Identification of the Base-Pairing Requirements for Repression of hctA Translation by the Small RNA IhtA Leads to the Discovery of a New mRNA Target in Chlamydia trachomatis

ABSTRACTThe bacterial small RNA (sRNA) SgrS has been a fruitful model for discovery of novel RNA-based regulatory mechanisms and new facets of bacterial physiology and metabolism. SgrS is one of only a few characterized dual-function sRNAs. SgrS can control gene expression posttranscriptionally via sRNA-mRNA base-pairing interactions. Its second function is coding for the small protein SgrT. Previous work demonstrated that both functions contribute to relief of growth inhibition caused by glucose-phosphate stress, a condition characterized by disrupted glycolytic flux and accumulation of sugar phosphates. The base-pairing activity of SgrS has been the subject of numerous studies, but the activity of SgrT is less well characterized. Here, we provide evidence that SgrT acts to specifically inhibit the transport activity of the major glucose permease PtsG. Superresolution microscopy demonstrated that SgrT localizes to the cell membrane in a PtsG-dependent manner. Mutational analysis determined that residues in the N-terminal domain of PtsG are important for conferring sensitivity to SgrT-mediated inhibition of transport activity. Growth assays support a model in which SgrT-mediated inhibition of PtsG transport activity reduces accumulation of nonmetabolizable sugar phosphates and promotes utilization of alternative carbon sources by modulating carbon catabolite repression. The results of this study expand our understanding of a basic and well-studied biological problem, namely, how cells coordinate carbohydrate transport and metabolism. Further, this work highlights the complex activities that can be carried out by sRNAs and small proteins in bacteria.IMPORTANCESequencing, annotation and investigation of hundreds of bacterial genomes have identified vast numbers of small RNAs and small proteins, the majority of which have no known function. In this study, we explore the function of a small protein that acts in tandem with a well-characterized small RNA during metabolic stress to help bacterial cells maintain balanced metabolism and continue growing. Our results indicate that this protein acts on the glucose transport system, inhibiting its activity under stress conditions in order to allow cells to utilize alternative carbon sources. This work sheds new light on a key biological problem: how cells coordinate carbohydrate transport and metabolism. The study also expands our understanding of the functional capacities of small proteins.

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trans-encoded base-pairing small RNA

The Dictionary of Genomics, Transcriptomics and Proteomics ◽

10.1002/9783527678679.dg13576 ◽

2015 ◽

pp. 1-1

Keyword(s):

Small Rna ◽

Base Pairing

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A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA

Molecular Microbiology ◽

10.1111/j.1365-2958.2010.07141.x ◽

2010 ◽

Vol 76 (3) ◽

pp. 782-792 ◽

Cited By ~ 41

Author(s):

Kimika Maki ◽

Teppei Morita ◽

Hironori Otaka ◽

Hiroji Aiba

Keyword(s):

Small Rna ◽

Translational Repression ◽

Base Pairing ◽

Minimal Base ◽

Bacterial Small Rna ◽

Pairing Region

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Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA

Nature Communications ◽

10.1038/s41467-021-21144-0 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Anustup Poddar ◽

Muhammad S. Azam ◽

Tunc Kayikcioglu ◽

Maksym Bobrovskyy ◽

Jichuan Zhang ◽

...

Keyword(s):

Small Rna ◽

Base Pair ◽

High Throughput Sequencing ◽

Base Pairing ◽

Target Search ◽

Single Base ◽

Base Pair Mismatch ◽

Single Base Pair ◽

Bacterial Small Rna

AbstractBase-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Mutations that disrupt binding of a chaperone protein, Hfq, and are distal to the mRNA annealing region still decrease the rate of target association, kon, and increase the dissociation rate, koff, showing that Hfq directly facilitates sRNA–mRNA annealing in vivo. Single base-pair mismatches in the annealing region reduce kon by 24–31% and increase koff by 14–25%, extending the time it takes to find and destroy the target by about a third. The effects of disrupting contiguous base-pairing are much more modest than that expected from thermodynamics, suggesting that Hfq buffers base-pair disruptions.

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