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Gupta KR, Arora G, Mattoo A, Sajid A. Stringent Response in Mycobacteria: From Biology to Therapeutic Potential. Pathogens 2021; 10:pathogens10111417. [PMID: 34832573 PMCID: PMC8622095 DOI: 10.3390/pathogens10111417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 01/16/2023] Open
Abstract
Mycobacterium tuberculosis is a human pathogen that can thrive inside the host immune cells for several years and cause tuberculosis. This is due to the propensity of M. tuberculosis to synthesize a sturdy cell wall, shift metabolism and growth, secrete virulence factors to manipulate host immunity, and exhibit stringent response. These attributes help M. tuberculosis to manage the host response, and successfully establish and maintain an infection even under nutrient-deprived stress conditions for years. In this review, we will discuss the importance of mycobacterial stringent response under different stress conditions. The stringent response is mediated through small signaling molecules called alarmones “(pp)pGpp”. The synthesis and degradation of these alarmones in mycobacteria are mediated by Rel protein, which is both (p)ppGpp synthetase and hydrolase. Rel is important for all central dogma processes—DNA replication, transcription, and translation—in addition to regulating virulence, drug resistance, and biofilm formation. Rel also plays an important role in the latent infection of M. tuberculosis. Here, we have discussed the literature on alarmones and Rel proteins in mycobacteria and highlight that (p)ppGpp-analogs and Rel inhibitors could be designed and used as antimycobacterial compounds against M. tuberculosis and non-tuberculous mycobacterial infections.
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Affiliation(s)
| | - Gunjan Arora
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - Abid Mattoo
- Pharmaceutical Development, Ultragenyx Gene Therapy, Woburn, MA 01801, USA;
| | - Andaleeb Sajid
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA;
- Correspondence: or
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Mauri M, Klumpp S. A model for sigma factor competition in bacterial cells. PLoS Comput Biol 2014; 10:e1003845. [PMID: 25299042 PMCID: PMC4191881 DOI: 10.1371/journal.pcbi.1003845] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 08/04/2014] [Indexed: 12/20/2022] Open
Abstract
Sigma factors control global switches of the genetic expression program in bacteria. Different sigma factors compete for binding to a limited pool of RNA polymerase (RNAP) core enzymes, providing a mechanism for cross-talk between genes or gene classes via the sharing of expression machinery. To analyze the contribution of sigma factor competition to global changes in gene expression, we develop a theoretical model that describes binding between sigma factors and core RNAP, transcription, non-specific binding to DNA and the modulation of the availability of the molecular components. The model is validated by comparison with in vitro competition experiments, with which excellent agreement is found. Transcription is affected via the modulation of the concentrations of the different types of holoenzymes, so saturated promoters are only weakly affected by sigma factor competition. However, in case of overlapping promoters or promoters recognized by two types of sigma factors, we find that even saturated promoters are strongly affected. Active transcription effectively lowers the affinity between the sigma factor driving it and the core RNAP, resulting in complex cross-talk effects. Sigma factor competition is not strongly affected by non-specific binding of core RNAPs, sigma factors and holoenzymes to DNA. Finally, we analyze the role of increased core RNAP availability upon the shut-down of ribosomal RNA transcription during the stringent response. We find that passive up-regulation of alternative sigma-dependent transcription is not only possible, but also displays hypersensitivity based on the sigma factor competition. Our theoretical analysis thus provides support for a significant role of passive control during that global switch of the gene expression program. Bacteria respond to changing environmental conditions by switching the global pattern of expressed genes. A key mechanism for global switches of the transcriptional program depends on alternative sigma factors that bind the RNA polymerase core enzyme and direct it towards the appropriate stress response genes. Competition of different sigma factors for a limited amount of RNA polymerase is believed to play a central role in this global switch. Here, a theoretical approach is used towards a quantitative understanding of sigma factor competition and its effects on gene expression. The model is used to quantitatively describe in vitro competition assays and to address the question of indirect or passive control in the stringent response upon amino acids starvation. We show that sigma factor competition provides a mechanism for a passive up-regulation of the stress specific sigma-driven genes due to the increased availability of RNA polymerase in the stringent response. Moreover, we find that active separation of sigma factor from the RNA polymerase during early transcript elongation weakens the sigma factor-RNA polymerase equilibrium constant, raising the question of how their in vitro measure is relevant in the cell.
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Affiliation(s)
- Marco Mauri
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- * E-mail:
| | - Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
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Barańska S, Glinkowska M, Herman-Antosiewicz A, Maciąg-Dorszyńska M, Nowicki D, Szalewska-Pałasz A, Węgrzyn A, Węgrzyn G. Replicating DNA by cell factories: roles of central carbon metabolism and transcription in the control of DNA replication in microbes, and implications for understanding this process in human cells. Microb Cell Fact 2013; 12:55. [PMID: 23714207 PMCID: PMC3698200 DOI: 10.1186/1475-2859-12-55] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/26/2013] [Indexed: 12/29/2022] Open
Abstract
Precise regulation of DNA replication is necessary to ensure the inheritance of genetic features by daughter cells after each cell division. Therefore, determining how the regulatory processes operate to control DNA replication is crucial to our understanding and application to biotechnological processes. Contrary to early concepts of DNA replication, it appears that this process is operated by large, stationary nucleoprotein complexes, called replication factories, rather than by single enzymes trafficking along template molecules. Recent discoveries indicated that in bacterial cells two processes, central carbon metabolism (CCM) and transcription, significantly and specifically influence the control of DNA replication of various replicons. The impact of these discoveries on our understanding of the regulation of DNA synthesis is discussed in this review. It appears that CCM may influence DNA replication by either action of specific metabolites or moonlighting activities of some enzymes involved in this metabolic pathway. The role of transcription in the control of DNA replication may arise from either topological changes in nucleic acids which accompany RNA synthesis or direct interactions between replication and transcription machineries. Due to intriguing similarities between some prokaryotic and eukaryotic regulatory systems, possible implications of studies on regulation of microbial DNA replication on understanding such a process occurring in human cells are discussed.
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Affiliation(s)
- Sylwia Barańska
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, Gdańsk 80-308, Poland
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Nejman B, Nadratowska-Wesołowska B, Szalewska-Pałasz A, Węgrzyn A, Węgrzyn G. Replication of plasmids derived from Shiga toxin-converting bacteriophages in starved Escherichia coli. MICROBIOLOGY-SGM 2010; 157:220-233. [PMID: 20829283 DOI: 10.1099/mic.0.042820-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The pathogenicity of Shiga toxin-producing Escherichia coli (STEC) depends on the expression of stx genes that are located on lambdoid prophages. Effective toxin production occurs only after prophage induction, and one may presume that replication of the phage genome is important for an increase in the dosage of stx genes, positively influencing their expression. We investigated the replication of plasmids derived from Shiga toxin (Stx)-converting bacteriophages in starved E. coli cells, as starvation conditions may be common in the intestine of infected humans. We found that, unlike plasmids derived from bacteriophage λ, the Shiga toxin phage-derived replicons did not replicate in amino acid-starved relA(+) and relA(-) cells (showing the stringent and relaxed responses to starvation, respectively). The presence of the stable fraction of the replication initiator O protein was detected in all tested replicons. However, while ppGpp, the stringent response effector, inhibited the activities of the λ P(R) promoter and its homologues from Shiga toxin-converting bacteriophages, these promoters, except for λ P(R), were only weakly stimulated by the DksA protein. We suggest that this less efficient (relative to λ) positive regulation of transcription responsible for transcriptional activation of the origin contributes to the inhibition of DNA replication initiation of Shiga toxin-converting bacteriophages in starved host cells, even in the absence of ppGpp (as in starved relA(-) hosts). Possible clinical implications of these results are discussed.
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Affiliation(s)
- Bożena Nejman
- Department of Molecular Biology, University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
| | | | | | - Alicja Węgrzyn
- Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
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Nadratowska-Wesołowska B, Słomińska-Wojewódzka M, Łyzeń R, Wegrzyn A, Szalewska-Pałasz A, Wegrzyn G. Transcription regulation of the Escherichia coli pcnB gene coding for poly(A) polymerase I: roles of ppGpp, DksA and sigma factors. Mol Genet Genomics 2010; 284:289-305. [PMID: 20700605 PMCID: PMC2939334 DOI: 10.1007/s00438-010-0567-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Accepted: 07/24/2010] [Indexed: 12/27/2022]
Abstract
Poly(A) polymerase I (PAP I), encoded by the pcnB gene, is a major enzyme responsible for RNA polyadenylation in Escherichia coli, a process involved in the global control of gene expression in this bacterium through influencing the rate of transcript degradation. Recent studies have suggested a complicated regulation of pcnB expression, including a complex promoter region, a control at the level of translation initiation and dependence on bacterial growth rate. In this report, studies on transcription regulation of the pcnB gene are described. Results of in vivo and in vitro experiments indicated that (a) there are three σ70-dependent (p1, pB, and p2) and two σS-dependent (pS1 and pS2) promoters of the pcnB gene, (b) guanosine tetraphosphate (ppGpp) and DksA directly inhibit transcription from pB, pS1 and pS2, and (c) pB activity is drastically impaired at the stationary phase of growth. These results indicate that regulation of the pcnB gene transcription is a complex process, which involves several factors acting to ensure precise control of PAP I production. Moreover, inhibition of activities of pS1 and pS2 by ppGpp and DksA suggests that regulation of transcription from promoters requiring alternative σ factors by these effectors of the stringent response might occur according to both passive and active models.
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Maciag M, Kochanowska M, Lyzeń R, Wegrzyn G, Szalewska-Pałasz A. ppGpp inhibits the activity of Escherichia coli DnaG primase. Plasmid 2009; 63:61-7. [PMID: 19945481 DOI: 10.1016/j.plasmid.2009.11.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 11/17/2009] [Accepted: 11/22/2009] [Indexed: 11/28/2022]
Abstract
DNA primase is an enzyme required for replication of both chromosomes and vast majority of plasmids. Guanosine tetra- and penta-phosphate (ppGpp and pppGpp, respectively) are alarmones of the bacterial stringent response to starvation and stress conditions, and act by modulation of the RNA polymerase activity. Recent studies indicated that the primase-catalyzed reaction is also inhibited by (p)ppGpp in Bacillus subtilis, where a specific regulation of DNA replication elongation, the replication fork arrest, was discovered. Although in Escherichia coli such a replication regulation was not reported to date, here we show that E. coli DnaG primase is directly inhibited by ppGpp and pppGpp. However, contrary to the B. subtilis primase response to the stringent control alarmones, the E, coli DnaG was inhibited more efficiently by ppGpp than by pppGpp.
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Affiliation(s)
- Monika Maciag
- Department of Molecular Biology, University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
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Stepanova EV, Shevelev AB, Borukhov SI, Severinov KV. Mechanisms of action of RNA polymerase-binding transcription factors that do not bind to DNA. Biophysics (Nagoya-shi) 2009. [DOI: 10.1134/s0006350909050017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Łyzen R, Kochanowska M, Wegrzyn G, Szalewska-Palasz A. Transcription from bacteriophage lambda pR promoter is regulated independently and antagonistically by DksA and ppGpp. Nucleic Acids Res 2009; 37:6655-64. [PMID: 19759216 PMCID: PMC2777414 DOI: 10.1093/nar/gkp676] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The stringent response effector, guanosine tetraphosphate (ppGpp), adjust gene expression and physiology in bacteria, by affecting the activity of various promoters. RNA polymerase-interacting protein, DksA, was proposed to be the co-factor of ppGpp effects; however, there are reports suggesting independent roles of these regulators. Bacteriophage λ major lytic promoter, pR, is down-regulated by the stringent response and ppGpp. Here, we present evidence that DksA significantly stimulates pR-initiated transcription in vitro in the reconstituted system. DksA is also indispensable for pR activity in vivo. DksA-mediated activation of pR-initiated transcription is predominant over ppGpp effects in the presence of both regulators in vitro. The possible role of the opposite regulation by ppGpp and DksA in λ phage development is discussed. The major mechanism of DksA-mediated activation of transcription from pR involves facilitating of RNA polymerase binding to the promoter region, which results in more productive transcription initiation. Thus, our results provide evidence for the first promoter inhibited by ppGpp that can be stimulated by the DksA protein both in vivo and in vitro. Therefore, DksA role could be not only independent but antagonistic to ppGpp in transcription regulation.
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Affiliation(s)
- Robert Łyzen
- Department of Molecular Biology, University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
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Janga SC, Babu MM. Transcript stability in the protein interaction network of Escherichia coli. MOLECULAR BIOSYSTEMS 2008; 5:154-62. [PMID: 19156261 DOI: 10.1039/b816845h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Gene expression is a dynamic process which can be controlled by a number of mechanisms as genetic information flows from nucleic acids to proteins. The study of gene expression in the steady state, while informative, overlooks the underlying dynamics of the processes. Steady-state transcript levels are a result of both RNA synthesis and degradation, and as such, measurements of degradation rates can be used to determine their rates of synthesis as well as reveal regulation that occurs via changes in RNA stability. Messenger RNA degradation plays a central role in diverse cellular processes and is controlled primarily by the activity of the degradosome in prokaryotes. In this study, we use the currently available network of protein-protein interactions (PPIs) and mRNA half-lives in Escherichia coli to demonstrate that centrality of a protein in the PPI network is strongly correlated with its mRNA half-life. We find that interacting proteins tend to show similar half-lives, commonly referred to as assortative behavior in networks, which is frequently found in biological and social networks. While a major fraction of the interacting proteins show significantly lower differences in mRNA stabilities, a smaller but significant number of protein pairs tend to show higher differences than expected by chance. Higher differences in transcript stabilities often involved those that encode for transcription factors and enzymes, suggesting a feedback link at the post-translational level. We also note that although essential genes, which act as a proxy for in vivo centrality in PPI networks, are highly expressed compared to non-essential ones, they do not encode for more stable transcripts than non-essential genes. Our results provide a direct link between mRNA stability and centrality of a protein in PPI network indicating the importance of post-transcriptional mechanisms on nascent RNAs in the cell.
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Abstract
The fundamental details of how nutritional stress leads to elevating (p)ppGpp are questionable. By common usage, the meaning of the stringent response has evolved from the specific response to (p)ppGpp provoked by amino acid starvation to all responses caused by elevating (p)ppGpp by any means. Different responses have similar as well as dissimilar positive and negative effects on gene expression and metabolism. The different ways that different bacteria seem to exploit their capacities to form and respond to (p)ppGpp are already impressive despite an early stage of discovery. Apparently, (p)ppGpp can contribute to regulation of many aspects of microbial cell biology that are sensitive to changing nutrient availability: growth, adaptation, secondary metabolism, survival, persistence, cell division, motility, biofilms, development, competence, and virulence. Many basic questions still exist. This review tries to focus on some issues that linger even for the most widely characterized bacterial strains.
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Affiliation(s)
- Katarzyna Potrykus
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-2785, USA.
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Lyzeń R, Kochanowska M, Wegrzyn G, Szalewska-Pałasz A. IHF- and SeqA-binding sites, present in plasmid cloning vectors, may significantly influence activities of promoters. Plasmid 2008; 60:125-30. [PMID: 18590762 DOI: 10.1016/j.plasmid.2008.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2008] [Accepted: 06/04/2008] [Indexed: 12/01/2022]
Abstract
Escherichia coli Integration Host Factor (IHF) regulates transcription from some bacterial and phage promoters by affecting DNA topology. Here we demonstrate that IHF affects transcription from bacteriophage lambdapR promoter and the ptac promoter located on plasmids that contain IHF-binding sites. The IHF consensus sites are abundant and they can bind the IHF protein as shown in in vitro studies. The SeqA protein has a role in the complex regulation of pR activity, together with other factors altering DNA topology. Down-regulation of the transcription from ptac in the absence of IHF, together with IHF- and SeqA-mediated effects on pR, suggest that DNA topology cannot be underestimated when assessing in vivo promoters' activity. This may have a significant impact on experiments employing recombinant genes cloned in plasmids and on choosing appropriate plasmid vectors.
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Affiliation(s)
- Robert Lyzeń
- Department of Molecular Biology, University of Gdańsk, Kładki 24, 80-822 Gdansk, Poland
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Lucchetti-Miganeh C, Burrowes E, Baysse C, Ermel G. The post-transcriptional regulator CsrA plays a central role in the adaptation of bacterial pathogens to different stages of infection in animal hosts. Microbiology (Reading) 2008; 154:16-29. [DOI: 10.1099/mic.0.2007/012286-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
| | - Elizabeth Burrowes
- Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation St, Worcester, MA 01605-4321, USA
| | - Christine Baysse
- UMR CNRS 6026, Université Rennes 1, Campus de Beaulieu, 35042 Rennes, France
| | - Gwennola Ermel
- UMR CNRS 6026, Université Rennes 1, Campus de Beaulieu, 35042 Rennes, France
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