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Gangakhedkar R, Jain V. Construing the function of N-terminal domain of D29 mycobacteriophage LysA endolysin in phage lytic efficiency and proliferation. Mol Microbiol 2024; 122:243-254. [PMID: 38994875 DOI: 10.1111/mmi.15295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/25/2024] [Accepted: 06/30/2024] [Indexed: 07/13/2024]
Abstract
Endolysins produced by bacteriophages hydrolyze host cell wall peptidoglycan to release newly assembled virions. D29 mycobacteriophage specifically infects mycobacteria including the pathogenic Mycobacterium tuberculosis. D29 encodes LysA endolysin, which hydrolyzes mycobacterial cell wall peptidoglycan. We previously showed that LysA harbors two catalytic domains (N-terminal domain [NTD] and lysozyme-like domain [LD]) and a C-terminal cell wall binding domain (CTD). While the importance of LD and CTD in mycobacteriophage biology has been examined in great detail, NTD has largely remained unexplored. Here, to address NTD's significance in D29 physiology, we generated NTD-deficient D29 (D29∆NTD) by deleting the NTD-coding region from D29 genome using CRISPY-BRED. We show that D29∆NTD is viable, but has a longer latent period, and a remarkably reduced burst size and plaque size. A large number of phages were found to be trapped in the host during the D29∆NTD-mediated cell lysis event. Such poor release of progeny phages during host cell lysis strongly suggests that NTD-deficient LysA produced by D29∆NTD, despite having catalytically-active LD, is unable to efficiently lyse host bacteria. We thus conclude that LysA NTD is essential for optimal release of progeny virions, thereby playing an extremely vital role in phage physiology and phage propagation in the environment.
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Affiliation(s)
- Rutuja Gangakhedkar
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
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Ghosh S, Sett U, Pal A, Nandy S, Nandi S, Chakrabarty S, Das A, Bandopadhyay P, Basu T. Antibiofilm potential of nanonized eugenol against Pseudomonas aeruginosa. J Appl Microbiol 2024; 135:lxad305. [PMID: 38093454 DOI: 10.1093/jambio/lxad305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 12/03/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
AIMS The purpose of this study was to synthesize a nanoform of eugenol (an important phytochemical with various pharmacological potentials) and to investigate its antibiofilm efficacy on Pseudomonas aeruginosa biofilm. METHODS AND RESULTS Colloidal suspension of eugenol-nanoparticles (ENPs) was synthesized by the simple ultrasonic cavitation method through the emulsification of hydrophobic eugenol into hydrophilic gelatin. Thus, the nanonization process made water-insoluble eugenol into water-soluble nano-eugenol, making the nanoform bioavailable. The size of the ENPs was 20-30 nm, entrapment efficiency of eugenol within gelatin was 80%, and release of eugenol from the gelatin cap was slow and sustained over 5 days. Concerning the clinically relevant pathogen P. aeruginosa, ENPs had higher antibiofilm (for both formation and eradication) activities than free eugenol. Minimal biofilm inhibitory concentration and minimal biofilm eradication concentration of ENP on P. aeruginosa biofilm were 2.0 and 4.0 mM, respectively. In addition, the measurement of P. aeruginosa biofilm biomass, biofilm thickness, amount of biofilm extra-polymeric substance, cell surface hydrophobicity, cell swarming and twitching efficiencies, cellular morphology, and biofilm formation in catheter demonstrated that the antibiofilm efficacy of nano-eugenol was 30%-40% higher than that of bulk eugenol. CONCLUSION These results signify that future pharmacological and clinical studies are very much required to investigate whether ENPs can act as an effective drug against P. aeruginosa biofilm-mediated diseases. Thus, the problem of intrinsic antibiotic tolerance of biofilm-forming cells may be minimized by ENPs. Moreover, ENP may be used as a potential catheter-coating agent to inhibit pseudomonal colonization on catheter surfaces and, therefore, to reduce catheter-associated infections and complications.
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Affiliation(s)
- Sourav Ghosh
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, India
| | - Upasana Sett
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, India
| | - Anabadya Pal
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, India
| | - Sanchita Nandy
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, India
| | - Susmita Nandi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, India
| | - Soumajit Chakrabarty
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, India
| | - Abhijit Das
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, India
| | - Pathikrit Bandopadhyay
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, India
| | - Tarakdas Basu
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, India
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Sinha S, RS N, Devarakonda Y, Rathi A, Reddy Regatti P, Batra S, Syal K. Tale of Twin Bifunctional Second Messenger (p)ppGpp Synthetases and Their Function in Mycobacteria. ACS OMEGA 2023; 8:32258-32270. [PMID: 37720788 PMCID: PMC10500699 DOI: 10.1021/acsomega.3c03557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023]
Abstract
M. tuberculosis, an etiological agent of tuberculosis, requires a long treatment regimen due to its ability to respond to stress and persist inside the host. The second messenger (p)ppGpp-mediated stress response plays a critical role in such long-term survival, persistence, and antibiotic tolerance which may also lead to the emergence of multiple drug resistance. In mycobacteria, (pp)pGpp molecules are synthesized predominantly by two bifunctional enzymes-long RSH-Rel and short SAS-RelZ. The long RSH-Rel is a major (p)ppGpp synthetase and hydrolase. How it switches its activity from synthesis to hydrolysis remains unclear. RelMtb mutant has been reported to be defective in biofilm formation, cell wall function, and persister cell formation. The survival of such mutants has also been observed to be compromised in infection models. In M. smegmatis, short SAS-RelZ has RNase HII activity in addition to (pp)Gpp synthesis activity. The RNase HII function of RelZ has been implicated in resolving replication-transcription conflicts by degrading R-loops. However, the mechanism and regulatory aspects of such a regulation remain elusive. In this article, we have discussed (p)ppGpp metabolism and its role in managing the stress response network of mycobacteria, which is responsible for long-term survival inside the host, making it an important therapeutic target.
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Affiliation(s)
- Shubham
Kumar Sinha
- Genetics and Molecular Microbiology
Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad campus, Hyderabad, Telangana, India, 500078
| | - Neethu RS
- Genetics and Molecular Microbiology
Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad campus, Hyderabad, Telangana, India, 500078
| | - Yogeshwar Devarakonda
- Genetics and Molecular Microbiology
Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad campus, Hyderabad, Telangana, India, 500078
| | - Ajita Rathi
- Genetics and Molecular Microbiology
Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad campus, Hyderabad, Telangana, India, 500078
| | - Pavan Reddy Regatti
- Genetics and Molecular Microbiology
Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad campus, Hyderabad, Telangana, India, 500078
| | - Sakshi Batra
- Genetics and Molecular Microbiology
Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad campus, Hyderabad, Telangana, India, 500078
| | - Kirtimaan Syal
- Genetics and Molecular Microbiology
Laboratory, Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad campus, Hyderabad, Telangana, India, 500078
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Enriquez KT, Plummer WD, Neufer PD, Chazin WJ, Dupont WD, Skaar EP. Temporal modelling of the biofilm lifecycle (TMBL) establishes kinetic analysis of plate-based bacterial biofilm dynamics. J Microbiol Methods 2023; 212:106808. [PMID: 37595876 PMCID: PMC10528067 DOI: 10.1016/j.mimet.2023.106808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/12/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023]
Abstract
Bacterial biofilms are critical to pathogenesis and infection. They are associated with rising rates of antimicrobial resistance. Biofilms are correlated with worse clinical outcomes, making them important to infectious diseases research. There is a gap in knowledge surrounding biofilm kinetics and dynamics which makes biofilm research difficult to translate from bench to bedside. To address this gap, this work employs a well-characterized crystal violet biomass accrual and planktonic cell density assay across a clinically relevant time course and expands statistical analysis to include kinetic information in a protocol termed the TMBL (Temporal Mapping of the Biofilm Lifecycle) assay. TMBL's statistical framework quantitatively compares biofilm communities across time, species, and media conditions in a 96-well format. Measurements from TMBL can reliably be condensed into response features that inform the time-dependent behavior of adherent biomass and planktonic cell populations. Staphylococcus aureus and Pseudomonas aeruginosa biofilms were grown in conditions of metal starvation in nutrient-variable media to demonstrate the rigor and translational potential of this strategy. Significant differences in single-species biofilm formation are seen in metal-deplete conditions as compared to their controls which is consistent with the consensus literature on nutritional immunity that metal availability drives transcriptomic and metabolomic changes in numerous pathogens. Taken together, these results suggest that kinetic analysis of biofilm by TMBL represents a statistically and biologically rigorous approach to studying the biofilm lifecycle as a time-dependent process. In addition to current methods to study the impact of microbe and environmental factors on the biofilm lifecycle, this kinetic assay can inform biological discovery in biofilm formation and maintenance.
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Affiliation(s)
- Kyle T Enriquez
- Vanderbilt University Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, United States of America; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, United States of America; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - W Dale Plummer
- Department of Biostatistics, Vanderbilt University, Nashville, TN, United States of America
| | - Preston D Neufer
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America; Department of Biochemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Walter J Chazin
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States of America; Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America; Department of Biochemistry, Vanderbilt University, Nashville, TN, United States of America
| | - William D Dupont
- Department of Biostatistics, Vanderbilt University, Nashville, TN, United States of America
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, United States of America; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States of America.
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Feng L, Xu M, Zhu J, Lu H. Genetic Basis of High-Pressure Tolerance of a Vibrio parahaemolyticus Mutant and Its Pathogenicity. Front Microbiol 2022; 13:827856. [PMID: 35432286 PMCID: PMC9008460 DOI: 10.3389/fmicb.2022.827856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/07/2022] [Indexed: 11/30/2022] Open
Abstract
Foodborne pathogens with high-pressure processing (HPP) tolerance and their pathogenicity have gained considerable attention in the field of food safety. However, tolerance to pressure treatment varies among microorganisms and growth phases, and the mechanism by which Vibrio parahaemolyticus can become tolerant of HPP is currently not known. In this study, 183 strains of V. parahaemolyticus were isolated from seafood products, and one strain, C4, carried a thermostable direct hemolysin (tdh) gene. A strain, N11, which was acquired from the C4 strain through adaptive laboratory evolution under HPP stress, could tolerate up to 200 MPa for 10 min. Compared with the C4 strain, the catalase and Na+/K+-ATPase activities in N11 strain were increased by about 2–3 times, and the cells maintained an intact cell membrane structure under HPP treatment. As shown by murine infection trials, the C4 and N11 strains impacted the physiological activities of mice and damaged liver and spleen cells. Comparative genomic analysis showed that 19 nucleotides were mutated in the N11 strain, which led to sustained high expression of mlaC and mlaD genes in this strain. Knockout of these genes confirmed that they were involved in the high-pressure stress response, and also related to pathogenicity of V. parahaemolyticus. Thereby, our findings revealed a HPP tolerance mechanism of V. parahaemolyticus, and the high-pressure-tolerant strain still retained pathogenicity in mice with skin and fur pleating and lethargy, indicating the pressure-tolerant foodborne pathogens present health risks.
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Ali MK, Zhen G, Nzungize L, Stojkoska A, Duan X, Li C, Duan W, Xu J, Xie J. Mycobacterium tuberculosis PE31 ( Rv3477) Attenuates Host Cell Apoptosis and Promotes Recombinant M. smegmatis Intracellular Survival via Up-regulating GTPase Guanylate Binding Protein-1. Front Cell Infect Microbiol 2020; 10:40. [PMID: 32117813 PMCID: PMC7020884 DOI: 10.3389/fcimb.2020.00040] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 01/21/2020] [Indexed: 12/23/2022] Open
Abstract
The Mycobacterium (M.) tuberculosis comprising proline–glutamic acid (PE) subfamily proteins associate with virulence, pathogenesis, and host-immune modulations. While the functions of most of this family members are not yet explored. Here, we explore the functions of “PE only” subfamily member PE31 (Rv3477) in virulence and host-pathogen interactions. We have expressed the M. tuberculosis PE31 in non-pathogenic Mycobacterium smegmatis strain (Ms_PE31) and demonstrated that PE31 significantly altered the cell facet features including colony morphology and biofilm formation. PE31 expressing M. smegmatis showed more resistant to the low pH, diamide, H2O2 and surface stress. Moreover, Ms_PE31 showed higher intracellular survival in macrophage THP-1 cells. Ms_PE31 significantly down-regulated the production of IL-12p40 and IL-6, while up-regulates the production of IL-10 in macrophages. Ms_PE31 also induced the expression of guanylate-binding protein-1 (GBP-1) in macrophages. Further analysis demonstrates that Ms_PE31 inhibits the caspase-3 activation and reduces the macrophages apoptosis. Besides, the NF-κB signaling pathway involves the interplay between Ms_PE31 and macrophages. Collectively, our finding identified that PE31 act as a functionally relevant virulence factor of M. tuberculosis.
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Affiliation(s)
- Md Kaisar Ali
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Gong Zhen
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Lambert Nzungize
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Andrea Stojkoska
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Xiangke Duan
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Chunyan Li
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Wei Duan
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Junqi Xu
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
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Mahapa A, Samanta GC, Maiti K, Chatterji D, Jayaraman N. Mannopyranoside Glycolipids Inhibit Mycobacterial and Biofilm Growth and Potentiate Isoniazid Inhibition Activities in M. smegmatis. Chembiochem 2019; 20:1966-1976. [PMID: 30951240 DOI: 10.1002/cbic.201900040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/04/2019] [Indexed: 12/17/2022]
Abstract
Lipomannan and lipoarabinomannan are integral components of the mycobacterial cell wall. Earlier studies demonstrated that synthetic arabinan and arabinomannan glycolipids acted as inhibitors of mycobacterial growth, in addition to exhibiting inhibitory activities of mycobacterial biofilm. Herein, it is demonstrated that synthetic mannan glycolipids are better inhibitors of mycobacterial growth, whereas lipoarabinomannan has a higher inhibition efficiency to biofilm. Syntheses of mannan glycolipids with a graded number of mannan moieties and an arabinomannan glycolipid are conducted by chemical methods and subsequent mycobacterial growth and biofilm inhibition studies are conducted on Mycobacterium smegmatis. Growth inhibition of (73±3) % is observed with a mannose trisaccharide containing a glycolipid, whereas this glycolipid did not promote biofilm inhibition activity better than that of arabinomannan glycolipid. The antibiotic supplementation activities of glycolipids on growth and biofilm inhibitions are evaluated. Increases in growth and biofilm inhibitions are observed if the antibiotic is supplemented with glycolipids, which leads to a significant reduction of inhibition concentrations of the antibiotic.
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Affiliation(s)
- Avisek Mahapa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
| | - Gopal Ch Samanta
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Krishnagopal Maiti
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
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Bhardwaj N, Syal K, Chatterji D. The role of ω-subunit of Escherichia coli RNA polymerase in stress response. Genes Cells 2018. [PMID: 29542212 DOI: 10.1111/gtc.12577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
ppGpp, an alarmone for stringent response, plays an important role in the reprogramming of the transcription complex at the time of stress. In Escherichia coli, ppGpp mediates its action by binding to at least two different sites on RNA polymerase (RNAP). One of the sites to which ppGpp binds to RNAP is at the β'-ω interface; however, the underlying molecular mechanism and the physiological relevance of ppGpp binding to this site remain unclear. In this study, we have performed UV cross-linking experiments using 32 P azido-labeled ppGpp to probe its association with RNAP in the absence and presence of ω, and observed weaker binding of ppGpp to the RNAP without ω. Furthermore, we followed the binding kinetics of ppGpp to RNAP with and without ω by isothermal titration calorimetry and found it to be concurrent with the cross-linking results. Native ω is intrinsically disordered, and we have used a previously characterized structured mutant of ω, which affects the plasticity of the active site of RNAP. Results show that the flexibility conferred by the unstructured ω is a prerequisite for ppGpp binding to RNAP. We have analyzed the stress-associated phenotypes in an E. coli strain devoid of ω (∆rpoZ). ppGpp levels in ∆rpoZ strain were found to be similar to that of the wild-type strain. Interestingly, when the ∆rpoZ strain of E. coli was transferred after nutritional stress to an enriched media, the recovery of growth was compromised. We have identified a new phenotype of ∆rpoZ strain corresponding to defect in biofilm formation in minimal media.
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Affiliation(s)
- Neerupma Bhardwaj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kirtimaan Syal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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