaryotic RNA polymerase that control promoter recognition and transcription initiation [ 23 , 24 ]. Primary sigma factors (RpoD, σ 70 family) direct transcription from the promoters of genes required for basic cellular functions.…”

Section: Introductionmentioning

confidence: 99%

The alternative sigma factor RpoQ regulates colony morphology, biofilm formation and motility in the fish pathogen Aliivibrio salmonicida

2018

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BackgroundQuorum sensing (QS) is a cell-to cell communication system that bacteria use to synchronize activities as a group. LitR, the master regulator of QS in Aliivibrio salmonicida, was recently shown to regulate activities such as motility, rugosity and biofilm formation in a temperature dependent manner. LitR was also found to be a positive regulator of rpoQ. RpoQ is an alternative sigma factor belonging to the sigma −70 family. Alternative sigma factors direct gene transcription in response to environmental signals. In this work we have studied the role of RpoQ in biofilm formation, colony morphology and motility of A. salmonicida LFI1238.ResultsThe rpoQ gene in A. salmonicida LFI1238 was deleted using allelic exchange. We found that RpoQ is a strong repressor of rugose colony morphology and biofilm formation, and that it controls motility of the bacteria. We also show that overexpression of rpoQ in a ΔlitR mutant of A. salmonicida disrupts the biofilm produced by the ΔlitR mutant and decreases its motility, whereas rpoQ overexpression in the wild-type completely eliminates the motility.ConclusionThe present work demonstrates that the RpoQ sigma factor is a novel regulatory component involved in modulating motility, colony morphology and biofilm formation in the fish pathogen A. salmonicida. The findings also confirm that RpoQ functions downstream of the QS master regulator LitR. However further studies are needed to elucidate how LitR and RpoQ work together in controlling phenotypes related to QS in A. salmonicida.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1258-9) contains supplementary material, which is available to authorized users.

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“…A noteworthy absentee is the Sigma 70, which is present in 38 species (80%) and essential only in 68% of the species it is found. A member of the sigma 70 is a ubiquitous requirement for bacteria, as its role in housekeeping transcription is supposedly vital (49). Here, we find that while the canonical Sigma 70 is well conserved, a large number of species contain non-homologous members of the sigma 70 protein family.…”

Section: Discussionmentioning

confidence: 85%

Comparative Gene Essentiality across the Bacterial Domain

Shaw

Hermoso

Lluch‐Senar

et al. 2020

Preprint

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Comparative genomics among bacteria has been used to gain insight into the minimal number of conserved genes in biological pathways. Essentiality studies have provided information regarding which genes are non-dispensable (essential, E) for cell growth. Here, we integrated studies of gene conservation, essentiality and function, performed in 47 diverse bacterial species. We showed there is a modest positive correlation between genome size and number of essential genes. Interestingly, we observed a clear shift in the functions assigned to these essential genes as genome size increases. For instance, essential genes related to transcription and translation dominate small genomes. In contrast, in large genomes functions of essential genes are related with cellular processing and metabolism. Finally, and most intriguing, we found a group of genes that while being highly conserved are also typically non-essential. This suggests that some housekeeping genes confer a significant survival benefit in nature while being non-essential in vitro.

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The essential activities of the bacterial sigma factor

Cited by 62 publications

References 90 publications

The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978

The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978

The alternative sigma factor RpoQ regulates colony morphology, biofilm formation and motility in the fish pathogen Aliivibrio salmonicida

Comparative Gene Essentiality across the Bacterial Domain

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