Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions

Jain, Sakshi; Gupta, Richa; Sen, Ranjan

doi:10.1038/s41467-019-09146-5

Cited by 24 publications

(14 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Over the last decade, it has been established that the Rho-dependent termination has a genome-wide effect ( 20 , 21 , 22 ), which directly or indirectly enabled Rho to function as a regulator of many physiological processes ( 4 ). Our laboratory has recently shown that Rho augments DNA repair ( 6 ) and controls bacterial antibiotic sensitivity via multipartite pathways ( 7 ). Likely, its RNA binding, as well as RNA translocase activities, could also impart its roles in various RNA metabolism processes, RNA chaperone activities, and RNA turnover functions.…”

Section: Discussionmentioning

confidence: 99%

“…It binds to the rut site (Rho utilization; a C-rich unstructured region) of the exiting nascent RNA, and this interaction is a prerequisite for its termination function ( 5 ). This termination function regulates many physiological processes ( 4 , 6 , 7 ), and the conserved nature of the Rho protein in a wide range of bacteria makes it an ideal target for bactericidal agents.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho

Ghosh

Sharma

Kumar

et al. 2021

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

The transcription terminator Rho regulates many physiological processes in bacteria, such as antibiotic sensitivity, DNA repair, RNA remodeling, and so forth, and hence, is a potential antimicrobial target, which is unexplored. The bacteriophage P4 capsid protein, Psu, moonlights as a natural Rho antagonist. Here, we report the design of novel peptides based on the C-terminal region of Psu using phenotypic screening methods. The resultant 38-mer peptides, in addition to containing mutagenized Psu sequences, also contained plasmid sequences, fused to their C termini. Expression of these peptides inhibited the growth of Escherichia coli and specifically inhibited Rhodependent termination in vivo. Peptides 16 and 33 exhibited the best Rho-inhibitory properties in vivo. Direct high-affinity binding of these two peptides to Rho also inhibited the latter's RNA-dependent ATPase and transcription termination functions in vitro. These two peptides remained functional even if eight to ten amino acids were deleted from their C termini. In silico modeling and genetic and biochemical evidence revealed that these two peptides bind to the primary RNA-binding site of the Rho hexamer near its subunit interfaces. In addition, the gene expression profiles of these peptides and Psu overlapped significantly. These peptides also inhibited the growth of Mycobacteria and inhibited the activities of Rho proteins from Mycobacterium tuberculosis, Xanthomonas, Vibrio cholerae, and Salmonella enterica. Our results showed that these novel anti-Rho peptides mimic the Rho-inhibition function of the 42-kDa dimeric bacteriophage P4 capsid protein, Psu. We conclude that these peptides and their C-terminal deletion derivatives could provide a basis on which to design novel antimicrobial peptides.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho

Ghosh

Sharma

Kumar

et al. 2021

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…Regulation of the elongation phase of transcription is important for coordination with other cellular mechanisms [60] and for preserving genome integrity [61]. Conservation of NusG and its functional homologs in all three kingdoms of life highlights the importance of this regulation.…”

Section: Discussionmentioning

confidence: 99%

NusG prevents transcriptional invasion of H-NS-silenced genes

Bossi¹,

Ratel²,

Laurent³

et al. 2019

PLoS Genet

View full text Add to dashboard Cite

Evolutionarily conserved NusG protein enhances bacterial RNA polymerase processivity but can also promote transcription termination by binding to, and stimulating the activity of, Rho factor. Rho terminates transcription upon anchoring to cytidine-rich motifs, the so-called Rho utilization sites (Rut) in nascent RNA. Both NusG and Rho have been implicated in the silencing of horizontally-acquired A/T-rich DNA by nucleoid structuring protein H-NS. However, the relative roles of the two proteins in H-NS-mediated gene silencing remain incompletely defined. In the present study, a Salmonella strain carrying the nusG gene under the control of an arabinose-inducible repressor was used to assess the genome-wide response to NusG depletion. Results from two complementary approaches, i) screening lacZ protein fusions generated by random transposition and ii) transcriptomic analysis, converged to show that loss of NusG causes massive upregulation of Salmonella pathogenicity islands (SPIs) and other H-NS-silenced loci. A similar, although not identical, SPI-upregulated profile was observed in a strain with a mutation in the rho gene, Rho K130Q. Surprisingly, Rho mutation Y80C, which affects Rho’s primary RNA binding domain, had either no effect or made H-NS-mediated silencing of SPIs even tighter. Thus, while corroborating the notion that bound H-NS can trigger Rho-dependent transcription termination in vivo, these data suggest that H-NS-elicited termination occurs entirely through a NusG-dependent pathway and is less dependent on Rut site binding by Rho. We provide evidence that through Rho recruitment, and possibly through other still unidentified mechanisms, NusG prevents pervasive transcripts from elongating into H-NS-silenced regions. Failure to perform this function causes the feedforward activation of the entire Salmonella virulence program. These findings provide further insight into NusG/Rho contribution in H-NS-mediated gene silencing and underscore the importance of this contribution for the proper functioning of a global regulatory response in growing bacteria. The complete set of transcriptomic data is freely available for viewing through a user-friendly genome browser interface.

show abstract

“…Images of the wounded cell monolayers were taken using a microscope (EVOS, Thermo Fisher Scientific, MA, United States) at 0 and 36 h after wounding and controlled by ImageJ software (National Institutes of Health, Bethesda, Maryland, USA). All experiments were performed in the presence of Mitomycin-C (10 μM, Selleck Chemicals, S8146) [ 37 ] to inhibit cell proliferation.…”

Section: Methodsmentioning

confidence: 99%

bFGF alleviates diabetes-associated endothelial impairment by downregulating inflammation via S-nitrosylation pathway

Chen

Huang

et al. 2021

Redox Biology

View full text Add to dashboard Cite

Protein S-nitrosylation is a reversible protein modification implicated in both physiological and pathophysiological regulation of protein function. However, the relationship between dysregulated S-nitrosylation homeostasis and diabetic vascular complications remains incompletely understood. Here, we demonstrate that basic fibroblast growth factor (bFGF) is a key regulatory link between S-nitrosylation homeostasis and inflammation, and alleviated endothelial dysfunction and angiogenic defects in diabetes. Subjecting human umbilical vein endothelial cells (HUVECs) to hyperglycemia and hyperlipidemia significantly decreased endogenous S -nitrosylated proteins, including S-nitrosylation of inhibitor kappa B kinase β (IKKβ C179 ) and transcription factor p65 (p65 C38 ), which was alleviated by bFGF co-treatment. Pretreatment with carboxy-PTIO (c-PTIO), a nitric oxide scavenger, abolished bFGF-mediated S-nitrosylation increase and endothelial protection. Meanwhile, nitrosylation-resistant IKKβ C179S and p65 C38S mutants exacerbated endothelial dysfunction in db/db mice, and in cultured HUVECs subjected to hyperglycemia and hyperlipidemia. Mechanistically, bFGF-mediated increase of S-nitrosylated IKKβ and p65 was attributed to synergistic effects of increased endothelial nitric oxide synthase (eNOS) and thioredoxin (Trx) activity. Taken together, the endothelial protective effect of bFGF under hyperglycemia and hyperlipidemia can be partially attributed to its role in suppressing inflammation via the S-nitrosylation pathway.

show abstract

Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions

Cited by 24 publications

References 47 publications

Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho

Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho

NusG prevents transcriptional invasion of H-NS-silenced genes

bFGF alleviates diabetes-associated endothelial impairment by downregulating inflammation via S-nitrosylation pathway

Contact Info

Product

Resources

About