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Kahan R, Worm DJ, de Castro GV, Ng S, Barnard A. Modulators of protein-protein interactions as antimicrobial agents. RSC Chem Biol 2021; 2:387-409. [PMID: 34458791 PMCID: PMC8341153 DOI: 10.1039/d0cb00205d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-Protein interactions (PPIs) are involved in a myriad of cellular processes in all living organisms and the modulation of PPIs is already under investigation for the development of new drugs targeting cancers, autoimmune diseases and viruses. PPIs are also involved in the regulation of vital functions in bacteria and, therefore, targeting bacterial PPIs offers an attractive strategy for the development of antibiotics with novel modes of action. The latter are urgently needed to tackle multidrug-resistant and multidrug-tolerant bacteria. In this review, we describe recent developments in the modulation of PPIs in pathogenic bacteria for antibiotic development, including advanced small molecule and peptide inhibitors acting on bacterial PPIs involved in division, replication and transcription, outer membrane protein biogenesis, with an additional focus on toxin-antitoxin systems as upcoming drug targets.
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Affiliation(s)
- Rashi Kahan
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Dennis J Worm
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Guilherme V de Castro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Simon Ng
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Anna Barnard
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
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2
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Stringer AM, Baniulyte G, Lasek-Nesselquist E, Seed KD, Wade JT. Transcription termination and antitermination of bacterial CRISPR arrays. eLife 2020; 9:e58182. [PMID: 33124980 PMCID: PMC7665894 DOI: 10.7554/elife.58182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences ('repeats') interspersed with short, variable sequences ('spacers'). CRISPR arrays are transcribed and processed into individual CRISPR RNAs that each include a single spacer, and direct Cas proteins to complementary sequences in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho can prematurely terminate transcription of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of transcription termination and antitermination in the evolution of bacterial CRISPR-Cas systems.
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Affiliation(s)
- Anne M Stringer
- Wadsworth Center, New York State Department of HealthAlbanyUnited States
| | - Gabriele Baniulyte
- Department of Biomedical Sciences, School of Public Health, University at AlbanyAlbanyUnited States
| | | | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Joseph T Wade
- Wadsworth Center, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyAlbanyUnited States
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3
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Chauvier A, Nadon JF, Grondin JP, Lamontagne AM, Lafontaine DA. Role of a hairpin-stabilized pause in the Escherichia coli thiC riboswitch function. RNA Biol 2019; 16:1066-1073. [PMID: 31081713 DOI: 10.1080/15476286.2019.1616354] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Transcriptional pauses have been reported in bacterial riboswitches and, in some cases, their specific positioning has been shown to be important for gene regulation. Here, we show that a hairpin structure in the Escherichia coli thiamin pyrophosphate (TPP) thiC riboswitch is involved in transcriptional pausing and ligand sensitivity. Using in vitro transcription kinetic experiments, we show that all three major transcriptional pauses in the thiC riboswitch are affected by NusA, a transcriptional factor known to stimulate hairpin-stabilized pauses. Using a truncated region of the riboswitch, we isolated the hairpin structure responsible for stabilization of the most upstream pause. Destabilization of this structure led to a weaker pause and a decreased NusA effect. In the context of the full-length riboswitch, this same mutation also led to a weaker pause, as well as a decreased TPP binding affinity. Our work suggests that RNA structures involved in transcriptional pausing in riboswitches are important for ligand sensitivity, most likely by increasing the time allowed to the ligand for binding to the riboswitch.
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Affiliation(s)
- Adrien Chauvier
- a Department of Biology, Faculty of Science , RNA Group, Université de Sherbrooke , Sherbrooke , Quebec , Canada
| | - Jean-François Nadon
- a Department of Biology, Faculty of Science , RNA Group, Université de Sherbrooke , Sherbrooke , Quebec , Canada
| | - Jonathan P Grondin
- a Department of Biology, Faculty of Science , RNA Group, Université de Sherbrooke , Sherbrooke , Quebec , Canada
| | - Anne-Marie Lamontagne
- a Department of Biology, Faculty of Science , RNA Group, Université de Sherbrooke , Sherbrooke , Quebec , Canada
| | - Daniel A Lafontaine
- a Department of Biology, Faculty of Science , RNA Group, Université de Sherbrooke , Sherbrooke , Quebec , Canada
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Qayyum MZ, Dey D, Sen R. Transcription Elongation Factor NusA Is a General Antagonist of Rho-dependent Termination in Escherichia coli. J Biol Chem 2016; 291:8090-8108. [PMID: 26872975 DOI: 10.1074/2fjbc.m115.701268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Indexed: 05/22/2023] Open
Abstract
NusA is an essential protein that binds to RNA polymerase and also to the nascent RNA and influences transcription by inducing pausing and facilitating the process of transcription termination/antitermination. Its participation in Rho-dependent transcription termination has been perceived, but the molecular nature of this involvement is not known. We hypothesized that, because both Rho and NusA are RNA-binding proteins and have the potential to target the same RNA, the latter is likely to influence the global pattern of the Rho-dependent termination. Analyses of the nascent RNA binding properties and consequent effects on the Rho-dependent termination functions of specific NusA-RNA binding domain mutants revealed an existence of Rho-NusA direct competition for the overlappingnut(NusA-binding site) andrut(Rho-binding site) sites on the RNA. This leads to delayed entry of Rho at therutsite that inhibits the latter's RNA release process. High density tiling microarray profiles of these NusA mutants revealed that a significant number of genes, together with transcripts from intergenic regions, are up-regulated. Interestingly, the majority of these genes were also up-regulated when the Rho function was compromised. These results provide strong evidence for the existence of NusA-binding sites in different operons that are also the targets of Rho-dependent terminations. Our data strongly argue in favor of a direct competition between NusA and Rho for the access of specific sites on the nascent transcripts in different parts of the genome. We propose that this competition enables NusA to function as a global antagonist of the Rho function, which is unlike its role as a facilitator of hairpin-dependent termination.
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Affiliation(s)
- M Zuhaib Qayyum
- From the Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, 4-1-714 Mozamjahi Road, Nampally, Hyderabad 500 001, India and Graduate Studies, Manipal University, Manipal, Karnataka 576104 India
| | - Debashish Dey
- From the Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, 4-1-714 Mozamjahi Road, Nampally, Hyderabad 500 001, India and
| | - Ranjan Sen
- From the Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, 4-1-714 Mozamjahi Road, Nampally, Hyderabad 500 001, India and
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Rho-dependent transcription termination is essential to prevent excessive genome-wide R-loops in Escherichia coli. Proc Natl Acad Sci U S A 2012; 110:258-63. [PMID: 23251031 DOI: 10.1073/pnas.1213123110] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two pathways of transcription termination, factor-independent and -dependent, exist in bacteria. The latter pathway operates on nascent transcripts that are not simultaneously translated and requires factors Rho, NusG, and NusA, each of which is essential for viability of WT Escherichia coli. NusG and NusA are also involved in antitermination of transcription at the ribosomal RNA operons, as well as in regulating the rates of transcription elongation of all genes. We have used a bisulfite-sensitivity assay to demonstrate genome-wide increase in the occurrence of RNA-DNA hybrids (R-loops), including from antisense and read-through transcripts, in a nusG missense mutant defective for Rho-dependent termination. Lethality associated with complete deficiency of Rho and NusG (but not NusA) was rescued by ectopic expression of an R-loop-helicase UvsW, especially so on defined growth media. Our results suggest that factor-dependent transcription termination subserves a surveillance function to prevent translation-uncoupled transcription from generating R-loops, which would block replication fork progression and therefore be lethal, and that NusA performs additional essential functions as well in E. coli. Prevention of R-loop-mediated transcription-replication conflicts by cotranscriptional protein engagement of nascent RNA is emerging as a unifying theme among both prokaryotes and eukaryotes.
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Muteeb G, Dey D, Mishra S, Sen R. A multipronged strategy of an anti-terminator protein to overcome Rho-dependent transcription termination. Nucleic Acids Res 2012; 40:11213-28. [PMID: 23024214 PMCID: PMC3526286 DOI: 10.1093/nar/gks872] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
One of the important role of Rho-dependent transcription termination in bacteria is to prevent gene expressions from the bacteriophage DNA. The transcription anti-termination systems of the lambdoid phages have been designed to overcome this Rho action. The anti-terminator protein N has three interacting regions, which interact with the mRNA, with the NusA and with the RNA polymerase. Here, we show that N uses all these interaction modules to overcome the Rho action. N and Rho co-occupy their overlapping binding sites on the nascent RNA (the nutR/tR1 site), and this configuration slows down the rate of ATP hydrolysis and the rate of RNA release by Rho from the elongation complex. N-RNA polymerase interaction is not too important for this Rho inactivation process near/at the nutR site. This interaction becomes essential when the elongation complex moves away from the nutR site. From the unusual NusA-dependence property of a Rho mutant E134K, a suppressor of N, we deduced that the N-NusA complex in the anti-termination machinery reduces the efficiency of Rho by removing NusA from the termination pathway. We propose that NusA-remodelling is also one of the mechanisms used by N to overcome the termination signals.
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Affiliation(s)
- Ghazala Muteeb
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, 4-1-714 Mozamjahi Road, Nampally, Hyderabad 500 001, India
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Shashni R, Mishra S, Kalayani BS, Sen R. Suppression of in vivo Rho-dependent transcription termination defects: evidence for kinetically controlled steps. MICROBIOLOGY-SGM 2012; 158:1468-1481. [PMID: 22442304 DOI: 10.1099/mic.0.056804-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The conventional model of Rho-dependent transcription termination in bacteria requires RNA-dependent translocase activity of the termination factor Rho as well as many kinetically controlled steps to execute efficient RNA release from the transcription elongation complex (EC). The involvement of the kinetically controlled steps, such as RNA binding, translocation and RNA release from the EC, means that this termination process must be kinetically coupled to the transcription elongation process. The existence of these steps in vivo has not previously been delineated in detail. Moreover, the requirement for translocase activity in Rho-dependent termination has recently been questioned by a radical view, wherein Rho binds to the elongating RNA polymerase (RNAP) prior to loading onto the mRNA. Using growth assays, microarray analyses and reporter-based transcription termination assays in vivo, we showed that slowing of the transcription elongation rate by using RNAP mutants (rpoB8 and rpoB3445) and growth of the strains in minimal medium suppressed the termination defects of five Rho mutants, three NusG mutants defective for Rho binding and the defects caused by two Rho inhibitors, Psu and bicyclomycin. These results established the existence of kinetically controlled steps in the in vivo Rho-dependent termination process and further reinforced the importance of 'kinetic coupling' between the two molecular motors, Rho and RNAP, and also argue strongly that the Rho translocation model is an accurate representation of the in vivo situation. Finally, these results indicated that one of the major roles of NusG in in vivo Rho-dependent termination is to enhance the speed of RNA release from the EC.
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Affiliation(s)
- Rajesh Shashni
- Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Tuljaguda complex, 4-1-714 Mozamjahi Road, Nampally, Hyderabad - 500 001, India
| | - Saurabh Mishra
- Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Tuljaguda complex, 4-1-714 Mozamjahi Road, Nampally, Hyderabad - 500 001, India
| | - B Sudha Kalayani
- Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Tuljaguda complex, 4-1-714 Mozamjahi Road, Nampally, Hyderabad - 500 001, India
| | - Ranjan Sen
- Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Tuljaguda complex, 4-1-714 Mozamjahi Road, Nampally, Hyderabad - 500 001, India
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Compromised factor-dependent transcription termination in a nusA mutant of Escherichia coli: spectrum of termination efficiencies generated by perturbations of Rho, NusG, NusA, and H-NS family proteins. J Bacteriol 2011; 193:3842-50. [PMID: 21602355 DOI: 10.1128/jb.00221-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The proteins NusA and NusG, which are essential for the viability of wild-type Escherichia coli, participate in various postinitiation steps of transcription including elongation, antitermination, and termination. NusG is required, along with the essential Rho protein, for factor-dependent transcription termination (also referred to as polarity), but the role of NusA is less clear, with conflicting reports that it both promotes and inhibits the process. In this study, we found that a recessive missense nusA mutant [nusA(R258C)] exhibits a transcription termination-defective (that is, polarity-relieved) phenotype, much like missense mutants in rho or nusG, but is unaffected for either the rate of transcription elongation or antitermination in λ phage. Various combinations of the rho, nusG, and nusA mutations were synthetically lethal, and the lethality was suppressed by expression of the N-terminal half of nucleoid protein H-NS. Our results suggest that NusA function is indeed needed for factor-dependent transcription termination and that an entire spectrum of termination efficiencies can be generated by perturbations of the Rho, NusG, NusA, and H-NS family of proteins, with the corresponding phenotypes extending from polarity through polarity relief to lethality.
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Pani B, Ranjan A, Sen R. Interaction surface of bacteriophage P4 protein Psu required for complex formation with the transcription terminator Rho. J Mol Biol 2009; 389:647-60. [PMID: 19409394 DOI: 10.1016/j.jmb.2009.04.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2009] [Revised: 04/20/2009] [Accepted: 04/24/2009] [Indexed: 11/27/2022]
Abstract
Rho-dependent transcription termination is an essential function in prokaryotes, and the transcription terminator Rho is highly conserved among different species. The bacteriophage P4 capsid-decoration protein, Psu, interacts specifically with and inhibits the function of Escherichia coli Rho. The interaction surface of Psu involved in interacting with Rho is not known, but knowledge of this is important to understand the mechanism of its action and will be useful to design peptide inhibitor(s) for Rho. We have isolated and characterized seven Psu mutants defective in interacting with Rho and in exerting anti-Rho activity. Conformational probing of Psu revealed that the N-terminal region of the protein folds over onto its central part, forming a globular domain and leaving a solvent-exposed "tail" in the C-terminus. The mutations are located in both of these domains. N-terminal mutants are instrumental in disrupting the N- to C-terminal "cross-talk" in Psu that is required for its structural integrity and its function. Site-specific cross-linking experiments showed that the C-terminal tail preferentially cross-links to Rho and this region of Psu is protected from limited proteolysis when bound to Rho. Therefore, the mutations in this region may have affected the direct interaction of Psu with Rho. We propose that the globular N-terminal domain of Psu confers structural integrity to the functionally important C-terminal tail, which interacts directly with the hexameric Rho.
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Affiliation(s)
- Bibhusita Pani
- Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, Tuljaguda, Nampally, Hyderabad-500001, India
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