1
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Wulff TF, Hahnke K, Lécrivain AL, Schmidt K, Ahmed-Begrich R, Finstermeier K, Charpentier E. Dynamics of diversified A-to-I editing in Streptococcus pyogenes is governed by changes in mRNA stability. Nucleic Acids Res 2024:gkae629. [PMID: 39087550 DOI: 10.1093/nar/gkae629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 07/01/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing plays an important role in the post-transcriptional regulation of eukaryotic cell physiology. However, our understanding of the occurrence, function and regulation of A-to-I editing in bacteria remains limited. Bacterial mRNA editing is catalysed by the deaminase TadA, which was originally described to modify a single tRNA in Escherichia coli. Intriguingly, several bacterial species appear to perform A-to-I editing on more than one tRNA. Here, we provide evidence that in the human pathogen Streptococcus pyogenes, tRNA editing has expanded to an additional tRNA substrate. Using RNA sequencing, we identified more than 27 editing sites in the transcriptome of S. pyogenes SF370 and demonstrate that the adaptation of S. pyogenes TadA to a second tRNA substrate has also diversified the sequence context and recoding scope of mRNA editing. Based on the observation that editing is dynamically regulated in response to several infection-relevant stimuli, such as oxidative stress, we further investigated the underlying determinants of editing dynamics and identified mRNA stability as a key modulator of A-to-I editing. Overall, our findings reveal the presence and diversification of A-to-I editing in S. pyogenes and provide novel insights into the plasticity of the editome and its regulation in bacteria.
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Affiliation(s)
- Thomas F Wulff
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | - Karin Hahnke
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | - Katja Schmidt
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | | | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
- Institute for Biology, Humboldt University Berlin, 10115 Berlin, Germany
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2
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Schiavolin L, Deneubourg G, Steinmetz J, Smeesters PR, Botteaux A. Group A Streptococcus adaptation to diverse niches: lessons from transcriptomic studies. Crit Rev Microbiol 2024; 50:241-265. [PMID: 38140809 DOI: 10.1080/1040841x.2023.2294905] [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: 07/12/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
Group A Streptococcus (GAS) is a major human pathogen, causing diseases ranging from mild superficial infections of the skin and pharyngeal epithelium to severe systemic and invasive diseases. Moreover, post infection auto-immune sequelae arise by a yet not fully understood mechanism. The ability of GAS to cause a wide variety of infections is linked to the expression of a large set of virulence factors and their transcriptional regulation in response to various physiological environments. The use of transcriptomics, among others -omics technologies, in addition to traditional molecular methods, has led to a better understanding of GAS pathogenesis and host adaptation mechanisms. This review focusing on bacterial transcriptomic provides new insight into gene-expression patterns in vitro, ex vivo and in vivo with an emphasis on metabolic shifts, virulence genes expression and transcriptional regulators role.
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Affiliation(s)
- Lionel Schiavolin
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
| | - Geoffrey Deneubourg
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
| | - Jenny Steinmetz
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
| | - Pierre R Smeesters
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
- Department of Paediatrics, Brussels University Hospital, Academic Children Hospital Queen Fabiola, Université libre de Bruxelles, Brussels, Belgium
| | - Anne Botteaux
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
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3
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Mirabal B, Andrade BS, Souza SPA, Oliveira IBDS, Melo TS, Barbosa FS, Jaiswal AK, Seyffert N, Portela RW, Soares SDC, Azevedo V, Meyer R, Tiwari S, Castro TLDP. In silico approaches for predicting natural compounds with therapeutic potential and vaccine candidates against Streptococcus equi. J Biomol Struct Dyn 2024:1-15. [PMID: 38239063 DOI: 10.1080/07391102.2023.2301056] [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: 02/27/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024]
Abstract
Equine strangles is a prevalent disease that affects the upper respiratory in horses and is caused by the Gram-positive bacterium Streptococcus equi. In addition to strangles, other clinical conditions are caused by the two S. equi subspecies, equi and zooepidemicus, which present relevant zoonotic potential. Treatment of infections caused by S. equi has become challenging due to the worldwide spreading of infected horses and the unavailability of effective therapeutics and vaccines. Penicillin treatment is often recommended, but multidrug resistance issues arised. We explored the whole genome sequence of 18 S. equi isolates to identify candidate proteins to be targeted by natural drug-like compounds or explored as immunogens. We considered only proteins shared among the sequenced strains of subspecies equi and zooepidemicus, absent in the equine host and predicted to be essential and involved in virulence. Of these, 4 proteins with cytoplasmic subcellular location were selected for molecular docking with a library of 5008 compounds, while 6 proteins were proposed as prominent immunogens against S. equi due to their probabilities of behaving as adhesins. The molecular docking analyses revealed the best ten ligands for each of the 4 drug target candidates, and they were ranked according to their binding affinities and the number of hydrogen bonds for complex stability. Finally, the natural 5-ring compound C25H20F3N5O3 excelled in molecular dynamics simulations for the increased stability in the interaction with UDP-N-acetylenolpyruvoylglucosamine reductase (MurB). This research paves the way to developing new therapeutics to minimize the impacts caused by S. equi infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bernardo Mirabal
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Bruno Silva Andrade
- Department of Biological Sciences, State University of Southwest Bahia, Jequié, Brazil
| | | | | | - Tarcisio Silva Melo
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Feira de Santana, Brazil
| | - Fabrício Santos Barbosa
- Postgraduate Program in Chemistry, State University of Southwest Bahia (UESB), Jequié, Brazil
| | - Arun Kumar Jaiswal
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Nubia Seyffert
- Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
| | | | - Siomar de Castro Soares
- Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Salvador, Brazil
| | - Roberto Meyer
- Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
| | - Sandeep Tiwari
- Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
| | - Thiago Luiz de Paula Castro
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
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4
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DebRoy S, Shropshire WC, Vega L, Tran C, Horstmann N, Mukherjee P, Selvaraj-Anand S, Tran TT, Bremer J, Gohel M, Arias CA, Flores AR, Shelburne SA. Identification of distinct impacts of CovS inactivation on the transcriptome of acapsular group A streptococci. mSystems 2023; 8:e0022723. [PMID: 37358280 PMCID: PMC10470059 DOI: 10.1128/msystems.00227-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/11/2023] [Indexed: 06/27/2023] Open
Abstract
Group A streptococcal (GAS) strains causing severe, invasive infections often have mutations in the control of virulence two-component regulatory system (CovRS) which represses capsule production, and high-level capsule production is considered critical to the GAS hypervirulent phenotype. Additionally, based on studies in emm1 GAS, hyperencapsulation is thought to limit transmission of CovRS-mutated strains by reducing GAS adherence to mucosal surfaces. It has recently been identified that about 30% of invasive GAS strains lacks capsule, but there are limited data regarding the impact of CovS inactivation in such acapsular strains. Using publicly available complete genomes (n = 2,455) of invasive GAS strains, we identified similar rates of CovRS inactivation and limited evidence for transmission of CovRS-mutated isolates for both encapsulated and acapsular emm types. Relative to encapsulated GAS, CovS transcriptomes of the prevalent acapsular emm types emm28, emm87, and emm89 revealed unique impacts such as increased transcript levels of genes in the emm/mga region along with decreased transcript levels of pilus operon-encoding genes and the streptokinase-encoding gene ska. CovS inactivation in emm87 and emm89 strains, but not emm28, increased GAS survival in human blood. Moreover, CovS inactivation in acapsular GAS reduced adherence to host epithelial cells. These data suggest that the hypervirulence induced by CovS inactivation in acapsular GAS follows distinct pathways from the better studied encapsulated strains and that factors other than hyperencapsulation may account for the lack of transmission of CovRS-mutated strains. IMPORTANCE Devastating infections due to group A streptococci (GAS) tend to occur sporadically and are often caused by strains that contain mutations in the control of virulence regulatory system (CovRS). In well-studied emm1 GAS, the increased production of capsule induced by CovRS mutation is considered key to both hypervirulence and limited transmissibility by interfering with proteins that mediate attachment to eukaryotic cells. Herein, we show that the rates of covRS mutations and genetic clustering of CovRS-mutated isolates are independent of capsule status. Moreover, we found that CovS inactivation in multiple acapsular GAS emm types results in dramatically altered transcript levels of a diverse array of cell-surface protein-encoding genes and a unique transcriptome relative to encapsulated GAS. These data provide new insights into how a major human pathogen achieves hypervirulence and indicate that factors other than hyperencapsulation likely account for the sporadic nature of the severe GAS disease.
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Affiliation(s)
- Sruti DebRoy
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - William C. Shropshire
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Luis Vega
- Division of Infectious Diseases and Department of Pediatrics, McGovern Medical School at UTHealth Houston and Children’s Memorial Hermann Hospital, Houston, Texas, USA
| | - Chau Tran
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nicola Horstmann
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Piyali Mukherjee
- Division of Infectious Diseases and Department of Pediatrics, McGovern Medical School at UTHealth Houston and Children’s Memorial Hermann Hospital, Houston, Texas, USA
| | | | - Truc T. Tran
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Jordan Bremer
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marc Gohel
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cesar A. Arias
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Anthony R. Flores
- Division of Infectious Diseases and Department of Pediatrics, McGovern Medical School at UTHealth Houston and Children’s Memorial Hermann Hospital, Houston, Texas, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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5
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Roux AE, Robert S, Bastat M, Rosinski-Chupin I, Rong V, Holbert S, Mereghetti L, Camiade E. The Role of Regulator Catabolite Control Protein A (CcpA) in Streptococcus agalactiae Physiology and Stress Response. Microbiol Spectr 2022; 10:e0208022. [PMID: 36264242 PMCID: PMC9784791 DOI: 10.1128/spectrum.02080-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/21/2022] [Indexed: 01/06/2023] Open
Abstract
Streptococcus agalactiae is a leading cause of infections in neonates. This opportunistic pathogen colonizes the vagina, where it has to cope with acidic pH and hydrogen peroxide produced by lactobacilli. Thus, in the host, this bacterium possesses numerous adaptation mechanisms in which the pleiotropic regulators play a major role. The transcriptional regulator CcpA (catabolite control protein A) has previously been shown to be the major regulator involved in carbon catabolite repression in Gram-positive bacteria but is also involved in other functions. By transcriptomic analysis, we characterized the CcpA-dependent gene regulation in S. agalactiae. Approximately 13.5% of the genome of S. agalactiae depends on CcpA for regulation and comprises genes involved in sugar uptake and fermentation, confirming the role of CcpA in carbon metabolism. We confirmed by electrophoretic mobility shift assays (EMSAs) that the DNA binding site called cis-acting catabolite responsive element (cre) determined for other streptococci was effective in S. agalactiae. We also showed that CcpA is of capital importance for survival under acidic and oxidative stresses and is implicated in macrophage survival by regulating several genes putatively or already described as involved in stress response. Among them, we focused our study on SAK_1689, which codes a putative UspA protein. We demonstrated that SAK_1689, highly downregulated by CcpA, is overexpressed under oxidative stress conditions, this overexpression being harmful for the bacterium in a ΔccpA mutant. IMPORTANCE Streptococcus agalactiae is a major cause of disease burden leading to morbidity and mortality in neonates worldwide. Deciphering its adaptation mechanisms is essential to understand how this bacterium manages to colonize its host. Here, we determined the regulon of the pleiotropic regulator CcpA in S. agalactiae. Our findings reveal that CcpA is not only involved in carbon catabolite repression, but is also important for acidic and oxidative stress resistance and survival in macrophages.
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Affiliation(s)
| | | | | | - Isabelle Rosinski-Chupin
- Unité Écologie et Évolution de la Résistance aux Antibiotiques, CNRS UMR3525, Institut Pasteur, Paris, France
| | | | | | - Laurent Mereghetti
- ISP, Université de Tours, INRAE, Tours, France
- CHRU Tours, Service de Bactériologie-Virologie-Hygiène, Tours, France
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6
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Zheng M, Zhu K, Peng H, Shang W, Zhao Y, Lu S, Rao X, Li M, Zhou R, Li G. CcpA Regulates Staphylococcus aureus Biofilm Formation through Direct Repression of Staphylokinase Expression. Antibiotics (Basel) 2022; 11:antibiotics11101426. [PMID: 36290085 PMCID: PMC9598941 DOI: 10.3390/antibiotics11101426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus represents a notorious opportunistic pathogen causing various infections in biofilm nature, imposing remarkable therapeutic challenges worldwide. The catabolite control protein A (CcpA), a major regulator of carbon catabolite repression (CCR), has been recognized to modulate S. aureus biofilm formation, while the underlying mechanism remains to be fully elucidated. In this study, the reduced biofilm was firstly determined in the ccpA deletion mutant of S. aureus clinical isolate XN108 using both crystal violet staining and confocal laser scanning microscopy. RNA-seq analysis suggested that sak-encoding staphylokinase (Sak) was significantly upregulated in the mutant ∆ccpA, which was further confirmed by RT-qPCR. Consistently, the induced Sak production correlated the elevated promoter activity of sak and increased secretion in the supernatants, as demonstrated by Psak-lacZ reporter fusion expression and chromogenic detection, respectively. Notably, electrophoretic mobility shift assays showed that purified recombinant protein CcpA binds directly to the promoter region of sak, suggesting the direct negative control of sak expression by CcpA. Double isogenic deletion of ccpA and sak restored biofilm formation for mutant ∆ccpA, which could be diminished by trans-complemented sak. Furthermore, the exogenous addition of recombinant Sak inhibited biofilm formation for XN108 in a dose-dependent manner. Together, this study delineates a novel model of CcpA-controlled S. aureus biofilm through direct inhibition of sak expression, highlighting the multifaceted roles and multiple networks regulated by CcpA.
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Affiliation(s)
- Mingxia Zheng
- Department of Emergency Medicine, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Keting Zhu
- Department of Emergency Medicine, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Huagang Peng
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Weilong Shang
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Yan Zhao
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Shuguang Lu
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Ming Li
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
- Correspondence: (M.L.); (R.Z.); (G.L.)
| | - Renjie Zhou
- Department of Emergency Medicine, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
- Correspondence: (M.L.); (R.Z.); (G.L.)
| | - Gang Li
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
- Correspondence: (M.L.); (R.Z.); (G.L.)
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7
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Woo JKK, McIver KS, Federle MJ. Carbon catabolite repression on the Rgg2/3 quorum sensing system in Streptococcus pyogenes is mediated by PTS Man and Mga. Mol Microbiol 2022; 117:525-538. [PMID: 34923680 PMCID: PMC8844239 DOI: 10.1111/mmi.14866] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 02/03/2023]
Abstract
Streptococcus pyogenes, also known as group A Streptococcus or GAS, is a human-restricted pathogen causing a diverse array of infections. The ability to adapt to different niches requires GAS to adjust gene expression in response to environmental cues. We previously identified the abundance of biometals and carbohydrates led to natural induction of the Rgg2/3 cell-cell communication system (quorum sensing, QS). Here we determined the mechanism by which the Rgg2/3 QS system is stimulated exclusively by mannose and repressed by glucose, a phenomenon known as carbon catabolite repression (CCR). Instead of carbon catabolite protein A, the primary mediator of CCR in Gram-positive bacteria; CCR of Rgg2/3 requires the PTS regulatory domain (PRD)-containing transcriptional regulator Mga. Deletion of Mga led to carbohydrate-independent activation of Rgg2/3 by down-regulating rgg3, the QS repressor. Through phosphoablative and phosphomimetic substitutions within Mga PRDs, we demonstrated that selective phosphorylation of PRD1 conferred repression of the Rgg2/3 system. Moreover, given the carbohydrate specificity mediating Mga-dependent governance over Rgg2/3, we tested mannose-specific PTS components and found the EIIA/B subunit ManL was required for Mga-dependent repression. These findings provide newfound connections between PTSMan , Mga, and QS, and further demonstrate that Mga is a central regulatory nexus for integrating nutritional status and virulence.
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Affiliation(s)
- Jerry K. K. Woo
- Department of Biopharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Kevin S. McIver
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA
| | - Michael J. Federle
- Department of Biopharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60607, USA,For correspondence. ; Tel. 312-413-0213; Fax. 312-413-9303
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8
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DebRoy S, Aliaga-Tobar V, Galvez G, Arora S, Liang X, Horstmann N, Maracaja-Coutinho V, Latorre M, Hook M, Flores AR, Shelburne SA. Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus. Mol Microbiol 2020; 115:1207-1228. [PMID: 33325565 PMCID: PMC8359418 DOI: 10.1111/mmi.14667] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/02/2020] [Accepted: 12/11/2020] [Indexed: 01/01/2023]
Abstract
Catabolite control protein A (CcpA) is a master regulator of carbon source utilization and contributes to the virulence of numerous medically important Gram‐positive bacteria. Most functional assessments of CcpA, including interaction with its key co‐factor HPr, have been performed in nonpathogenic bacteria. In this study we aimed to identify the in vivo DNA binding profile of CcpA and assess the extent to which HPr is required for CcpA‐mediated regulation and DNA binding in the major human pathogen group A Streptococcus (GAS). Using a combination RNAseq/ChIP‐seq approach, we found that CcpA affects transcript levels of 514 of 1667 GAS genes (31%) whereas direct DNA binding was identified for 105 GAS genes. Three of the directly regulated genes encode the key GAS virulence factors Streptolysin S, PrtS (IL‐8 degrading proteinase), and SpeB (cysteine protease). Mutating CcpA Val301 to Ala (strain 2221‐CcpA‐V301A) abolished interaction between CcpA and HPr and impacted the transcript levels of 205 genes (40%) in the total CcpA regulon. By ChIP‐seq analysis, CcpAV301A bound to DNA from 74% of genes bound by wild‐type CcpA, but generally with lower affinity. These data delineate the direct CcpA regulon and clarify the HPr‐dependent and independent activities of CcpA in a key pathogenic bacterium.
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Affiliation(s)
- Sruti DebRoy
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Victor Aliaga-Tobar
- Facultad de Ciencias Químicas y Farmacéuticas, Advanced Center for Chronic Diseases-ACCDiS, Universidad de Chile, Independencia, Chile.,Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Gabriel Galvez
- Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Nicola Horstmann
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vinicius Maracaja-Coutinho
- Facultad de Ciencias Químicas y Farmacéuticas, Advanced Center for Chronic Diseases-ACCDiS, Universidad de Chile, Independencia, Chile.,Centro de Modelamiento Molecular, Biofísica y Bioinformática (CM2B2), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.,Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Anthony R Flores
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA.,Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
| | - Samuel A Shelburne
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston TX, USA
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9
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Cortés MP, Acuña V, Travisany D, Siegel A, Maass A, Latorre M. Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways. Front Mol Biosci 2020; 6:155. [PMID: 31998751 PMCID: PMC6966769 DOI: 10.3389/fmolb.2019.00155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/13/2019] [Indexed: 11/13/2022] Open
Abstract
Acidithiobacillus thiooxidans is one of the most studied biomining species, highlighting its ability to oxidize reduced inorganic sulfur compounds, coupled with its elevated capacity to live under an elevated concentration of heavy metals. In this work, using an in silico semi-automatic genome scale approach, two biological networks for A. thiooxidans Licanantay were generated: (i) An affinity transcriptional regulatory network composed of 42 regulatory family genes and 1,501 operons (57% genome coverage) linked through 2,646 putative DNA binding sites (arcs), (ii) A metabolic network reconstruction made of 523 genes and 1,203 reactions (22 pathways related to biomining processes). Through the identification of confident connections between both networks (V-shapes), it was possible to identify a sub-network of transcriptional factor (34 regulators) regulating genes (61 operons) encoding for proteins involved in biomining-related pathways. Network analysis suggested that transcriptional regulation of biomining genes is organized into different modules. The topological parameters showed a high hierarchical organization by levels inside this network (14 layers), highlighting transcription factors CysB, LysR, and IHF as complex modules with high degree and number of controlled pathways. In addition, it was possible to identify transcription factor modules named primary regulators (not controlled by other regulators in the sub-network). Inside this group, CysB was the main module involved in gene regulation of several bioleaching processes. In particular, metabolic processes related to energy metabolism (such as sulfur metabolism) showed a complex integrated regulation, where different primary regulators controlled several genes. In contrast, pathways involved in iron homeostasis and oxidative stress damage are mainly regulated by unique primary regulators, conferring Licanantay an efficient, and specific metal resistance response. This work shows new evidence in terms of transcriptional regulation at a systems level and broadens the study of bioleaching in A. thiooxidans species.
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Affiliation(s)
- María Paz Cortés
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile
| | - Vicente Acuña
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile
| | - Dante Travisany
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile
| | - Anne Siegel
- IRISA, UMR 6074, CNRS, Rennes, France.,INRIA, Dyliss Team, Centre Rennes-Bretagne-Atlantique, Rennes, France
| | - Alejandro Maass
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile.,Department of Mathematical Engineering, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
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10
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Lu Y, Song S, Tian H, Yu H, Zhao J, Chen C. Functional analysis of the role of CcpA in Lactobacillus plantarum grown on fructooligosaccharides or glucose: a transcriptomic perspective. Microb Cell Fact 2018; 17:201. [PMID: 30593274 PMCID: PMC6309078 DOI: 10.1186/s12934-018-1050-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/24/2018] [Indexed: 12/19/2022] Open
Abstract
Background The catabolite control protein A (CcpA) is a master regulator of many important cellular processes in Gram-positive bacteria. In Lactobacillus plantarum, CcpA directly or indirectly controls the transcription of a large number of genes that are involved in carbohydrate metabolism, aerobic and anaerobic growth, stress response and metabolite production, but its role in response to different carbon sources remains unclear. Results Here a combined transcriptomic and physiological approach was used to survey the global alterations that occurred during the logarithmic growth phase of wild-type and ccpA mutant strains of L. plantarum ST-III using fructooligosaccharides (FOS) or glucose as the sole carbon source. The inactivation of ccpA significantly affected the growth and production of metabolites under both carbon sources. About 15% of the total genes were significantly altered between wild-type and ccpA strains grown on glucose and the value is deceased to 12% when these two strains were compared on FOS, while only 7% were obviously changed due to the loss of CcpA when comparing strains grown on glucose and FOS. Although most of the differentially expressed genes mediated by CcpA are glucose dependent, FOS can also induce carbon catabolite repression (CCR) through the CcpA pathway. Moreover, the inactivation of ccpA led to a transformation from homolactic fermentation to mixed fermentation under aerobic conditions. CcpA can control genes directly by binding in the regulatory region of the target genes (mixed fermentation), indirectly through local regulators (fatty acid biosynthesis), or have a double effect via direct and indirect regulation (FOS metabolism). Conclusion Overall, our results show that CcpA plays a central role in response to carbon source and availability of L. plantarum and provide new insights into the complex and extended regulatory network of lactic acid bacteria.![]() Electronic supplementary material The online version of this article (10.1186/s12934-018-1050-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanqing Lu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
| | - Sichao Song
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China
| | - Huaixiang Tian
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, People's Republic of China
| | - Chen Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China.
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11
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DebRoy S, Li X, Kalia A, Galloway-Pena J, Shah BJ, Fowler VG, Flores AR, Shelburne SA. Identification of a chimeric emm gene and novel emm pattern in currently circulating strains of emm4 Group A Streptococcus. Microb Genom 2018; 4. [PMID: 30412460 PMCID: PMC6321872 DOI: 10.1099/mgen.0.000235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Group A Streptococcus (GAS) is classified on the basis of the sequence of the gene encoding the M protein (emm) and the patterns into which emm types are grouped. We discovered a novel emm pattern in emm4 GAS, historically considered pattern E, arising from a fusion event between emm and the adjacent enn gene. We identified the emm–enn fusion event in 51 out of 52 emm4 GAS strains isolated by national surveillance in 2015. GAS isolates with an emm–enn fusion event completely replaced pattern E emm4 strains over a 4-year span in Houston (2013–2017). The novel emm–enn gene fusion and new emm pattern has potential vaccine implications.
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Affiliation(s)
- Sruti DebRoy
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiqi Li
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jessica Galloway-Pena
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brittany J. Shah
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
| | - Vance G. Fowler
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Anthony R. Flores
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern Medical School, Houston, TX, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern Medical School, Houston, TX, USA
- *Correspondence: Samuel A. Shelburne,
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12
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Valdes KM, Sundar GS, Belew AT, Islam E, El-Sayed NM, Le Breton Y, McIver KS. Glucose Levels Alter the Mga Virulence Regulon in the Group A Streptococcus. Sci Rep 2018; 8:4971. [PMID: 29563558 PMCID: PMC5862849 DOI: 10.1038/s41598-018-23366-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/06/2018] [Indexed: 12/25/2022] Open
Abstract
Many bacterial pathogens coordinately regulate genes encoding important metabolic pathways during disease progression, including the phosphoenolpyruvate (PEP)-phosphotransferase system (PTS) for uptake of carbohydrates. The Gram-positive Group A Streptococcus (GAS) is a pathogen that infects multiple tissues in the human host. The virulence regulator Mga in GAS can be phosphorylated by the PTS, affecting Mga activity based on carbohydrate availability. Here, we explored the effects of glucose availability on the Mga regulon. RNA-seq was used to identify transcriptomic differences between the Mga regulon grown to late log phase in the presence of glucose (THY) or after glucose has been expended (C media). Our results revealed a correlation between the genes activated in C media with those known to be repressed by CcpA, indicating that C media mimics a non-preferred sugar environment. Interestingly, we found very little overlap in the Mga regulon from GAS grown in THY versus C media beyond the core virulence genes. We also observed an alteration in the phosphorylation status of Mga, indicating that the observed media differences in the Mga regulon may be directly attributed to glucose levels. Thus, these results support an in vivo link between glucose availability and virulence regulation in GAS.
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Affiliation(s)
- Kayla M Valdes
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA
| | - Ganesh S Sundar
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA
| | - Ashton T Belew
- Center for Bioinformatics and Computation Biology, UMCP, College Park, MD, USA
| | - Emrul Islam
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA
| | - Najib M El-Sayed
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA.,Center for Bioinformatics and Computation Biology, UMCP, College Park, MD, USA
| | - Yoann Le Breton
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA.
| | - Kevin S McIver
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, Maryland, USA.
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13
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Sundar GS, Islam E, Braza RD, Silver AB, Le Breton Y, McIver KS. Route of Glucose Uptake in the Group a Streptococcus Impacts SLS-Mediated Hemolysis and Survival in Human Blood. Front Cell Infect Microbiol 2018; 8:71. [PMID: 29594067 PMCID: PMC5861209 DOI: 10.3389/fcimb.2018.00071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/27/2018] [Indexed: 12/29/2022] Open
Abstract
The transport and metabolism of glucose has been shown to have far reaching consequences in the transcriptional profile of many bacteria. As glucose is most often the preferred carbon source for bacteria, its presence in the environment leads to the repression of many alternate carbohydrate pathways, a condition known as carbon catabolite repression (CCR). Additionally, the expression of many virulence factors is also dependent on the presence of glucose. Despite its importance, little is known about the transport routes of glucose in the human pathogen Streptococcus pyogenes. Considering that Streptococcus pyogenes is an important human pathogen responsible for over 500,000 deaths every year, we characterized the routes of glucose transport in an effort to understand its importance in GAS pathogenesis. Using a deletion of glucokinase (ΔnagC) to block utilization of glucose imported by non-PTS pathways, we determined that of the two glucose transport pathways in GAS (PTS and non-PTS), the non-PTS pathway played a more significant role in glucose transport. However, the expression of both pathways is linked by a currently unknown mechanism, as blocking the non-PTS uptake of glucose reduces ptsI (EI) expression. Similar to the effects of the deletion of the PTS pathway, lack of the non-PTS pathway also leads to the early activity of Streptolysin S. However, this early activity did not adversely or favorably affect survival of ΔnagC in whole human blood. In a subcutaneous murine infection model, ΔnagC-infected mice showed increased lesion severity at the local site of infection; although, lesion size and dissemination from the site of infection was similar to wild type. Here, we show that glucose transport in GAS is primarily via a non-PTS pathway. The route of glucose transport differentially affects the survival of GAS in whole human blood, as well as the lesion size at the local site of infection in a murine skin infection model.
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Affiliation(s)
- Ganesh S Sundar
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, College Park, MD, United States
| | - Emrul Islam
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, College Park, MD, United States
| | - Rezia D Braza
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, College Park, MD, United States
| | - Aliyah B Silver
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, College Park, MD, United States
| | - Yoann Le Breton
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, College Park, MD, United States
| | - Kevin S McIver
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, College Park, MD, United States
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