1
|
Kim NK, Baek JE, Lee YJ, Oh Y, Oh JI. Rel-dependent decrease in the expression of ribosomal protein genes by inhibition of the respiratory electron transport chain in Mycobacterium smegmatis. Front Microbiol 2024; 15:1448277. [PMID: 39188315 PMCID: PMC11345224 DOI: 10.3389/fmicb.2024.1448277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/24/2024] [Indexed: 08/28/2024] Open
Abstract
In this study, we demonstrated that both the expression of most ribosomal protein genes and the amount of ribosomes were decreased in the Δaa 3 mutant of Mycobacterium smegmatis, in which the major terminal oxidase (aa 3 cytochrome c oxidase) of the respiratory electron transport chain (ETC) is inactivated, compared to those in the wild-type strain. Deletion of the rel gene encoding the major (p)ppGpp synthetase in the background of the Δaa 3 mutant restored the reduced expression of ribosomal protein genes, suggesting that inhibition of the respiratory ETC leads to the Rel-dependent stringent response (SR) in this bacterium. Both a decrease in the expression of ribosomal protein genes by overexpression of rel and the increased expression of rel in the Δaa 3 mutant relative to the wild-type strain support the Rel-dependent induction of SR in the Δaa 3 mutant. We also demonstrated that the expression of ribosomal protein genes was decreased in M. smegmatis exposed to respiration-inhibitory conditions, such as KCN and bedaquiline treatment, null mutation of the cytochrome bcc 1 complex, and hypoxia. The MprBA-SigE-SigB regulatory pathway was implicated in both the increased expression of rel and the decreased expression of ribosomal protein genes in the Δaa 3 mutant of M. smegmatis.
Collapse
Affiliation(s)
- Na-Kyeong Kim
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Jong-Eun Baek
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Ye-Jin Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Microbiological Resource Research Institute, Pusan National University, Busan, Republic of Korea
| |
Collapse
|
2
|
van der Niet S, Green KD, Schimmel IM, de Bakker J, Lodder B, Reits EA, Garneau-Tsodikova S, van der Wel NN. Zafirlukast induces DNA condensation and has bactericidal effect on replicating Mycobacterium abscessus. Antimicrob Agents Chemother 2024; 68:e0002924. [PMID: 38990015 PMCID: PMC11304721 DOI: 10.1128/aac.00029-24] [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: 01/05/2024] [Accepted: 06/09/2024] [Indexed: 07/12/2024] Open
Abstract
Mycobacterium abscessus infections are emerging in cystic fibrosis patients, and treatment success rate in these patients is only 33% due to extreme antibiotic resistance. Thus, new treatment options are essential. An interesting target could be Lsr2, a nucleoid-associated protein involved in mycobacterial virulence. Zafirlukast is a Food and Drug Administration (FDA)-approved drug against asthma that was shown to bind Lsr2. In this study, zafirlukast treatment is shown to reduce M. abscessus growth, with a minimal inhibitory concentration of 16 µM and a bactericidal concentration of 64 µM in replicating bacteria only. As an initial response, DNA condensation, a known stress response of mycobacteria, occurs after 1 h of treatment with zafirlukast. During continued zafirlukast treatment, the morphology of the bacteria alters and the structural integrity of the bacteria is lost. After 4 days of treatment, reduced viability is measured in different culture media, and growth of M. abscessus is reduced in a dose-dependent manner. Using transmission electron microscopy, we demonstrated that the hydrophobic multilayered cell wall and periplasm are disorganized and ribosomes are reduced in size and relocalized. In summary, our data demonstrate that zafirlukast alters the morphology of M. abscessus and is bactericidal at 64 µM. The bactericidal concentration of zafirlukast is relatively high, and it is only effective on replicating bacteria but as zafirlukast is an FDA-approved drug, and currently used as an anti-asthma treatment, it could be an interesting drug to further study in in vivo experiments to determine whether it could be used as an antibiotic for M. abscessus infections.
Collapse
Affiliation(s)
- Sanne van der Niet
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Keith D. Green
- College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Irene M. Schimmel
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Jordy de Bakker
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Bastiaan Lodder
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Eric A. Reits
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | | | - Nicole N. van der Wel
- Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| |
Collapse
|
3
|
Płocińska R, Struś K, Korycka-Machała M, Płociński P, Kuzioła M, Żaczek A, Słomka M, Dziadek J. MnoSR removal in Mycobacterium smegmatis triggers broad transcriptional response to 1,3-propanediol and glucose as sole carbon sources. Front Cell Infect Microbiol 2024; 14:1427829. [PMID: 39113823 PMCID: PMC11303327 DOI: 10.3389/fcimb.2024.1427829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 07/02/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction The two-component signal transduction systems play an essential role in the adaptation of bacteria to changing environmental conditions. One of them is the MnoSR system involved in the regulation of methylotrophic metabolism in M. smegmatis. Methods Mycobacterium smegmatis mutant strains ΔmnoS, ΔmnoR and ΔmnoS/R lacking functional mnoS, mnoR and both genes were generated using a homologous recombination approach. MnoR recombinant protein was purified by affinity column chromatography. The present study employs molecular biology techniques: cloning strategies, global RNA sequencing, qRT-PCR, EMSA, Microscale thermophoresis, and bioinformatics analysis. Results and discussion The ∆mnoS, ∆mnoR, and ∆mnoS/R mutant strains were generated and cultured in the presence of defined carbon sources. Growth curve analysis confirmed that inactivation of the MnoSR impairs the ability of M. smegmatis cells to use alcohols such as 1,3-propanediol and ethanol but improves the bacterial growth on ethylene glycol, xylitol, and glycerol. The total RNA sequencing method was employed to understand the importance of MnoSR in the global responses of mycobacteria to limited carbon access and in carbon-rich conditions. The loss of MnoSR significantly affected carbon utilization in the case of mycobacteria cultured on glucose or 1,3-propanediol as sole carbon sources as it influenced the expression of multiple metabolic pathways. The numerous transcriptional changes could not be linked to the presence of evident MnoR DNA-binding sites within the promotor regions for the genes outside of the mno operon. This was confirmed by EMSA and microscale thermophoresis with mutated MnoR binding consensus region. Our comprehensive analysis highlights the system's vital role in metabolic adaptability, providing insights into its potential impact on the environmental survival of mycobacteria.
Collapse
Affiliation(s)
- Renata Płocińska
- Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Katarzyna Struś
- Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | | | - Przemysław Płociński
- Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Łódz, Łódź, Poland
| | - Magdalena Kuzioła
- Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
- BioMedChem Doctoral School of the UL and Łódź Institutes of the Polish Academy of Sciences, Łódź, Poland
| | - Anna Żaczek
- Department of Microbiology, College of Medical Sciences, University of Rzeszów, Rzeszów, Poland
| | - Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| |
Collapse
|
4
|
Oh Y, Oh JI. The RsfSR two-component system regulates SigF function by monitoring the state of the respiratory electron transport chain in Mycobacterium smegmatis. J Biol Chem 2024; 300:105764. [PMID: 38367670 PMCID: PMC10950880 DOI: 10.1016/j.jbc.2024.105764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024] Open
Abstract
In Mycobacterium smegmatis, the transcriptional activity of the alternative sigma factor SigF is posttranslationally regulated by the partner switching system consisting of SigF, the anti-SigF RsbW1, and three anti-SigF antagonists (RsfA, RsfB, and RsbW3). We previously demonstrated that expression of the SigF regulon is strongly induced in the Δaa3 mutant of M. smegmatis lacking the aa3 cytochrome c oxidase, the major terminal oxidase in the respiratory electron transport chain. Here, we identified and characterized the RsfSR two-component system involved in regulating the phosphorylation state of the major anti-SigF antagonist RsfB. RsfS (MSMEG_6130) is a histidine kinase with the cyclase/histidine kinase-associated sensing extracellular 3 domain at its N terminus, and RsfR (MSMEG_6131) is a receiver domain-containing protein phosphatase 2C-type phosphatase that can dephosphorylate phosphorylated RsfB. We demonstrated that phosphorylation of RsfR on Asp74 by RsfS reduces the phosphatase activity of RsfR toward phosphorylated RsfB and that the cellular abundance of the active unphosphorylated RsfB is increased in the Δaa3 mutant relative to the WT strain. We also demonstrated that the RsfSR two-component system is required for induction of the SigF regulon under respiration-inhibitory conditions such as inactivation of the cytochrome bcc1 complex and aa3 cytochrome c oxidase, as well as hypoxia, electron donor-limiting, high ionic strength, and low pH conditions. Collectively, our results reveal a key regulatory element involved in regulating the SigF signaling system by monitoring the state of the respiratory electron transport chain.
Collapse
Affiliation(s)
- Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, Korea
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, Korea; Microbiological Resource Research Institute, Pusan National University, Busan, Korea.
| |
Collapse
|
5
|
Singh P, Kumar A, Chhabra R, Singh K, Kaur J. MSMEG_5850, a stress-induced TetR protein, involved in global transcription regulation in Mycobacterium smegmatis. Future Microbiol 2023; 18:563-580. [PMID: 37284769 DOI: 10.2217/fmb-2022-0238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Abstract
Aim: To decipher the role of MSMEG_5850 in the physiology of mycobacteria. Methods: MSMEG_5850 was knocked out and RNA sequencing was performed. MSMEG_5850 protein was purified from the Escherichia coli pET28a system. Electrophoretic mobility shift assay and size exclusion chromatography were used to determine the binding of MSMEG_5850 to its motif and binding stoichiometry. The effect of nutritional stress was monitored. Results: Transcriptome analysis revealed the differential expression of 148 genes in an MSMEG_5850 knockout strain. MSMEG_5850 had control over 50 genes because those genes had a binding motif upstream of their sequence. The electrophoretic mobility shift assay showed MSMEG_5850 bound to its motif as a monomer. MSMEG_5850 was upregulated under nutritional stress and promoted the survival of mycobacteria. Conclusion: The study confirms the role of MSMEG_5850 in global transcriptional regulation.
Collapse
Affiliation(s)
- Parul Singh
- Department of Biotechnology, BMS Block-1, Sector-25, Panjab University, Chandigarh, 160014, India
| | - Arbind Kumar
- Department of Biotechnology, BMS Block-1, Sector-25, Panjab University, Chandigarh, 160014, India
- Current Address: Fellow Scientist, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Ravindresh Chhabra
- Department of Biochemistry, Central University of Punjab, Bathinda, 151001, India
| | - Kashmir Singh
- Department of Biotechnology, BMS Block-1, Sector-25, Panjab University, Chandigarh, 160014, India
| | - Jagdeep Kaur
- Department of Biotechnology, BMS Block-1, Sector-25, Panjab University, Chandigarh, 160014, India
| |
Collapse
|
6
|
A Feedback Regulatory Loop Containing McdR and WhiB2 Controls Cell Division and DNA Repair in Mycobacteria. mBio 2022; 13:e0334321. [PMID: 35357209 PMCID: PMC9040748 DOI: 10.1128/mbio.03343-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cell division must be coordinated with DNA repair, which is strictly regulated in response to different drugs and environmental stresses in bacteria. However, the mechanisms by which mycobacteria orchestrate these two processes remain largely uncharacterized. Here, we report a regulatory loop between two essential mycobacterial regulators, McdR (Rv1830) and WhiB2, in coordinating the processes of cell division and DNA repair. McdR inhibits cell division-associated whiB2 expression by binding to the AATnACAnnnnTGTnATT motif in the promoter region. Furthermore, McdR overexpression simultaneously activates imuAB and dnaE2 expression to promote error-prone DNA repair, which facilitates genetic adaptation to stress conditions. Through a feedback mechanism, WhiB2 activates mcdR expression by binding to the cGACACGc motif in the promoter region. Importantly, analyses of mutations in clinical Mycobacterium tuberculosis strains indicate that disruption of this McdR-WhiB2 feedback regulatory loop influences expression of both cell growth- and DNA repair-associated genes, which further supports the contribution of McdR-WhiB2 regulatory loop in regulating mycobacterial cell growth and drug resistance. This highly conserved feedback regulatory loop provides fresh insight into the link between mycobacterial cell growth control and stress responses. IMPORTANCE Drug-resistant M. tuberculosis poses a threat to the control and prevention of tuberculosis (TB) worldwide. Thus, there is a need to identify the mechanisms enabling M. tuberculosis to adapt and grow under drug-induced stress. Rv1830 has been shown to be associated with drug resistance in M. tuberculosis, but its mechanisms have not yet been elucidated. Here, we reveal a regulatory role of Rv1830, which coordinates cell division and DNA repair in mycobacteria, and rename it McdR (mycobacterial cell division regulator). An increase in McdR levels represses the expression of cell division-associated whiB2 but activates the DNA repair-associated, error-prone enzymes ImuA/B and DnaE2, which in turn facilitates adaptation to stress responses and drug resistance. Furthermore, WhiB2 activates the transcription of mcdR to form a conserved regulatory loop. These data provide new insights into the mechanisms controlling mycobacterial cell growth and stress responses.
Collapse
|
7
|
Pradhan A, Mukkayyan N, Jakkala K, Ajitkumar P. Mycobacterial Populations Partly Change the Proportions of the Cells Undergoing Asymmetric/Symmetric Divisions in Response to Glycerol Levels in Growth Medium. Cells 2021; 10:1160. [PMID: 34064643 PMCID: PMC8151439 DOI: 10.3390/cells10051160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/25/2022] Open
Abstract
Twenty to thirty percent of the septating mycobacterial cells of the mid-log phase population showed highly deviated asymmetric constriction during division (ACD), while the remaining underwent symmetric constriction during division (SCD). The ACD produced short-sized cells (SCs) and normal/long-sized cells (NCs) as the sister-daughter cells, but with significant differential susceptibility to antibiotic/oxidative/nitrite stress. Here we report that, at 0.2% glycerol, formulated in the Middlebrook 7H9 medium, a significantly high proportion of the cells were divided by SCD. When the glycerol concentration decreased to 0.1% due to cell-growth/division, the ACD proportion gradually increased until the ACD:SCD ratio reached ~50:50. With further decrease in the glycerol levels, the SCD proportion increased with concomitant decrease in the ACD proportion. Maintenance of glycerol at 0.1%, through replenishment, held the ACD:SCD proportion at ~50:50. Transfer of the cells from one culture with a specific glycerol level to the supernatant from another culture, with a different glycerol level, made the cells change the ACD:SCD proportion to that of the culture from which the supernatant was taken. RT-qPCR data showed the possibility of diadenosine tetraphosphate phosphorylase (MSMEG_2932), phosphatidylinositol synthase (MSMEG_2933), and a Nudix family hydrolase (MSMEG_2936) involved in the ACD:SCD proportion-change in response to glycerol levels. We also discussed its physiological significance.
Collapse
Affiliation(s)
| | | | | | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India; (A.P.); (N.M.); (K.J.)
| |
Collapse
|
8
|
Bespyatykh J, Bespiatykh D, Malakhova M, Klimina K, Bespyatykh A, Varizhuk A, Tevyashova A, Nikolenko T, Pozmogova G, Ilina E, Shitikov E. Aureolic Acid Group of Agents as Potential Antituberculosis Drugs. Antibiotics (Basel) 2020; 9:E715. [PMID: 33086595 PMCID: PMC7650759 DOI: 10.3390/antibiotics9100715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium tuberculosis is one of the most dangerous pathogens. Bacterial resistance to antituberculosis drugs grows each year, but searching for new drugs is a long process. Testing for available drugs to find active against mycobacteria may be a good alternative. In this work, antibiotics of the aureolic acid group were tested on a model organism Mycobacterium smegmatis. We presumed that antibiotics of this group may be potential G4 ligands. However, this was not confirmed in our analyses. We determined the antimicrobial activity of these drugs and revealed morphological changes in the cell structure upon treatment. Transcriptomic analysis documented increased expression of MSMEG_3743/soj and MSMEG_4228/ftsW, involved in cell division. Therefore, drugs may affect cell division, possibly disrupting the function of the Z-ring and the formation of a septum. Additionally, a decrease in the transcription level of several indispensable genes, such as nitrate reductase subunits (MSMEG_5137/narI and MSMEG_5139/narX) and MSMEG_3205/hisD was shown. We concluded that the mechanism of action of aureolic acid and its related compounds may be similar to that bedaquiline and disturb the NAD+/NADH balance in the cell. All of this allowed us to conclude that aureolic acid derivatives can be considered as potential antituberculosis drugs.
Collapse
Affiliation(s)
- Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Dmitry Bespiatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Maja Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Ksenia Klimina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Andrey Bespyatykh
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia;
| | - Anna Varizhuk
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | | | - Tatiana Nikolenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700 Moscow, Russia
| | - Galina Pozmogova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Elena Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (D.B.); (M.M.); (K.K.); (A.V.); (T.N.); (G.P.); (E.I.); (E.S.)
| |
Collapse
|
9
|
Integrating multi-omics data to investigate pseudogene expression in Mycolicibacterium smegmatis. Gene X 2020; 755:144908. [DOI: 10.1016/j.gene.2020.144908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/05/2020] [Accepted: 06/17/2020] [Indexed: 11/21/2022] Open
|
10
|
Luo X, Pan J, Meng Q, Huang J, Wang W, Zhang N, Wang G. High-Throughput Screen for Cell Wall Synthesis Network Module in Mycobacterium tuberculosis Based on Integrated Bioinformatics Strategy. Front Bioeng Biotechnol 2020; 8:607. [PMID: 32695753 PMCID: PMC7338375 DOI: 10.3389/fbioe.2020.00607] [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: 04/06/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis is one of the deadliest pathogens in humans. Co-infection of M. tuberculosis with HIV and the emergence of multi-drug-resistant tuberculosis (TB) constitute a serious global threat. However, no effective anti-TB drugs are available, with the exception of first-line drugs such as isoniazid. The cell wall of M. tuberculosis, which is primarily responsible for the lack of effective anti-TB drugs and the escape of the bacteria from host immunity, is an important drug target. The core components of the cell wall of M. tuberculosis are peptidoglycan, arabinogalactan, and mycotic acid. However, the functional genome and metabolic regulation pathways for the M. tuberculosis cell wall are still unknown. In this study, we used the biclustering algorithm integrated into cMonkey, sequence alignment, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and other bioinformatics methods to scan the whole genome of M. tuberculosis as well as to identify and statistically analyze the genes related to the synthesis of the M. tuberculosis cell wall. METHOD We performed high-throughput genome-wide screening for M. tuberculosis using Biocarta, KEGG, National Cancer Institute Pathway Interaction Database (NCI-PID), HumanCyc, and Reactome. We then used the Database of Origin and Registration (DOOR) established in our laboratory to classify the collection of operons for M. tuberculosis cell wall synthetic genes. We used the cMonkey double clustering algorithm to perform clustering analysis on the gene expression profile of M. tuberculosis for cell wall synthesis. Finally, we visualized the results using Cytoscape. RESULT AND CONCLUSION Through bioinformatics and statistical analyses, we identified 893 M. tuberculosis H37Rv cell wall synthesis genes, distributed in 20 pathways, involved in 46 different functions related to cell wall synthesis, and clustered in 386 modules. We identified important pivotal genes and proteins in the cell wall synthesis pathway such as murA, a class of operons containing genes involved in cell wall synthesis such as ID6951, and a class of operons indispensable for the survival of the bacteria. In addition, we found 41 co-regulatory modules for cell wall synthesis and five co-expression networks of molecular complexes involved in peptidoglycan biosynthesis, membrane transporter synthesis, and other cell wall processes.
Collapse
Affiliation(s)
- Xizi Luo
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Jiahui Pan
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Qingyu Meng
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Juanjuan Huang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Wenfang Wang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Nan Zhang
- College of Mathematics, Jilin University, Changchun, China
| | - Guoqing Wang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
- *Correspondence: Guoqing Wang,
| |
Collapse
|
11
|
Suzina NE, Polivtseva VN, Shorokhova AP, Ross DV, Abashina TN, Machulin AV, El’-Registan GI, Solyanikova IP. Ultrastructural Organization and Enzymes of the Antioxidant Defense System in the Dormant Cells of Gram-Negative Bacteria Stenotrophomonas sp. Strain FM3 and Morganella morganii subsp. sibonii Strain FF1. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719020115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
|
12
|
Briffotaux J, Liu S, Gicquel B. Genome-Wide Transcriptional Responses of Mycobacterium to Antibiotics. Front Microbiol 2019; 10:249. [PMID: 30842759 PMCID: PMC6391361 DOI: 10.3389/fmicb.2019.00249] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Antibiotics can stimulate or depress gene expression in bacteria. The analysis of transcriptional responses of Mycobacterium to antimycobacterial compounds has improved our understanding of the mode of action of various drug classes and the efficacy and effect of such compounds on the global metabolism of Mycobacterium. This approach can provide new insights for known antibiotics, for example those currently used for tuberculosis treatment, as well as help to identify the mode of action and predict the targets of new compounds identified by whole-cell screening assays. In addition, changes in gene expression profiles after antimycobacterial treatment can provide information about the adaptive ability of bacteria to escape the effects of antibiotics and allow monitoring of the physiology of the bacteria during treatment. Genome-wide expression profiling also makes it possible to pinpoint genes differentially expressed between drug sensitive Mycobacterium and multidrug-resistant clinical isolates. Finally, genes involved in adaptive responses and drug tolerance could become new targets for improving the efficacy of existing antibiotics.
Collapse
Affiliation(s)
- Julien Briffotaux
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China.,Emerging Bacterial Pathogens Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Shengyuan Liu
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Brigitte Gicquel
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China.,Emerging Bacterial Pathogens Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,Mycobacterial Genetics Unit, Institut Pasteur, Paris, France
| |
Collapse
|
13
|
You D, Xu Y, Yin BC, Ye BC. Nitrogen Regulator GlnR Controls Redox Sensing and Lipids Anabolism by Directly Activating the whiB3 in Mycobacterium smegmatis. Front Microbiol 2019; 10:74. [PMID: 30761112 PMCID: PMC6361795 DOI: 10.3389/fmicb.2019.00074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/15/2019] [Indexed: 11/30/2022] Open
Abstract
WhiB3 is a conserved cytoplasmic redox sensor which is required in the infection and lipid anabolism of Mycobacterium tuberculosis. The response of WhiB3 to environmental nutrient and its regulatory cascades are crucial during the persistent infection, while little is known about the relationship between WhiB3 and emergence of nutrient stress in this process. Here, we found that nitrogen regulator GlnR directly interacted with the WhiB3 promoter region and activated its transcription in response to nitrogen availability. In whiB3 promoter region, the typical GlnR-box was also identified. Moreover, GlnR controlled cell resistance to redox stress and SL-1 lipid anabolism by directly activating whiB3 expression. These results demonstrated that GlnR regulated redox sensor WhiB3 at the transcriptional level and mediated the interplay among nitrogen metabolism, redox sensing, and lipid anabolism.
Collapse
Affiliation(s)
- Di You
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ying Xu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bin-Cheng Yin
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| |
Collapse
|
14
|
Scutigliani EM, Scholl ER, Grootemaat AE, Khanal S, Kochan JA, Krawczyk PM, Reits EA, Garzan A, Ngo HX, Green KD, Garneau-Tsodikova S, Ruijter JM, van Veen HA, van der Wel NN. Interfering With DNA Decondensation as a Strategy Against Mycobacteria. Front Microbiol 2018; 9:2034. [PMID: 30233521 PMCID: PMC6135046 DOI: 10.3389/fmicb.2018.02034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis is once again a major global threat, leading to more than 1 million deaths each year. Treatment options for tuberculosis patients are limited, expensive and characterized by severe side effects, especially in the case of multidrug-resistant forms. Uncovering novel vulnerabilities of the pathogen is crucial to generate new therapeutic strategies. Using high resolution microscopy techniques, we discovered one such vulnerability of Mycobacterium tuberculosis. We demonstrate that the DNA of M. tuberculosis can condense under stressful conditions such as starvation and antibiotic treatment. The DNA condensation is reversible and specific for viable bacteria. Based on these observations, we hypothesized that blocking the recovery from the condensed state could weaken the bacteria. We showed that after inducing DNA condensation, and subsequent blocking of acetylation of DNA binding proteins, the DNA localization in the bacteria is altered. Importantly under these conditions, Mycobacterium smegmatis did not replicate and its survival was significantly reduced. Our work demonstrates that agents that block recovery from the condensed state of the nucleoid can be exploited as antibiotic. The combination of fusidic acid and inhibition of acetylation of DNA binding proteins, via the Eis enzyme, potentiate the efficacy of fusidic acid by 10 and the Eis inhibitor to 1,000-fold. Hence, we propose that successive treatment with antibiotics and drugs interfering with recovery from DNA condensation constitutes a novel approach for treatment of tuberculosis and related bacterial infections.
Collapse
Affiliation(s)
- Enzo M Scutigliani
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Edwin R Scholl
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Anita E Grootemaat
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Sadhana Khanal
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Jakub A Kochan
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | | | - Eric A Reits
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | - Huy X Ngo
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | - Keith D Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | | | - Jan M Ruijter
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Henk A van Veen
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Nicole N van der Wel
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| |
Collapse
|
15
|
Li X, Mei H, Chen F, Tang Q, Yu Z, Cao X, Andongma BT, Chou SH, He J. Transcriptome Landscape of Mycobacterium smegmatis. Front Microbiol 2017; 8:2505. [PMID: 29326668 PMCID: PMC5741613 DOI: 10.3389/fmicb.2017.02505] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/01/2017] [Indexed: 11/13/2022] Open
Abstract
The non-pathogenic bacterium Mycobacterium smegmatis mc2155 has been widely used as a model organism in mycobacterial research, yet a detailed study about its transcription landscape remains to be established. Here we report the transcriptome, expression profiles and transcriptional structures through growth-phase-dependent RNA sequencing (RNA-seq) as well as other related experiments. We found: (1) 2,139 transcriptional start sites (TSSs) in the genome-wide scale, of which eight samples were randomly selected and further verified by 5′-RACE; (2) 2,233 independent monocistronic or polycistronic mRNAs in the transcriptome within the operon/sub-operon structures which are classified into five groups; (3) 47.50% (1016/2139) genes were transcribed into leaderless mRNAs, with the TSSs of 41.3% (883/2139) mRNAs overlapping with the first base of the annotated start codon. Initial amino acids of MSMEG_4921 and MSMEG_6422 proteins were identified by Edman degradation, indicating the presence of distinctive widespread leaderless features in M. smegmatis mc2155. (4) 150 genes with potentially wrong structural annotation, of which 124 proposed genes have been corrected; (5) eight highly active promoters, with their activities further determined by β-galactosidase assays. These data integrated the transcriptional landscape to genome information of model organism mc2155 and lay a solid foundation for further works in Mycobacterium.
Collapse
Affiliation(s)
- Xinfeng Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Han Mei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fang Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qing Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhaoqing Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Binda T Andongma
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shan-Ho Chou
- Institute of Biochemistry and NCHU Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
16
|
WhiB4 Regulates the PE/PPE Gene Family and is Essential for Virulence of Mycobacterium marinum. Sci Rep 2017; 7:3007. [PMID: 28592799 PMCID: PMC5462746 DOI: 10.1038/s41598-017-03020-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/18/2017] [Indexed: 11/18/2022] Open
Abstract
During the course of infection, pathogenic mycobacteria including Mycobacterium tuberculosis (M. tb) encounter host environments of variable oxygen tension, ranging from the hypoxic center of granulomas to the most oxygenated region in the lung cavities. Mycobacterial responses to changes of oxygen tension are critically related to infection outcomes, such as latency and reactivation. WhiB4 is an iron-sulfur containing transcription factor that is highly sensitive to oxygen exposure. In this study, we found that WhiB4 of Mycobacterium marinum (M. marinum), a pathogenic mycobacterial species that is closely related to M. tb, is required for its virulence. M. marinum ΔwhiB4 exhibited defective intracellular replication in macrophages and diminished virulence in zebrafish. Histology analysis revealed that the host had successfully controlled ΔwhiB4 bacteria, forming well-organized granulomas. RNA-seq analysis identified a large number of pe/ppe genes that were regulated by WhiB4, which provides an explanation for the essential role of WhiB4 in M. marinum virulence. Several antioxidant enzymes were also upregulated in ΔwhiB4, supporting its role in modulation of oxidative stress response. Taken together, we have provided new insight into and proposed a model to explain the physiological role of WhiB4.
Collapse
|