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Sarshar M, Scribano D, Palamara AT, Ambrosi C, Masotti A. The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions. Front Mol Biosci 2022; 9:1088783. [PMID: 36619166 PMCID: PMC9810633 DOI: 10.3389/fmolb.2022.1088783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein-RNA and RNA-RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.
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Affiliation(s)
- Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,Department of Infectious Diseases, National Institute of Health, Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy,IRCCS San Raffaele Roma, Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
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2
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Álvarez-Fraga L, Rumbo-Feal S, Pérez A, Gómez MJ, Gayoso C, Vallejo JA, Ohneck EJ, Valle J, Actis LA, Beceiro A, Bou G, Poza M. Global assessment of small RNAs reveals a non-coding transcript involved in biofilm formation and attachment in Acinetobacter baumannii ATCC 17978. PLoS One 2017; 12:e0182084. [PMID: 28763494 PMCID: PMC5538643 DOI: 10.1371/journal.pone.0182084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/12/2017] [Indexed: 12/30/2022] Open
Abstract
Many strains of Acinetobacter baumannii have been described as being able to form biofilm. Small non-coding RNAs (sRNAs) control gene expression in many regulatory circuits in bacteria. The aim of the present work was to provide a global description of the sRNAs produced both by planktonic and biofilm-associated (sessile) cells of A. baumannii ATCC 17978, and to compare the corresponding gene expression profiles to identify sRNAs molecules associated to biofilm formation and virulence. sRNA was extracted from both planktonic and sessile cells and reverse transcribed. cDNA was subjected to 454-pyrosequencing using the GS-FLX Titanium chemistry. The global analysis of the small RNA transcriptome revealed different sRNA expression patterns in planktonic and biofilm associated cells, with some of the transcripts only expressed or repressed in sessile bacteria. A total of 255 sRNAs were detected, with 185 of them differentially expressed in the different types of cells. A total of 9 sRNAs were expressed only in biofilm cells, while the expression of other 21 coding regions were repressed only in biofilm cells. Strikingly, the expression level of the sRNA 13573 was 120 times higher in biofilms than in planktonic cells, an observation that prompted us to further investigate the biological role of this non-coding transcript. Analyses of an isogenic mutant and over-expressing strains revealed that the sRNA 13573 gene is involved in biofilm formation and attachment to A549 human alveolar epithelial cells. The present work serves as a basis for future studies examining the complex regulatory network that regulate biofilm biogenesis and attachment to eukaryotic cells in A. baumannii ATCC 17978.
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Affiliation(s)
- Laura Álvarez-Fraga
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
| | - Soraya Rumbo-Feal
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
| | - Astrid Pérez
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Manuel J. Gómez
- Department of Molecular Evolution, Center for Astrobiology, INTA-CSIC, Torrejón de Ardoz, Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Carmen Gayoso
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
| | - Juan A. Vallejo
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
| | - Emily J. Ohneck
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Jaione Valle
- Departamento de Biofilms Microbianos, Instituto de Agrobiotecnología, Navarra, Spain
| | - Luis A. Actis
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Alejandro Beceiro
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
| | - Germán Bou
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
- * E-mail: (GB); (MP)
| | - Margarita Poza
- Departamento de Microbiología, Instituto de Investigación Biomédica (INIBIC), Complejo Hospitalario Universitario (CHUAC), A Coruña, Spain
- * E-mail: (GB); (MP)
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3
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Kröger C, Kary SC, Schauer K, Cameron ADS. Genetic Regulation of Virulence and Antibiotic Resistance in Acinetobacter baumannii. Genes (Basel) 2016; 8:genes8010012. [PMID: 28036056 PMCID: PMC5295007 DOI: 10.3390/genes8010012] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/18/2016] [Accepted: 12/20/2016] [Indexed: 01/14/2023] Open
Abstract
Multidrug resistant microorganisms are forecast to become the single biggest challenge to medical care in the 21st century. Over the last decades, members of the genus Acinetobacter have emerged as bacterial opportunistic pathogens, in particular as challenging nosocomial pathogens because of the rapid evolution of antimicrobial resistances. Although we lack fundamental biological insight into virulence mechanisms, an increasing number of researchers are working to identify virulence factors and to study antibiotic resistance. Here, we review current knowledge regarding the regulation of virulence genes and antibiotic resistance in Acinetobacter baumannii. A survey of the two-component systems AdeRS, BaeSR, GacSA and PmrAB explains how each contributes to antibiotic resistance and virulence gene expression, while BfmRS regulates cell envelope structures important for pathogen persistence. A. baumannii uses the transcription factors Fur and Zur to sense iron or zinc depletion and upregulate genes for metal scavenging as a critical survival tool in an animal host. Quorum sensing, nucleoid-associated proteins, and non-classical transcription factors such as AtfA and small regulatory RNAs are discussed in the context of virulence and antibiotic resistance.
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Stefani C Kary
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Kristina Schauer
- Department of Veterinary Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Oberschleißheim 85764, Germany.
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, SK S4S 042, Canada.
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C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA. Proc Natl Acad Sci U S A 2016; 113:E6089-E6096. [PMID: 27681631 DOI: 10.1073/pnas.1613053113] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The bacterial Sm protein and RNA chaperone Hfq stabilizes small noncoding RNAs (sRNAs) and facilitates their annealing to mRNA targets involved in stress tolerance and virulence. Although an arginine patch on the Sm core is needed for Hfq's RNA chaperone activity, the function of Hfq's intrinsically disordered C-terminal domain (CTD) has remained unclear. Here, we use stopped flow spectroscopy to show that the CTD of Escherichia coli Hfq is not needed to accelerate RNA base pairing but is required for the release of dsRNA. The Hfq CTD also mediates competition between sRNAs, offering a kinetic advantage to sRNAs that contact both the proximal and distal faces of the Hfq hexamer. The change in sRNA hierarchy caused by deletion of the Hfq CTD in E. coli alters the sRNA accumulation and the kinetics of sRNA regulation in vivo. We propose that the Hfq CTD displaces sRNAs and annealed sRNA⋅mRNA complexes from the Sm core, enabling Hfq to chaperone sRNA-mRNA interactions and rapidly cycle between competing targets in the cell.
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Montaña S, Schramm STJ, Traglia GM, Chiem K, Parmeciano Di Noto G, Almuzara M, Barberis C, Vay C, Quiroga C, Tolmasky ME, Iriarte A, Ramírez MS. The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer. PLoS One 2016; 11:e0161528. [PMID: 27548264 PMCID: PMC4993456 DOI: 10.1371/journal.pone.0161528] [Citation(s) in RCA: 26] [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: 03/23/2016] [Accepted: 08/08/2016] [Indexed: 02/08/2023] Open
Abstract
Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT) events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as blaPER-2, blaOXA-58, blaTEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of blaOXA-211, called blaOXA-498. In particular, blaPER-2 and blaTEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes.
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Affiliation(s)
- Sabrina Montaña
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Sareda T. J. Schramm
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
| | - German Matías Traglia
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Kevin Chiem
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
| | - Gisela Parmeciano Di Noto
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Marisa Almuzara
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Claudia Barberis
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Carlos Vay
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Cecilia Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Marcelo E. Tolmasky
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
| | - Andrés Iriarte
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - María Soledad Ramírez
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
- * E-mail:
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Abstract
Over the last decade, small (often noncoding) RNA molecules have been discovered as important regulators influencing myriad aspects of bacterial physiology and virulence. In particular, small RNAs (sRNAs) have been implicated in control of both primary and secondary metabolic pathways in many bacterial species. This chapter describes characteristics of the major classes of sRNA regulators, and highlights what is known regarding their mechanisms of action. Specific examples of sRNAs that regulate metabolism in gram-negative bacteria are discussed, with a focus on those that regulate gene expression by base pairing with mRNA targets to control their translation and stability.
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7
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Weiss A, Broach WH, Lee MC, Shaw LN. Towards the complete small RNome of Acinetobacter baumannii. Microb Genom 2016; 2:e000045. [PMID: 28348845 PMCID: PMC5320573 DOI: 10.1099/mgen.0.000045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/13/2015] [Accepted: 12/15/2015] [Indexed: 01/08/2023] Open
Abstract
In recent years, the Gram-negative bacterium Acinetobacter baumannii has garnered considerable attention for its unprecedented capacity to rapidly develop resistance to antibacterial therapeutics. This is coupled with the seemingly epidemic emergence of new hyper-virulent strains. Although strain-specific differences for A. baumannii isolates have been well described, these studies have primarily focused on proteinaceous factors. At present, only limited publications have investigated the presence and role of small regulatory RNA (sRNA) transcripts. Herein, we perform such an analysis, describing the RNA-seq-based identification of 78 A. baumannii sRNAs in the AB5075 background. Together with six previously identified elements, we include each of these in a new genome annotation file, which will serve as a tool to investigate regulatory events in this organism. Our work reveals that the sRNAs display high expression, accounting for >50 % of the 20 most strongly expressed genes. Through conservation analysis we identified six classes of similar sRNAs, with one found to be particularly abundant and homologous to regulatory, C4 antisense RNAs found in bacteriophages. These elements appear to be processed from larger transcripts in an analogous manner to the phage C4 molecule and are putatively controlled by two further sRNAs that are strongly antisense to them. Collectively, this study offers a detailed view of the sRNA content of A. baumannii, exposing sequence and structural conservation amongst these elements, and provides novel insight into the potential evolution, and role, of these understudied regulatory molecules.
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Affiliation(s)
- Andy Weiss
- Cell Biology, Microbiology & Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - William H Broach
- Cell Biology, Microbiology & Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Mackenzie C Lee
- Cell Biology, Microbiology & Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Lindsey N Shaw
- Cell Biology, Microbiology & Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
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8
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Backofen R, Amman F, Costa F, Findeiß S, Richter AS, Stadler PF. Bioinformatics of prokaryotic RNAs. RNA Biol 2014; 11:470-83. [PMID: 24755880 PMCID: PMC4152356 DOI: 10.4161/rna.28647] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/17/2014] [Accepted: 03/25/2014] [Indexed: 02/02/2023] Open
Abstract
The genome of most prokaryotes gives rise to surprisingly complex transcriptomes, comprising not only protein-coding mRNAs, often organized as operons, but also harbors dozens or even hundreds of highly structured small regulatory RNAs and unexpectedly large levels of anti-sense transcripts. Comprehensive surveys of prokaryotic transcriptomes and the need to characterize also their non-coding components is heavily dependent on computational methods and workflows, many of which have been developed or at least adapted specifically for the use with bacterial and archaeal data. This review provides an overview on the state-of-the-art of RNA bioinformatics focusing on applications to prokaryotes.
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Affiliation(s)
- Rolf Backofen
- Bioinformatics Group; Department of Computer Science; University of Freiburg; Georges-Köhler-Allee 106; D-79110 Freiburg, Germany
- Center for non-coding RNA in Technology and Health; University of Copenhagen; Grønnegårdsvej 3; DK-1870 Frederiksberg C, Denmark
| | - Fabian Amman
- Institute for Theoretical Chemistry; University of Vienna; Währingerstraße 17; A-1090 Wien, Austria
- Bioinformatics Group; Department of Computer Science, and Interdisciplinary Center for Bioinformatics; University of Leipzig; Härtelstraße 16-18; D-04107 Leipzig, Germany
| | - Fabrizio Costa
- Bioinformatics Group; Department of Computer Science; University of Freiburg; Georges-Köhler-Allee 106; D-79110 Freiburg, Germany
| | - Sven Findeiß
- Institute for Theoretical Chemistry; University of Vienna; Währingerstraße 17; A-1090 Wien, Austria
- Bioinformatics and Computational Biology Research Group; University of Vienna; Währingerstraße 29; A-1090 Wien, Austria
| | - Andreas S Richter
- Bioinformatics Group; Department of Computer Science; University of Freiburg; Georges-Köhler-Allee 106; D-79110 Freiburg, Germany
- Max Planck Institute of Immunobiology and Epigenetics; Stübeweg 51; D-79108 Freiburg, Germany
| | - Peter F Stadler
- Center for non-coding RNA in Technology and Health; University of Copenhagen; Grønnegårdsvej 3; DK-1870 Frederiksberg C, Denmark
- Institute for Theoretical Chemistry; University of Vienna; Währingerstraße 17; A-1090 Wien, Austria
- Bioinformatics Group; Department of Computer Science, and Interdisciplinary Center for Bioinformatics; University of Leipzig; Härtelstraße 16-18; D-04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences; Inselstraße 22; D-04103 Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology – IZI; Perlickstraße 1; D-04103 Leipzig, Germany
- Santa Fe Institute; Santa Fe, NM USA
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Berghoff BA, Glaeser J, Sharma CM, Zobawa M, Lottspeich F, Vogel J, Klug G. Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides. Mol Microbiol 2011; 80:1479-95. [PMID: 21535243 DOI: 10.1111/j.1365-2958.2011.07658.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The photosynthetic alphaproteobacterium Rhodobacter sphaeroides has to cope with photooxidative stress that is caused by the bacteriochlorophyll a-mediated formation of singlet oxygen ((1)O(2)). Exposure to (1)O(2) induces the alternative sigma factors RpoE and RpoH(II) which then promote transcription of photooxidative stress-related genes, including small RNAs (sRNAs). The ubiquitous RNA chaperone Hfq is well established to interact with and facilitate the base-pairing of sRNAs and target mRNAs to influence mRNA stability and/or translation. Here we report on the pleiotropic phenotype of a Δhfq mutant of R. sphaeroides, which is less pigmented, produces minicells and is more sensitive to (1)O(2). The higher (1)O(2) sensitivity of the Δhfq mutant is paralleled by a reduced RpoE activity and a disordered induction of RpoH(II)-dependent genes. We used co-immunoprecipitation of FLAG-tagged Hfq combined with RNA-seq to identify association of at least 25 sRNAs and of mRNAs encoding cell division proteins and ribosomal proteins with Hfq. Remarkably, > 70% of the Hfq-bound sRNAs are (1)O(2)-affected. Proteomics analysis of the Hfq-deficient strain revealed an impact of Hfq on amino acid transport and metabolic functions. Our data demonstrate for the first time an involvement of Hfq in regulation of photosynthesis genes and in the photooxidative stress response.
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Affiliation(s)
- Bork A Berghoff
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 26, 35392 Gießen, Germany
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