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Furuta Y, Cheng C, Zorigt T, Paudel A, Izumi S, Tsujinouchi M, Shimizu T, Meijer WG, Higashi H. Direct Regulons of AtxA, the Master Virulence Regulator of Bacillus anthracis. mSystems 2021; 6:e0029121. [PMID: 34282944 PMCID: PMC8407390 DOI: 10.1128/msystems.00291-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
AtxA, the master virulence regulator of Bacillus anthracis, regulates the expression of three toxins and genes for capsule formation that are required for the pathogenicity of B. anthracis. Recent transcriptome analyses showed that AtxA affects a large number of genes on the chromosome and plasmids, suggesting a role as a global regulator. However, information on genes directly regulated by AtxA is scarce. In this work, we conducted genome-wide analyses and cataloged the binding sites of AtxA in vivo and transcription start sites on the B. anthracis genome. By integrating these results, we detected eight genes as direct regulons of AtxA. These consisted of five protein-coding genes, including two of the three toxin genes, and three genes encoding the small RNAs XrrA and XrrB and a newly discovered 95-nucleotide small RNA, XrrC. Transcriptomes from single-knockout mutants of these small RNAs revealed changes in the transcription levels of genes related to the aerobic electron transport chain, heme biosynthesis, and amino acid metabolism, suggesting their function for the control of cell physiology. These results reveal the first layer of the gene regulatory network for the pathogenicity of B. anthracis and provide a data set for the further study of the genomics and genetics of B. anthracis. IMPORTANCE Bacillus anthracis is the Gram-positive bacterial species that causes anthrax. Anthrax is still prevalent in countries mainly in Asia and Africa, where it causes economic damage and remains a public health issue. The mechanism of pathogenicity is mainly explained by the three toxin proteins expressed from the pXO1 plasmid and by proteins involved in capsule formation expressed from the pXO2 plasmid. AtxA is a protein expressed from the pXO1 plasmid that is known to upregulate genes involved in toxin production and capsule formation and is thus considered the master virulence regulator of B. anthracis. Therefore, understanding the detailed mechanism of gene regulation is important for the control of anthrax. The significance of this work lies in the identification of genes that are directly regulated by AtxA via genome-wide analyses. The results reveal the first layer of the gene regulatory network for the pathogenicity of B. anthracis and provide useful resources for a further understanding of B. anthracis.
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Affiliation(s)
- Yoshikazu Furuta
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Cheng Cheng
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Tuvshinzaya Zorigt
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Atmika Paudel
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Shun Izumi
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mai Tsujinouchi
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Tomoko Shimizu
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Wim G. Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Hideaki Higashi
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
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Christopoulou N, Granneman S. The role of RNA-binding proteins in mediating adaptive responses in Gram-positive bacteria. FEBS J 2021; 289:1746-1764. [PMID: 33690958 DOI: 10.1111/febs.15810] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 02/06/2023]
Abstract
Bacteria are constantly subjected to stressful conditions, such as antibiotic exposure, nutrient limitation and oxidative stress. For pathogenic bacteria, adapting to the host environment, escaping defence mechanisms and coping with antibiotic stress are crucial for their survival and the establishment of a successful infection. Stress adaptation relies heavily on the rate at which the organism can remodel its gene expression programme to counteract the stress. RNA-binding proteins mediating co- and post-transcriptional regulation have recently emerged as important players in regulating gene expression during adaptive responses. Most of the research on these layers of gene expression regulation has been done in Gram-negative model organisms where, thanks to a wide variety of global studies, large post-transcriptional regulatory networks have been uncovered. Unfortunately, our understanding of post-transcriptional regulation in Gram-positive bacteria is lagging behind. One possible explanation for this is that many proteins employed by Gram-negative bacteria are not well conserved in Gram-positives. And even if they are conserved, they do not always play similar roles as in Gram-negative bacteria. This raises the important question whether Gram-positive bacteria regulate gene expression in a significantly different way. The goal of this review was to discuss this in more detail by reviewing the role of well-known RNA-binding proteins in Gram-positive bacteria and by highlighting their different behaviours with respect to some of their Gram-negative counterparts. Finally, the second part of this review introduces several unusual RNA-binding proteins of Gram-positive species that we believe could also play an important role in adaptive responses.
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Affiliation(s)
- Niki Christopoulou
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Sander Granneman
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, UK
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Corsi ID, Dutta S, van Hoof A, Koehler TM. AtxA-Controlled Small RNAs of Bacillus anthracis Virulence Plasmid pXO1 Regulate Gene Expression in trans. Front Microbiol 2021; 11:610036. [PMID: 33519762 PMCID: PMC7843513 DOI: 10.3389/fmicb.2020.610036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Abstract
Small regulatory RNAs (sRNAs) are short transcripts that base-pair to mRNA targets or interact with regulatory proteins. sRNA function has been studied extensively in Gram-negative bacteria; comparatively less is known about sRNAs in Firmicutes. Here we investigate two sRNAs encoded by virulence plasmid pXO1 of Bacillus anthracis, the causative agent of anthrax. The sRNAs, named “XrrA and XrrB” (for pXO1-encoded regulatory RNA) are abundant and highly stable primary transcripts, whose expression is dependent upon AtxA, the master virulence regulator of B. anthracis. sRNA levels are highest during culture conditions that promote AtxA expression and activity, and sRNA levels are unaltered in Hfq RNA chaperone null-mutants. Comparison of the transcriptome of a virulent Ames-derived strain to the transcriptome of isogenic sRNA-null mutants revealed multiple 4.0- to >100-fold differences in gene expression. Most regulatory effects were associated with XrrA, although regulation of some transcripts suggests functional overlap between the XrrA and XrrB. Many sRNA-regulated targets were chromosome genes associated with branched-chain amino acid metabolism, proteolysis, and transmembrane transport. Finally, in a mouse model for systemic anthrax, the lungs and livers of animals infected with xrrA-null mutants had a small reduction in bacterial burden, suggesting a role for XrrA in B. anthracis pathogenesis.
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Affiliation(s)
- Ileana D Corsi
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, TX, United States
| | - Soumita Dutta
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, TX, United States
| | - Theresa M Koehler
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, TX, United States
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Cai Q, Wang G, Li Z, Zhang L, Fu Y, Yang X, Lin W, Lin X. SWATH based quantitative proteomics analysis reveals Hfq2 play an important role on pleiotropic physiological functions in Aeromonas hydrophila. J Proteomics 2019; 195:1-10. [DOI: 10.1016/j.jprot.2018.12.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/15/2018] [Accepted: 12/26/2018] [Indexed: 12/14/2022]
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Riboregulator elements as tools to engineer gene expression in cyanobacteria. Appl Microbiol Biotechnol 2018; 102:7717-7723. [DOI: 10.1007/s00253-018-9221-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 01/01/2023]
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Indication and Identification of Bacillus anthracis Isolates from the Middle Volga Region by Multi-Primer PCR. BIONANOSCIENCE 2018. [DOI: 10.1007/s12668-017-0477-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Zheng JJ, Perez AJ, Tsui HCT, Massidda O, Winkler ME. Absence of the KhpA and KhpB (JAG/EloR) RNA-binding proteins suppresses the requirement for PBP2b by overproduction of FtsA in Streptococcus pneumoniae D39. Mol Microbiol 2017; 106:793-814. [PMID: 28941257 DOI: 10.1111/mmi.13847] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2017] [Indexed: 12/11/2022]
Abstract
Suppressor mutations were isolated that obviate the requirement for essential PBP2b in peripheral elongation of peptidoglycan from the midcells of dividing Streptococcus pneumoniae D39 background cells. One suppressor was in a gene encoding a single KH-domain protein (KhpA). ΔkhpA suppresses deletions in most, but not all (mltG), genes involved in peripheral PG synthesis and in the gpsB regulatory gene. ΔkhpA mutations reduce growth rate, decrease cell size, minimally affect shape and induce expression of the WalRK cell-wall stress regulon. Reciprocal co-immunoprecipitations show that KhpA forms a complex in cells with another KH-domain protein (KhpB/JAG/EloR). ΔkhpA and ΔkhpB mutants phenocopy each other exactly, consistent with a direct interaction. RNA-immunoprecipitation showed that KhpA/KhpB bind an overlapping set of RNAs in cells. Phosphorylation of KhpB reported previously does not affect KhpB function in the D39 progenitor background. A chromosome duplication implicated FtsA overproduction in Δpbp2b suppression. We show that cellular FtsA concentration is negatively regulated by KhpA/B at the post-transcriptional level and that FtsA overproduction is necessary and sufficient for suppression of Δpbp2b. However, increased FtsA only partially accounts for the phenotypes of ΔkhpA mutants. Together, these results suggest that multimeric KhpA/B may function as a pleiotropic RNA chaperone controlling pneumococcal cell division.
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Affiliation(s)
- Jiaqi J Zheng
- Department of Biology, Indiana University Bloomington (IUB), Bloomington, IN 47405, USA
| | - Amilcar J Perez
- Department of Biology, Indiana University Bloomington (IUB), Bloomington, IN 47405, USA
| | - Ho-Ching Tiffany Tsui
- Department of Biology, Indiana University Bloomington (IUB), Bloomington, IN 47405, USA
| | - Orietta Massidda
- Dipartimento di Scienze Chirurgiche, Università di Cagliari, 09100 Cagliari, Italy
| | - Malcolm E Winkler
- Department of Biology, Indiana University Bloomington (IUB), Bloomington, IN 47405, USA
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