1
|
Luo G, Ming T, Yang L, He L, Tao T, Wang Y. Modulators targeting protein-protein interactions in Mycobacterium tuberculosis. Microbiol Res 2024; 284:127675. [PMID: 38636239 DOI: 10.1016/j.micres.2024.127675] [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: 09/27/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/20/2024]
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), mainly transmitted through droplets to infect the lungs, and seriously affecting patients' health and quality of life. Clinically, anti-TB drugs often entail side effects and lack efficacy against resistant strains. Thus, the exploration and development of novel targeted anti-TB medications are imperative. Currently, protein-protein interactions (PPIs) offer novel avenues for anti-TB drug development, and the study of targeted modulators of PPIs in M. tuberculosis has become a prominent research focus. Furthermore, a comprehensive PPI network has been constructed using computational methods and bioinformatics tools. This network allows for a more in-depth analysis of the structural biology of PPIs and furnishes essential insights for the development of targeted small-molecule modulators. Furthermore, this article provides a detailed overview of the research progress and regulatory mechanisms of PPI modulators in M. tuberculosis, the causative agent of TB. Additionally, it summarizes potential targets for anti-TB drugs and discusses the prospects of existing PPI modulators.
Collapse
Affiliation(s)
- Guofeng Luo
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianqi Ming
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Luchuan Yang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Lei He
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Tao Tao
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Yanmei Wang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China.
| |
Collapse
|
2
|
Smith EL, Goley ED. House of CarDs: Functional insights into the transcriptional regulator CdnL. Mol Microbiol 2024. [PMID: 38664995 DOI: 10.1111/mmi.15268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/12/2024] [Accepted: 04/11/2024] [Indexed: 07/07/2024]
Abstract
Regulation of bacterial transcription is a complex and multi-faceted phenomenon that is critical for growth and adaptation. Proteins in the CarD_CdnL_TRCF family are widespread, often essential, regulators of transcription of genes required for growth and metabolic homeostasis. Research in the last decade has described the mechanistic and structural bases of CarD-CdnL-mediated regulation of transcription initiation. More recently, studies in a range of bacteria have begun to elucidate the physiological roles of CarD-CdnL proteins as well as mechanisms by which these proteins, themselves, are regulated. A theme has emerged wherein regulation of CarD-CdnL proteins is central to bacterial adaptation to stress and/or changing environmental conditions.
Collapse
Affiliation(s)
- Erika L Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
3
|
Smith EL, Panis G, Woldemeskel SA, Viollier PH, Chien P, Goley ED. Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter. PNAS NEXUS 2024; 3:pgae154. [PMID: 38650860 PMCID: PMC11034885 DOI: 10.1093/pnasnexus/pgae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). During SR activation in Caulobacter crescentus, SpoT synthesizes the secondary messengers guanosine 5'-diphosphate 3'-diphosphate and guanosine 5'-triphosphate 3'-diphosphate (collectively known as (p)ppGpp), which affect transcription by binding RNA polymerase (RNAP) to down-regulate anabolic genes. (p)ppGpp also impacts the expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important are unclear. In this study, we show that CdnL is down-regulated posttranslationally during starvation in a manner dependent on SpoT and the ClpXP protease. Artificial stabilization of CdnL during starvation causes misregulation of ribosomal and metabolic genes. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. Moreover, cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to nutrient fluctuations. We hypothesize that clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, is critical for altering the transcriptome in order to permit cell survival during nutrient stress.
Collapse
Affiliation(s)
- Erika L Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Selamawit Abi Woldemeskel
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA 01003, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
4
|
Smith EL, Panis G, Woldemeskel SA, Viollier PH, Chien P, Goley ED. Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572625. [PMID: 38187569 PMCID: PMC10769358 DOI: 10.1101/2023.12.20.572625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). During SR activation in Caulobacter crescentus, SpoT synthesizes the secondary messengers (p)ppGpp, which affect transcription by binding RNA polymerase to downregulate anabolic genes. (p)ppGpp also impacts expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important is unclear. Here, we show that CdnL is downregulated post-translationally during starvation in a manner dependent on SpoT and the ClpXP protease. Inappropriate stabilization of CdnL during starvation causes misregulation of ribosomal and metabolic genes. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. Moreover, cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to nutrient fluctuations. We hypothesize that clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, is critical for altering the transcriptome in order to permit cell survival during nutrient stress.
Collapse
Affiliation(s)
- Erika L. Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
| | - Gaäl Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland, 1211
| | - Selamawit Abi Woldemeskel
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
- BlueRock Therapeutics, Cambridge, Massachusetts, 02142 (current)
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland, 1211
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts, 01003
| | - Erin D. Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
| |
Collapse
|
5
|
Zhu DX, Stallings CL. Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics. J Biol Chem 2023; 299:104724. [PMID: 37075846 PMCID: PMC10232725 DOI: 10.1016/j.jbc.2023.104724] [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: 01/23/2023] [Revised: 03/30/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023] Open
Abstract
Bacterial pathogens like Mycobacterium tuberculosis (Mtb) employ transcription factors to adapt their physiology to the diverse environments within their host. CarD is a conserved bacterial transcription factor that is essential for viability in Mtb. Unlike classical transcription factors that recognize promoters by binding to specific DNA sequence motifs, CarD binds directly to the RNA polymerase to stabilize the open complex intermediate (RPo) during transcription initiation. We previously showed using RNA-sequencing that CarD is capable of both activating and repressing transcription in vivo. However, it is unknown how CarD achieves promoter-specific regulatory outcomes in Mtb despite binding indiscriminate of DNA sequence. We propose a model where CarD's regulatory outcome depends on the promoter's basal RPo stability and test this model using in vitro transcription from a panel of promoters with varying levels of RPo stability. We show that CarD directly activates full-length transcript production from the Mtb ribosomal RNA promoter rrnAP3 (AP3) and that the degree of transcription activation by CarD is negatively correlated with RPo stability. Using targeted mutations in the extended -10 and discriminator region of AP3, we show that CarD directly represses transcription from promoters that form relatively stable RPo. DNA supercoiling also influenced RPo stability and affected the direction of CarD regulation, indicating that the outcome of CarD activity can be regulated by factors beyond promoter sequence. Our results provide experimental evidence for how RNA polymerase-binding transcription factors like CarD can exert specific regulatory outcomes based on the kinetic properties of a promoter.
Collapse
Affiliation(s)
- Dennis X Zhu
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri, USA.
| |
Collapse
|
6
|
Zhu DX, Stallings CL. Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533025. [PMID: 36993566 PMCID: PMC10055060 DOI: 10.1101/2023.03.16.533025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Bacterial pathogens like Mycobacterium tuberculosis ( Mtb ) employ transcription factors to adapt their physiology to the diverse environments within their host. CarD is a conserved bacterial transcription factor that is essential for viability in Mtb . Unlike classical transcription factors that recognize promoters by binding to specific DNA sequence motifs, CarD binds directly to the RNA polymerase (RNAP) to stabilize the open complex intermediate (RP o ) during transcription initiation. We previously showed using RNA-sequencing that CarD is capable of both activating and repressing transcription in vivo . However, it is unknown how CarD achieves promoter specific regulatory outcomes in Mtb despite binding indiscriminate of DNA sequence. We propose a model where CarD's regulatory outcome depends on the promoter's basal RP o stability and test this model using in vitro transcription from a panel of promoters with varying levels of RP o stability. We show that CarD directly activates full-length transcript production from the Mtb ribosomal RNA promoter rrnA P3 (AP3) and that the degree of transcription activation by CarD is negatively correlated with RP o stability. Using targeted mutations in the extended -10 and discriminator region of AP3, we show that CarD directly represses transcription from promoters that form relatively stable RP o . DNA supercoiling also influenced RP o stability and affected the direction of CarD regulation, indicating that the outcome of CarD activity can be regulated by factors beyond promoter sequence. Our results provide experimental evidence for how RNAP-binding transcription factors like CarD can exert specific regulatory outcomes based on the kinetic properties of a promoter.
Collapse
|
7
|
Oh Y, Lee HN, Ko EM, Jeong JA, Park SW, Oh JI. Mycobacterial Regulatory Systems Involved in the Regulation of Gene Expression Under Respiration-Inhibitory Conditions. J Microbiol 2023; 61:297-315. [PMID: 36847970 DOI: 10.1007/s12275-023-00026-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/01/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis. M. tuberculosis can survive in a dormant state within the granuloma, avoiding the host-mounting immune attack. M. tuberculosis bacilli in this state show increased tolerance to antibiotics and stress conditions, and thus the transition of M. tuberculosis to the nonreplicating dormant state acts as an obstacle to tuberculosis treatment. M. tuberculosis in the granuloma encounters hostile environments such as hypoxia, nitric oxide, reactive oxygen species, low pH, and nutrient deprivation, etc., which are expected to inhibit respiration of M. tuberculosis. To adapt to and survive in respiration-inhibitory conditions, it is required for M. tuberculosis to reprogram its metabolism and physiology. In order to get clues to the mechanism underlying the entry of M. tuberculosis to the dormant state, it is important to understand the mycobacterial regulatory systems that are involved in the regulation of gene expression in response to respiration inhibition. In this review, we briefly summarize the information regarding the regulatory systems implicated in upregulation of gene expression in mycobacteria exposed to respiration-inhibitory conditions. The regulatory systems covered in this review encompass the DosSR (DevSR) two-component system, SigF partner switching system, MprBA-SigE-SigB signaling pathway, cAMP receptor protein, and stringent response.
Collapse
Affiliation(s)
- Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Ha-Na Lee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Eon-Min Ko
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea Disease Control and Prevention Agency, National Institute of Infectious Diseases, National Institute of Health, Osong, 28159, Republic of Korea
| | - Ji-A Jeong
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea Disease Control and Prevention Agency, National Institute of Infectious Diseases, National Institute of Health, Osong, 28159, Republic of Korea
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea. .,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
| |
Collapse
|
8
|
Stephanie F, Tambunan USF, Siahaan TJ. M. tuberculosis Transcription Machinery: A Review on the Mycobacterial RNA Polymerase and Drug Discovery Efforts. Life (Basel) 2022; 12:1774. [PMID: 36362929 PMCID: PMC9695777 DOI: 10.3390/life12111774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 09/08/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) is the main source of tuberculosis (TB), one of the oldest known diseases in the human population. Despite the drug discovery efforts of past decades, TB is still one of the leading causes of mortality and claimed more than 1.5 million lives worldwide in 2020. Due to the emergence of drug-resistant strains and patient non-compliance during treatments, there is a pressing need to find alternative therapeutic agents for TB. One of the important areas for developing new treatments is in the inhibition of the transcription step of gene expression; it is the first step to synthesize a copy of the genetic material in the form of mRNA. This further translates to functional protein synthesis, which is crucial for the bacteria living processes. MTB contains a bacterial DNA-dependent RNA polymerase (RNAP), which is the key enzyme for the transcription process. MTB RNAP has been targeted for designing and developing antitubercular agents because gene transcription is essential for the mycobacteria survival. Initiation, elongation, and termination are the three important sequential steps in the transcription process. Each step is complex and highly regulated, involving multiple transcription factors. This review is focused on the MTB transcription machinery, especially in the nature of MTB RNAP as the main enzyme that is regulated by transcription factors. The mechanism and conformational dynamics that occur during transcription are discussed and summarized. Finally, the current progress on MTB transcription inhibition and possible drug target in mycobacterial RNAP are also described to provide insight for future antitubercular drug design and development.
Collapse
Affiliation(s)
- Filia Stephanie
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Usman Sumo Friend Tambunan
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Teruna J. Siahaan
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, KS 66045, USA
| |
Collapse
|
9
|
Ke N, Kumka JE, Fang M, Weaver B, Burstyn JN, Bauer CE. Redox Brake Regulator RedB and FnrL Function as Yin-Yang Regulators of Anaerobic-Aerobic Metabolism in Rhodobacter capsulatus. Microbiol Spectr 2022; 10:e0235422. [PMID: 36106752 PMCID: PMC9603517 DOI: 10.1128/spectrum.02354-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/25/2022] [Indexed: 01/04/2023] Open
Abstract
We recently described a new member of the CRP (cyclic AMP receptor protein)/FNR (fumarate and nitrate reductase regulatory protein) family called RedB, an acronym for redox brake, that functions to limit the production of ATP and NADH. This study shows that the RedB regulon significantly overlaps the FnrL regulon, with 199 genes being either directly or indirectly regulated by both of these global regulatory proteins. Among these 199 coregulated genes, 192 are divergently regulated, indicating that RedB functions as an antagonist of FnrL. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis indicates that RedB and Fnr directly coregulate only 4 out of 199 genes. The primary mechanism for the divergent regulation of target genes thus involves indirect regulation by both RedB and FnrL (156 cases). Additional regulation involves direct binding by RedB and indirect regulation by FnrL (36 cases) or direct binding by FnrL and indirect regulation by RedB (3 cases). Analysis of physiological pathways under direct and indirect control by these global regulators demonstrates that RedB functions primarily to limit energy production, while FnrL functions to enhance energy production. This regulation includes glycolysis, gluconeogenesis, photosynthesis, hydrogen oxidation, electron transport, carbon fixation, lipid biosynthesis, and protein synthesis. Finally, we show that 75% of genomes from diverse species that code for RedB proteins also harbor genes coding for FNR homologs. This cooccurrence indicates that RedB likely has an important role in buffering FNR-mediated energy production in a broad range of species. IMPORTANCE The CRP/FNR family of regulatory proteins constitutes a large collection of related transcription factors, several of which globally regulate cellular energy production. A well-characterized example is FNR (called FnrL in Rhodobacter capsulatus), which is responsible for regulating the expression of numerous genes that promote maximal energy production and growth under anaerobic conditions. In a companion article (N. Ke, J. E. Kumka, M. Fang, B. Weaver, et al., Microbiol Spectr 10:e02353-22, 2022, https://doi.org/10.1128/Spectrum02353-22), we identified a new subgroup of the CRP/FNR family and demonstrated that a member of this new subgroup, called RedB, has a role in limiting cellular energy production. In this study, we show that numerous genes encompassing the RedB regulon significantly overlap genes that are members of the FnrL regulon. Furthermore, 97% of the genes that are members of both the RedB and FnrL regulons are divergently regulated by these two transcription factors. RedB thus functions as a buffer limiting the amount of energy production that is promoted by FnrL.
Collapse
Affiliation(s)
- Nijia Ke
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Joseph E. Kumka
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Mingxu Fang
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Brian Weaver
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Judith N. Burstyn
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Carl E. Bauer
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| |
Collapse
|
10
|
Taboada-Castro H, Gil J, Gómez-Caudillo L, Escorcia-Rodríguez JM, Freyre-González JA, Encarnación-Guevara S. Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network. Front Microbiol 2022; 13:947678. [PMID: 36312930 PMCID: PMC9611204 DOI: 10.3389/fmicb.2022.947678] [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: 05/19/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
A comparative proteomic study at 6 h of growth in minimal medium (MM) and bacteroids at 18 days of symbiosis of Rhizobium etli CFN42 with the Phaseolus vulgaris leguminous plant was performed. A gene ontology classification of proteins in MM and bacteroid, showed 31 and 10 pathways with higher or equal than 30 and 20% of proteins with respect to genome content per pathway, respectively. These pathways were for energy and environmental compound metabolism, contributing to understand how Rhizobium is adapted to the different conditions. Metabolic maps based on orthology of the protein profiles, showed 101 and 74 functional homologous proteins in the MM and bacteroid profiles, respectively, which were grouped in 34 different isoenzymes showing a great impact in metabolism by covering 60 metabolic pathways in MM and symbiosis. Taking advantage of co-expression of transcriptional regulators (TF’s) in the profiles, by selection of genes whose matrices were clustered with matrices of TF’s, Transcriptional Regulatory networks (TRN´s) were deduced by the first time for these metabolic stages. In these clustered TF-MM and clustered TF-bacteroid networks, containing 654 and 246 proteins, including 93 and 46 TFs, respectively, showing valuable information of the TF’s and their regulated genes with high stringency. Isoenzymes were specific for adaptation to the different conditions and a different transcriptional regulation for MM and bacteroid was deduced. The parameters of the TRNs of these expected biological networks and biological networks of E. coli and B. subtilis segregate from the random theoretical networks. These are useful data to design experiments on TF gene–target relationships for bases to construct a TRN.
Collapse
Affiliation(s)
- Hermenegildo Taboada-Castro
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | - Jeovanis Gil
- Division of Oncology, Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden
| | - Leopoldo Gómez-Caudillo
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | - Juan Miguel Escorcia-Rodríguez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Julio Augusto Freyre-González
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Sergio Encarnación-Guevara
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
- *Correspondence: Sergio Encarnacion Guevara,
| |
Collapse
|
11
|
Zannier F, Portero LR, Douki T, Gärtner W, Farías ME, Albarracín VH. Proteomic Signatures of Microbial Adaptation to the Highest Ultraviolet-Irradiation on Earth: Lessons From a Soil Actinobacterium. Front Microbiol 2022; 13:791714. [PMID: 35369494 PMCID: PMC8965627 DOI: 10.3389/fmicb.2022.791714] [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] [Received: 10/08/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
In the Central Andean region in South America, high-altitude ecosystems (3500-6000 masl) are distributed across Argentina, Chile, Bolivia, and Peru, in which poly-extremophilic microbes thrive under extreme environmental conditions. In particular, in the Puna region, total solar irradiation and UV incidence are the highest on Earth, thus, restraining the physiology of individual microorganisms and the composition of microbial communities. UV-resistance of microbial strains thriving in High-Altitude Andean Lakes was demonstrated and their mechanisms were partially characterized by genomic analysis, biochemical and physiological assays. Then, the existence of a network of physiological and molecular mechanisms triggered by ultraviolet light exposure was hypothesized and called "UV-resistome". It includes some or all of the following subsystems: (i) UV sensing and effective response regulators, (ii) UV-avoidance and shielding strategies, (iii) damage tolerance and oxidative stress response, (iv) energy management and metabolic resetting, and (v) DNA damage repair. Genes involved in the described UV-resistome were recently described in the genome of Nesterenkonia sp. Act20, an actinobacterium which showed survival to high UV-B doses as well as efficient photorepairing capability. The aim of this work was to use a proteomic approach together with photoproduct measurements to help dissecting the molecular events involved in the adaptive response of a model High-Altitude Andean Lakes (HAAL) extremophilic actinobacterium, Nesterenkonia sp. Act20, under artificial UV-B radiation. Our results demonstrate that UV-B exposure induced over-abundance of a well-defined set of proteins while recovery treatments restored the proteomic profiles present before the UV-challenge. The proteins involved in this complex molecular network were categorized within the UV-resistome subsystems: damage tolerance and oxidative stress response, energy management and metabolic resetting, and DNA damage repair.
Collapse
Affiliation(s)
- Federico Zannier
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
| | - Luciano R. Portero
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
| | - Thierry Douki
- Université Grenoble Alpes, Commissariat a l’Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Institut de Recherche Interdisciplinaire de Grenoble–Systèmes Moléculaires et nanoMatériaux p our l’Énergie et la Santé, Grenoble, France
| | - Wolfgang Gärtner
- Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
| | - María E. Farías
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
| | - Virginia H. Albarracín
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| |
Collapse
|
12
|
Prusa J, Zhu DX, Flynn AJ, Jensen D, Ruiz Manzano A, Galburt EA, Stallings CL. Molecular dissection of RbpA-mediated regulation of fidaxomicin sensitivity in mycobacteria. J Biol Chem 2022; 298:101752. [PMID: 35189142 PMCID: PMC8956947 DOI: 10.1016/j.jbc.2022.101752] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 01/13/2023] Open
Abstract
RNA polymerase (RNAP) binding protein A (RbpA) is essential for mycobacterial viability and regulates transcription initiation by increasing the stability of the RNAP-promoter open complex (RPo). RbpA consists of four domains: an N-terminal tail (NTT), a core domain (CD), a basic linker, and a sigma interaction domain. We have previously shown that truncation of the RbpA NTT and CD increases RPo stabilization by RbpA, implying that these domains inhibit this activity of RbpA. Previously published structural studies showed that the NTT and CD are positioned near multiple RNAP-σA holoenzyme functional domains and predict that the RbpA NTT contributes specific amino acids to the binding site of the antibiotic fidaxomicin (Fdx), which inhibits the formation of the RPo complex. Furthermore, deletion of the NTT results in decreased Mycobacterium smegmatis sensitivity to Fdx, but whether this is caused by a loss in Fdx binding is unknown. We generated a panel of rbpA mutants and found that the RbpA NTT residues predicted to directly interact with Fdx are partially responsible for RbpA-dependent Fdx activity in vitro, while multiple additional RbpA domains contribute to Fdx activity in vivo. Specifically, our results suggest that the RPo-stabilizing activity of RbpA decreases Fdx activity in vivo. In support of the association between RPo stability and Fdx activity, we find that another factor that promotes RPo stability in bacteria, CarD, also impacts to Fdx sensitivity. Our findings highlight how RbpA and other factors may influence RNAP dynamics to affect Fdx sensitivity.
Collapse
Affiliation(s)
- Jerome Prusa
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dennis X. Zhu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Aidan J. Flynn
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Drake Jensen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ana Ruiz Manzano
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eric A. Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christina L. Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA,For correspondence: Christina L. Stallings
| |
Collapse
|
13
|
Li X, Chen F, Liu X, Xiao J, Andongma BT, Tang Q, Cao X, Chou SH, Galperin MY, He J. Clp protease and antisense RNA jointly regulate the global regulator CarD to mediate mycobacterial starvation response. eLife 2022; 11:73347. [PMID: 35080493 PMCID: PMC8820732 DOI: 10.7554/elife.73347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/25/2022] [Indexed: 12/02/2022] Open
Abstract
Under starvation conditions, bacteria tend to slow down their translation rate by reducing rRNA synthesis, but the way they accomplish that may vary in different bacteria. In Mycobacterium species, transcription of rRNA is activated by the RNA polymerase (RNAP) accessory transcription factor CarD, which interacts directly with RNAP to stabilize the RNAP-promoter open complex formed on rRNA genes. The functions of CarD have been extensively studied, but the mechanisms that control its expression remain obscure. Here, we report that the level of CarD was tightly regulated when mycobacterial cells switched from nutrient-rich to nutrient-deprived conditions. At the translational level, an antisense RNA of carD (AscarD) was induced in a SigF-dependent manner to bind with carD mRNA and inhibit CarD translation, while at the post-translational level, the residual intracellular CarD was quickly degraded by the Clp protease. AscarD thus worked synergistically with Clp protease to decrease the CarD level to help mycobacterial cells cope with the nutritional stress. Altogether, our work elucidates the regulation mode of CarD and delineates a new mechanism for the mycobacterial starvation response, which is important for the adaptation and persistence of mycobacterial pathogens in the host environment.
Collapse
Affiliation(s)
- Xinfeng Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fang Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaoyu Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinfeng Xiao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Binda T Andongma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qing Tang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Cao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shan-Ho Chou
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jin He
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
14
|
Sharma A, Sagar K, Chauhan NK, Venkataraman B, Gupta N, Gosain TP, Bhalla N, Singh R, Gupta A. HigB1 Toxin in Mycobacterium tuberculosis Is Upregulated During Stress and Required to Establish Infection in Guinea Pigs. Front Microbiol 2021; 12:748890. [PMID: 34917044 PMCID: PMC8669151 DOI: 10.3389/fmicb.2021.748890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/29/2021] [Indexed: 12/20/2022] Open
Abstract
The extraordinary expansion of Toxin Antitoxin (TA) modules in the genome of Mycobacterium tuberculosis has received significant attention over the last few decades. The cumulative evidence suggests that TA systems are activated in response to stress conditions and are essential for M. tuberculosis pathogenesis. In M. tuberculosis, Rv1955-Rv1956-Rv1957 constitutes the only tripartite TAC (Toxin Antitoxin Chaperone) module. In this locus, Rv1955 (HigB1) encodes for the toxin and Rv1956 (HigA1) encodes for antitoxin. Rv1957 encodes for a SecB-like chaperone that regulates HigBA1 toxin antitoxin system by preventing HigA1 degradation. Here, we have investigated the physiological role of HigB1 toxin in stress adaptation and pathogenesis of Mycobacterium tuberculosis. qPCR studies revealed that higBA1 is upregulated in nutrient limiting conditions and upon exposure to levofloxacin. We also show that the promoter activity of higBA1 locus in M. tuberculosis is (p)ppGpp dependent. We observed that HigB1 locus is non-essential for M. tuberculosis growth under different stress conditions in vitro. However, guinea pigs infected with higB1 deletion strain exhibited significantly reduced bacterial loads and pathological damage in comparison to the animals infected with the parental strain. Transcriptome analysis suggested that deletion of higB1 reduced the expression of genes involved in virulence, detoxification and adaptation. The present study describes the role of higB1 toxin in M. tuberculosis physiology and highlights the importance of higBA1 locus during infection in host tissues.
Collapse
Affiliation(s)
- Arun Sharma
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Kalpana Sagar
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India.,Centre for Innovation in Infectious Disease Research, Education and Training, New Delhi, India
| | - Neeraj Kumar Chauhan
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Balaji Venkataraman
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Nidhi Gupta
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Tannu Priya Gosain
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Nikhil Bhalla
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Amita Gupta
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India.,Centre for Innovation in Infectious Disease Research, Education and Training, New Delhi, India
| |
Collapse
|
15
|
Myers KS, Noguera DR, Donohue TJ. Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa. mSystems 2021; 6:e0052621. [PMID: 34254822 PMCID: PMC8407463 DOI: 10.1128/msystems.00526-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Much of our knowledge of bacterial transcription initiation has been derived from studying the promoters of Escherichia coli and Bacillus subtilis. Given the expansive diversity across the bacterial phylogeny, it is unclear how much of this knowledge can be applied to other organisms. Here, we report on bioinformatic analyses of promoter sequences of the primary σ factor (σ70) by leveraging publicly available transcription start site (TSS) sequencing data sets for nine bacterial species spanning five phyla. This analysis identifies previously unreported differences in the -35 and -10 elements of σ70-dependent promoters in several groups of bacteria. We found that Actinobacteria and Betaproteobacteria σ70-dependent promoters lack the TTG triad in their -35 element, which is predicted to be conserved across the bacterial phyla. In addition, the majority of the Alphaproteobacteria σ70-dependent promoters analyzed lacked the thymine at position -7 that is highly conserved in other phyla. Bioinformatic examination of the Alphaproteobacteria σ70-dependent promoters identifies a significant overrepresentation of essential genes and ones encoding proteins with common cellular functions downstream of promoters containing an A, C, or G at position -7. We propose that transcription of many σ70-dependent promoters in Alphaproteobacteria depends on the transcription factor CarD, which is an essential protein in several members of this phylum. Our analysis expands the knowledge of promoter architecture across the bacterial phylogeny and provides new information that can be used to engineer bacteria for use in medical, environmental, agricultural, and biotechnological processes. IMPORTANCE Transcription of DNA to RNA by RNA polymerase is essential for cells to grow, develop, and respond to stress. Understanding the process and control of transcription is important for health, disease, the environment, and biotechnology. Decades of research on a few bacteria have identified promoter DNA sequences that are recognized by the σ subunit of RNA polymerase. We used bioinformatic analyses to reveal previously unreported differences in promoter DNA sequences across the bacterial phylogeny. We found that many Actinobacteria and Betaproteobacteria promoters lack a sequence in their -35 DNA recognition element that was previously assumed to be conserved and that Alphaproteobacteria lack a thymine residue at position -7, also previously assumed to be conserved. Our work reports important new information about bacterial transcription, illustrates the benefits of studying bacteria across the phylogenetic tree, and proposes new lines of future investigation.
Collapse
Affiliation(s)
- Kevin S. Myers
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Civil & Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| |
Collapse
|
16
|
Pan L, Gardner CL, Beliakoff R, da Silva D, Zuo R, Pagliai FA, Padgett-Pagliai KA, Merli ML, Bahadiroglu E, Gonzalez CF, Lorca GL. PrbP modulates biofilm formation in Liberibacter crescens. Environ Microbiol 2021; 23:7121-7138. [PMID: 34431209 DOI: 10.1111/1462-2920.15740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 12/31/2022]
Abstract
In Liberibacter asiaticus, PrbP is a transcriptional regulatory protein involved in survival and persistence during host infection. Tolfenamic acid was previously found to inhibit interactions between PrbP and the promotor region of rplK, resulting in reduced survival of L. asiaticus in the citrus host. In this study, we performed transcriptome analyses to elucidate the PrbP regulon in L. crescens, as it is phylogenetically the closest related species to L. asiaticus that can be grown in laboratory conditions. Chemical inhibition of PrbP with tolfenamic acid revealed that PrbP is involved in the regulation of diverse cellular processes, including stress response, cell motility, cell cycle and biofilm formation. In vitro DNA binding and bacterial two-hybrid assays also suggested that PrbP is a global regulator of multiple transcription factors (RpoH, VisN, PleD, MucR, MocR and CtrA) at both transcriptional and/or post-transcriptional levels. Sub-lethal concentrations of tolfenamic acid significantly reduced the attachment of L. crescens during biofilm formation and decreased long-term persistence in biofilm structures. Overall, our findings show the importance of PrbP in regulating diverse biological processes through direct and indirect interactions with other transcriptional regulators in L. crescens.
Collapse
Affiliation(s)
- Lei Pan
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Christopher L Gardner
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Reagan Beliakoff
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Danilo da Silva
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Ran Zuo
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Fernando A Pagliai
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Kaylie A Padgett-Pagliai
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Marcelo L Merli
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Erol Bahadiroglu
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Claudio F Gonzalez
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Graciela L Lorca
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| |
Collapse
|
17
|
Aviles FA, Kyndt JA. Cellulosimicrobium fucosivorans sp. nov., isolated from San Elijo Lagoon, contains a fucose metabolic pathway linked to carotenoid production. Arch Microbiol 2021; 203:4525-4538. [PMID: 34148152 DOI: 10.1007/s00203-021-02443-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/10/2021] [Accepted: 06/13/2021] [Indexed: 10/21/2022]
Abstract
Cellulosimicrobium strain SE3T was isolated from the San Elijo coastal lagoon near San Diego. A whole genome-based phylogenetic comparison shows great heterogeneity within the Cellulosimicrobium genus. Based on average nucleotide identity, whole genome-based comparison, and the presence of a unique L-fucose metabolic pathway, strain SE3T was shown to belong to a novel species within the genus, together with five other strains. The name Cellulosimicrobium fucosivorans sp. nov. is proposed, with strain SE3T as the type strain. The strain encodes a unique alpha-L-fucosidase and the L-fucose metabolic pathway is homologous to the one recently described in Campylobacter jejuni. C. fucosivorans is able to grow on L-fucose, and interestingly, the biosynthesis of the yellow carotenoid is dependent on the presence of L-fucose in the media. The ability to metabolize fucose and the linked production of carotenoids are expected to provide C. fucosivorans with a competitive advantage in the sunny coastal lagoon area.
Collapse
Affiliation(s)
- Fabiola A Aviles
- College of Science and Technology, Bellevue University, 1000 Galvin Rd. S., Bellevue, NE, 68005, USA
| | - John A Kyndt
- College of Science and Technology, Bellevue University, 1000 Galvin Rd. S., Bellevue, NE, 68005, USA.
| |
Collapse
|
18
|
Chauhan A, Kumar M, Kumar A, Kanchan K. Comprehensive review on mechanism of action, resistance and evolution of antimycobacterial drugs. Life Sci 2021; 274:119301. [PMID: 33675895 DOI: 10.1016/j.lfs.2021.119301] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/14/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023]
Abstract
Tuberculosis is one of the deadliest infectious diseases existing in the world since ancient times and still possesses serious threat across the globe. Each year the number of cases increases due to high drug resistance shown by Mycobacterium tuberculosis (Mtb). Available antimycobacterial drugs have been classified as First line, Second line and Third line antibiotics depending on the time of their discoveries and their effectiveness in the treatment. These antibiotics have a broad range of targets ranging from cell wall to metabolic processes and their non-judicious and uncontrolled usage in the treatment for years has created a significant problem called multi-drug resistant (MDR) tuberculosis. In this review, we have summarized the mechanism of action of all the classified antibiotics currently in use along with the resistance mechanisms acquired by Mtb. We have focused on the new drug candidates/repurposed drugs, and drug in combinations, which are in clinical trials for either treating the MDR tuberculosis more effectively or involved in reducing the time required for the chemotherapy of drug sensitive TB. This information is not discussed very adequately on a single platform. Additionally, we have discussed the recent technologies that are being used to discover novel resistance mechanisms acquired by Mtb and for exploring novel drugs. The story of intrinsic resistance mechanisms and evolution in Mtb is far from complete. Therefore, we have also discussed intrinsic resistance mechanisms of Mtb and their evolution with time, emphasizing the hope for the development of novel antimycobacterial drugs for effective therapy of tuberculosis.
Collapse
Affiliation(s)
- Aditi Chauhan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India
| | - Manoj Kumar
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Noida 201313, India
| | - Awanish Kumar
- Department of Bio Technology, National Institute of Technology, Raipur, India
| | - Kajal Kanchan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India.
| |
Collapse
|
19
|
The DUF1013 protein TrcR tracks with RNA polymerase to control the bacterial cell cycle and protect against antibiotics. Proc Natl Acad Sci U S A 2021; 118:2010357118. [PMID: 33602809 DOI: 10.1073/pnas.2010357118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How DNA-dependent RNA polymerase (RNAP) acts on bacterial cell cycle progression during transcription elongation is poorly investigated. A forward genetic selection for Caulobacter crescentus cell cycle mutants unearthed the uncharacterized DUF1013 protein (TrcR, transcriptional cell cycle regulator). TrcR promotes the accumulation of the essential cell cycle transcriptional activator CtrA in late S-phase but also affects transcription at a global level to protect cells from the quinolone antibiotic nalidixic acid that induces a multidrug efflux pump and from the RNAP inhibitor rifampicin that blocks transcription elongation. We show that TrcR associates with promoters and coding sequences in vivo in a rifampicin-dependent manner and that it interacts physically and genetically with RNAP. We show that TrcR function and its RNAP-dependent chromatin recruitment are conserved in symbiotic Sinorhizobium sp. and pathogenic Brucella spp Thus, TrcR represents a hitherto unknown antibiotic target and the founding member of the DUF1013 family, an uncharacterized class of transcriptional regulators that track with RNAP during the elongation phase to promote transcription during the cell cycle.
Collapse
|
20
|
Stefan MA, Velazquez GM, Garcia GA. High-throughput screening to discover inhibitors of the CarD·RNA polymerase protein-protein interaction in Mycobacterium tuberculosis. Sci Rep 2020; 10:21309. [PMID: 33277558 PMCID: PMC7718890 DOI: 10.1038/s41598-020-78269-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/23/2020] [Indexed: 12/18/2022] Open
Abstract
Multidrug-resistant Mycobacterium tuberculosis (MDR-TB) accounts for 3.7% of new cases of TB annually worldwide and is a major threat to global public health. Due to the prevalence of the MDR-TB and extensively drug resistant tuberculosis (XDR-TB) cases, there is an urgent need for new drugs with novel mechanisms of action. CarD, a global transcription regulator in MTB, binds RNAP and activates transcription by stabilizing the transcription initiation open-promoter complex (RPo). CarD is required for MTB viability and it has highly conserved homologues in many eubacteria. A fluorescence polarization (FP) assay which monitors the association of MTB RNAP, native rRNA promoter DNA and CarD has been developed. Overall, our objective is to identify and characterize small molecule inhibitors which block the CarD/RNAP interaction and to understand the mechanisms by which CarD interacts with the molecules. We expect that the development of a new and improved anti-TB compound with a novel mechanism of action will relieve the burden of resistance. This CarD FP assay is amenable to HTS and is an enabling tool for future novel therapeutic discovery.
Collapse
Affiliation(s)
- Maxwell A Stefan
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Glory M Velazquez
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - George A Garcia
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
21
|
Henry KK, Ross W, Myers KS, Lemmer KC, Vera JM, Landick R, Donohue TJ, Gourse RL. A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation. Proc Natl Acad Sci U S A 2020; 117:29658-29668. [PMID: 33168725 PMCID: PMC7703639 DOI: 10.1073/pnas.2010087117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Using an in vitro transcription system with purified RNA polymerase (RNAP) to investigate rRNA synthesis in the photoheterotrophic α-proteobacterium Rhodobacter sphaeroides, we identified a surprising feature of promoters recognized by the major holoenzyme. Transcription from R. sphaeroides rRNA promoters was unexpectedly weak, correlating with absence of -7T, the very highly conserved thymine found at the last position in -10 elements of promoters in most bacterial species. Thymine substitutions for adenine at position -7 in the three rRNA promoters strongly increased intrinsic promoter activity, indicating that R. sphaeroides RNAP can utilize -7T when present. rRNA promoters were activated by purified R. sphaeroides CarD, a transcription factor found in many bacterial species but not in β- and γ-proteobacteria. Overall, CarD increased the activity of 15 of 16 native R. sphaeroides promoters tested in vitro that lacked -7T, whereas it had no effect on three of the four native promoters that contained -7T. Genome-wide bioinformatic analysis of promoters from R. sphaeroides and two other α-proteobacterial species indicated that 30 to 43% contained -7T, whereas 90 to 99% of promoters from non-α-proteobacteria contained -7T. Thus, promoters lacking -7T appear to be widespread in α-proteobacteria and may have evolved away from consensus to enable their coordinated regulation by transcription factors like CarD. We observed a strong reduction in R. sphaeroides CarD levels when cells enter stationary phase, suggesting that reduced activation by CarD may contribute to inhibition of rRNA transcription when cells enter stationary phase, the stage of growth when bacterial ribosome synthesis declines.
Collapse
Affiliation(s)
- Kemardo K Henry
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Wilma Ross
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706;
| | - Kevin S Myers
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Kimberly C Lemmer
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Jessica M Vera
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Robert Landick
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Timothy J Donohue
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706;
| |
Collapse
|
22
|
Kaur G, Kapoor S, Kaundal S, Dutta D, Thakur KG. Structure-Guided Designing and Evaluation of Peptides Targeting Bacterial Transcription. Front Bioeng Biotechnol 2020; 8:797. [PMID: 33014990 PMCID: PMC7505949 DOI: 10.3389/fbioe.2020.00797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/22/2020] [Indexed: 11/17/2022] Open
Abstract
The mycobacterial RNA polymerase (RNAP) is an essential and validated drug target for developing antibacterial drugs. The β-subunit of Mycobacterium tuberculosis (Mtb) RNAP (RpoB) interacts with an essential and global transcription factor, CarD, and confers antibiotic and oxidative stress resistance to Mtb. Compromising the RpoB/CarD interactions results in the killing of mycobacteria, hence disrupting the RpoB/CarD interaction has been proposed as a novel strategy for the development of anti-tubercular drugs. Here, we describe the first approach to rationally design and test the efficacy of the peptide-based inhibitors which specifically target the conserved PPI interface between the bacterial RNAP β/transcription factor complex. We performed in silico protein-peptide docking studies along with biochemical assays to characterize the novel peptide-based inhibitors. Our results suggest that the top ranked peptides are highly stable, soluble in aqueous buffer, and capable of inhibiting transcription with IC50 > 50 μM concentration. Using peptide-based molecules, our study provides the first piece of evidence to target the conserved RNAP β/transcription factor interface for designing new inhibitors. Our results may hence form the basis to further improve the potential of these novel peptides in modulating bacterial gene expression, thus inhibiting bacterial growth and combating bacterial infections.
Collapse
Affiliation(s)
- Gundeep Kaur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Srajan Kapoor
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Soni Kaundal
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Dipak Dutta
- Molecular Microbiology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| |
Collapse
|
23
|
Mycobacterium smegmatis MSMEG_0129 is a nutrition-associated regulator that interacts with CarD and ClpP2. Int J Biochem Cell Biol 2020; 124:105763. [PMID: 32389745 DOI: 10.1016/j.biocel.2020.105763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 04/14/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022]
Abstract
Mycobacterium smegmatis MSMEG_0129 and Rv0164, its homologue in Mycobacterium tuberculosis, are single START-domain proteins essential for bacterial growth and survival, but their biochemical activities and biological roles remain undetermined. Here, we probed the possible functions of MSMEG_0129 and its underlying mechanisms by determining its cellular location, searching for its interaction partners and monitoring its transcription profile. MSMEG_0129, and Rv0164 by extension, were found to be cytosolic proteins rather than secreted components as previously understood. Increases in MSMEG_0129 expression at physiological levels accelerated bacterial growth in a proportional manner, but additional growth acceleration was not observed when MSMEG_0129 was overexpressed up to 20 fold. MSMEG_0129 is a short-lived protein, unstable at both the mRNA and protein levels. Co-IP and GST pull-down assays showed that MSMEG_0129 interacts with the ClpP2 protease and a global transcription factor, CarD, their expression being correlated with that of MSMEG_0129. Nutrient deficiency led to the downregulation of MSMEG_0129 but upregulation of CarD. However, in the context of constitutive MSMEG_0129 overexpression under nutrient-rich or starvation conditions, the mRNA level of CarD was reduced 3 fold. Conversely, expression of ClpP2 decreased with MSMEG_0129 downregulation under starvation conditions, but increased 4-8 fold when MSMEG_0129 was overexpressed. Our data suggest that MSMEG_0129, and Rv0164 by analogy, are likely to be nutrition sensing factors that regulate mycobacterial growth and may be involved in signal transfer under nutrient deficiency, possibly via physical and regulatory interactions with CarD and ClpP2.
Collapse
|
24
|
Gardner CL, da Silva DR, Pagliai FA, Pan L, Padgett-Pagliai KA, Blaustein RA, Merli ML, Zhang D, Pereira C, Teplitski M, Chaparro JX, Folimonova SY, Conesa A, Gezan S, Lorca GL, Gonzalez CF. Assessment of unconventional antimicrobial compounds for the control of 'Candidatus Liberibacter asiaticus', the causative agent of citrus greening disease. Sci Rep 2020; 10:5395. [PMID: 32214166 PMCID: PMC7096471 DOI: 10.1038/s41598-020-62246-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/11/2020] [Indexed: 01/22/2023] Open
Abstract
In this study, newly identified small molecules were examined for efficacy against ‘Candidatus Liberibacter asiaticus’ in commercial groves of sweet orange (Citrus sinensis) and white grapefruit (Citrus paradisi) trees. We used benzbromarone and/or tolfenamic acid delivered by trunk injection. We evaluated safety and efficacy parameters by performing RNAseq of the citrus host responses, 16S rRNA gene sequencing to characterize citrus-associated microbial communities during treatment, and qRT-PCR as an indirect determination of ‘Ca. L. asiaticus’ viability. Analyses of the C. sinensis transcriptome indicated that each treatment consistently induced genes associated with normal metabolism and growth, without compromising tree viability or negatively affecting the indigenous citrus-associated microbiota. It was found that treatment-associated reduction in ‘Ca. L. asiaticus’ was positively correlated with the proliferation of several core taxa related with citrus health. No symptoms of phytotoxicity were observed in any of the treated trees. Trials were also performed in commercial groves to examine the effect of each treatment on fruit productivity, juice quality and efficacy against ‘Ca. L. asiaticus’. Increased fruit production (15%) was observed in C. paradisi following twelve months of treatment with benzbromarone and tolfenamic acid. These results were positively correlated with decreased ‘Ca. L. asiaticus’ transcriptional activity in root samples.
Collapse
Affiliation(s)
- Christopher L Gardner
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Danilo R da Silva
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Fernando A Pagliai
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Lei Pan
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Kaylie A Padgett-Pagliai
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Ryan A Blaustein
- Soil and Water Sciences Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Marcelo L Merli
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Dan Zhang
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Cécile Pereira
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Max Teplitski
- Soil and Water Sciences Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Jose X Chaparro
- Fruit Tree Breeding and Genetics, Horticultural Sciences Department, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Svetlana Y Folimonova
- Plant Pathology Department, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, 32611, USA
| | - Ana Conesa
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Salvador Gezan
- School of Forest Resources and Conservation, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Graciela L Lorca
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America
| | - Claudio F Gonzalez
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, United States of America.
| |
Collapse
|
25
|
Jensen D, Manzano AR, Rammohan J, Stallings CL, Galburt EA. CarD and RbpA modify the kinetics of initial transcription and slow promoter escape of the Mycobacterium tuberculosis RNA polymerase. Nucleic Acids Res 2020; 47:6685-6698. [PMID: 31127308 PMCID: PMC6648326 DOI: 10.1093/nar/gkz449] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/11/2019] [Accepted: 05/09/2019] [Indexed: 12/17/2022] Open
Abstract
The pathogen Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, enacts unique transcriptional regulatory mechanisms when subjected to host-derived stresses. Initiation of transcription by the Mycobacterial RNA polymerase (RNAP) has previously been shown to exhibit different open complex kinetics and stabilities relative to Escherichia coli (Eco) RNAP. However, transcription initiation rates also depend on the kinetics following open complex formation such as initial nucleotide incorporation and subsequent promoter escape. Here, using a real-time fluorescence assay, we present the first in-depth kinetic analysis of initial transcription and promoter escape for the Mtb RNAP. We show that in relation to Eco RNAP, Mtb displays slower initial nucleotide incorporation but faster overall promoter escape kinetics on the Mtb rrnAP3 promoter. Furthermore, in the context of the essential transcription factors CarD and RbpA, Mtb promoter escape is slowed via differential effects on initially transcribing complexes. Finally, based on their ability to increase the rate of open complex formation and decrease the rate of promoter escape, we suggest that CarD and RbpA are capable of activation or repression depending on the rate-limiting step of a given promoter's basal initiation kinetics.
Collapse
Affiliation(s)
- Drake Jensen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ana Ruiz Manzano
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jayan Rammohan
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric A Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
26
|
Woldemeskel SA, Daitch AK, Alvarez L, Panis G, Zeinert R, Gonzalez D, Smith E, Collier J, Chien P, Cava F, Viollier PH, Goley ED. The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter. PLoS Genet 2020; 16:e1008591. [PMID: 31961855 PMCID: PMC6994171 DOI: 10.1371/journal.pgen.1008591] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/31/2020] [Accepted: 01/01/2020] [Indexed: 12/23/2022] Open
Abstract
Bacterial growth and division require regulated synthesis of the macromolecules used to expand and replicate components of the cell. Transcription of housekeeping genes required for metabolic homeostasis and cell proliferation is guided by the sigma factor σ70. The conserved CarD-like transcriptional regulator, CdnL, associates with promoter regions where σ70 localizes and stabilizes the open promoter complex. However, the contributions of CdnL to metabolic homeostasis and bacterial physiology are not well understood. Here, we show that Caulobacter crescentus cells lacking CdnL have severe morphological and growth defects. Specifically, ΔcdnL cells grow slowly in both rich and defined media, and are wider, more curved, and have shorter stalks than WT cells. These defects arise from transcriptional downregulation of most major classes of biosynthetic genes, leading to significant decreases in the levels of critical metabolites, including pyruvate, α-ketoglutarate, ATP, NAD+, UDP-N-acetyl-glucosamine, lipid II, and purine and pyrimidine precursors. Notably, we find that ΔcdnL cells are glutamate auxotrophs, and ΔcdnL is synthetic lethal with other genetic perturbations that limit glutamate synthesis and lipid II production. Our findings implicate CdnL as a direct and indirect regulator of genes required for metabolic homeostasis that impacts morphogenesis through availability of lipid II and other metabolites.
Collapse
Affiliation(s)
- Selamawit Abi Woldemeskel
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Allison K. Daitch
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Laura Alvarez
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Rilee Zeinert
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, MA, United States of America
| | - Diego Gonzalez
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Erika Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Justine Collier
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, MA, United States of America
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Erin D. Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| |
Collapse
|
27
|
Potter RF, Burnham CAD, Dantas G. In Silico Analysis of Gardnerella Genomospecies Detected in the Setting of Bacterial Vaginosis. Clin Chem 2019; 65:1375-1387. [PMID: 31462445 PMCID: PMC7055668 DOI: 10.1373/clinchem.2019.305474] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/25/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Gardnerella vaginalis is implicated as one of the causative agents of bacterial vaginosis, but it can also be isolated from the vagina of healthy women. Previous efforts to study G. vaginalis identified 4 to 6 clades, but average nucleotide identity analysis indicates that G. vaginalis may be multiple species. Recently, Gardnerella was determined to be 13 genomospecies, with Gardnerella piottii, Gardnerella leopoldii, and Gardnerella swidsinkii delineated as separate species. METHODS We accessed 103 publicly available genomes annotated as G. vaginalis. We performed comprehensive taxonomic and phylogenomic analysis to quantify the number of species called G. vaginalis, the similarity of their core genes, and their burden of their accessory genes. We additionally analyzed publicly available metatranscriptomic data sets of bacterial vaginosis to determine whether the newly delineated genomospecies are present, and to identify putative conserved features of Gardnerella pathogenesis. RESULTS Gardnerella could be classified into 8 to 14 genomospecies depending on the in silico classification tools used. Consensus classification identified 9 different Gardnerella genomospecies, here annotated as GS01 through GS09. The genomospecies could be readily distinguished by the phylogeny of their shared genes and burden of accessory genes. All of the new genomospecies were identified in metatranscriptomes of bacterial vaginosis. CONCLUSIONS Multiple Gardnerella genomospecies operating in isolation or in concert with one another may be responsible for bacterial vaginosis. These results have important implications for future efforts to understand the evolution of the Gardnerella genomospecies, host-pathogen interactions of the genomospecies during bacterial vaginosis, diagnostic assay development for bacterial vaginosis, and metagenomic investigations of the vaginal microbiota.
Collapse
Affiliation(s)
- Robert F Potter
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO;
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO
| |
Collapse
|
28
|
Zhu DX, Garner AL, Galburt EA, Stallings CL. CarD contributes to diverse gene expression outcomes throughout the genome of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2019; 116:13573-13581. [PMID: 31217290 PMCID: PMC6613185 DOI: 10.1073/pnas.1900176116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ability to regulate gene expression through transcription initiation underlies the adaptability and survival of all bacteria. Recent work has revealed that the transcription machinery in many bacteria diverges from the paradigm that has been established in Escherichia coliMycobacterium tuberculosis (Mtb) encodes the RNA polymerase (RNAP)-binding protein CarD, which is absent in E. coli but is required to form stable RNAP-promoter open complexes (RPo) and is essential for viability in Mtb The stabilization of RPo by CarD has been proposed to result in activation of gene expression; however, CarD has only been examined on limited promoters that do not represent the typical promoter structure in Mtb In this study, we investigate the outcome of CarD activity on gene expression from Mtb promoters genome-wide by performing RNA sequencing on a panel of mutants that differentially affect CarD's ability to stabilize RPo In all CarD mutants, the majority of Mtb protein encoding transcripts were differentially expressed, demonstrating that CarD had a global effect on gene expression. Contrary to the expected role of CarD as a transcriptional activator, mutation of CarD led to both up- and down-regulation of gene expression, suggesting that CarD can also act as a transcriptional repressor. Furthermore, we present evidence that stabilization of RPo by CarD could lead to transcriptional repression by inhibiting promoter escape, and the outcome of CarD activity is dependent on the intrinsic kinetic properties of a given promoter region. Collectively, our data support CarD's genome-wide role of regulating diverse transcription outcomes.
Collapse
Affiliation(s)
- Dennis X Zhu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Ashley L Garner
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Eric A Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110;
| |
Collapse
|
29
|
The Ferredoxin-Like Protein FerR Regulates PrbP Activity in Liberibacter asiaticus. Appl Environ Microbiol 2019; 85:AEM.02605-18. [PMID: 30552192 DOI: 10.1128/aem.02605-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 12/08/2018] [Indexed: 12/26/2022] Open
Abstract
In Liberibacter asiaticus, PrbP is an important transcriptional accessory protein that regulates gene expression through interactions with the RNA polymerase β-subunit and a specific sequence on the promoter region. The constitutive expression of prbP observed upon chemical inactivation of PrbP-DNA interactions in vivo indicated that the expression of prbP was not autoregulated at the level of transcription. This observation suggested that a modulatory mechanism via protein-protein interactions may be involved. In silico genome association analysis identified FerR (CLIBASIA_01505), a putative ferredoxin-like protein, as a PrbP-interacting protein. Using a bacterial two-hybrid system and immunoprecipitation assays, interactions between PrbP and FerR were confirmed. In vitro transcription assays were used to show that FerR can increase the activity of PrbP by 16-fold when present in the PrbP-RNA polymerase reaction mixture. The FerR protein-protein interaction surface was predicted by structural modeling and followed by site-directed mutagenesis. Amino acids V20, V23, and C40 were identified as the most important residues in FerR involved in the modulation of PrbP activity in vitro The regulatory mechanism of FerR abundance was examined at the transcription level. In contrast to prbP of L. asiaticus (prbP Las), mRNA levels of ferR of L. asiaticus (ferR Las) are induced by an increase in osmotic pressure. The results of this study revealed that the activity of the transcriptional activator PrbPLas is modulated via interactions with FerRLas The induction of ferR Las expression by osmolarity provides insight into the mechanisms of adjusting gene expression in response to host environmental signals in L. asiaticus IMPORTANCE The rapid spread and aggressive progression of huanglongbing (HLB) in the major citrus-producing areas have raised global recognition of and vigilance to this disease. As a result, the causative agent, Liberibacter asiaticus, has been investigated from various perspectives. However, gene expression regulatory mechanisms that are important for the survival and persistence of this intracellular pathogen remain largely unexplored. PrbP is a transcriptional accessory protein important for L. asiaticus survival in the plant host. In this study, we investigated the interactions between PrbP in L. asiaticus (PrbPLas) and a ferredoxin-like protein (FerR) in L. asiaticus, FerRLas We show that the presence of FerR stabilizes and augments the activity of PrbPLas In addition, we demonstrate that the expression of ferR is induced by increases in osmolarity in Liberibacter crescens Altogether, these results suggest that FerRLas and PrbPLas may play important roles in the regulation of gene expression in response to changing environmental signals during L. asiaticus infection in the citrus host.
Collapse
|
30
|
Rifampicin can induce antibiotic tolerance in mycobacteria via paradoxical changes in rpoB transcription. Nat Commun 2018; 9:4218. [PMID: 30310059 PMCID: PMC6181997 DOI: 10.1038/s41467-018-06667-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/19/2018] [Indexed: 12/17/2022] Open
Abstract
Metrics commonly used to describe antibiotic efficacy rely on measurements performed on bacterial populations. However, certain cells in a bacterial population can continue to grow and divide, even at antibiotic concentrations that kill the majority of cells, in a phenomenon known as antibiotic tolerance. Here, we describe a form of semi-heritable tolerance to the key anti-mycobacterial agent rifampicin, which is known to inhibit transcription by targeting the β subunit of the RNA polymerase (RpoB). We show that rifampicin exposure results in rpoB upregulation in a sub-population of cells, followed by growth. More specifically, rifampicin preferentially inhibits one of the two rpoB promoters (promoter I), allowing increased rpoB expression from a second promoter (promoter II), and thus triggering growth. Disruption of promoter architecture leads to differences in rifampicin susceptibility of the population, confirming the contribution of rifampicin-induced rpoB expression to tolerance. The antibiotic rifampicin inhibits transcription by targeting RpoB, a bacterial RNA polymerase subunit. Here, Zhu et al. show that certain cells in mycobacterial populations can continue to grow and divide in the presence of rifampicin due, paradoxically, to rifampicin-induced upregulation of the rpoB gene.
Collapse
|
31
|
Portman JR, Strick TR. Transcription-Coupled Repair and Complex Biology. J Mol Biol 2018; 430:4496-4512. [DOI: 10.1016/j.jmb.2018.04.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 10/24/2022]
|
32
|
Mycobacterium tuberculosis CarD, an essential global transcriptional regulator forms amyloid-like fibrils. Sci Rep 2018; 8:10124. [PMID: 29973616 PMCID: PMC6031611 DOI: 10.1038/s41598-018-28290-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/21/2018] [Indexed: 02/06/2023] Open
Abstract
CarD is an essential global transcription regulator from Mycobacterium tuberculosis (Mtb) that binds RNA polymerase and activates transcription by stabilizing the transcription initiation complex. Available crystal structures have captured two distinct, monomeric and domain-swapped homodimeric, oligomeric states of CarD. However, the actual oligomeric state of CarD in solution and its biological relevance has remained unclear. Here, we confirm the presence of the homodimeric state of CarD in solution by using synchrotron-based small-angle X-ray scattering. Furthermore, by using biochemical and biophysical experiments, in addition to mass-spectrometry, transmission electron microscopy, and confocal imaging, we show that CarD is the first soluble cytosolic protein in Mtb which displays the tendency to form amyloid-like fibrils both in vitro as well as in vivo. We demonstrate that the deletion of the fourteen N-terminal residues involved in domain-swapping hampers amyloid formation, thus, suggesting that domain-swapping is crucial in amyloidogenesis. The discovery of the amyloidogenic property of an essential cytosolic global transcription regulator, CarD, in a pathogenic bacteria will further open up new frontiers in research.
Collapse
|
33
|
Prusa J, Jensen D, Santiago-Collazo G, Pope SS, Garner AL, Miller JJ, Ruiz Manzano A, Galburt EA, Stallings CL. Domains within RbpA Serve Specific Functional Roles That Regulate the Expression of Distinct Mycobacterial Gene Subsets. J Bacteriol 2018; 200:e00690-17. [PMID: 29686140 PMCID: PMC5996690 DOI: 10.1128/jb.00690-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/18/2018] [Indexed: 11/20/2022] Open
Abstract
The RNA polymerase (RNAP) binding protein A (RbpA) contributes to the formation of stable RNAP-promoter open complexes (RPo) and is essential for viability in mycobacteria. Four domains have been identified in the RbpA protein, i.e., an N-terminal tail (NTT) that interacts with RNAP β' and σ subunits, a core domain (CD) that contacts the RNAP β' subunit, a basic linker (BL) that binds DNA, and a σ-interaction domain (SID) that binds group I and group II σ factors. Limited in vivo studies have been performed in mycobacteria, however, and how individual structural domains of RbpA contribute to RbpA function and mycobacterial gene expression remains mostly unknown. We investigated the roles of the RbpA structural domains in mycobacteria using a panel of rbpA mutants that target individual RbpA domains. The function of each RbpA domain was required for Mycobacterium tuberculosis viability and optimal growth in Mycobacterium smegmatis We determined that the RbpA SID is both necessary and sufficient for RbpA interaction with the RNAP, indicating that the primary functions of the NTT and CD are not solely association with the RNAP. We show that the RbpA BL and SID are required for RPo stabilization in vitro, while the NTT and CD antagonize this activity. Finally, RNA-sequencing analyses suggest that the NTT and CD broadly activate gene expression, whereas the BL and SID activate or repress gene expression in a gene-dependent manner for a subset of mycobacterial genes. Our findings highlight specific outcomes for the activities of the individual functional domains in RbpA.IMPORTANCEMycobacterium tuberculosis is the causative agent of tuberculosis and continues to be the most lethal infectious disease worldwide. Improved molecular understanding of the essential proteins involved in M. tuberculosis transcription, such as RbpA, could provide targets for much needed future therapeutic agents aimed at combatting this pathogen. In this study, we expand our understanding of RbpA by identifying the RbpA structural domains responsible for the interaction of RbpA with the RNAP and the effects of RbpA on transcription initiation and gene expression. These experiments expand our knowledge of RbpA while also broadening our understanding of bacterial transcription in general.
Collapse
Affiliation(s)
- Jerome Prusa
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Drake Jensen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gustavo Santiago-Collazo
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Steven S Pope
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ashley L Garner
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Justin J Miller
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ana Ruiz Manzano
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eric A Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
34
|
Peptide Similarity Search Based and Virtual Screening Based Strategies to Identify Small Molecules to Inhibit CarD–RNAP Interaction in M. tuberculosis. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9716-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
35
|
Pan L, Gardner CL, Pagliai FA, Gonzalez CF, Lorca GL. Identification of the Tolfenamic Acid Binding Pocket in PrbP from Liberibacter asiaticus. Front Microbiol 2017; 8:1591. [PMID: 28878750 PMCID: PMC5572369 DOI: 10.3389/fmicb.2017.01591] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/04/2017] [Indexed: 12/31/2022] Open
Abstract
In Liberibacter asiaticus, PrbP is an important transcriptional accessory protein that was found to regulate gene expression through interactions with the RNA polymerase β-subunit and a specific sequence on the promoter region. It was found that inactivation of PrbP, using the inhibitor tolfenamic acid, resulted in a significant decrease in the overall transcriptional activity of L. asiaticus, and the suppression of L. asiaticus infection in HLB symptomatic citrus seedlings. The molecular interactions between PrbP and tolfenamic acid, however, were yet to be elucidated. In this study, we modeled the structure of PrbP and identified a ligand binding pocket, TaP, located at the interface of the predicted RNA polymerase interaction domain (N-terminus) and the DNA binding domain (C-terminus). The molecular interactions of PrbP with tolfenamic acid were predicted using in silico docking. Site-directed mutagenesis of specific amino acids was followed by electrophoresis mobility shift assays and in vitro transcription assays, where residues N107, G109, and E148 were identified as the primary amino acids involved in interactions with tolfenamic acid. These results provide insight into the binding mechanism of PrbP to a small inhibitory molecule, and a starting scaffold for the identification and development of therapeutics targeting PrbP and other homologs in the CarD_CdnL_TRCF family.
Collapse
Affiliation(s)
| | | | | | | | - Graciela L. Lorca
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Science, University of FloridaGainesville, FL, United States
| |
Collapse
|
36
|
Caulobacter crescentus CdnL is a non-essential RNA polymerase-binding protein whose depletion impairs normal growth and rRNA transcription. Sci Rep 2017; 7:43240. [PMID: 28233804 PMCID: PMC5324124 DOI: 10.1038/srep43240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/23/2017] [Indexed: 12/22/2022] Open
Abstract
CdnL is an essential RNA polymerase (RNAP)-binding activator of rRNA transcription in mycobacteria and myxobacteria but reportedly not in Bacillus. Whether its function and mode of action are conserved in other bacteria thus remains unclear. Because virtually all alphaproteobacteria have a CdnL homolog and none of these have been characterized, we studied the homolog (CdnLCc) of the model alphaproteobacterium Caulobacter crescentus. We show that CdnLCc is not essential for viability but that its absence or depletion causes slow growth and cell filamentation. CdnLCc is degraded in vivo in a manner dependent on its C-terminus, yet excess CdnLCc resulting from its stabilization did not adversely affect growth. We find that CdnLCc interacts with itself and with the RNAP β subunit, and localizes to at least one rRNA promoter in vivo, whose activity diminishes upon depletion of CdnLCc. Interestingly, cells expressing CdnLCc mutants unable to interact with the RNAP were cold-sensitive, suggesting that CdnLCc interaction with RNAP is especially required at lower than standard growth temperatures in C. crescentus. Our study indicates that despite limited sequence similarities and regulatory differences compared to its myco/myxobacterial homologs, CdnLCc may share similar biological functions, since it affects rRNA synthesis, probably by stabilizing open promoter-RNAP complexes.
Collapse
|
37
|
Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence. J Bacteriol 2017; 199:JB.00698-16. [PMID: 27920294 DOI: 10.1128/jb.00698-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/23/2016] [Indexed: 01/29/2023] Open
Abstract
CarD is an essential RNA polymerase (RNAP) interacting protein in Mycobacterium tuberculosis that stimulates formation of RNAP-promoter open complexes. CarD plays a complex role in M. tuberculosis growth and virulence that is not fully understood. Therefore, to gain further insight into the role of CarD in M. tuberculosis growth and virulence, we determined the effect of increasing the affinity of CarD for RNAP. Using site-directed mutagenesis guided by crystal structures of CarD bound to RNAP, we identified amino acid substitutions that increase the affinity of CarD for RNAP. Using these substitutions, we show that increasing the affinity of CarD for RNAP increases the stability of the CarD protein in M. tuberculosis In addition, we show that increasing the affinity of CarD for RNAP increases the growth rate in M. tuberculosis without affecting 16S rRNA levels. We further show that increasing the affinity of CarD for RNAP reduces M. tuberculosis virulence in a mouse model of infection despite the improved growth rate in vitro Our findings suggest that the CarD-RNAP interaction protects CarD from proteolytic degradation in M. tuberculosis, establish that growth rate and rRNA levels can be uncoupled in M. tuberculosis and demonstrate that the strength of the CarD-RNAP interaction has been finely tuned to optimize virulence. IMPORTANCE Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a major global health problem. In order to develop new strategies to battle this pathogen, we must gain a better understanding of the molecular processes involved in its survival and pathogenesis. We have previously identified CarD as an essential transcriptional regulator in mycobacteria. In this study, we detail the effects of increasing the affinity of CarD for RNAP on transcriptional regulation, CarD protein stability, and virulence. These studies expand our understanding of the global transcription regulator CarD, provide insight into how CarD activity is regulated, and broaden our understanding of prokaryotic transcription.
Collapse
|
38
|
Deaconescu AM, Suhanovsky MM. From Mfd to TRCF and Back Again-A Perspective on Bacterial Transcription-coupled Nucleotide Excision Repair. Photochem Photobiol 2017; 93:268-279. [PMID: 27859304 PMCID: PMC5672955 DOI: 10.1111/php.12661] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/08/2016] [Indexed: 12/17/2022]
Abstract
Photochemical and other reactions on DNA cause damage and corrupt genetic information. To counteract this damage, organisms have evolved intricate repair mechanisms that often crosstalk with other DNA-based processes such as transcription. Intriguing observations in the late 1980s and early 1990s led to the discovery of transcription-coupled repair (TCR), a subpathway of nucleotide excision repair. TCR, found in all domains of life, prioritizes for repair lesions located in the transcribed DNA strand, directly read by RNA polymerase. Here, we give a historical overview of developments in the field of bacterial TCR, starting from the pioneering work of Evelyn Witkin and Aziz Sancar, which led to the identification of the first transcription-repair coupling factor (the Mfd protein), to recent studies that have uncovered alternative TCR pathways and regulators.
Collapse
Affiliation(s)
- Alexandra M. Deaconescu
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Margaret M. Suhanovsky
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
| |
Collapse
|
39
|
Gardner CL, Pagliai FA, Pan L, Bojilova L, Torino MI, Lorca GL, Gonzalez CF. Drug Repurposing: Tolfenamic Acid Inactivates PrbP, a Transcriptional Accessory Protein in Liberibacter asiaticus. Front Microbiol 2016; 7:1630. [PMID: 27803694 PMCID: PMC5067538 DOI: 10.3389/fmicb.2016.01630] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/30/2016] [Indexed: 01/11/2023] Open
Abstract
CLIBASIA_01510, PrbP, is a predicted RNA polymerase binding protein in Liberibacter asiaticus. PrbP was found to regulate expression of a small subset of ribosomal genes through interactions with the β-subunit of the RNA polymerase and a short, specific sequence on the promoter region. Molecular screening assays were performed to identify small molecules that interact with PrbP in vitro. Chemical hits were analyzed for therapeutic efficacy against L. asiaticus via an infected leaf assay, where the transcriptional activity of L. asiaticus was found to decrease significantly after exposure to tolfenamic acid. Similarly, tolfenamic acid was found to inhibit L. asiaticus infection in highly symptomatic citrus seedlings. Our results indicate that PrbP is an important transcriptional regulator for survival of L. asiaticus in planta, and the chemicals identified by molecular screening assays could be used as a therapeutic treatment for huanglongbing disease.
Collapse
Affiliation(s)
- Christopher L Gardner
- Microbiology and Cell Science Department, Genetics Institute & Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| | - Fernando A Pagliai
- Microbiology and Cell Science Department, Genetics Institute & Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| | - Lei Pan
- Microbiology and Cell Science Department, Genetics Institute & Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| | - Lora Bojilova
- Microbiology and Cell Science Department, Genetics Institute & Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| | - Maria I Torino
- Microbiology and Cell Science Department, Genetics Institute & Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| | - Graciela L Lorca
- Microbiology and Cell Science Department, Genetics Institute & Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| | - Claudio F Gonzalez
- Microbiology and Cell Science Department, Genetics Institute & Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| |
Collapse
|
40
|
Rammohan J, Ruiz Manzano A, Garner AL, Prusa J, Stallings CL, Galburt EA. Cooperative stabilization of Mycobacterium tuberculosis rrnAP3 promoter open complexes by RbpA and CarD. Nucleic Acids Res 2016; 44:7304-13. [PMID: 27342278 PMCID: PMC5009747 DOI: 10.1093/nar/gkw577] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/16/2016] [Indexed: 01/24/2023] Open
Abstract
The essential mycobacterial transcriptional regulators RbpA and CarD act to modulate transcription by associating to the initiation complex and increasing the flux of transcript production. Each of these factors interacts directly with the promoter DNA template and with RNA polymerase (RNAP) holoenzyme. We recently reported on the energetics of CarD-mediated open complex stabilization on the Mycobacterium tuberculosis rrnAP3 ribosomal promoter using a stopped-flow fluorescence assay. Here, we apply this approach to RbpA and show that RbpA stabilizes RNAP-promoter open complexes (RPo) via a distinct mechanism from that of CarD. Furthermore, concentration-dependent stopped-flow experiments with both factors reveal positive linkage (cooperativity) between RbpA and CarD with regard to their ability to stabilize RPo The observation of positive linkage between RbpA and CarD demonstrates that the two factors can act on the same transcription initiation complex simultaneously. Lastly, with both factors present, the kinetics of open complex formation is significantly faster than in the presence of either factor alone and approaches that of E. coli RNAP on the same promoter. This work provides a quantitative framework for the molecular mechanisms of these two essential transcription factors and the critical roles they play in the biology and pathology of mycobacteria.
Collapse
Affiliation(s)
- Jayan Rammohan
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ana Ruiz Manzano
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ashley L Garner
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jerome Prusa
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric A Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
41
|
Mycobacterium tuberculosis Transcription Machinery: Ready To Respond to Host Attacks. J Bacteriol 2016; 198:1360-73. [PMID: 26883824 DOI: 10.1128/jb.00935-15] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Regulating responses to stress is critical for all bacteria, whether they are environmental, commensal, or pathogenic species. For pathogenic bacteria, successful colonization and survival in the host are dependent on adaptation to diverse conditions imposed by the host tissue architecture and the immune response. Once the bacterium senses a hostile environment, it must enact a change in physiology that contributes to the organism's survival strategy. Inappropriate responses have consequences; hence, the execution of the appropriate response is essential for survival of the bacterium in its niche. Stress responses are most often regulated at the level of gene expression and, more specifically, transcription. This minireview focuses on mechanisms of regulating transcription initiation that are required by Mycobacterium tuberculosis to respond to the arsenal of defenses imposed by the host during infection. In particular, we highlight how certain features of M. tuberculosis physiology allow this pathogen to respond swiftly and effectively to host defenses. By enacting highly integrated and coordinated gene expression changes in response to stress,M. tuberculosis is prepared for battle against the host defense and able to persist within the human population.
Collapse
|
42
|
Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA. CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. eLife 2015; 4. [PMID: 26349034 PMCID: PMC4593161 DOI: 10.7554/elife.08505] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/04/2015] [Indexed: 01/25/2023] Open
Abstract
A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD. DOI:http://dx.doi.org/10.7554/eLife.08505.001 Inside cells, molecules of double-stranded DNA encode the instructions needed to make proteins. To make a protein, the two strands of DNA that make up a gene are separated and one strand acts as a template to make molecules of messenger ribonucleic acid (or mRNA for short). This process is called transcription. The mRNA is then used as a template to assemble the protein. An enzyme called RNA polymerase carries out transcription and is found in all cells ranging from bacteria to humans and other animals. Bacteria have the simplest form of RNA polymerase and provide an excellent system to study how it controls transcription. It is made up of several proteins that work together to make RNA using DNA as a template. However, it requires the help of another protein called sigma factor to direct it to regions of DNA called promoters, which are just before the start of the gene. When RNA polymerase and the sigma factor interact the resulting group of proteins is known as the RNA polymerase ‘holoenzyme’. Transcription takes place in several stages. To start with, the RNA polymerase holoenzyme locates and binds to promoter DNA. Next, it separates the two strands of DNA and exposes a portion of the template strand. At this point, the DNA and the holoenzyme are said to be in an ‘open promoter complex’ and the section of promoter DNA that is within it is known as a ‘transcription bubble’. Another protein called CarD helps to speed up transcription but it is not clear how this stage of the process works. Bae et al. have now used X-ray crystallography to reveal the structure of CarD bound to the RNA polymerase holoenyzme and a DNA promoter. The structures show that one part of CarD interacts with the DNA at the start of the transcription bubble, and another part binds to the RNA polymerase. CarD fits between the two strands of DNA in the promoter, like a wedge, to keep the strands apart. Therefore, CarD stabilizes the open promoter complex and prevents the transcription bubble from collapsing. These findings reveal a previously unseen mechanism involved in activating transcription and will guide further experiments probing the role of CarD in living cells. Another study by Bae, Feklistov et al.—which involves some of the same researchers as this study—reveals that the sigma factor also binds to DNA at the start of the transcription bubble. The general principles outlined by these studies may help to identify other proteins that regulate transcription. DOI:http://dx.doi.org/10.7554/eLife.08505.002
Collapse
Affiliation(s)
- Brian Bae
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - James Chen
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Elizabeth Davis
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Katherine Leon
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Seth A Darst
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Elizabeth A Campbell
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| |
Collapse
|
43
|
Wong FC, Tan ST, Chai TT. Phytochemical-mediated Protein Expression Profiling and the Potential Applications in Therapeutic Drug Target Identifications. Crit Rev Food Sci Nutr 2015; 56 Suppl 1:S162-70. [DOI: 10.1080/10408398.2015.1045967] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
44
|
Rammohan J, Ruiz Manzano A, Garner AL, Stallings CL, Galburt EA. CarD stabilizes mycobacterial open complexes via a two-tiered kinetic mechanism. Nucleic Acids Res 2015; 43:3272-85. [PMID: 25697505 PMCID: PMC4381055 DOI: 10.1093/nar/gkv078] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/21/2015] [Indexed: 11/28/2022] Open
Abstract
CarD is an essential and global transcriptional regulator in mycobacteria. While its biological role is unclear, CarD functions by interacting directly with RNA polymerase (RNAP) holoenzyme promoter complexes. Here, using a fluorescent reporter of open complex, we quantitate RPo formation in real time and show that Mycobacterium tuberculosis CarD has a dramatic effect on the energetics of RNAP bound complexes on the M. tuberculosis rrnAP3 ribosomal RNA promoter. The data reveal that Mycobacterium bovis RNAP exhibits an unstable RPo that is stabilized by CarD and suggest that CarD uses a two-tiered, concentration-dependent mechanism by associating with open and closed complexes with different affinities. Specifically, the kinetics of open-complex formation can be explained by a model where, at saturating concentrations of CarD, the rate of bubble collapse is slowed and the rate of opening is accelerated. The kinetics and open-complex stabilities of CarD mutants further clarify the roles played by the key residues W85, K90 and R25 previously shown to affect CarD-dependent gene regulation in vivo. In contrast to M. bovis RNAP, Escherichia coli RNAP efficiently forms RPo on rrnAP3, suggesting an important difference between the polymerases themselves and highlighting how transcriptional machinery can vary across bacterial genera.
Collapse
Affiliation(s)
- Jayan Rammohan
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ana Ruiz Manzano
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ashley L Garner
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric A Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
45
|
Landick R, Krek A, Glickman MS, Socci ND, Stallings CL. Genome-Wide Mapping of the Distribution of CarD, RNAP σ A, and RNAP β on the Mycobacterium smegmatis Chromosome using Chromatin Immunoprecipitation Sequencing. GENOMICS DATA 2014; 2:110-113. [PMID: 25089258 PMCID: PMC4115788 DOI: 10.1016/j.gdata.2014.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis [6]. We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits β and σA were also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σA would be predominantly enriched at promoters based on work in Escherichia coli [3], however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 [5] as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164).
Collapse
Affiliation(s)
- Robert Landick
- Departments of Biochemistry and Bacteriology, University of Wisconsin, Madison, WI, 53706, USA
| | - Azra Krek
- Bioinformatics Core, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Michael S Glickman
- Immunology Program, Sloan-Kettering Institute, and Division of Infectious Diseases, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
46
|
Cui T, He ZG. Improved understanding of pathogenesis from protein interactions inMycobacteriumtuberculosis. Expert Rev Proteomics 2014; 11:745-55. [DOI: 10.1586/14789450.2014.971762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
47
|
Gallego-García A, Mirassou Y, García-Moreno D, Elías-Arnanz M, Jiménez MA, Padmanabhan S. Structural insights into RNA polymerase recognition and essential function of Myxococcus xanthus CdnL. PLoS One 2014; 9:e108946. [PMID: 25272012 PMCID: PMC4182748 DOI: 10.1371/journal.pone.0108946] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/28/2014] [Indexed: 11/18/2022] Open
Abstract
CdnL and CarD are two functionally distinct members of the CarD_CdnL_TRCF family of bacterial RNA polymerase (RNAP)-interacting proteins, which co-exist in Myxococcus xanthus. While CarD, found exclusively in myxobacteria, has been implicated in the activity of various extracytoplasmic function (ECF) σ-factors, the function and mode of action of the essential CdnL, whose homologs are widespread among bacteria, remain to be elucidated in M. xanthus. Here, we report the NMR solution structure of CdnL and present a structure-based mutational analysis of its function. An N-terminal five-stranded β-sheet Tudor-like module in the two-domain CdnL mediates binding to RNAP-β, and mutations that disrupt this interaction impair cell growth. The compact CdnL C-terminal domain consists of five α-helices folded as in some tetratricopeptide repeat-like protein-protein interaction domains, and contains a patch of solvent-exposed nonpolar and basic residues, among which a set of basic residues is shown to be crucial for CdnL function. We show that CdnL, but not its loss-of-function mutants, stabilizes formation of transcriptionally competent, open complexes by the primary σA-RNAP holoenzyme at an rRNA promoter in vitro. Consistent with this, CdnL is present at rRNA promoters in vivo. Implication of CdnL in RNAP-σA activity and of CarD in ECF-σ function in M. xanthus exemplifies how two related members within a widespread bacterial protein family have evolved to enable distinct σ-dependent promoter activity.
Collapse
Affiliation(s)
- Aránzazu Gallego-García
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Yasmina Mirassou
- Instituto de Química Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Madrid, Spain
| | - Diana García-Moreno
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
- * E-mail: (MEA); (MAJ); (SP)
| | - María Angeles Jiménez
- Instituto de Química Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Madrid, Spain
- * E-mail: (MEA); (MAJ); (SP)
| | - S. Padmanabhan
- Instituto de Química Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Madrid, Spain
- * E-mail: (MEA); (MAJ); (SP)
| |
Collapse
|
48
|
Garner AL, Weiss LA, Manzano AR, Galburt EA, Stallings CL. CarD integrates three functional modules to promote efficient transcription, antibiotic tolerance, and pathogenesis in mycobacteria. Mol Microbiol 2014; 93:682-97. [PMID: 24962732 PMCID: PMC4127138 DOI: 10.1111/mmi.12681] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2014] [Indexed: 11/27/2022]
Abstract
Although the basic mechanisms of prokaryotic transcription are conserved, it has become evident that some bacteria require additional factors to allow for efficient gene transcription. CarD is an RNA polymerase (RNAP)-binding protein conserved in numerous bacterial species and essential in mycobacteria. Despite the importance of CarD, its function at transcription complexes remains unclear. We have generated a panel of mutations that individually target three independent functional modules of CarD: the RNAP interaction domain, the DNA-binding domain, and a conserved tryptophan residue. We have dissected the roles of each functional module in CarD activity and built a model where each module contributes to stabilizing RNAP-promoter complexes. Our work highlights the requirement of all three modules of CarD in the obligate pathogen Mycobacterium tuberculosis, but not in Mycobacterium smegmatis. We also report divergent use of the CarD functional modules in resisting oxidative stress and pigmentation. These studies provide new information regarding the functional domains involved in transcriptional regulation by CarD while also improving understanding of the physiology of M. tuberculosis.
Collapse
Affiliation(s)
- Ashley L. Garner
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110 USA
| | - Leslie A. Weiss
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110 USA
| | - Ana Ruiz Manzano
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110 USA
| | - Eric A. Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110 USA
| | - Christina L. Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110 USA
| |
Collapse
|
49
|
Verma AK, Chatterji D. Dual role of MsRbpA: transcription activation and rescue of transcription from the inhibitory effect of rifampicin. MICROBIOLOGY-SGM 2014; 160:2018-2029. [PMID: 24987104 DOI: 10.1099/mic.0.079186-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
MsRbpA is an RNA polymerase (RNAP) binding protein from Mycobacterium smegmatis. According to previous studies, MsRbpA rescues rifampicin-induced transcription inhibition upon binding to the RNAP. Others have shown that RbpA from Mycobacterium tuberculosis (MtbRbpA) is a transcription activator. In this study, we report that both MsRbpA and MtbRbpA activate transcription as well as rescue rifampicin-induced transcription inhibition. Transcription activation is achieved through the increased formation of closed RNAP-promoter complex as well as enhanced rate of conversion of this complex to a stable transcriptionally competent RNAP-promoter complex. When a 16 aa peptide fragment (Asp 58 to Lys 73) was deleted from MsRbpA, the resulting protein showed 1000-fold reduced binding with core RNAP. The deletion results in abolition of transcription activation and rescue of transcription from the inhibitory effect of rifampicin. Through alanine scanning of this essential region of MsRbpA, Gly 67, Val 69, Pro 70 and Pro 72 residues are identified to be important for MsRbpA function. Furthermore, we report here that the protein is indispensable for M. smegmatis, and it appears to help the organism grow in the presence of the antibiotic rifampicin.
Collapse
Affiliation(s)
- Amit Kumar Verma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka-560012, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka-560012, India
| |
Collapse
|
50
|
Gangwar SP, Meena SR, Saxena AK. Structure of the carboxy-terminal domain of Mycobacterium tuberculosis CarD protein: an essential rRNA transcriptional regulator. Acta Crystallogr F Struct Biol Commun 2014; 70:160-5. [PMID: 24637748 PMCID: PMC3936448 DOI: 10.1107/s2053230x13034407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/21/2013] [Indexed: 12/19/2022] Open
Abstract
The CarD protein is highly expressed in mycobacterial strains under basal conditions and is transcriptionally induced during multiple types of genotoxic stress and starvation. The CarD protein binds the β subunit of RNA polymerase and influences gene expression. The disruption of interactions between CarD and the β subunit of RNA polymerase has a significant effect on mycobacterial survival, resistance to stress and pathogenesis. To understand the structure of CarD and its interaction with the β subunit of RNA polymerase, Mycobacterium tuberculosis CarD (MtbCarD) and the Thermus aquaticus RNA polymerase β subunit were recombinantly expressed and purified. Secondary-structure analysis using circular-dichroism spectroscopy indicated that MtbCarD contains ∼ 60% α-helix, ∼ 7% β-sheet and ∼ 33% random-coil structure. The C-terminal domain of MtbCarD (CarD(83-161)) was crystallized and its X-ray structure was determined at 2.1 Å resolution. CarD(83-161) forms a distorted Y-shaped structure containing bundles of three helices connected by a loop. The residues forming the distorted Y-shaped structure are highly conserved in CarD sequences from other mycobacterial species. Comparison of the CarD(83-161) structure with the recently determined full-length M. tuberculosis and T. thermophilus CarD crystal structures revealed structural differences in residues 141-161 of the C-terminal domain of the CarD(83-161) structure. The structural changes in the CarD(83-161) structure occurred owing to proteolysis and crystallization artifacts.
Collapse
Affiliation(s)
- Shanti P. Gangwar
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
| | - Sita R. Meena
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
| | - Ajay K. Saxena
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
| |
Collapse
|