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Muñoz-Bucio A, Arellano-Reynoso B, Sangari FJ, Sieira R, Thébault P, Espitia C, García Lobo JM, Seoane A, Suárez-Güemes F. Increased Brucella abortus asRNA_0067 expression under intraphagocytic stressors is associated with enhanced virB2 transcription. Arch Microbiol 2024; 206:285. [PMID: 38816572 PMCID: PMC11139718 DOI: 10.1007/s00203-024-03984-8] [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: 02/21/2024] [Accepted: 04/27/2024] [Indexed: 06/01/2024]
Abstract
Intracellular pathogens like Brucella face challenges during the intraphagocytic adaptation phase, where the modulation of gene expression plays an essential role in taking advantage of stressors to persist inside the host cell. This study aims to explore the expression of antisense virB2 RNA strand and related genes under intracellular simulation media. Sense and antisense virB2 RNA strands increased expression when nutrient deprivation and acidification were higher, being starvation more determinative. Meanwhile, bspB, one of the T4SS effector genes, exhibited the highest expression during the exposition to pH 4.5 and nutrient abundance. Based on RNA-seq analysis and RACE data, we constructed a regional map depicting the 5' and 3' ends of virB2 and the cis-encoded asRNA_0067. Without affecting the CDS or a possible autonomous RBS, we generate the deletion mutant ΔasRNA_0067, significantly reducing virB2 mRNA expression and survival rate. These results suggest that the antisense asRNA_0067 expression is promoted under exposure to the intraphagocytic adaptation phase stressors, and its deletion is associated with a lower transcription of the virB2 gene. Our findings illuminate the significance of these RNA strands in modulating the survival strategy of Brucella within the host and emphasize the role of nutrient deprivation in gene expression.
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Affiliation(s)
- Adrian Muñoz-Bucio
- Facultad de Medicina Veterinaria y Zootecnia, Departamento de Microbiología e Inmunología. Circuito Exterior S/N, Universidad Nacional Autónoma de México, CDMX, Ciudad Universitaria, Coyoacán, 04510, Mexico
| | - Beatriz Arellano-Reynoso
- Facultad de Medicina Veterinaria y Zootecnia, Departamento de Microbiología e Inmunología. Circuito Exterior S/N, Universidad Nacional Autónoma de México, CDMX, Ciudad Universitaria, Coyoacán, 04510, Mexico
| | - Félix J Sangari
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, C. Albert Einstein 22, 39011, Santander, Cantabria, Spain
| | - Rodrigo Sieira
- Fundación Instituto Leloir-IIBBA CONICET, Av. Patricias Argentinas 435CABA, CP. 1405, Buenos Aires Argentina, Argentina
| | - Patricia Thébault
- Laboratoire Bordelais de Recherche en Informatique (LaBRI), UMR 5800, CNRS, Bordeaux INP, Université de Bordeaux, 33400, Talence, France
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México MX, CDMX, Circuito Escolar 33, Ciudad Universitaria, Coyoacán, 04510, Mexico
| | - Juan M García Lobo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, C. Albert Einstein 22, 39011, Santander, Cantabria, Spain
| | - Asunción Seoane
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, C. Albert Einstein 22, 39011, Santander, Cantabria, Spain
| | - Francisco Suárez-Güemes
- Facultad de Medicina Veterinaria y Zootecnia, Departamento de Microbiología e Inmunología. Circuito Exterior S/N, Universidad Nacional Autónoma de México, CDMX, Ciudad Universitaria, Coyoacán, 04510, Mexico.
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2
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King KA, Benton AH, Caudill MT, Stoyanof ST, Kang L, Michalak P, Lahmers KK, Dunman PM, DeHart TG, Ahmad SS, Jutras BL, Poncin K, De Bolle X, Caswell CC. Post-transcriptional control of the essential enzyme MurF by a small regulatory RNA in Brucella abortus. Mol Microbiol 2024; 121:129-141. [PMID: 38082493 DOI: 10.1111/mmi.15207] [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: 09/27/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 01/15/2024]
Abstract
Brucella abortus is a facultative, intracellular, zoonotic pathogen that resides inside macrophages during infection. This is a specialized niche where B. abortus encounters various stresses as it navigates through the macrophage. In order to survive this harsh environment, B. abortus utilizes post-transcriptional regulation of gene expression through the use of small regulatory RNAs (sRNAs). Here, we characterize a Brucella sRNAs called MavR (for MurF- and virulence-regulating sRNA), and we demonstrate that MavR is required for the full virulence of B. abortus in macrophages and in a mouse model of chronic infection. Transcriptomic and proteomic studies revealed that a major regulatory target of MavR is MurF. MurF is an essential protein that catalyzes the final cytoplasmic step in peptidoglycan (PG) synthesis; however, we did not detect any differences in the amount or chemical composition of PG in the ΔmavR mutant. A 6-nucleotide regulatory seed region within MavR was identified, and mutation of this seed region resulted in dysregulation of MurF production, as well as significant attenuation of infection in a mouse model. Overall, the present study underscores the importance of sRNA regulation in the physiology and virulence of Brucella.
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Affiliation(s)
- Kellie A King
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Angela H Benton
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Mitchell T Caudill
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - S Tristan Stoyanof
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Lin Kang
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, USA
- College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana, USA
- Center for One Health Research, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, USA
| | - Pawel Michalak
- Department of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, USA
- Center for One Health Research, Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, USA
- Institute for Evolution, University of Haifa, Haifa, Israel
| | - Kevin K Lahmers
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Tanner G DeHart
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Saadman S Ahmad
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Brandon L Jutras
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Katy Poncin
- URBM, Narilis, University of Namur, Namur, Belgium
| | | | - Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, Center for One Health Research, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
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3
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Rivas-Solano O, Núñez-Montero K, Altamirano-Silva P, Ruiz-Villalobos N, Barquero-Calvo E, Moreno E, Chaves-Olarte E, Guzmán-Verri C. A bvrR/bvrS Non-Polar Brucella abortus Mutant Confirms the Role of the Two-Component System BvrR/BvrS in Virulence and Membrane Integrity. Microorganisms 2023; 11:2014. [PMID: 37630574 PMCID: PMC10459465 DOI: 10.3390/microorganisms11082014] [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: 06/28/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Brucella abortus is a bacterial pathogen causing bovine brucellosis worldwide. This facultative extracellular-intracellular pathogen can be transmitted to humans, leading to a zoonotic disease. The disease remains a public health concern, particularly in regions where livestock farming is present. The two-component regulatory system BvrR/BvrS was described by isolating the attenuated transposition mutants bvrR::Tn5 and bvrS::Tn5, whose characterization led to the understanding of the role of the system in bacterial survival. However, a phenotypic comparison with deletion mutants has not been performed because their construction has been unsuccessful in brucellae and difficult in phylogenetically related Rhizobiales with BvrR/BvrS orthologs. Here, we used an unmarked gene excision strategy to generate a B. abortus mutant strain lacking both genes, called B. abortus ∆bvrRS. The deletion was verified through PCR, Southern blot, Western blot, Sanger sequencing, and whole-genome sequencing, confirming a clean mutation without further alterations at the genome level. B. abortus ∆bvrRS shared attenuated phenotypic traits with both transposition mutants, confirming the role of BvrR/BvrS in pathogenesis and membrane integrity. This B. abortus ∆bvrRS with a non-antimicrobial marker is an excellent tool for continuing studies on the role of BvrR/BvrS in the B. abortus lifestyle.
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Affiliation(s)
- Olga Rivas-Solano
- Centro de Investigación en Biotecnología, Instituto Tecnológico de Costa Rica, Cartago 30109, Costa Rica
| | - Kattia Núñez-Montero
- Laboratorio Facultad Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Temuco 4813003, Chile;
| | - Pamela Altamirano-Silva
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San Pedro de Montes de Oca, San José 2060, Costa Rica; (P.A.-S.); (E.C.-O.)
| | - Nazareth Ruiz-Villalobos
- Programa de Investigación en Enfermedades Tropicales, Universidad Nacional, Heredia 40104, Costa Rica; (N.R.-V.); (E.B.-C.); (E.M.); (C.G.-V.)
| | - Elías Barquero-Calvo
- Programa de Investigación en Enfermedades Tropicales, Universidad Nacional, Heredia 40104, Costa Rica; (N.R.-V.); (E.B.-C.); (E.M.); (C.G.-V.)
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Universidad Nacional, Heredia 40104, Costa Rica; (N.R.-V.); (E.B.-C.); (E.M.); (C.G.-V.)
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San Pedro de Montes de Oca, San José 2060, Costa Rica; (P.A.-S.); (E.C.-O.)
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Universidad Nacional, Heredia 40104, Costa Rica; (N.R.-V.); (E.B.-C.); (E.M.); (C.G.-V.)
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4
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King KA, Caudill MT, Caswell CC. A comprehensive review of small regulatory RNAs in Brucella spp. Front Vet Sci 2022; 9:1026220. [PMID: 36532353 PMCID: PMC9751625 DOI: 10.3389/fvets.2022.1026220] [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: 08/23/2022] [Accepted: 11/15/2022] [Indexed: 09/29/2023] Open
Abstract
Brucella spp. are Gram-negative bacteria that naturally infect a variety of domesticated and wild animals, often resulting in abortions and sterility. Humans exposed to these animals or animal products can also develop debilitating, flu-like disease. The brucellae are intracellular pathogens that reside predominantly within immune cells, typically macrophages, where they replicate in a specialized compartment. This capacity of Brucella to survive and replicate within macrophages is essential to their ability to cause disease. In recent years, several groups have identified and characterized small regulatory RNAs (sRNAs) as critical factors in the control of Brucella physiology within macrophages and overall disease virulence. sRNAs are generally < 300 nucleotides in length, and these independent sRNA transcripts are encoded either next to (i.e., cis-encoded) or at a distant location to (i.e., trans-encoded) the genes that they regulate. Trans-encoded sRNAs interact with the mRNA transcripts through short stretches of imperfect base pairing that often require the RNA chaperone Hfq to facilitate sRNA-mRNA interaction. In many instances, these sRNA-mRNA interactions inhibit gene expression, usually by occluding the ribosome-binding site (RBS) and/or by decreasing the stability of the mRNA, leading to degradation of the transcript. A number of sRNAs have been predicted and authenticated in Brucella strains, and a variety of approaches, techniques, and means of validation have been employed in these efforts. Nonetheless, some important issues and considerations regarding the study of sRNA regulation in Brucella need to be addressed. For example, the lack of uniform sRNA nomenclature in Brucella has led to difficulty in comparisons of sRNAs across the different Brucella species, and there exist multiple names in the literature for what are functionally the same sRNA. Moreover, even though bona fide sRNAs have been discovered in Brucella, scant functional information is known about the regulatory activities of these sRNAs, or the extent to which these sRNAs are required for the intracellular life and/or host colonization by the brucellae. Therefore, this review summarizes the historical context of Hfq and sRNAs in Brucella; our current understanding of Brucella sRNAs; and some future perspectives and considerations for the field of sRNA biology in the brucellae.
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Affiliation(s)
| | | | - Clayton C. Caswell
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
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5
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Majumder R, Ghosh S, Das A, Singh MK, Samanta S, Saha A, Saha RP. Prokaryotic ncRNAs: Master regulators of gene expression. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100136. [PMID: 36568271 PMCID: PMC9780080 DOI: 10.1016/j.crphar.2022.100136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/11/2022] [Accepted: 10/14/2022] [Indexed: 12/14/2022] Open
Abstract
ncRNA plays a very pivotal role in various biological activities ranging from gene regulation to controlling important developmental networks. It is imperative to note that this small molecule is not only present in all three domains of cellular life, but is an important modulator of gene regulation too in all these domains. In this review, we discussed various aspects of ncRNA biology, especially their role in bacteria. The last two decades of scientific research have proved that this molecule plays an important role in the modulation of various regulatory pathways in bacteria including the adaptive immune system and gene regulation. It is also very surprising to note that this small molecule is also employed in various processes related to the pathogenicity of virulent microorganisms.
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Affiliation(s)
- Rajib Majumder
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Sanmitra Ghosh
- Department of Biological Sciences, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Arpita Das
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Manoj Kumar Singh
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Saikat Samanta
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Abinit Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India,Corresponding authors.
| | - Rudra P. Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India,Corresponding authors.
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6
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Oliveira KC, Brancaglion GA, Santos NCM, Araújo LP, Novaes E, Santos RDL, Oliveira SC, Corsetti PP, de Almeida LA. Epitope-Based Vaccine of a Brucella abortus Putative Small RNA Target Induces Protection and Less Tissue Damage in Mice. Front Immunol 2021; 12:778475. [PMID: 34992597 PMCID: PMC8724193 DOI: 10.3389/fimmu.2021.778475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/03/2021] [Indexed: 01/18/2023] Open
Abstract
Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis in humans and animals. Currently available live attenuated vaccines against brucellosis still have drawbacks. Therefore, subunit vaccines, produced using epitope-based antigens, have the advantage of being safe, cost-effective and efficacious. Here, we identified B. abortus small RNAs expressed during early infection with bone marrow-derived macrophages (BMDMs) and an apolipoprotein N-acyltransferase (Int) was identified as the putative target of the greatest expressed small RNA. Decreased expression of Int was observed during BMDM infection and the protein sequence was evaluated to rationally select a putative immunogenic epitope by immunoinformatic, which was explored as a vaccinal candidate. C57BL/6 mice were immunized and challenged with B. abortus, showing lower recovery in the number of viable bacteria in the liver, spleen, and axillary lymph node and greater production of IgG and fractions when compared to non-vaccinated mice. The vaccinated and infected mice showed the increased expression of TNF-α, IFN-γ, and IL-6 following expression of the anti-inflammatory genes IL-10 and TGF-β in the liver, justifying the reduction in the number and size of the observed granulomas. BMDMs stimulated with splenocyte supernatants from vaccinated and infected mice increase the CD86+ marker, as well as expressing greater amounts of iNOS and the consequent increase in NO production, suggesting an increase in the phagocytic and microbicidal capacity of these cells to eliminate the bacteria.
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Affiliation(s)
- Karen Cristina Oliveira
- Laboratory of Molecular Biology of Microorganisms, Federal University of Alfenas, Alfenas, Brazil
| | | | - Natália C. M. Santos
- Laboratory of Molecular Biology of Microorganisms, Federal University of Alfenas, Alfenas, Brazil
| | - Leonardo P. Araújo
- Laboratory of Molecular Biology of Microorganisms, Federal University of Alfenas, Alfenas, Brazil
| | - Evandro Novaes
- Department of Biology, Federal University of Lavras, Lavras, Brazil
| | - Renato de Lima Santos
- Department of Clinic and Veterinary Surgery, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sergio Costa Oliveira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Patrícia Paiva Corsetti
- Laboratory of Molecular Biology of Microorganisms, Federal University of Alfenas, Alfenas, Brazil
- *Correspondence: Leonardo Augusto de Almeida, ; Patrícia Paiva Corsetti,
| | - Leonardo Augusto de Almeida
- Laboratory of Molecular Biology of Microorganisms, Federal University of Alfenas, Alfenas, Brazil
- *Correspondence: Leonardo Augusto de Almeida, ; Patrícia Paiva Corsetti,
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Eisfeld J, Kraus A, Ronge C, Jagst M, Brandenburg VB, Narberhaus F. A LysR-type transcriptional regulator controls the expression of numerous small RNAs in Agrobacterium tumefaciens. Mol Microbiol 2021; 116:126-139. [PMID: 33560537 DOI: 10.1111/mmi.14695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 01/08/2023]
Abstract
Small RNAs (sRNAs) are universal posttranscriptional regulators of gene expression and hundreds of sRNAs are frequently found in each and every bacterium. In order to coordinate cellular processes in response to ambient conditions, many sRNAs are differentially expressed. Here, we asked how these small regulators are regulated using Agrobacterium tumefaciens as a model system. Among the best-studied sRNAs in this plant pathogen are AbcR1 regulating numerous ABC transporters and PmaR, a regulator of peptidoglycan biosynthesis, motility, and ampicillin resistance. We report that the LysR-type regulator VtlR (also known as LsrB) controls expression of AbcR1 and PmaR. A vtlR/lsrB deletion strain showed growth defects, was sensitive to antibiotics and severely compromised in plant tumor formation. Transcriptome profiling by RNA-sequencing revealed more than 1,200 genes with altered expression in the mutant. Consistent with the function of VtlR/LsrB as regulator of AbcR1, many ABC transporter genes were affected. Interestingly, the transcription factor did not only control the expression of AbcR1 and PmaR. In the mutant, 102 sRNA genes were significantly up- or downregulated. Thus, our study uncovered VtlR/LsrB as the master regulator of numerous sRNAs. Thereby, the transcriptional regulator harnesses the regulatory power of sRNAs to orchestrate the expression of distinct sub-regulons.
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Affiliation(s)
- Jessica Eisfeld
- Microbial Biology, Ruhr University Bochum, Bochum, Germany.,Medical Microbiology, Ruhr University Bochum, Bochum, Germany
| | | | | | - Michelle Jagst
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
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Pervasive RNA Regulation of Metabolism Enhances the Root Colonization Ability of Nitrogen-Fixing Symbiotic α-Rhizobia. mBio 2021; 13:e0357621. [PMID: 35164560 PMCID: PMC8844928 DOI: 10.1128/mbio.03576-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The rhizosphere and rhizoplane are nutrient-rich but selective environments for the root microbiome. Here, we deciphered a posttranscriptional network regulated by the homologous trans-small RNAs (sRNAs) AbcR1 and AbcR2, which rewire the metabolism of the nitrogen-fixing α-rhizobium Sinorhizobium meliloti during preinfection stages of symbiosis with its legume host alfalfa. The LysR-type regulator LsrB, which transduces the cell redox state, is indispensable for AbcR1 expression in actively dividing bacteria, whereas the stress-induced transcription of AbcR2 depends on the alternative σ factor RpoH1. MS2 affinity purification coupled with RNA sequencing unveiled exceptionally large and overlapping AbcR1/2 mRNA interactomes, jointly representing ⁓6% of the S. meliloti protein-coding genes. Most mRNAs encode transport/metabolic proteins whose translation is silenced by base pairing to two distinct anti-Shine Dalgarno motifs that function independently in both sRNAs. A metabolic model-aided analysis of the targetomes predicted changes in AbcR1/2 expression driven by shifts in carbon/nitrogen sources, which were confirmed experimentally. Low AbcR1/2 levels in some defined media anticipated overexpression growth phenotypes linked to the silencing of specific mRNAs. As a proof of principle, we confirmed AbcR1/2-mediated downregulation of the l-amino acid AapQ permease. AbcR1/2 interactomes are well represented in rhizosphere-related S. meliloti transcriptomic signatures. Remarkably, a lack of AbcR1 specifically compromised the ability of S. meliloti to colonize the root rhizoplane. The AbcR1 regulon likely ranks the utilization of available substrates to optimize metabolism, thus conferring on S. meliloti an advantage for efficient rhizosphere/rhizoplane colonization. AbcR1 regulation is predicted to be conserved in related α-rhizobia, which opens unprecedented possibilities for engineering highly competitive biofertilizers. IMPORTANCE Nitrogen-fixing root nodule symbioses between rhizobia and legume plants provide more than half of the combined nitrogen incorporated annually into terrestrial ecosystems, rendering plant growth independent of environmentally unfriendly chemical fertilizers. The success of symbiosis depends primarily on the capacity of rhizobia to establish competitive populations in soil and rhizosphere environments. Here, we provide insights into the regulation and architecture of an extensive RNA posttranscriptional network that fine-tunes the metabolism of the alfalfa symbiont S. meliloti, thereby enhancing the ability of this beneficial bacterium to colonize nutrient-rich but extremely selective niches, such as the rhizosphere of its host plant. This pervasive RNA regulation of metabolism is a major adaptive mechanism, predicted to operate in diverse rhizobial species. Because RNA regulation relies on modifiable base-pairing interactions, our findings open unexplored avenues for engineering the legumes rhizobiome within sustainable agricultural practices.
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9
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Roop RM, Barton IS, Hopersberger D, Martin DW. Uncovering the Hidden Credentials of Brucella Virulence. Microbiol Mol Biol Rev 2021; 85:e00021-19. [PMID: 33568459 PMCID: PMC8549849 DOI: 10.1128/mmbr.00021-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Bacteria in the genus Brucella are important human and veterinary pathogens. The abortion and infertility they cause in food animals produce economic hardships in areas where the disease has not been controlled, and human brucellosis is one of the world's most common zoonoses. Brucella strains have also been isolated from wildlife, but we know much less about the pathobiology and epidemiology of these infections than we do about brucellosis in domestic animals. The brucellae maintain predominantly an intracellular lifestyle in their mammalian hosts, and their ability to subvert the host immune response and survive and replicate in macrophages and placental trophoblasts underlies their success as pathogens. We are just beginning to understand how these bacteria evolved from a progenitor alphaproteobacterium with an environmental niche and diverged to become highly host-adapted and host-specific pathogens. Two important virulence determinants played critical roles in this evolution: (i) a type IV secretion system that secretes effector molecules into the host cell cytoplasm that direct the intracellular trafficking of the brucellae and modulate host immune responses and (ii) a lipopolysaccharide moiety which poorly stimulates host inflammatory responses. This review highlights what we presently know about how these and other virulence determinants contribute to Brucella pathogenesis. Gaining a better understanding of how the brucellae produce disease will provide us with information that can be used to design better strategies for preventing brucellosis in animals and for preventing and treating this disease in humans.
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Affiliation(s)
- R Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ian S Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Dariel Hopersberger
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Daniel W Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
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10
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The Endoribonuclease RNase E Coordinates Expression of mRNAs and Small Regulatory RNAs and Is Critical for the Virulence of Brucella abortus. J Bacteriol 2020; 202:JB.00240-20. [PMID: 32747427 DOI: 10.1128/jb.00240-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
RNases are key regulatory components in prokaryotes, responsible for the degradation and maturation of specific RNA molecules at precise times. Specifically, RNases allow cells to cope with changes in their environment through rapid alteration of gene expression. To date, few RNases have been characterized in the mammalian pathogen Brucella abortus In the present work, we sought to investigate several RNases in B. abortus and determine what role, if any, they have in pathogenesis. Of the 4 RNases reported in this study, the highly conserved endoribonuclease, RNase E, was found to play an integral role in the virulence of B. abortus Although rne, which encodes RNase E, is essential in B. abortus, we were able to generate a strain encoding a defective version of RNase E lacking the C-terminal portion of the protein, and this strain (rne-tnc) was attenuated in a mouse model of Brucella infection. RNA-sequencing analysis revealed massive RNA dysregulation in B. abortus rne-tnc, with 122 upregulated and 161 downregulated transcripts compared to the parental strain. Interestingly, several mRNAs related to metal homeostasis were significantly decreased in the rne-tnc strain. We also identified a small regulatory RNA (sRNA), called Bsr4, that exhibited significantly elevated levels in rne-tnc, demonstrating an important role for RNase E in sRNA-mediated regulatory pathways in Brucella Overall, these data highlight the importance of RNase E in B. abortus, including the role of RNase E in properly controlling mRNA levels and contributing to virulence in an animal model of infection.IMPORTANCE Brucellosis is a debilitating disease of humans and animals globally, and there is currently no vaccine to combat human infection by Brucella spp. Moreover, effective antibiotic treatment in humans is extremely difficult and can lead to disease relapse. Therefore, it is imperative that systems and pathways be identified and characterized in the brucellae so new vaccines and therapies can be generated. In this study, we describe the impact of the endoribonuclease RNase E on the control of mRNA and small regulatory RNA (sRNA) levels in B. abortus, as well as the importance of RNase E for the full virulence of B. abortus This work greatly enhances our understanding of ribonucleases in the biology and pathogenesis of Brucella spp.
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Budnick JA, Sheehan LM, Ginder MJ, Failor KC, Perkowski JM, Pinto JF, Kohl KA, Kang L, Michalak P, Luo L, Heindl JE, Caswell CC. A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens. Sci Rep 2020; 10:14968. [PMID: 32917931 PMCID: PMC7486931 DOI: 10.1038/s41598-020-72117-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/17/2020] [Indexed: 12/28/2022] Open
Abstract
LysR-type transcriptional regulators (LTTRs) are the most common type of transcriptional regulators in prokaryotes and function by altering gene expression in response to environmental stimuli. In the class Alphaproteobacteria, a conserved LTTR named VtlR is critical to the establishment of host-microbe interactions. In the mammalian pathogen Brucella abortus, VtlR is required for full virulence in a mouse model of infection, and VtlR activates the expression of abcR2, which encodes a small regulatory RNA (sRNA). In the plant symbiont Sinorhizobium meliloti, the ortholog of VtlR, named LsrB, is involved in the symbiosis of the bacterium with alfalfa. Agrobacterium tumefaciens is a close relative of both B. abortus and S. meliloti, and this bacterium is the causative agent of crown gall disease in plants. In the present study, we demonstrate that VtlR is involved in the ability of A. tumefaciens to grow appropriately in artificial medium, and an A. tumefaciens vtlR deletion strain is defective in motility, biofilm formation, and tumorigenesis of potato discs. RNA-sequencing analyses revealed that more than 250 genes are dysregulated in the ∆vtlR strain, and importantly, VtlR directly controls the expression of three sRNAs in A. tumefaciens. Taken together, these data support a model in which VtlR indirectly regulates hundreds of genes via manipulation of sRNA pathways in A. tumefaciens, and moreover, while the VtlR/LsrB protein is present and structurally conserved in many members of the Alphaproteobacteria, the VtlR/LsrB regulatory circuitry has diverged in order to accommodate the unique environmental niche of each organism.
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Affiliation(s)
- James A Budnick
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Lauren M Sheehan
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Miranda J Ginder
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, 19104, USA
| | - Kevin C Failor
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, 19104, USA
| | - Julia M Perkowski
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, 19104, USA
| | - John F Pinto
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, 19104, USA
| | - Kirsten A Kohl
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Lin Kang
- Edward via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA
| | - Pawel Michalak
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, 24060, USA
- Edward via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA
- Institute of Evolution, Haifa University, 3498838, Haifa, Israel
| | - Li Luo
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Plant Science Center, Shanghai University, Shanghai, 200444, China
| | - Jason E Heindl
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, 19104, USA.
| | - Clayton C Caswell
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, 24060, USA.
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Budnick JA, Sheehan LM, Benton AH, Pitzer JE, Kang L, Michalak P, Roop RM, Caswell CC. Characterizing the transport and utilization of the neurotransmitter GABA in the bacterial pathogen Brucella abortus. PLoS One 2020; 15:e0237371. [PMID: 32845904 PMCID: PMC7449393 DOI: 10.1371/journal.pone.0237371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/04/2020] [Indexed: 01/18/2023] Open
Abstract
The neurotransmitter gamma-aminobutyric acid (GABA) is the most abundant inhibitory neurotransmitter in the human brain; however, it is becoming more evident that this non-proteinogenic amino acid plays multiple physiological roles in biology. In the present study, the transport and function of GABA is studied in the highly infectious intracellular bacterium Brucella abortus. The data show that 3H-GABA is imported by B. abortus under nutrient limiting conditions and that the small RNAs AbcR1 and AbcR2 negatively regulate this transport. A specific transport system, gts, is responsible for the transport of GABA as determined by measuring 3H-GABA transport in isogenic deletion strains of known AbcR1/2 regulatory targets; however, this locus is unnecessary for Brucella infection in BALB/c mice. Similar assays revealed that 3H-GABA transport is uninhibited by the 20 standard proteinogenic amino acids, representing preference for the transport of 3H-GABA. Metabolic studies did not show any potential metabolic utilization of GABA by B. abortus as a carbon or nitrogen source, and RNA sequencing analysis revealed limited transcriptional differences between B. abortus 2308 with or without exposure to GABA. While this study provides evidence for GABA transport by B. abortus, questions remain as to why and when this transport is utilized during Brucella pathogenesis.
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Affiliation(s)
- James A. Budnick
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, United States of America
- Center for One Health Research, Blacksburg, Virginia, United States of America
| | - Lauren M. Sheehan
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, United States of America
- Center for One Health Research, Blacksburg, Virginia, United States of America
| | - Angela H. Benton
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, United States of America
- Center for One Health Research, Blacksburg, Virginia, United States of America
| | - Joshua E. Pitzer
- Department of Microbiology and Immunology, East Carolina University Brody School of Medicine, Greenville, North Carolina, United States of America
| | - Lin Kang
- Center for One Health Research, Blacksburg, Virginia, United States of America
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
| | - Pawel Michalak
- Center for One Health Research, Blacksburg, Virginia, United States of America
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia, United States of America
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - R. Martin Roop
- Department of Microbiology and Immunology, East Carolina University Brody School of Medicine, Greenville, North Carolina, United States of America
| | - Clayton C. Caswell
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, United States of America
- Center for One Health Research, Blacksburg, Virginia, United States of America
- * E-mail:
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Assessment of Survival and Replication of Brucella spp. in Murine Peritoneal Macrophages. Methods Mol Biol 2019. [PMID: 30798532 DOI: 10.1007/978-1-4939-9167-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Brucella spp. are bacteria that naturally infect a variety of domesticated and wild animals leading to abortions and infertility, and these bacteria are also capable of causing debilitating human infections, which often result from human exposure to infected animals and animal products. The brucellae are intracellular pathogens that reside in host cells, including macrophages and dendritic cells, and it is paramount for the pathogenesis of Brucella that the bacteria are able to survive and replicate in these host cells. The methods outlined in this chapter can be employed to study the interactions between Brucella strains and primary murine peritoneal macrophages.
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Abstract
Bacterial regulatory RNAs are key players in adaptation to changing environmental conditions and response to diverse cellular stresses. However, while regulatory RNAs of bacterial pathogens have been intensely studied under defined conditions in vitro, characterization of their role during the infection of eukaryotic host organisms is lagging behind. This review summarizes our current understanding of the contribution of the different classes of regulatory RNAs and RNA-binding proteins to bacterial virulence and illustrates their role in infection by reviewing the mechanisms of some prominent representatives of each class. Emerging technologies are described that bear great potential for global, unbiased studies of virulence-related RNAs in bacterial model and nonmodel pathogens in the future. The review concludes by deducing common principles of RNA-mediated gene expression control of virulence programs in different pathogens, and by defining important open questions for upcoming research in the field.
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Dong H, Peng X, Liu Y, Wu T, Wang X, De Y, Han T, Yuan L, Ding J, Wang C, Wu Q. BASI74, a Virulence-Related sRNA in Brucella abortus. Front Microbiol 2018; 9:2173. [PMID: 30271397 PMCID: PMC6146029 DOI: 10.3389/fmicb.2018.02173] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/24/2018] [Indexed: 11/13/2022] Open
Abstract
Brucella spp. are intracellular pathogens that infect a wide variety of mammals including humans, posing threats to the livestock industry and human health in developing countries. A number of genes associated with the intracellular trafficking and multiplication have so far been identified in Brucella spp. However, the sophisticated post-transcriptional regulation and coordination of gene expression that enable Brucella spp. to adapt to changes in environment and to evade host cell defenses are not fully understood. Bacteria small RNAs (sRNAs) play a significant role in post-transcriptional regulation, which has already been confirmed in a number of bacteria but the role of sRNAs in Brucella remains elusive. In this study, we identified several different sRNAs in Brucella spp., and found that over-expression of a sRNA, tentatively termed BASI74, led to alternation in virulence of Brucella in macrophage infection model. The expression level of BASI74 increased while Brucella abortus 2308 was grown in acidic media. In addition, BASI74 affected the growth ratio of the Brucella cells in minimal media and iron limiting medium. Using a two-plasmid reporter system, we identified four genes as the target of BASI74. One target gene, BABI1154, was predicted to encode a cytosine-N4-specific DNA methyltransferase, which protects cellular DNA from the restriction endonuclease in Brucella. These results show that BASI74 plays an important role in Brucella survival in macrophage infection model, speculatively by its connection with stress response or impact on restriction-modification system. Our study promotes the understanding of Brucella sRNAs, as well as the mechanism by which sRNAs use to influence Brucella physiology and pathogenesis.
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Affiliation(s)
- Hao Dong
- China Animal Disease Control Center, Beijing, China
| | - Xiaowei Peng
- Department of Inspection Technology Research, China Institute of Veterinary Drug Control, Beijing, China
| | - Yufu Liu
- Department of Inspection Technology Research, China Institute of Veterinary Drug Control, Beijing, China.,College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Tonglei Wu
- Key Laboratory of Preventive Veterinary Medicine of Hebei Province, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xiaolei Wang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanyan De
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Tao Han
- China Animal Disease Control Center, Beijing, China
| | - Lin Yuan
- China Animal Disease Control Center, Beijing, China
| | - Jiabo Ding
- Department of Inspection Technology Research, China Institute of Veterinary Drug Control, Beijing, China
| | | | - Qingmin Wu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Characterization of Three Small Proteins in Brucella abortus Linked to Fucose Utilization. J Bacteriol 2018; 200:JB.00127-18. [PMID: 29967118 DOI: 10.1128/jb.00127-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/22/2018] [Indexed: 11/20/2022] Open
Abstract
Elucidating the function of proteins <50 amino acids in length is no small task. Nevertheless, small proteins can play vital roles in the lifestyle of bacteria and influence the virulence of pathogens; thus, the investigation of the small proteome is warranted. Recently, our group identified the Brucella abortus protein VtlR as a transcriptional activator of four genes, one of which is the well-studied small regulatory RNA AbcR2, while the other three genes encode hypothetical small proteins, two of which are highly conserved among the order Rhizobiales This study provides evidence that all three genes encode authentic small proteins and that all three are highly expressed under oxidative stress, low-pH, and stationary-phase growth conditions. Fractionation of the cells revealed that the proteins are localized to the membranes of B. abortus We demonstrate that the small proteins under the transcriptional control of VtlR are not accountable for attenuation observed with the B. abortusvtlR deletion strain. However, there is an association between VtlR-regulated genes and growth inhibition in the presence of the sugar l-fucose. Subsequent transcriptomic analyses revealed that B. abortus initiates the transcription of a locus encoding a putative sugar transport and utilization system when the bacteria are cultured in the presence of l-fucose. Altogether, our observations characterize the role of the VtlR-controlled small proteins BAB1_0914, BAB2_0512, and BAB2_0574 in the biology of B. abortus, particularly in the capacity of the bacteria to utilize l-fucose.IMPORTANCE Despite being one of the most common zoonoses worldwide, there is currently no human vaccine to combat brucellosis. Therefore, a better understanding of the pathogenesis and biology of Brucella spp., the causative agent of brucellosis, is essential for the discovery of novel therapeutics against these highly infectious bacteria. In this study, we further characterize the virulence-associated transcriptional regulator VtlR in Brucella abortus Our findings not only shed light on our current understanding of a virulence related genetic system in Brucella spp. but also increase our knowledge of small proteins in the field of bacteriology.
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Xu D, Song J, Li G, Cai W, Zong S, Li Z, Liu W, Hu S, Bu Z. A novel small RNA Bmsr1 enhances virulence in Brucella melitensis M28. Vet Microbiol 2018; 223:1-8. [PMID: 30173733 DOI: 10.1016/j.vetmic.2018.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/12/2018] [Accepted: 07/11/2018] [Indexed: 01/22/2023]
Abstract
Brucellosis, caused by Brucella spp., is one of the most serious zoonotic bacterial diseases. Small RNAs (sRNAs) are recognized as a key player in bacterial post-transcription regulation, since they participate in many biological processes with high efficiency and may govern the intracellular biochemistry and virulence of some pathogenic bacteria. Here, a novel small regulatory RNA, Bmsr1 (Brucella melitensis M28 small RNA 1), was identified in a virulent Brucella melitensis M28 strain based on bioinformatic analysis, reverse transcription PCR (RT-PCR), and Northern blot. The Bmsr1 expression level was highly induced after infection of macrophage cells RAW264.7 at 48 h, suggesting a role for Bmsr1 during in vitro infection. Indeed, bmsr1 deletion mutant of M28 attenuated its intracellular survival in RAW264.7 at 24 h and 48 h post-infection. In a mouse model of chronic infection, bmsr1 deletion strain displayed decreased colonization in the spleen while Bmsr1-overexpressed strain showed higher colonization levels than wild type pathogen. Isobaric tags for relative and absolute quantification (iTRAQ) revealed that 314 proteins were differentially expressed in M28Δbmsr1 compared with wild type. Functional annotation analysis demonstrated that most of those proteins are involved in biological processes and those proteins in the ribosome and nitrogen metabolism pathways were enriched. iTRAQ results combined with target prediction identified several potential target genes related to virulence, including virB2, virB9, virB10, virB11, and vjbR and many metabolism genes. Taken together, this study revealed the contribution of a novel sRNA Bmsr1 to virulence of B. melitensis M28, probably by influencing genes involved in T4SS, virulence regulator VjbR and other metabolism genes.
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Affiliation(s)
- Da Xu
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Jiabao Song
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Ganwu Li
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Wentong Cai
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Shucheng Zong
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Zhaoli Li
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Wenxing Liu
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Sen Hu
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, 225009, China.
| | - Zhigao Bu
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, 225009, China.
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Endoribonuclease YbeY Is Linked to Proper Cellular Morphology and Virulence in Brucella abortus. J Bacteriol 2018; 200:JB.00105-18. [PMID: 29632093 DOI: 10.1128/jb.00105-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/03/2018] [Indexed: 12/14/2022] Open
Abstract
The YbeY endoribonuclease is one of the best-conserved proteins across the kingdoms of life. In the present study, we demonstrated that YbeY in Brucella abortus is linked to a variety of important activities, including proper cellular morphology, mRNA transcript levels, and virulence. Deletion of ybeY in B. abortus led to a small-colony phenotype when the bacteria were grown on agar medium, as well as to significant aberrations in the morphology of the bacterial cell as evidenced by electron microscopy. Additionally, compared to the parental strain, the ΔybeY strain was significantly attenuated in both macrophage and mouse models of infection. The ΔybeY strain also showed increased sensitivities to several in vitro-applied stressors, including bile acid, hydrogen peroxide, SDS, and paraquat. Transcriptomic analysis revealed that a multitude of mRNA transcripts are dysregulated in the ΔybeY strain, and many of the identified mRNAs encode proteins involved in metabolism, nutrient transport, transcriptional regulation, and flagellum synthesis. We subsequently constructed gene deletion strains of the most highly dysregulated systems, and several of the YbeY-linked gene deletion strains exhibited defects in the ability of the bacteria to survive and replicate in primary murine macrophages. Taken together, these data establish a clear role for YbeY in the biology and virulence of Brucella; moreover, this work further illuminates the highly varied roles of this widely conserved endoribonuclease in bacteria.IMPORTANCEBrucella spp. are highly efficient bacterial pathogens of animals and humans, causing significant morbidity and economic loss worldwide, and relapse of disease often occurs following antibiotic treatment of human brucellosis. As such, novel therapeutic strategies to combat Brucella infections are needed. Ribonucleases in the brucellae are understudied, and these enzymes represent elements that may be potential targets for future treatment approaches. The present work demonstrates the importance of the YbeY endoribonuclease for cellular morphology, efficient control of mRNA levels, and virulence in B. abortus Overall, the results of this study advance our understanding of the critical roles of YbeY in the pathogenesis of the intracellular brucellae and expand our understanding of this highly conserved RNase.
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Ahmed W, Razzaq M. RETRACTED: A small non-coding RNA AbcR2 regulate gntR transcription factor that modulate the intracellular survival of Brucella melitensis. Microb Pathog 2018; 118:118-125. [PMID: 29555506 DOI: 10.1016/j.micpath.2018.03.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Waqas Ahmed
- College of Life Sciences, Guangzhou University, Guangzhou, P. R. China.
| | - Maria Razzaq
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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Small Noncoding RNA AbcR1 Addressing Multiple Target mRNAs From Transcriptional Factor and Two-Component Response Regulator of Brucella melitensis. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.60269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Sheehan LM, Caswell CC. An account of evolutionary specialization: the AbcR small RNAs in the Rhizobiales. Mol Microbiol 2017; 107:24-33. [PMID: 29076560 DOI: 10.1111/mmi.13869] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2017] [Indexed: 01/26/2023]
Abstract
The AbcR small RNAs (sRNAs) are a fascinating example of two highly conserved sRNAs that differ tremendously at the functional level among organisms. From their transcriptional activation to their regulatory capabilities, the AbcR sRNAs exhibit varying characteristics in three well-studied bacteria belonging to the Rhizobiales order: the plant symbiont Sinorhizobium meliloti, the plant pathogen Agrobacterium tumefaciens, and the animal pathogen Brucella abortus. This review outlines the similarities and differences of the AbcR sRNAs between each of these organisms, and discusses reasons as to why this group of sRNAs has diverged in their genetic organization and regulatory functions across species. In the end, this review will shed light on how regulatory systems, although seemingly conserved among bacteria, can vary based on the environmental niche and lifestyle of an organism.
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Affiliation(s)
- Lauren M Sheehan
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
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Saramago M, Peregrina A, Robledo M, Matos RG, Hilker R, Serrania J, Becker A, Arraiano CM, Jiménez-Zurdo JI. Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation. Nucleic Acids Res 2017; 45:1371-1391. [PMID: 28180335 PMCID: PMC5388416 DOI: 10.1093/nar/gkw1234] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 01/23/2023] Open
Abstract
Structural and biochemical features suggest that the almost ubiquitous bacterial YbeY protein may serve catalytic and/or Hfq-like protective functions central to small RNA (sRNA)-mediated regulation and RNA metabolism. We have biochemically and genetically characterized the YbeY ortholog of the legume symbiont Sinorhizobium meliloti (SmYbeY). Co-immunoprecipitation (CoIP) with a FLAG-tagged SmYbeY yielded a poor enrichment in RNA species, compared to Hfq CoIP-RNA uncovered previously by a similar experimental setup. Purified SmYbeY behaved as a monomer that indistinctly cleaved single- and double-stranded RNA substrates, a unique ability among bacterial endoribonucleases. SmYbeY-mediated catalysis was supported by the divalent metal ions Mg2+, Mn2+ and Ca2+, which influenced in a different manner cleavage efficiency and reactivity patterns, with Ca2+ specifically blocking activity on double-stranded and some structured RNA molecules. SmYbeY loss-of-function compromised expression of core energy and RNA metabolism genes, whilst promoting accumulation of motility, late symbiotic and transport mRNAs. Some of the latter transcripts are known Hfq-binding sRNA targets and might be SmYbeY substrates. Genetic reporter and in vitro assays confirmed that SmYbeY is required for sRNA-mediated down-regulation of the amino acid ABC transporter prbA mRNA. We have thus discovered a bacterial endoribonuclease with unprecedented catalytic features, acting also as gene silencing enzyme.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
- These authors contributed equally to the work as the first authors
| | - Alexandra Peregrina
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- These authors contributed equally to the work as the first authors
| | - Marta Robledo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- These authors contributed equally to the work as the first authors
| | - Rute G. Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Rolf Hilker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Javier Serrania
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Cecilia M. Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - José I. Jiménez-Zurdo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- To whom correspondence should be addressed. Tel: +34 958181600; Fax: +34 958181609;
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Jiménez-Zurdo JI, Robledo M. RNA silencing in plant symbiotic bacteria: Insights from a protein-centric view. RNA Biol 2017; 14:1672-1677. [PMID: 28805544 DOI: 10.1080/15476286.2017.1356565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Extensive work in model enterobacteria has evidenced that the RNA chaperone Hfq and several endoribonucleases, such as RNase E or RNase III, serve pivotal roles in small RNA-mediated post-transcriptional silencing of gene expression. Characterization of these protein hubs commonly provide global functional and mechanistic insights into complex sRNA regulatory networks. The legume endosymbiont Sinorhizobium meliloti is a non-classical model bacterium with a very complex lifestyle in which riboregulation is expected to play important adaptive functions. Here, we discuss current knowledge about RNA silencing in S. meliloti from the perspective of the activity of Hfq and a recently discovered endoribonuclease (YbeY) exhibiting unprecedented catalytic versatility for the cleavage of single- and double-stranded RNA molecules.
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Affiliation(s)
- José I Jiménez-Zurdo
- a Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín , Consejo Superior de Investigaciones Científicas (CSIC) , Granada , Spain
| | - Marta Robledo
- a Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín , Consejo Superior de Investigaciones Científicas (CSIC) , Granada , Spain
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24
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Fuli X, Wenlong Z, Xiao W, Jing Z, Baohai H, Zhengzheng Z, Bin-Guang M, Youguo L. A Genome-Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis in Mesorhizobium huakuii 7653R. Front Microbiol 2017; 8:1730. [PMID: 28943874 PMCID: PMC5596092 DOI: 10.3389/fmicb.2017.01730] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/24/2017] [Indexed: 01/23/2023] Open
Abstract
In bacteria, small non-coding RNAs (sRNAs) are critical regulators of cellular adaptation to changes in metabolism, physiology, or the external environment. In the last decade, more than 2000 of sRNA families have been reported in the Rfam database and have been shown to exert various regulatory functions in bacterial transcription and translation. However, little is known about sRNAs and their functions in Mesorhizobium. Here, we predicted putative sRNAs in the intergenic regions (IGRs) of M. huakuii 7653R by genome-wide comparisons with four related Mesorhizobial strains. The expression and transcribed regions of candidate sRNAs were analyzed using a set of high-throughput RNA deep sequencing data. In all, 39 candidate sRNAs were found, with 5 located in the symbiotic megaplasmids and 34 in the chromosome of M. huakuii 7653R. Of these, 24 were annotated as functional sRNAs in the Rfam database and 15 were recognized as putative novel sRNAs. The expression of nine selected sRNAs was confirmed by Northern blotting, and most of the nine selected sRNAs were highly expressed in 28 dpi nodules and under symbiosis-mimicking conditions. For those putative novel sRNAs, functional categorizations of their target genes were performed by analyzing the enriched GO terms. In addition, MH_s15 was shown to be an abundant and conserved sRNA.
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Affiliation(s)
- Xie Fuli
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Zhao Wenlong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Wang Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Zhang Jing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Hao Baohai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Zou Zhengzheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Ma Bin-Guang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
| | - Li Youguo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural UniversityWuhan, China
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25
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Abstract
Bacterial pathogens must endure or adapt to different environments and stresses during transmission and infection. Posttranscriptional gene expression control by regulatory RNAs, such as small RNAs and riboswitches, is now considered central to adaptation in many bacteria, including pathogens. The study of RNA-based regulation (riboregulation) in pathogenic species has provided novel insight into how these bacteria regulate virulence gene expression. It has also uncovered diverse mechanisms by which bacterial small RNAs, in general, globally control gene expression. Riboregulators as well as their targets may also prove to be alternative targets or provide new strategies for antimicrobials. In this article, we present an overview of the general mechanisms that bacteria use to regulate with RNA, focusing on examples from pathogens. In addition, we also briefly review how deep sequencing approaches have aided in opening new perspectives in small RNA identification and the study of their functions. Finally, we discuss examples of riboregulators in two model pathogens that control virulence factor expression or survival-associated phenotypes, such as stress tolerance, biofilm formation, or cell-cell communication, to illustrate how riboregulation factors into regulatory networks in bacterial pathogens.
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26
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Barbier T, Zúñiga-Ripa A, Moussa S, Plovier H, Sternon JF, Lázaro-Antón L, Conde-Álvarez R, De Bolle X, Iriarte M, Moriyón I, Letesson JJ. Brucella central carbon metabolism: an update. Crit Rev Microbiol 2017; 44:182-211. [PMID: 28604247 DOI: 10.1080/1040841x.2017.1332002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The brucellae are facultative intracellular pathogens causing brucellosis, an important zoonosis. Here, we review the nutritional, genetic, proteomic and transcriptomic studies on Brucella carbon uptake and central metabolism, information that is needed for a better understanding of Brucella virulence. There is no uniform picture across species but the studies suggest primary and/or secondary transporters for unknown carbohydrates, lactate, glycerol phosphate, erythritol, xylose, ribose, glucose and glucose/galactose, and routes for their incorporation to central metabolism, including an erythritol pathway feeding the pentose phosphate cycle. Significantly, all brucellae lack phosphoenolpyruvate synthase and phosphofructokinase genes, which confirms previous evidence on glycolysis absence, but carry all Entner-Doudoroff (ED) pathway and Krebs cycle (and glyoxylate pathway) genes. However, glucose catabolism proceeds through the pentose phosphate cycle in the classical species, and the ED pathway operates in some rodent-associated brucellae, suggesting an ancestral character for this pathway in this group. Gluconeogenesis is functional but does not rely exclusively on classical fructose bisphosphatases. Evidence obtained using infection models is fragmentary but suggests the combined or sequential use of hexoses/pentoses, amino acids and gluconeogenic substrates. We also discuss the role of the phosphotransferase system, stringent reponse, quorum sensing, BvrR/S and sRNAs in metabolism control, an essential aspect of the life style of facultative intracellular parasites.
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Affiliation(s)
- T Barbier
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - A Zúñiga-Ripa
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - S Moussa
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - H Plovier
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - J F Sternon
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - L Lázaro-Antón
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - R Conde-Álvarez
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - X De Bolle
- a Unité de Recherche en Biologie des Microorganismes , Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur , Namur , Belgium
| | - M Iriarte
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - I Moriyón
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
| | - J J Letesson
- b Instituto de Salud Tropical (ISTUN), Instituto de Investigación Sanitaria de Navarra (IdISNA) and Depto. Microbiología y Parasitología , Universidad de Navarra, Edificio de Investigación , Pamplona , Spain
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27
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A 6-Nucleotide Regulatory Motif within the AbcR Small RNAs of Brucella abortus Mediates Host-Pathogen Interactions. mBio 2017; 8:mBio.00473-17. [PMID: 28588127 PMCID: PMC5461406 DOI: 10.1128/mbio.00473-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Brucella abortus, two small RNAs (sRNAs), AbcR1 and AbcR2, are responsible for regulating transcripts encoding ABC-type transport systems. AbcR1 and AbcR2 are required for Brucella virulence, as a double chromosomal deletion of both sRNAs results in attenuation in mice. Although these sRNAs are responsible for targeting transcripts for degradation, the mechanism utilized by the AbcR sRNAs to regulate mRNA in Brucella has not been described. Here, two motifs (M1 and M2) were identified in AbcR1 and AbcR2, and complementary motif sequences were defined in AbcR-regulated transcripts. Site-directed mutagenesis of M1 or M2 or of both M1 and M2 in the sRNAs revealed transcripts to be targeted by one or both motifs. Electrophoretic mobility shift assays revealed direct, concentration-dependent binding of both AbcR sRNAs to a target mRNA sequence. These experiments genetically and biochemically characterized two indispensable motifs within the AbcR sRNAs that bind to and regulate transcripts. Additionally, cellular and animal models of infection demonstrated that only M2 in the AbcR sRNAs is required for Brucella virulence. Furthermore, one of the M2-regulated targets, BAB2_0612, was found to be critical for the virulence of B. abortus in a mouse model of infection. Although these sRNAs are highly conserved among Alphaproteobacteria, the present report displays how gene regulation mediated by the AbcR sRNAs has diverged to meet the intricate regulatory requirements of each particular organism and its unique biological niche. Small RNAs (sRNAs) are important components of bacterial regulation, allowing organisms to quickly adapt to changes in their environments. The AbcR sRNAs are highly conserved throughout the Alphaproteobacteria and negatively regulate myriad transcripts, many encoding ABC-type transport systems. In Brucella abortus, AbcR1 and AbcR2 are functionally redundant, as only a double abcR1 abcR2 (abcR1/2) deletion results in attenuation in vitro and in vivo. In the present study, we confirmed that the AbcR sRNAs have redundant regulatory functions and defined two six-nucleotide motifs, M1 and M2, that the AbcR sRNAs utilize to control gene expression. Importantly, only M2 was linked to B. abortus virulence. Further investigation of M2-regulated targets identified BAB2_0612 as critical for colonization of B. abortus in mice, highlighting the significance of AbcR M2-regulated transcripts for Brucella infection. Overall, our findings define the molecular mechanism of the virulence-associated AbcR system in the pathogenic bacterium B. abortus.
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Robledo M, Peregrina A, Millán V, García-Tomsig NI, Torres-Quesada O, Mateos PF, Becker A, Jiménez-Zurdo JI. A conserved α-proteobacterial small RNA contributes to osmoadaptation and symbiotic efficiency of rhizobia on legume roots. Environ Microbiol 2017; 19:2661-2680. [PMID: 28401641 DOI: 10.1111/1462-2920.13757] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/05/2017] [Accepted: 04/05/2017] [Indexed: 02/02/2023]
Abstract
Small non-coding RNAs (sRNAs) are expected to have pivotal roles in the adaptive responses underlying symbiosis of nitrogen-fixing rhizobia with legumes. Here, we provide primary insights into the function and activity mechanism of the Sinorhizobium meliloti trans-sRNA NfeR1 (Nodule Formation Efficiency RNA). Northern blot probing and transcription tracking with fluorescent promoter-reporter fusions unveiled high nfeR1 expression in response to salt stress and throughout the symbiotic interaction. The strength and differential regulation of nfeR1 transcription are conferred by a motif, which is conserved in nfeR1 promoter regions in α-proteobacteria. NfeR1 loss-of-function compromised osmoadaptation of free-living bacteria, whilst causing misregulation of salt-responsive genes related to stress adaptation, osmolytes catabolism and membrane trafficking. Nodulation tests revealed that lack of NfeR1 affected competitiveness, infectivity, nodule development and symbiotic efficiency of S. meliloti on alfalfa roots. Comparative computer predictions and a genetic reporter assay evidenced a redundant role of three identical NfeR1 unpaired anti Shine-Dalgarno motifs for targeting and downregulation of translation of multiple mRNAs from transporter genes. Our data provide genetic evidence of the hyperosmotic conditions of the endosymbiotic compartments. NfeR1-mediated gene regulation in response to this cue could contribute to coordinate nutrient uptake with the metabolic reprogramming concomitant to symbiotic transitions.
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Affiliation(s)
- Marta Robledo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Alexandra Peregrina
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Vicenta Millán
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Natalia I García-Tomsig
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Omar Torres-Quesada
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Pedro F Mateos
- Departamento de Microbiología y Genética and CIALE, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - José I Jiménez-Zurdo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
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29
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The ω Subunit Governs RNA Polymerase Stability and Transcriptional Specificity in Staphylococcus aureus. J Bacteriol 2016; 199:JB.00459-16. [PMID: 27799328 DOI: 10.1128/jb.00459-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/26/2016] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen that causes infection in a wide variety of sites within the human body. Its ability to adapt to the human host and to produce a successful infection requires precise orchestration of gene expression. While DNA-dependent RNA polymerase (RNAP) is generally well characterized, the roles of several small accessory subunits within the complex have yet to be fully explored. This is particularly true for the omega (ω or RpoZ) subunit, which has been extensively studied in Gram-negative bacteria but largely neglected in Gram-positive counterparts. In Escherichia coli, it has been shown that ppGpp binding, and thus control of the stringent response, is facilitated by ω. Interestingly, key residues that facilitate ppGpp binding by ω are not conserved in S. aureus, and consequently, survival under starvation conditions is unaffected by rpoZ deletion. Further to this, ω-lacking strains of S. aureus display structural changes in the RNAP complex, which result from increased degradation and misfolding of the β' subunit, alterations in δ and σ factor abundance, and a general dissociation of RNAP in the absence of ω. Through RNA sequencing analysis we detected a variety of transcriptional changes in the rpoZ-deficient strain, presumably as a response to the negative effects of ω depletion on the transcription machinery. These transcriptional changes translated to an impaired ability of the rpoZ mutant to resist stress and to fully form a biofilm. Collectively, our data underline, for the first time, the importance of ω for RNAP stability, function, and cellular physiology in S. aureus IMPORTANCE: In order for bacteria to adjust to changing environments, such as within the host, the transcriptional process must be tightly controlled. Transcription is carried out by DNA-dependent RNA polymerase (RNAP). In addition to its major subunits (α2ββ') a fifth, smaller subunit, ω, is present in all forms of life. Although this small subunit is well studied in eukaryotes and Gram-negative bacteria, only limited information is available for Gram-positive and pathogenic species. In this study, we investigated the structural and functional importance of ω, revealing key roles in subunit folding/stability, complex assembly, and maintenance of transcriptional integrity. Collectively, our data underline, for the first time, the importance of ω for RNAP function and cellular harmony in S. aureus.
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30
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Vishnu US, Sankarasubramanian J, Gunasekaran P, Rajendhran J. Identification of OtpR regulated sRNAs in Brucella melitensis expressed under acidic stress and their roles in pathogenesis and metabolism. Comp Immunol Microbiol Infect Dis 2016; 50:40-47. [PMID: 28131377 DOI: 10.1016/j.cimid.2016.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/14/2016] [Indexed: 11/25/2022]
Abstract
Small RNAs (sRNAs) are the small regulatory molecules that regulate various biological processes in bacteria. Though the functions of sRNAs are well documented, very little information is available on the sRNAs of Brucella spp. The otpR is the response regulator of a two-component regulatory system, which plays a significant role in Brucella virulence. In this study, we identified the sRNAs expressed in B. melitensis 16M and its otpR mutant under acidic stress from the RNAseq dataset. We identified 94 trans-encoded and 948 cis-encoded sRNAs in B. melitensis 16M. In B. melitensis 16M ΔotpR under acidic stress 99 trans-encoded and 877 cis-encoded sRNAs were identified. Among these, 12 trans-encoded and 43 cis-encoded sRNAs were upregulated in B. melitensis 16M ΔotpR, with an adjusted P-value≤0.05. The mRNA targets of these sRNAs were predicted. Further, the levels of mRNA targets were examined, and the sRNA-mediated regulatory network was predicted. Functional classification and pathway analysis of mRNA targets provided evidence that sRNAs are involved in different metabolic pathways including carbohydrates, amino acids, lipids, nucleotides transport and metabolism, cell membrane biogenesis and intracellular trafficking of Brucella. We also found that eight transcriptional regulators including a quorum sensing regulator, vjbR are down-regulated by sRNAs. These transcriptional regulators might be responsible for the regulation of several other genes in the otpR mutant. The trans-encoded BsnR88 and cis-encoded BsnR980, BsnR998, BsnR881, BsnR1001, BsnR891, BsnR883, BsnR905 are regulating virB operon genes coding for type IV secretion system (T4SS), which is the major virulence factor of Brucella.
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Affiliation(s)
- Udayakumar S Vishnu
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Jagadesan Sankarasubramanian
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | | | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
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31
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Ahmed W, Zheng K, Liu ZF. Small Non-Coding RNAs: New Insights in Modulation of Host Immune Response by Intracellular Bacterial Pathogens. Front Immunol 2016; 7:431. [PMID: 27803700 PMCID: PMC5067535 DOI: 10.3389/fimmu.2016.00431] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/03/2016] [Indexed: 12/20/2022] Open
Abstract
Pathogenic bacteria possess intricate regulatory networks that temporally control the production of virulence factors and enable the bacteria to survive and proliferate within host cell. Small non-coding RNAs (sRNAs) have been identified as important regulators of gene expression in diverse biological contexts. Recent research has shown bacterial sRNAs involved in growth and development, cell proliferation, differentiation, metabolism, cell signaling, and immune response through regulating protein–protein interactions or via their ability to base pair with RNA and DNA. In this review, we provide a brief overview of mechanism of action employed by immune-related sRNAs, their known functions in immunity, and how they can be integrated into regulatory circuits that govern virulence, which will facilitate our understanding of pathogenesis and the development of novel, more effective therapeutic approaches to treat infections caused by intracellular bacterial pathogens.
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Affiliation(s)
- Waqas Ahmed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University , Wuhan , China
| | - Ke Zheng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University , Wuhan , China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University , Wuhan , China
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32
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cis-Encoded Small RNAs, a Conserved Mechanism for Repression of Polysaccharide Utilization in Bacteroides. J Bacteriol 2016; 198:2410-8. [PMID: 27353652 PMCID: PMC4999932 DOI: 10.1128/jb.00381-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/23/2016] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED Bacteroides is a major component of the human gut microbiota which has a broad impact on the development and physiology of its host and a potential role in a wide range of disease syndromes. The predominance of this genus is due in large part to expansion of paralogous gene clusters, termed polysaccharide utilization loci (PULs), dedicated to the uptake and catabolism of host-derived and dietary polysaccharides. The nutritive value and availability of polysaccharides in the gut vary greatly; thus, their utilization is hierarchical and strictly controlled. A typical PUL includes regulatory genes that induce PUL expression in response to the presence of specific glycan substrates. However, the existence of additional regulatory mechanisms has been predicted to explain phenomena such as hierarchical control and catabolite repression. In this report, a previously unknown layer of regulatory control was discovered in Bacteroides fragilis Exploratory transcriptome sequencing (RNA-seq) analysis revealed the presence of cis-encoded antisense small RNAs (sRNAs) associated with 15 (30%) of the B. fragilis PULs. A model system using the Don (degradation of N-glycans) PUL showed that the donS sRNA negatively regulated Don expression at the transcriptional level, resulting in a decrease in N-glycan utilization. Additional studies performed with other Bacteroides species indicated that this regulatory mechanism is highly conserved and, interestingly, that the regulated PULs appear to be closely linked to the utilization of host-derived glycans rather than dietary plant polysaccharides. The findings described here demonstrate a global control mechanism underlying known PUL regulatory circuits and provide insight into regulation of Bacteroides physiology. IMPORTANCE The human gut is colonized by a dense microbiota which is essential to the health and normal development of the host. A key to gut homeostasis is the preservation of a stable, diverse microbiota. Bacteroides is a dominant genus in the gut, and the ability of Bacteroides species to efficiently compete for a wide range of glycan energy sources is a crucial advantage for colonization. Glycan utilization is mediated by a large number of polysaccharide utilization loci (PULs) which are regulated by substrate induction. In this report, a novel family of antisense sRNAs is described whose members repress gene expression in a distinct subset of PULs. This repression downregulates PUL expression in the presence of energy sources that are more readily utilized such as glucose, thereby allowing efficient glycan utilization.
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33
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Broach WH, Weiss A, Shaw LN. Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis. Microb Genom 2016; 2:e000065. [PMID: 28348860 PMCID: PMC5343137 DOI: 10.1099/mgen.0.000065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/22/2016] [Indexed: 12/26/2022] Open
Abstract
Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. Recently, our group catalogued and annotated all previously known and newly identified sRNAs in several Staphylococcus aureus strains. These complete annotation files now serve as tools to compare the sRNA content of S. aureus with other bacterial strains to investigate the conservation of their sRNomes. Accordingly, in this study we performed RNAseq on two staphylococcal species, Staphylococcus epidermidis and Staphylococcus carnosus, identifying 118 and 89 sRNAs in these organisms, respectively. The sRNA contents of all three species were then compared to elucidate their common and species-specific sRNA content, identifying a core set of between 53 and 36 sRNAs encoded in each organism. In addition, we determined that S. aureus has the largest set of unique sRNAs (137) while S. epidermidishas the fewest (25). Finally, we identify a highly conserved sequence and structural motif differentially represented within, yet common to, both S. aureus and S. epidermidis. Collectively, in this study, we uncover the sRNome common to three staphylococcal species, shedding light on sRNAs that are likely to be involved in basic physiological processes common to the genus. More significantly, we have identified species-specific sRNAs that are likely to influence the individual lifestyle and behaviour of these diverse staphylococcal strains.
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Affiliation(s)
- William H Broach
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Andy Weiss
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
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34
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Vishnu US, Sankarasubramanian J, Gunasekaran P, Sridhar J, Rajendhran J. Omics of Brucella: Species-Specific sRNA-Mediated Gene Ontology Regulatory Networks Identified by Computational Biology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:375-85. [DOI: 10.1089/omi.2016.0034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Udayakumar S. Vishnu
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | | | - Paramasamy Gunasekaran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Jayavel Sridhar
- Department of Biotechnology, DDE, Madurai Kamaraj University, Madurai, India
| | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
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35
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Zhong Z, Xu X, Li X, Liu S, Lei S, Yang M, Yu J, Yuan J, Ke Y, Du X, Wang Z, Ren Z, Peng G, Wang Y, Chen Z. Large-scale identification of small noncoding RNA with strand-specific deep sequencing and characterization of a novel virulence-related sRNA in Brucella melitensis. Sci Rep 2016; 6:25123. [PMID: 27112796 PMCID: PMC4845025 DOI: 10.1038/srep25123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/11/2016] [Indexed: 12/03/2022] Open
Abstract
Brucella is the causative agent of brucellosis, a worldwide epidemic zoonosis. Small noncoding RNAs (sRNAs) are important modulators of gene expression and involved in pathogenesis and stress adaptation of Brucella. In this study, using a strand-specific RNA deep-sequencing approach, we identified a global set of sRNAs expressed by B. melitensis 16M. In total, 1321 sRNAs were identified, ranging from 100 to 600 nucleotides. These sRNAs differ in their expression levels and strand and chromosomal distributions. The role of BSR0441, one of these sRNAs, in the virulence of B. melitensis 16M was further characterized. BSR0441 was highly induced during the infection of macrophages and mice. The deletion mutant of BSR0441 showed significantly reduced spleen colonization in the middle and late phases of infection. The expression of the BSR0441 target mRNA genes was also altered in the BSR0441 mutant strain during macrophage and mice infection, which is consistent with its reduced intracellular survival capacity. In summary, Brucella encodes a large number of sRNAs, which may be involved in the stress adaptation and virulence of Brucella. Further investigation of these regulators will extend our understanding of the Brucella pathogenesis mechanism and the interactions between Brucella and its hosts.
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Affiliation(s)
- Zhijun Zhong
- College of Veterinary Medicine, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Sichuan Province, Chengdu 611130, P. R. China.,Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China
| | - Xiaoyang Xu
- College of Veterinary Medicine, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Sichuan Province, Chengdu 611130, P. R. China.,Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China
| | - Xinran Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China
| | - Shiwei Liu
- Wangjing Hospital, Academy of Traditional Chinese Medicine, Beijing 100102, P. R. China
| | - Shuangshuang Lei
- College of Veterinary Medicine, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Sichuan Province, Chengdu 611130, P. R. China.,Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China
| | - Mingjuan Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China
| | - Jiuxuan Yu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China
| | - Jiuyun Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China
| | - Yuehua Ke
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China
| | - Xinying Du
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China
| | - Zhoujia Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China
| | - Zhihua Ren
- College of Veterinary Medicine, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Sichuan Province, Chengdu 611130, P. R. China
| | - Guangneng Peng
- College of Veterinary Medicine, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Sichuan Province, Chengdu 611130, P. R. China
| | - Yufei Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China.,Department of Laboratory Medicine, The General Hospital of Chinese People's Armed Police Forces, Beijing 100039, P. R. China
| | - Zeliang Chen
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P. R. China.,Key Laboratory of Zoonotic of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, P. R. China
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Ahmed W, Zheng K, Liu ZF. Establishment of Chronic Infection: Brucella's Stealth Strategy. Front Cell Infect Microbiol 2016; 6:30. [PMID: 27014640 PMCID: PMC4791395 DOI: 10.3389/fcimb.2016.00030] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/29/2016] [Indexed: 01/18/2023] Open
Abstract
Brucella is a facultative intracellular pathogen that causes zoonotic infection known as brucellosis which results in abortion and infertility in natural host. Humans, especially in low income countries, can acquire infection by direct contact with infected animal or by consumption of animal products and show high morbidity, severe economic losses and public health problems. However for survival, host cells develop complex immune mechanisms to defeat and battle against attacking pathogens and maintain a balance between host resistance and Brucella virulence. On the other hand as a successful intracellular pathogen, Brucella has evolved multiple strategies to evade immune response mechanisms to establish persistent infection and replication within host. In this review, we mainly summarize the "Stealth" strategies employed by Brucella to modulate innate and the adaptive immune systems, autophagy, apoptosis and possible role of small noncoding RNA in the establishment of chronic infection. The purpose of this review is to give an overview for recent understanding how this pathogen evades immune response mechanisms of host, which will facilitate to understanding the pathogenesis of brucellosis and the development of novel, more effective therapeutic approaches to treat brucellosis.
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Affiliation(s)
- Waqas Ahmed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Ke Zheng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
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37
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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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38
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Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN. Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus. mBio 2016; 7:e01990-15. [PMID: 26861020 PMCID: PMC4752604 DOI: 10.1128/mbio.01990-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/22/2015] [Indexed: 12/25/2022] Open
Abstract
UNLABELLED In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome annotation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. IMPORTANCE Despite a large number of studies identifying regulatory or small RNA (sRNA) genes in Staphylococcus aureus, their annotation is notably lacking in available genome files. In addition to this, there has been a considerable lack of cross-referencing in the wealth of studies identifying these elements, often leading to the same sRNA being identified multiple times and bearing multiple names. In this work, we have consolidated and curated known sRNA genes from the literature and mapped them to their position on the S. aureus genome, creating new genome annotation files. These files can now be used by the scientific community at large in experiments to search for previously undiscovered sRNA genes and to monitor sRNA gene expression by transcriptome sequencing (RNA-seq). We demonstrate this application, identifying 39 new sRNAs and studying their expression during S. aureus growth in human serum.
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Affiliation(s)
- Ronan K Carroll
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Andy Weiss
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - William H Broach
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Richard E Wiemels
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Austin B Mogen
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Kelly C Rice
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, USA
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RNA-seq reveals the critical role of CspA in regulating Brucella melitensis metabolism and virulence. SCIENCE CHINA-LIFE SCIENCES 2016; 59:417-24. [PMID: 26740105 DOI: 10.1007/s11427-015-4981-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 11/23/2015] [Indexed: 10/22/2022]
Abstract
Brucella melitensis is a facultative intracellular bacterium that replicates within macrophages. The ability of Brucella to survive and multiply in the hostile environment of host macrophages is essential for its virulence. The cold shock protein CspA plays an important role in the virulence of B. melitensis. To analyze the genes regulated by CspA, the whole transcriptomes of B. melitensis NIΔcspA and its parental wild-type strain, B. melitensis NI, were sequenced and analyzed using the Solexa/Illumina sequencing platform. A total of 446 differentially expressed genes were identified, including 324 up-regulated and 122 down-regulated genes. Numerous genes identified are involved in amino acid, fatty acid, nitrogen, and energy metabolism. Interestingly, all genes involved in the type IV secretion system and LuxR-type regulatory protein VjbR were significantly down-regulated in NIΔcspA. In addition, an effector translocation assay confirmed that the function of T4SS in NIΔcspA is influenced by deletion of the cspA gene. These results revealed the differential phenomena associated with virulence and metabolism in NIΔcspA and NI, providing important information for understanding detailed CspA-regulated interaction networks and Brucella pathogenesis.
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40
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Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis by Deep Sequencing. J Bacteriol 2015; 198:427-35. [PMID: 26553849 DOI: 10.1128/jb.00711-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/26/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Recent breakthroughs in next-generation sequencing technologies have led to the identification of small noncoding RNAs (sRNAs) as a new important class of regulatory molecules. In prokaryotes, sRNAs are often bound to the chaperone protein Hfq, which allows them to interact with their partner mRNA(s). We screened the genome of the zoonotic and human pathogen Brucella suis 1330 for the presence of this class of RNAs. We designed a coimmunoprecipitation strategy that relies on the use of Hfq as a bait to enrich the sample with sRNAs and eventually their target mRNAs. By deep sequencing analysis of the Hfq-bound transcripts, we identified a number of mRNAs and 33 sRNA candidates associated with Hfq. The expression of 10 sRNAs in the early stationary growth phase was experimentally confirmed by Northern blotting and/or reverse transcriptase PCR. IMPORTANCE Brucella organisms are facultative intracellular pathogens that use stealth strategies to avoid host defenses. Adaptation to the host environment requires tight control of gene expression. Recently, small noncoding RNAs (sRNAs) and the sRNA chaperone Hfq have been shown to play a role in the fine-tuning of gene expression. Here we have used RNA sequencing to identify RNAs associated with the B. suis Hfq protein. We have identified a novel list of 33 sRNAs and 62 Hfq-associated mRNAs for future studies aiming to understand the intracellular lifestyle of this pathogen.
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41
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Unraveling the universe of small RNA regulators in the legume symbiont Sinorhizobium meliloti. Symbiosis 2015. [DOI: 10.1007/s13199-015-0345-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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42
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George R, Cavalcante R, Jr CC, Marques E, Waugh JB, Unlap MT. Use of siRNA molecular beacons to detect and attenuate mycobacterial infection in macrophages. World J Exp Med 2015; 5:164-181. [PMID: 26309818 PMCID: PMC4543811 DOI: 10.5493/wjem.v5.i3.164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/05/2015] [Accepted: 06/11/2015] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis is one of the leading infectious diseases plaguing mankind and is mediated by the facultative pathogen, Mycobacterium tuberculosis (MTB). Once the pathogen enters the body, it subverts the host immune defenses and thrives for extended periods of time within the host macrophages in the lung granulomas, a condition called latent tuberculosis (LTB). Persons with LTB are prone to reactivation of the disease when the body’s immunity is compromised. Currently there are no reliable and effective diagnosis and treatment options for LTB, which necessitates new research in this area. The mycobacterial proteins and genes mediating the adaptive responses inside the macrophage is largely yet to be determined. Recently, it has been shown that the mce operon genes are critical for host cell invasion by the mycobacterium and for establishing a persistent infection in both in vitro and in mouse models of tuberculosis. The YrbE and Mce proteins which are encoded by the MTB mce operons display high degrees of homology to the permeases and the surface binding protein of the ABC transports, respectively. Similarities in structure and cell surface location impute a role in cell invasion at cholesterol rich regions and immunomodulation. The mce4 operon is also thought to encode a cholesterol transport system that enables the mycobacterium to derive both energy and carbon from the host membrane lipids and possibly generating virulence mediating metabolites, thus enabling the bacteria in its long term survival within the granuloma. Various deletion mutation studies involving individual or whole mce operon genes have shown to be conferring varying degrees of attenuation of infectivity or at times hypervirulence to the host MTB, with the deletion of mce4A operon gene conferring the greatest degree of attenuation of virulence. Antisense technology using synthetic siRNAs has been used in knocking down genes in bacteria and over the years this has evolved into a powerful tool for elucidating the roles of various genes mediating infectivity and survival in mycobacteria. Molecular beacons are a newer class of antisense RNA tagged with a fluorophore/quencher pair and their use for in vivo detection and knockdown of mRNA is rapidly gaining popularity.
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43
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Sheehan LM, Budnick JA, Blanchard C, Dunman PM, Caswell CC. A LysR-family transcriptional regulator required for virulence in Brucella abortus is highly conserved among the α-proteobacteria. Mol Microbiol 2015; 98:318-28. [PMID: 26175079 DOI: 10.1111/mmi.13123] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 12/31/2022]
Abstract
Small RNAs are principal elements of bacterial gene regulation and physiology. Two small RNAs in Brucella abortus, AbcR1 and AbcR2, are required for wild-type virulence. Examination of the abcR loci revealed the presence of a gene encoding a LysR-type transcriptional regulator flanking abcR2 on chromosome 1. Deletion of this lysR gene (bab1_1517) resulted in the complete loss of abcR2 expression while no difference in abcR1 expression was observed. The B. abortus bab1_1517 mutant strain was significantly attenuated in macrophages and mice, and bab1_1517 was subsequently named vtlR for virulence-associated transcriptional LysR-family regulator. Microarray analysis revealed three additional genes encoding small hypothetical proteins also under the control of VtlR. Electrophoretic mobility shift assays demonstrated that VtlR binds directly to the promoter regions of abcR2 and the three hypothetical protein-encoding genes, and DNase I footprint analysis identified the specific nucleotide sequence in these promoters that VtlR binds to and drives gene expression. Strikingly, orthologs of VtlR are encoded in a wide range of host-associated α-proteobacteria, and it is likely that the VtlR genetic system represents a common regulatory circuit critical for host-bacterium interactions.
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Affiliation(s)
- Lauren M Sheehan
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, 24060, USA
| | - James A Budnick
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Catlyn Blanchard
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, 24060, USA
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Miyakoshi M, Chao Y, Vogel J. Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA. EMBO J 2015; 34:1478-92. [PMID: 25630703 PMCID: PMC4474525 DOI: 10.15252/embj.201490546] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 11/16/2022] Open
Abstract
There is an expanding list of examples by which one mRNA can posttranscriptionally influence the expression of others. This can involve RNA sponges that sequester regulatory RNAs of mRNAs in the same regulon, but the underlying molecular mechanism of such mRNA cross talk remains little understood. Here, we report sponge-mediated mRNA cross talk in the posttranscriptional network of GcvB, a conserved Hfq-dependent small RNA with one of the largest regulons known in bacteria. We show that mRNA decay from the gltIJKL locus encoding an amino acid ABC transporter generates a stable fragment (SroC) that base-pairs with GcvB. This interaction triggers the degradation of GcvB by RNase E, alleviating the GcvB-mediated mRNA repression of other amino acid-related transport and metabolic genes. Intriguingly, since the gltIJKL mRNA itself is a target of GcvB, the SroC sponge seems to enable both an internal feed-forward loop to activate its parental mRNA in cis and activation of many trans-encoded mRNAs in the same pathway. Disabling this mRNA cross talk affects bacterial growth when peptides are the sole carbon and nitrogen sources.
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Affiliation(s)
- Masatoshi Miyakoshi
- RNA Biology Group, Institute for Molecular Infection Biology University of Würzburg, Würzburg, Germany
| | - Yanjie Chao
- RNA Biology Group, Institute for Molecular Infection Biology University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology University of Würzburg, Würzburg, Germany
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Oliva G, Sahr T, Buchrieser C. Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence. FEMS Microbiol Rev 2015; 39:331-349. [DOI: 10.1093/femsre/fuv022] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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46
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Wang Y, Ke Y, Xu J, Wang L, Wang T, Liang H, Zhang W, Gong C, Yuan J, Zhuang Y, An C, Lei S, Du X, Wang Z, Li W, Yuan X, Huang L, Yang X, Chen Z. Identification of a Novel Small Non-Coding RNA Modulating the Intracellular Survival of Brucella melitensis. Front Microbiol 2015; 6:164. [PMID: 25852653 PMCID: PMC4365724 DOI: 10.3389/fmicb.2015.00164] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/02/2015] [Indexed: 12/20/2022] Open
Abstract
Bacterial small non-coding RNAs (sRNAs) are gene expression modulators respond to environmental changes, stressful conditions, and pathogenesis. In this study, by using a combined bioinformatic and experimental approach, eight novel sRNA genes were identified in intracellular pathogen Brucella melitensis. BSR0602, one sRNA that was highly induced in stationary phase, was further examined and found to modulate the intracellular survival of B. melitensis. BSR0602 was present at very high levels in vitro under stresses similar to those encountered during infection in host macrophages. Furthermore, BSR0602 was found to be highly expressed in the spleens of infected mice, suggesting its potential role in the control of pathogenesis. BSR0602 targets the mRNAs coding for gntR, a global transcriptional regulator, which is required for B. melitensis virulence. Overexpression of BSR0602 results in distinct reduction in the gntR mRNA level. B. melitensis with high level of BSR0602 is defective in bacteria intracellular survival in macrophages and defective in growth in the spleens of infected mice. Therefore, BSR0602 may directly inhibit the expression of gntR, which then impairs Brucellae intracellular survival and contributes to Brucella infection. Our findings suggest that BSR0602 is responsible for bacterial adaptation to stress conditions and thus modulate B. melitensis intracellular survival.
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Affiliation(s)
- Yufei Wang
- Department of Laboratory Medicine, The General Hospital of Chinese People's Armed Police Forces , Beijing , China
| | - Yuehua Ke
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Jie Xu
- Laboratory of Clinical Immunology in Jiangsu Province, Department of Clinical Laboratory, The First Affiliated Hospital of Soochow University , Suzhou , China
| | - Ligui Wang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Tongkun Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing , China
| | - Hui Liang
- Department of Laboratory Medicine, The General Hospital of Chinese People's Armed Police Forces , Beijing , China
| | - Wei Zhang
- Department of Laboratory Medicine, The General Hospital of Chinese People's Armed Police Forces , Beijing , China
| | - Chunli Gong
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Jiuyun Yuan
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Yubin Zhuang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Chang An
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Shuangshuang Lei
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Xinying Du
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Zhoujia Wang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Wenna Li
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Xitong Yuan
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Liuyu Huang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Xiaoli Yang
- Department of Laboratory Medicine, The General Hospital of Chinese People's Armed Police Forces , Beijing , China
| | - Zeliang Chen
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
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Ronneau S, Moussa S, Barbier T, Conde-Álvarez R, Zuniga-Ripa A, Moriyon I, Letesson JJ. Brucella, nitrogen and virulence. Crit Rev Microbiol 2014; 42:507-25. [PMID: 25471320 DOI: 10.3109/1040841x.2014.962480] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The brucellae are α-Proteobacteria causing brucellosis, an important zoonosis. Although multiplying in endoplasmic reticulum-derived vacuoles, they cause no cell death, suggesting subtle but efficient use of host resources. Brucellae are amino-acid prototrophs able to grow with ammonium or use glutamate as the sole carbon-nitrogen source in vitro. They contain more than twice amino acid/peptide/polyamine uptake genes than the amino-acid auxotroph Legionella pneumophila, which multiplies in a similar vacuole, suggesting a different nutritional strategy. During these two last decades, many mutants of key actors in nitrogen metabolism (transporters, enzymes, regulators, etc.) have been described to be essential for full virulence of brucellae. Here, we review the genomic and experimental data on Brucella nitrogen metabolism and its connection with virulence. An analysis of various aspects of this metabolism (transport, assimilation, biosynthesis, catabolism, respiration and regulation) has highlighted differences and similarities in nitrogen metabolism with other α-Proteobacteria. Together, these data suggest that, during their intracellular life cycle, the brucellae use various nitrogen sources for biosynthesis, catabolism and respiration following a strategy that requires prototrophy and a tight regulation of nitrogen use.
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Affiliation(s)
| | - Simon Moussa
- a UNamur, URBM 61 rue de Bruxelles , Namur , Belgium and
| | | | - Raquel Conde-Álvarez
- b Departamento de Microbiología , Edificio de Investigación, Universidad de Navarra , Pamplona , Spain
| | - Amaia Zuniga-Ripa
- b Departamento de Microbiología , Edificio de Investigación, Universidad de Navarra , Pamplona , Spain
| | - Ignacio Moriyon
- b Departamento de Microbiología , Edificio de Investigación, Universidad de Navarra , Pamplona , Spain
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Peng X, Dong H, Wu Q. A new cis-encoded sRNA, BsrH, regulating the expression of hemH gene in Brucella abortus 2308. FEMS Microbiol Lett 2014; 362:1-7. [DOI: 10.1093/femsle/fnu017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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49
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Ortega AD, Quereda JJ, Pucciarelli MG, García-del Portillo F. Non-coding RNA regulation in pathogenic bacteria located inside eukaryotic cells. Front Cell Infect Microbiol 2014; 4:162. [PMID: 25429360 PMCID: PMC4228915 DOI: 10.3389/fcimb.2014.00162] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 10/20/2014] [Indexed: 01/06/2023] Open
Abstract
Intracellular bacterial pathogens have evolved distinct lifestyles inside eukaryotic cells. Some pathogens coexist with the infected cell in an obligate intracellular state, whereas others transit between the extracellular and intracellular environment. Adaptation to these intracellular lifestyles is regulated in both space and time. Non-coding small RNAs (sRNAs) are post-transcriptional regulatory molecules that fine-tune important processes in bacterial physiology including cell envelope architecture, intermediate metabolism, bacterial communication, biofilm formation, and virulence. Recent studies have shown production of defined sRNA species by intracellular bacteria located inside eukaryotic cells. The molecules targeted by these sRNAs and their expression dynamics along the intracellular infection cycle remain, however, poorly characterized. Technical difficulties linked to the isolation of “intact” intracellular bacteria from infected host cells might explain why sRNA regulation in these specialized pathogens is still a largely unexplored field. Transition from the extracellular to the intracellular lifestyle provides an ideal scenario in which regulatory sRNAs are intended to participate; so much work must be done in this direction. This review focuses on sRNAs expressed by intracellular bacterial pathogens during the infection of eukaryotic cells, strategies used with these pathogens to identify sRNAs required for virulence, and the experimental technical challenges associated to this type of studies. We also discuss varied techniques for their potential application to study RNA regulation in intracellular bacterial infections.
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Affiliation(s)
- Alvaro D Ortega
- Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC) Madrid, Spain
| | - Juan J Quereda
- Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC) Madrid, Spain
| | - M Graciela Pucciarelli
- Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC) Madrid, Spain ; Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Biología Molecular 'Severo Ochoa' (CBMSO-CSIC) Madrid, Spain
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50
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Caswell CC, Oglesby-Sherrouse AG, Murphy ER. Sibling rivalry: related bacterial small RNAs and their redundant and non-redundant roles. Front Cell Infect Microbiol 2014; 4:151. [PMID: 25389522 PMCID: PMC4211561 DOI: 10.3389/fcimb.2014.00151] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/07/2014] [Indexed: 11/13/2022] Open
Abstract
Small RNA molecules (sRNAs) are now recognized as key regulators controlling bacterial gene expression, as sRNAs provide a quick and efficient means of positively or negatively altering the expression of specific genes. To date, numerous sRNAs have been identified and characterized in a myriad of bacterial species, but more recently, a theme in bacterial sRNAs has emerged: the presence of more than one highly related sRNAs produced by a given bacterium, here termed sibling sRNAs. Sibling sRNAs are those that are highly similar at the nucleotide level, and while it might be expected that sibling sRNAs exert identical regulatory functions on the expression of target genes based on their high degree of relatedness, emerging evidence is demonstrating that this is not always the case. Indeed, there are several examples of bacterial sibling sRNAs with non-redundant regulatory functions, but there are also instances of apparent regulatory redundancy between sibling sRNAs. This review provides a comprehensive overview of the current knowledge of bacterial sibling sRNAs, and also discusses important questions about the significance and evolutionary implications of this emerging class of regulators.
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Affiliation(s)
- Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD Regional College of Veterinary Medicine, Virginia Tech Blacksburg, VA, USA
| | - Amanda G Oglesby-Sherrouse
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, MD, USA ; Department of Microbiology and Immunology, School of Medicine, University of Maryland Baltimore, MD, USA
| | - Erin R Murphy
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine Athens, OH, USA
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