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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Devarakonda Y, Reddy MVNJ, Neethu RS, Chandran A, Syal K. Multi epitope vaccine candidate design against Streptococcus pneumonia. J Biomol Struct Dyn 2023; 41:12654-12667. [PMID: 36636838 DOI: 10.1080/07391102.2023.2167123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023]
Abstract
Streptococcus pneumonia, the causative agent of sepsis, meningitis and pneumonia, is held responsible for causing invasive diseases predominantly in children along with adults from both developing and developed countries. The available vaccines coverage in the context of different serotypes is limited and emergence of non-vaccine serotypes could further emerge as a threat in future. Advanced immunoinformatics tools have been used for developing a multi epitope subunit vaccine. In the current study we have subjected these four surface antigenic proteins Ply, PsaA, PspA and PspK to construct vaccine designs. We have predicted different B-cell and T-cell epitopes by using NetCTL 1.2, IEDB (Immune Epitope Databases) and ABCpred. An adjuvant (griselimycin) has been added to the vaccine construct sequence in order to improve its immunogenicity. The vaccine construct has been evaluated for its antigenicity, allergenicity, toxicity and different physio-chemical properties. The bioinformatic tools have been used for prediction, refinement and validation of the 3 D structure. Further, the vaccine structure has been docked with a toll-like receptor (TLR-4) by ClusPro 2.0. In conclusion, the proposed multi-epitope vaccine designs could potentially activate both humoral and cellular immune responses and has a potential to be a vaccine candidate against S.pneumoniae, and requires experimental validation for ensuring immunogenicity and safety profile.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yogeshwar Devarakonda
- Department of Biological Sciences, Center for Genetics and Molecular Microbiology, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, India
| | - M V N Janaradhan Reddy
- Department of Biological Sciences, Center for Genetics and Molecular Microbiology, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, India
| | - R S Neethu
- Department of Biological Sciences, Center for Genetics and Molecular Microbiology, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, India
| | - Aneesh Chandran
- Department of Biotechnology and Microbiology, Kannur University, Kannur, India
| | - Kirtimaan Syal
- Department of Biological Sciences, Center for Genetics and Molecular Microbiology, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, India
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Affiliation(s)
- Kirtimaan Syal
- Department of Biological Sciences, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad Campus, Telangana India
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Syal K, Rs N, Reddy MVNJ. The extended (p)ppGpp family: New dimensions in Stress response. Curr Res Microb Sci 2021; 2:100052. [PMID: 34841343 PMCID: PMC8610335 DOI: 10.1016/j.crmicr.2021.100052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/21/2021] [Accepted: 07/25/2021] [Indexed: 11/30/2022] Open
Abstract
Second messenger (p)ppGpp mediated stress response plays a crucial role in bacterial persistence and multiple drug resistance. In E. coli, (p)ppGpp binds to RNA polymerase and upregulates the transcription of genes essential for stress response while concurrently downregulating the expression of genes critical for growth and metabolism. Recently, the family of alarmone molecules has expanded to pppGpp, ppGpp, pGpp & (pp)pApp as distinct members. These molecules may help in fine-tuning stress responses in different hostile conditions. Do all of these molecules bind to RNA polymerase? Do they compete with each other or complement each other's functions is still not clear. Earlier, others and we have synthesized artificial analogs of (p)ppGpp that inhibited (p)ppGpp synthesis and long-term survival in M. smegmatis and in B. subtilis suggesting that analogs could compete with each other. Understanding the interplay of these molecules will allow deciphering novel pathways that can be potentially subjected to the therapeutic intervention. In this article, we have reviewed newly characterized second messengers and discussed their mode of action. We have also documented the progress made to-date in understanding the molecular basis of regulation of transcription by second messenger ppGpp, pppGpp, and pGpp.
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Affiliation(s)
- Kirtimaan Syal
- Department of Biological Sciences, Birla Institute of Technology and Sciences-Pilani, Hyderabad campus, Hyderabad, Telangana, India
| | - Neethu Rs
- Department of Biological Sciences, Birla Institute of Technology and Sciences-Pilani, Hyderabad campus, Hyderabad, Telangana, India
| | - M V N Janardhan Reddy
- Department of Biological Sciences, Birla Institute of Technology and Sciences-Pilani, Hyderabad campus, Hyderabad, Telangana, India
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Syal K. Guidelines on newly identified limitations of diagnostic tools for COVID-19 and consequences. J Med Virol 2020; 93:1837-1842. [PMID: 33200414 PMCID: PMC7753543 DOI: 10.1002/jmv.26673] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/05/2020] [Accepted: 11/12/2020] [Indexed: 01/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by coronavirus has spread worldwide and has become the deadliest pandemic of the 21st century. Such rapid spread is predominantly attributed to the poor diagnosis and its asymptomatic transmission. In the absence of treatment regime, timely diagnosis is the best available remedy that can restrict its spread. An early diagnosis of COVID-19 is critical for determining the line of treatment and preventing long term complications in the infected subject. Unfortunately, available rapid antigen and antibody kits are known to be erroneous whereas reverse transcription polymerase chain reaction based tests are expensive, viral load dependent and at times inconclusive. In current scenario, the false-negative results imposed a major risk to the individual patient care and also to the efforts for containing the spread at the population level, where as false positives are traumatic for families and can lead to improper treatment resulting in severe complications. In this article, the limitations of available diagnostic procedures have been elaborated and plausible combination approach has been advised.
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Affiliation(s)
- Kirtimaan Syal
- Department of Biological Sciences, BITS-Pilani, Telangana, India
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Syal K. COVID-19: Herd immunity and convalescent plasma transfer therapy. J Med Virol 2020; 92:1380-1382. [PMID: 32281679 PMCID: PMC7262166 DOI: 10.1002/jmv.25870] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Kirtimaan Syal
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, Tennessee.,Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
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Nemec CM, Singh AK, Ali A, Tseng SC, Syal K, Ringelberg KJ, Ho YH, Hintermair C, Ahmad MF, Kar RK, Gasch AP, Akhtar MS, Eick D, Ansari AZ. Noncanonical CTD kinases regulate RNA polymerase II in a gene-class-specific manner. Nat Chem Biol 2018; 15:123-131. [PMID: 30598543 PMCID: PMC6339578 DOI: 10.1038/s41589-018-0194-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/09/2018] [Indexed: 11/09/2022]
Abstract
Phosphorylation of the carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) governs stage-specific interactions with different cellular machines. The CTD consists of Y1S2P3T4S5P6S7 heptad repeats, and sequential phosphorylations of Ser7, Ser5 and Ser2 occur universally across Pol II-transcribed genes. Phosphorylation of Thr4, however, appears to selectively modulate transcription of specific classes of genes. Here, we identify 10 new Thr4 kinases from different kinase structural groups. Irreversible chemical inhibition of the most active Thr4 kinase, Hrr25, reveals a novel role for this kinase in transcription termination of specific class of noncoding snoRNA genes. Genome-wide profiles of Hrr25 reveal a selective enrichment at 3ʹ regions of noncoding genes that display termination defects. Importantly, phospho-Thr4 marks placed by Hrr25 are recognized by Rtt103, a key component of the termination machinery. Our results suggest that these uncommon CTD kinases selectively place phospho-Thr4 marks to regulate expression of targeted genes.
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Affiliation(s)
- Corey M Nemec
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Amit K Singh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India
| | - Asfa Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sandra C Tseng
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kirtimaan Syal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Yi-Hsuan Ho
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Corinna Hintermair
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Mohammad Faiz Ahmad
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Rajesh Kumar Kar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Md Sohail Akhtar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India.,Academy of Scientific and Innovative Research, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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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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Maiti K, Syal K, Chatterji D, Jayaraman N. Synthetic Arabinomannan Heptasaccharide Glycolipids Inhibit Biofilm Growth and Augment Isoniazid Effects in Mycobacterium smegmatis. Chembiochem 2017; 18:1959-1970. [PMID: 28771901 DOI: 10.1002/cbic.201700247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Indexed: 02/04/2023]
Abstract
Biofilm formation, involving attachment to an adherent surface, is a critical survival strategy of mycobacterial colonies in hostile environmental conditions. Here we report the synthesis of heptasaccharide glycolipids based on mannopyranoside units anchored on to a branched arabinofuranoside core. Two types of glycolipids-2,3-branched and 2,5-branched-were synthesized and evaluated for their efficacies in inhibiting biofilm growth by the non-pathogenic mycobacterium variant Mycobacterium smegmatis. Biofilm formation was inhibited at a minimum biofilm growth inhibition concentration (MBIC) of 100 μg mL-1 in the case of the 2,5-branched heptasaccharide glycolipid. Further, we were able to ascertain that a combination of the drug isoniazid with the branched heptasaccharide glycolipid (50 μg mL-1 ) potentiates the drug, making it three times more effective, with an improved MBIC of 30 μg mL-1 . These studies establish that synthetic glycolipids not only act as inhibitors of biofilm growth, but also provide a synergistic effect when combined with significantly lowered concentrations of isoniazid to disrupt the biofilm structures of the mycobacteria.
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Affiliation(s)
- Krishnagopal Maiti
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Kirtimaan Syal
- Molecular Biophysics Unit, 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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Syal K, Bhardwaj N, Chatterji D. Vitamin C targets (p)ppGpp synthesis leading to stalling of long-term survival and biofilm formation in Mycobacterium smegmatis. FEMS Microbiol Lett 2016; 364:fnw282. [PMID: 27986825 DOI: 10.1093/femsle/fnw282] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/23/2016] [Accepted: 12/15/2016] [Indexed: 12/26/2022] Open
Abstract
Earlier, vitamin C was demonstrated to sterilize Mycobacterium tuberculosis culture via Fenton's reaction at high concentration. It alters the regulatory pathways associated with stress response and dormancy. Since (p)ppGpp is considered to be the master regulator of stress response and is responsible for bacterial survival under stress, we tested the effect of vitamin C on the formation of (p)ppGpp. In vivo estimation of (p)ppGpp showed a decrease in (p)ppGpp levels in vitamin C-treated M. smegmatis cells in comparison to the untreated cells. Furthermore, in vitro (p)ppGpp synthesis using RelMSM enzyme was conducted in order to confirm the specificity of the inhibition in the presence of variable concentrations of vitamin C. We observed that vitamin C at high concentration can inhibit the synthesis of (p)ppGpp. We illustrated binding of vitamin C to RelMSM by isothermal titration calorimetry. Enzyme kinetics was followed where K0.5 was found to be increased with the concomitant reduction of Vmax value suggesting mixed inhibition. Both long-term survival and biofilm formation were inhibited by vitamin C. The experiments suggest that vitamin C has the potential to be developed as the inhibitor of (p)ppGpp synthesis and stress response, at least in the concentration range used here.
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Affiliation(s)
- Kirtimaan Syal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Neerupma Bhardwaj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Syal K, Maiti K, Naresh K, Avaji PG, Chatterji D, Jayaraman N. Synthetic arabinomannan glycolipids impede mycobacterial growth, sliding motility and biofilm structure. Glycoconj J 2016; 33:763-77. [DOI: 10.1007/s10719-016-9670-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/17/2016] [Accepted: 04/26/2016] [Indexed: 11/24/2022]
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Syal K, Tadala R. Modifications in trypsin digestion protocol for increasing the efficiency and coverage. Protein Pept Lett 2015; 22:372-8. [PMID: 25813035 DOI: 10.2174/0929866522666150327132415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/28/2015] [Accepted: 02/28/2015] [Indexed: 11/22/2022]
Abstract
Standard trypsin digestion protocol of proteins followed by MALDI-MS analysis has been realized as an important tool for the identification and characterization of proteins. In this article, we proposed the elimination of the step of 'staining/de-staining of gel pieces' in in-gel digestion protocol in order to improve the efficiency of trypsin digestion. Coomassie dye is known to interfere with digestion of proteins by trypsin and the procedure of staining-de-staining could result in loss of photoaffinity probe, post translational modifications and catalytic activities of enzymes. Further, we studied parameters like hydrophobicity and isoelectric point, and attempted to quantitatively relate it to the efficiency of trypsin digestion. We suggest that properties of proteins should be considered and trypsin digestion protocol should be appropriately modified as per sequence and other information.
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Affiliation(s)
- Kirtimaan Syal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
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Affiliation(s)
- Kirtimaan Syal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
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Syal K, Chatterji D. Differential binding of ppGpp and pppGpp to E. coli RNA polymerase: photo-labeling and mass spectral studies. Genes Cells 2015; 20:1006-16. [PMID: 26606426 DOI: 10.1111/gtc.12304] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/06/2015] [Indexed: 11/28/2022]
Abstract
(p)ppGpp, a secondary messenger, is induced under stress and shows pleiotropic response. It binds to RNA polymerase and regulates transcription in Escherichia coli. More than 25 years have passed since the first discovery was made on the direct interaction of ppGpp with E. coli RNA polymerase. Several lines of evidence suggest different modes of ppGpp binding to the enzyme. Earlier cross-linking experiments suggested that the β-subunit of RNA polymerase is the preferred site for ppGpp, whereas recent crystallographic studies pinpoint the interface of β'/ω-subunits as the site of action. With an aim to validate the binding domain and to follow whether tetra- and pentaphosphate guanosines have different location on RNA polymerase, this work was initiated. RNA polymerase was photo-labeled with 8-azido-ppGpp/8-azido-pppGpp, and the product was digested with trypsin and subjected to mass spectrometry analysis. We observed three new peptides in the trypsin digest of the RNA polymerase labeled with 8-azido-ppGpp, of which two peptides correspond to the same pocket on β'-subunit as predicted by X-ray structural analysis, whereas the third peptide was mapped on the β-subunit. In the case of 8-azido-pppGpp-labeled RNA polymerase, we have found only one cross-linked peptide from the β'-subunit. However, we were unable to identify any binding site of pppGpp on the β-subunit. Interestingly, we observed that pppGpp at high concentration competes out ppGpp bound to RNA polymerase more efficiently, whereas ppGpp cannot titrate out pppGpp. The competition between tetraphosphate guanosine and pentaphosphate guanosine for E. coli RNA polymerase was followed by gel-based assay as well as by a new method known as DRaCALA assay.
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Affiliation(s)
- Kirtimaan Syal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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Syal K, Joshi H, Chatterji D, Jain V. Novel pppGpp binding site at the C-terminal region of the Rel enzyme from Mycobacterium smegmatis. FEBS J 2015; 282:3773-85. [PMID: 26179484 DOI: 10.1111/febs.13373] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/26/2015] [Accepted: 07/09/2015] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis elicits the stringent response under unfavorable growth conditions, such as those encountered by the pathogen inside the host. The hallmark of this response is production of guanosine tetra- and pentaphosphates, collectively termed (p)ppGpp, which have pleiotropic effects on the bacterial physiology. As the stringent response is connected to survival under stress, it is now being targeted for developing inhibitors against bacterial persistence. The Rel enzyme in mycobacteria has two catalytic domains at its N-terminus that are involved in the synthesis and hydrolysis of (p)ppGpp, respectively. However, the function of the C-terminal region of the protein remained unknown. Here, we have identified a binding site for pppGpp in the C-terminal region of Rel. The binding affinity of pppGpp was quantified by isothermal titration calorimetry. The binding site was determined by crosslinking using the nucleotide analog azido-pppGpp, and examining the crosslink product by mass spectrometry. Additionally, mutations in the Rel protein were created to confirm the site of pppGpp binding by isothermal titration calorimetry. These mutants showed increased pppGpp synthesis and reduced hydrolytic activity. We believe that binding of pppGpp to Rel provides a feedback mechanism that allows the protein to detect and adjust the (p)ppGpp level in the cell. Our work suggests that such sites should also be considered while designing inhibitors to target the stringent response.
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Affiliation(s)
- Kirtimaan Syal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Himanshu Joshi
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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Syal K, Srinivasan A, Banerjee D. VDR, RXR, Coronin-1 and Interferonγ Levels in PBMCs of Type-2 Diabetes Patients: Molecular Link between Diabetes and Tuberculosis. Indian J Clin Biochem 2015; 30:323-8. [PMID: 26089620 PMCID: PMC4469064 DOI: 10.1007/s12291-014-0431-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/02/2014] [Indexed: 01/05/2023]
Abstract
Diabetes and tuberculosis are world's most deadly epidemics. People suffering from diabetes are susceptible to tuberculosis. Molecular link between the two is largely unknown. It is known that Vitamin A receptor (RXR) heterodimerizes with Vitamin D receptor (VDR) and Peroxisome proliferator-activator receptor-γ (PPARγ) to regulate Tryptophan-aspartate containing coat protein (TACO) expression and fatty acid metabolism respectively, so it would be interesting to check the expression of these genes in diabetes mellitus (DM) patients which might explain the susceptibility of diabetics to tuberculosis. In this study, we checked the expression of RXR, VDR, TACO and Interferon-γ (IFNγ) genes in type-2 DM patients for understanding the link between the two diseases. We observed down regulation of RXR gene and corresponding up regulation of TACO gene expression. We have not observed significant change in expression of VDR and IFNγ genes in type-2 DM patients. Repression of RXR gene could hamper VDR-RXR heterodimer formation and thus would up regulate TACO gene expression which may predispose the type-2 DM patients to tuberculosis. Also, decrease in RXR-PPARγ heterodimer could be involved in DM.
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Affiliation(s)
- Kirtimaan Syal
- />Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
- />Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012 India
| | - Anand Srinivasan
- />Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Dibyajyoti Banerjee
- />Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
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Syal K, Chakraborty S, Bhattacharyya R, Banerjee D. Combined inhalation and oral supplementation of Vitamin A and Vitamin D: A possible prevention and therapy for tuberculosis. Med Hypotheses 2015; 84:199-203. [DOI: 10.1016/j.mehy.2014.12.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/26/2014] [Indexed: 11/25/2022]
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Syal K. Comments on "Serum Urea:Albumin Ratio as a Prognostic Marker in Critical Patients With Non-chronic Kidney Disease". Indian J Clin Biochem 2014; 29:393. [PMID: 24966494 DOI: 10.1007/s12291-014-0433-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 04/02/2014] [Indexed: 11/25/2022]
Affiliation(s)
- Kirtimaan Syal
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India ; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Syal K. Point of care testing for measurement of white blood cell count and C-reactive protein levels in blood. Clin Chim Acta 2014; 437:218. [PMID: 24911981 DOI: 10.1016/j.cca.2014.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 05/29/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Kirtimaan Syal
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
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Srinivasan A, Syal K, Banerjee D, Hota D, Gupta D, Kaul D, Chakrabarti A. Low plasma levels of cholecalciferol and 13-cis-retinoic acid in tuberculosis: implications in host-based chemotherapy. Nutrition 2013; 29:1245-51. [PMID: 23880094 DOI: 10.1016/j.nut.2013.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/27/2013] [Accepted: 03/31/2013] [Indexed: 12/25/2022]
Abstract
OBJECTIVE The aim of this study was to estimate the concentration of cholecalciferol and 13-cis-retinoic acid (RA) in the plasma and pleural fluid of patients with tuberculosis (TB) against controls. METHODS Plasma levels of cholecalciferol and 13-cis-RA were measured in 22 patients with TB and healthy controls and their pleural fluids levels were measured in 6 TB patients and diseased controls by established high-performance liquid chromatography-based procedure. RESULTS Cholecalciferol levels in plasma and pleural fluid of patients with TB and healthy controls were 67.45 (10.71) nmol/L and 21.40 (8.58) nmol/L compared with 117.43 (18.40) nmol/L (P < 0.001) and 94.73 (33.34) nmol/L (P = 0.0049), respectively. 13-cis-RA level in the plasma of patients with TB and healthy controls were 1.51 (0.72) nmol/L and 6.67 (0.81) nmol/L (P < 0.001), respectively. 13-cis-RA was not detectable in pleural fluid. The levels of both the agents were lower in patients with TB than in controls. CONCLUSION It was observed that in patients with TB there is a combined deficiency of cholecalciferol and 13-cis-RA compared with healthy volunteers. Because cholecalciferol and 13-cis-RA are in equilibrium with active ingredients of vitamins A and D, we feel that there is a combined deficiency of these vitamins in patients with TB. There is an evidence that concomitant vitamin A and D supplementation can kill intracellular Mycobacterium tuberculosis in vitro. Therefore, the observations made in this study can pave the path for a trial of combined supplementation of available formulations of vitamin A and D (cholecalciferol and 13-cis-RA) for novel anti-tubercular drug therapy. Because such an approach is host-based it has potential to treat even multidrug-resistant and extensively drug-resistant forms of TB.
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Affiliation(s)
- Anand Srinivasan
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Syal K, Srinivasan A, Banerjee D. Streptomycin interference in Jaffe reaction - possible false positive creatinine estimation in excessive dose exposure. Clin Biochem 2012; 46:177-9. [PMID: 23123914 DOI: 10.1016/j.clinbiochem.2012.10.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 08/05/2012] [Accepted: 10/21/2012] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To study the potential of commonly used aminoglycoside antibiotics to form non-creatinine chromogen with alkaline picrate reagent. DESIGN AND METHODS We studied the non-creatinine chromogen formation of various concentrations of streptomycin, amikacin, kanamycin, netilmicin, gentamicin and tobramycin added to known creatinine concentrations by the Jaffe reaction based creatinine estimation. RESULTS Only streptomycin above therapeutic concentrations of 10mg/mL interfered in the Jaffe reaction and acted as non-creatinine chromogen. CONCLUSIONS Therapeutic doses of the aminoglycosides do not form non-creatinine chromogens.
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Affiliation(s)
- Kirtimaan Syal
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
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Naresh K, Avaji PG, Maiti K, Bharati BK, Syal K, Chatterji D, Jayaraman N. Synthesis of β-arabinofuranoside glycolipids, studies of their binding to surfactant protein-A and effect on sliding motilities of M. smegmatis. Glycoconj J 2012; 29:107-18. [DOI: 10.1007/s10719-012-9369-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 01/01/2012] [Accepted: 01/05/2012] [Indexed: 10/14/2022]
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Syal K, Dogra RK, Ohri A, Chauhan G, Goel A. Epidural labour analgesia using Bupivacaine and Clonidine. J Anaesthesiol Clin Pharmacol 2011; 27:87-90. [PMID: 21804714 PMCID: PMC3146166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND To compare the effects of addition of Clonidine (60 μg) to Epidural Bupivacaine (0.125%) for labour analgesia, with regard to duration of analgesia, duration of labour, ambulation, incidence of instrumentation and caesarean section, foetal outcome, patient satisfaction and side effects. PATIENTS #ENTITYSTARTX00026; METHODS On demand, epidural labour analgesia was given to 50 nulliparous healthy term parturients (cephalic presentation), divided in two groups randomly. Group I received bupivacaine (0.125%) alone, whereas Group II received bupivacaine (0.125%) along with Clonidine (60 μg). 10 ml of 0.125% bupivacaine was injected as first dose and further doses titrated with patient relief (Numerical Rating Scale <3). Top ups were given whenever Numerical Rating Scale went above 5. RESULTS There was statistically significant prolongation of duration of analgesia in Group II, with no difference in duration of labour, ambulation, incidence of instrumentation and caesarean section or foetal outcome. Also clonidine gave dose sparing effect to bupivacaine and there was better patient satisfaction without any significant side effects in Group II. CONCLUSION Clonidine is a useful adjunct to bupivacaine for epidural labour analgesia and can be considered as alternative to opioids.
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Affiliation(s)
- K Syal
- Senior Residents, Department of Anaesthesia, IGMC, Shimla (H.P.),Correspondence: Dr. Kartik Syal, E-mail:
| | - RK Dogra
- Senior Residents, Department of Anaesthesia, IGMC, Shimla (H.P.)
| | - A Ohri
- Associate Professor, Department of Anaesthesia, IGMC, Shimla (H.P.)
| | - G Chauhan
- Assistant Professor, Department of Anaesthesia, IGMC, Shimla (H.P.)
| | - A Goel
- Associate Professor, Department of Pharmacology, GMC, Amritsar (Pb)
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