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Newberry EA, Minsavage GV, Holland A, Jones JB, Potnis N. Genome-Wide Association to Study the Host-Specificity Determinants of Xanthomonas perforans. PHYTOPATHOLOGY 2023; 113:400-412. [PMID: 36318253 DOI: 10.1094/phyto-08-22-0294-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Xanthomonas perforans and X. euvesicatoria are the causal agents of bacterial spot disease of tomato and pepper, endemic to the Southeastern United States. Although very closely related, the two bacterial species differ in host specificity, where X. perforans is the dominant pathogen of tomato and X. euvesicatoria that of pepper. This is in part due to the activity of avirulence proteins that are secreted by X. perforans strains and elicit effector-triggered immunity in pepper leaves, thereby restricting pathogen growth. In recent years, the emergence of several pepper-pathogenic X. perforans lineages has revealed variability within the bacterial species to multiply and cause disease in pepper, even in the absence of avirulence gene activity. Here, we investigated the basal evolutionary processes underlying the host range of this species using multiple genome-wide association analyses. Surprisingly, we identified two novel gene candidates that were significantly associated with pepper-pathogenic X. perforans and X. euvesicatoria. Both candidates were predicted to be involved in the transport/acquisition of nutrients common to the plant cell wall or apoplast and included a TonB-dependent receptor, which was disrupted through independent mutations within the X. perforans lineage. The other included a symporter of protons/glutamate, gltP, enriched with pepper-associated mutations near the promoter and start codon of the gene. Functional analysis of these candidates revealed that only the TonB-dependent receptor had a minor effect on the symptom development and growth of X. perforans in pepper leaves, indicating that pathogenicity to this host might have evolved independently within the bacterial species and is likely a complex, multigenic trait.
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Affiliation(s)
- Eric A Newberry
- Department of Entomology and Plant Pathology, Auburn University, AL 36849
| | | | - Auston Holland
- Department of Entomology and Plant Pathology, Auburn University, AL 36849
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, FL 32611
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, AL 36849
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2
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An SQ, Potnis N, Dow M, Vorhölter FJ, He YQ, Becker A, Teper D, Li Y, Wang N, Bleris L, Tang JL. Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiol Rev 2020; 44:1-32. [PMID: 31578554 PMCID: PMC8042644 DOI: 10.1093/femsre/fuz024] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/29/2019] [Indexed: 01/15/2023] Open
Abstract
Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.
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Affiliation(s)
- Shi-Qi An
- National Biofilms Innovation Centre (NBIC), Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn AL36849, USA
| | - Max Dow
- School of Microbiology, Food Science & Technology Building, University College Cork, Cork T12 K8AF, Ireland
| | | | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, Marburg 35032, Germany
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Yi Li
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX75080, USA
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
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3
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Schulte F, Leßmeier L, Voss J, Ortseifen V, Vorhölter FJ, Niehaus K. Regulatory associations between the metabolism of sulfur-containing amino acids and xanthan biosynthesis in Xanthomonas campestris pv. campestris B100. FEMS Microbiol Lett 2019; 366:5289864. [PMID: 30649298 DOI: 10.1093/femsle/fnz005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/14/2019] [Indexed: 02/06/2023] Open
Abstract
The γ-proteobacterium Xanthomonas campestris pv. campestris (Xcc) B100 synthesizes the exopolysaccharide xanthan, a commercially relevant thickening agent produced commonly by industrial scale fermentation. This work was inspired by the observation that methionine is an inhibitor of xanthan formation in growth experiments. Therefore, the global effects of methionine supplementation were characterized through cultivation experiments, genome-wide microarray hybridizations and qRT-PCR. Specific pull down of DNA-binding proteins by using the intergenic regions upstream of xanA, gumB and gumD led to the identification of six transcriptional regulators, among them the LysR-family transcriptional regulator CysB. An insertion mutant of this gene was analyzed by growth experiments, microarray experiments and qRT-PCR. Based on our experimental data, we developed a model that describes the methionine-dependent co-regulation of xanthan and sulfur-containing compounds in Xanthomonas. These data substantially contribute to better understand the impact of methionine as a compound in xanthan production media used in industrial fermentations.
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Affiliation(s)
- Fabian Schulte
- Department of Proteome and Metabolome Research - Bio27, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Lennart Leßmeier
- Chair of Genetics of Prokaryotes, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Julia Voss
- Department of Proteome and Metabolome Research - Bio27, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Vera Ortseifen
- Department of Proteome and Metabolome Research - Bio27, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Frank-Jörg Vorhölter
- Department of Proteome and Metabolome Research - Bio27, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Karsten Niehaus
- Department of Proteome and Metabolome Research - Bio27, Faculty of Biology, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
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4
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McIntosh M, Serrania J, Lacanna E. A novel LuxR-type solo of Sinorhizobium meliloti, NurR, is regulated by the chromosome replication coordinator, DnaA and activates quorum sensing. Mol Microbiol 2019; 112:678-698. [PMID: 31124196 DOI: 10.1111/mmi.14312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2019] [Indexed: 12/16/2022]
Abstract
The genome of Sinorhizobium meliloti, a model for studying plant-bacteria symbiosis, contains eight genes coding for LuxR-like proteins. Two of these, SinR and ExpR, are essential for quorum sensing (QS). Roles and regulation surrounding the others are mostly unknown. Here, we reveal the DNA recognition sequence and regulon of the LuxR-like protein SMc00877. Unlike ExpR, which uses the long-chain acyl homoserine lactones (AHLs) as inducers, SMc00877 functioned independently of AHLs and was even functional in Escherichia coli. A target of SMc00877 is SinR, the major regulator of AHL production in S. meliloti. Disruption of SMc00877 decreased AHL production. A weaker production of AHLs resulted in smaller microcolonies, starting from single cells, and delayed AHL-dependent regulation. SMc00877 was expressed only in growing cells in the presence of replete nutrients. Therefore, we renamed it NurR (nutrient sensitive LuxR-like regulator). We traced this nutrient-sensitive expression to transcription control by the DNA replication initiation factor, DnaA, which is essential for growth. These results indicate that NurR has a role in modulating the threshold of QS activation according to growth. We propose growth behavior as an additional prerequisite to population density for the activation of QS in S. meliloti.
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Affiliation(s)
- Matthew McIntosh
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, 35043, Germany.,Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany.,Institut für Mikrobiologie und Molekularbiologie, Universität Giessen, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Javier Serrania
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, 35043, Germany.,Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Egidio Lacanna
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, 35043, Germany.,Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
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Abstract
Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.
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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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7
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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8
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Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data. J Biotechnol 2017; 253:55-61. [DOI: 10.1016/j.jbiotec.2017.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 11/18/2022]
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9
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AraC-like transcriptional activator CuxR binds c-di-GMP by a PilZ-like mechanism to regulate extracellular polysaccharide production. Proc Natl Acad Sci U S A 2017; 114:E4822-E4831. [PMID: 28559336 DOI: 10.1073/pnas.1702435114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyclic dimeric GMP (c-di-GMP) has emerged as a key regulatory player in the transition between planktonic and sedentary biofilm-associated bacterial lifestyles. It controls a multitude of processes including production of extracellular polysaccharides (EPSs). The PilZ domain, consisting of an N-terminal "RxxxR" motif and a β-barrel domain, represents a prototype c-di-GMP receptor. We identified a class of c-di-GMP-responsive proteins, represented by the AraC-like transcription factor CuxR in plant symbiotic α-proteobacteria. In Sinorhizobium meliloti, CuxR stimulates transcription of an EPS biosynthesis gene cluster at elevated c-di-GMP levels. CuxR consists of a Cupin domain, a helical hairpin, and bipartite helix-turn-helix motif. Although unrelated in sequence, the mode of c-di-GMP binding to CuxR is highly reminiscent to that of PilZ domains. c-di-GMP interacts with a conserved N-terminal RxxxR motif and the Cupin domain, thereby promoting CuxR dimerization and DNA binding. We unravel structure and mechanism of a previously unrecognized c-di-GMP-responsive transcription factor and provide insights into the molecular evolution of c-di-GMP binding to proteins.
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10
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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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11
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Baumgardt K, Melior H, Madhugiri R, Thalmann S, Schikora A, McIntosh M, Becker A, Evguenieva-Hackenberg E. RNase E and RNase J are needed for S-adenosylmethionine homeostasis in Sinorhizobium meliloti. MICROBIOLOGY-SGM 2017; 163:570-583. [PMID: 28141492 DOI: 10.1099/mic.0.000442] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The ribonucleases (RNases) E and J play major roles in E. coli and Bacillus subtilis, respectively, and co-exist in Sinorhizobium meliloti. We analysed S. meliloti 2011 mutants with mini-Tn5 insertions in the corresponding genes rne and rnj and found many overlapping effects. We observed similar changes in mRNA levels, including lower mRNA levels of the motility and chemotaxis related genes flaA, flgB and cheR and higher levels of ndvA (important for glucan export). The acyl-homoserine lactone (AHL) levels were also higher during exponential growth in both RNase mutants, despite no increase in the expression of the sinI AHL synthase gene. Furthermore, several RNAs from both mutants migrated aberrantly in denaturing gels at 300 V but not under stronger denaturing conditions at 1300 V. The similarities between the two mutants could be explained by increased levels of the key methyl donor S-adenosylmethionine (SAM), since this may result in faster AHL synthesis leading to higher AHL accumulation as well as in uncontrolled methylation of macromolecules including RNA, which may strengthen RNA secondary structures. Indeed, we found that in both mutants the N6-methyladenosine content was increased almost threefold and the SAM level was increased at least sevenfold. Complementation by induced ectopic expression of the respective RNase restored the AHL and SAM levels in each of the mutants. In summary, our data show that both RNase E and RNase J are needed for SAM homeostasis in S. meliloti.
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Affiliation(s)
- Kathrin Baumgardt
- Institute of Microbiology and Molecular Biology, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.,Present address: CNRS, Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Hendrik Melior
- Institute of Microbiology and Molecular Biology, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Ramakanth Madhugiri
- Institute of Microbiology and Molecular Biology, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.,Present address: Institute of Medical Virology, Biomedical Research Center, Justus Liebig University, Schubertstr. 81, D 35392 Giessen, Germany
| | - Sebastian Thalmann
- Institute of Microbiology and Molecular Biology, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Adam Schikora
- Institute of Phytopathology and Applied Zoology, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.,Present address: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Brunswick, Germany
| | - Matthew McIntosh
- Centre of Synthetic Microbiology, Hans-Meerwein-Straße 6, D-35043 Marburg, Germany
| | - Anke Becker
- Centre of Synthetic Microbiology, Hans-Meerwein-Straße 6, D-35043 Marburg, Germany
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12
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Krol E, Klaner C, Gnau P, Kaever V, Essen LO, Becker A. Cyclic mononucleotide- and Clr-dependent gene regulation in Sinorhizobium meliloti. MICROBIOLOGY-SGM 2016; 162:1840-1856. [PMID: 27535558 DOI: 10.1099/mic.0.000356] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To identify physiological processes affected by cAMP in the plant-symbiotic nitrogen-fixing α-proteobacterium Sinorhizobium meliloti Rm2011, cAMP levels were artificially increased by overexpression of its cognate adenylate/guanylate cyclase gene cyaJ. This resulted in high accumulation of cAMP in the culture supernatant, decreased swimming motility and increased production of succinoglycan, an exopolysaccharide involved in host invasion. Weaker, similar phenotypic changes were induced by overexpression of cyaB and cyaG1. Effects on swimming motility and succinoglycan production were partially dependent on clr encoding a cyclic AMP receptor-like protein. Transcriptome profiling of an cyaJ-overexpressing strain identified 72 upregulated and 82 downregulated genes. A considerable number of upregulated genes are related to polysaccharide biosynthesis and osmotic stress response. These included succinoglycan biosynthesis genes, genes of the putative polysaccharide synthesis nodP2-exoF3 cluster and feuN, the first gene of the operon encoding the FeuNPQ regulatory system. Downregulated genes were mostly related to respiration, central metabolism and swimming motility. Promoter-probe studies in the presence of externally added cAMP revealed 18 novel Clr-cAMP-regulated genes. Moreover, the addition of cGMP into the growth medium also promoted clr-dependent gene regulation. In vitro binding of Clr-cAMP and Clr-cGMP to the promoter regions of SMc02178, SMb20906,SMc04190, SMc00925, SMc01136 and cyaF2 required the DNA motif (A/C/T)GT(T/C)(T/C/A)C (N4) G(G/A)(T/A)ACA. Furthermore, SMc02178, SMb20906,SMc04190and SMc00653 promoters were activated by Clr-cAMP/cGMP in Escherichia coli as heterologous host. These findings suggest direct activation of these 7 genes by Clr-cAMP/cGMP.
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Affiliation(s)
- Elizaveta Krol
- Faculty of Biology and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Christina Klaner
- Faculty of Biology and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Petra Gnau
- Faculty of Chemistry and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Lars-Oliver Essen
- Faculty of Chemistry and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Anke Becker
- Faculty of Biology and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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Leßmeier L, Alkhateeb RS, Schulte F, Steffens T, Loka TP, Pühler A, Niehaus K, Vorhölter FJ. Applying DNA affinity chromatography to specifically screen for sucrose-related DNA-binding transcriptional regulators of Xanthomonas campestris. J Biotechnol 2016; 232:89-98. [DOI: 10.1016/j.jbiotec.2016.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 11/28/2022]
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14
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Frage B, Döhlemann J, Robledo M, Lucena D, Sobetzko P, Graumann PL, Becker A. Spatiotemporal choreography of chromosome and megaplasmids in theSinorhizobium meliloticell cycle. Mol Microbiol 2016; 100:808-23. [DOI: 10.1111/mmi.13351] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Frage
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Johannes Döhlemann
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Marta Robledo
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Daniella Lucena
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps-Universität Marburg, 35032; Marburg Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Peter L. Graumann
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps-Universität Marburg, 35032; Marburg Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
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Alkhateeb RS, Vorhölter FJ, Rückert C, Mentz A, Wibberg D, Hublik G, Niehaus K, Pühler A. Genome wide transcription start sites analysis of Xanthomonas campestris pv. campestris B100 with insights into the gum gene cluster directing the biosynthesis of the exopolysaccharide xanthan. J Biotechnol 2016; 225:18-28. [PMID: 26975844 DOI: 10.1016/j.jbiotec.2016.03.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 01/18/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is the major producer of the exopolysaccharide xanthan, the commercially most important natural polysaccharide of microbial origin. The current work provides deeper insights into the yet uncharacterized transcriptomic features of the xanthan producing strain Xcc-B100. Towards this goal, RNA sequencing of a library based on the selective enrichment of the 5' ends of native transcripts was performed. This approach resulted in the genome wide identification of 3067 transcription start sites (TSSs) that were further classified based on their genomic positions. Among them, 1545 mapped upstream of an actively transcribed CDS and 1363 were classified as novel TSSs representing antisense, internal, and TSSs belonging to previously unidentified genomic features. Analyzing the transcriptional strength of primary and antisense TSSs revealed that in some instances antisense transcription seemed to be initiated at a higher level than its sense counterpart. Mapping the exact positions of TSSs aided in the identification of promoter consensus motifs, ribosomal binding sites, and enhanced the genome annotation of 159 in silico predicted translational start (TLS) sites. The global view on length distribution of the 5' untranslated regions (5'-UTRs) deduced from the data pointed to the occurrence of leaderless transcripts and transcripts with unusually long 5'-UTRs, in addition to identifying seven putative riboswitch elements for Xcc-B100. Concerning the biosynthesis of xanthan, we focused on the transcriptional organization of the gum gene cluster. Under the conditions tested, we present evidence for a complex transcription pattern of the gum genes with multiple TSSs and an obvious considerable role of antisense transcription. The gene gumB, encoding an outer membrane xanthan exporter, is presented here as an example for genes that possessed a strong antisense TSS.
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Affiliation(s)
- Rabeaa S Alkhateeb
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Frank-Jörg Vorhölter
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany; Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Christian Rückert
- Technologie Platform Genomics, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Almut Mentz
- Technologie Platform Genomics, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Gerd Hublik
- Jungbunzlauer Austria AG, Pernhofen 1, 2064 Wulzeshofen, Austria
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Alfred Pühler
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany
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Schmid J, Sieber V, Rehm B. Bacterial exopolysaccharides: biosynthesis pathways and engineering strategies. Front Microbiol 2015; 6:496. [PMID: 26074894 PMCID: PMC4443731 DOI: 10.3389/fmicb.2015.00496] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/06/2015] [Indexed: 12/13/2022] Open
Abstract
Bacteria produce a wide range of exopolysaccharides which are synthesized via different biosynthesis pathways. The genes responsible for synthesis are often clustered within the genome of the respective production organism. A better understanding of the fundamental processes involved in exopolysaccharide biosynthesis and the regulation of these processes is critical toward genetic, metabolic and protein-engineering approaches to produce tailor-made polymers. These designer polymers will exhibit superior material properties targeting medical and industrial applications. Exploiting the natural design space for production of a variety of biopolymer will open up a range of new applications. Here, we summarize the key aspects of microbial exopolysaccharide biosynthesis and highlight the latest engineering approaches toward the production of tailor-made variants with the potential to be used as valuable renewable and high-performance products for medical and industrial applications.
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Affiliation(s)
- Jochen Schmid
- Chair of Chemistry of Biogenic Resources, Technische Universität MünchenStraubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technische Universität MünchenStraubing, Germany
| | - Bernd Rehm
- Institute of Fundamental Sciences, Massey UniversityPalmerston North, New Zealand
- The MacDiarmid Institute for Advanced Materials and NanotechnologyPalmerston North, New Zealand
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A stress-induced small RNA modulates alpha-rhizobial cell cycle progression. PLoS Genet 2015; 11:e1005153. [PMID: 25923724 PMCID: PMC4414408 DOI: 10.1371/journal.pgen.1005153] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 03/18/2015] [Indexed: 01/22/2023] Open
Abstract
Mechanisms adjusting replication initiation and cell cycle progression in response to environmental conditions are crucial for microbial survival. Functional characterization of the trans-encoded small non-coding RNA (trans-sRNA) EcpR1 in the plant-symbiotic alpha-proteobacterium Sinorhizobium meliloti revealed a role of this class of riboregulators in modulation of cell cycle regulation. EcpR1 is broadly conserved in at least five families of the Rhizobiales and is predicted to form a stable structure with two defined stem-loop domains. In S. meliloti, this trans-sRNA is encoded downstream of the divK-pleD operon. ecpR1 belongs to the stringent response regulon, and its expression was induced by various stress factors and in stationary phase. Induced EcpR1 overproduction led to cell elongation and increased DNA content, while deletion of ecpR1 resulted in reduced competitiveness. Computationally predicted EcpR1 targets were enriched with cell cycle-related mRNAs. Post-transcriptional repression of the cell cycle key regulatory genes gcrA and dnaA mediated by mRNA base-pairing with the strongly conserved loop 1 of EcpR1 was experimentally confirmed by two-plasmid differential gene expression assays and compensatory changes in sRNA and mRNA. Evidence is presented for EcpR1 promoting RNase E-dependent degradation of the dnaA mRNA. We propose that EcpR1 contributes to modulation of cell cycle regulation under detrimental conditions. Microorganisms frequently encounter adverse conditions unfavorable for cell proliferation. They have evolved diverse mechanisms, including transcriptional control and targeted protein degradation, to adjust cell cycle progression in response to environmental cues. Non-coding RNAs are widespread regulators of various cellular processes in all domains of life. In prokaryotes, trans-encoded small non-coding RNAs (trans-sRNAs) contribute to a rapid cellular response to changing environments, but so far have not been directly related to cell cycle regulation. Here, we report the first example of a trans-sRNA (EcpR1) with two experimentally confirmed targets in the core of cell cycle regulation and demonstrate that in the plant-symbiotic alpha-proteobacterium Sinorhizobium meliloti the regulatory mechanism involves base-pairing of this sRNA with the dnaA and gcrA mRNAs. Most trans-sRNAs are restricted to closely related species, but the stress-induced EcpR1 is broadly conserved in the order of Rhizobiales suggesting an evolutionary advantage conferred by ecpR1. It broadens the functional diversity of prokaryotic sRNAs and adds a new regulatory level to the mechanisms that contribute to interlinking stress responses with the cell cycle machinery.
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Chapelle E, Alunni B, Malfatti P, Solier L, Pédron J, Kraepiel Y, Van Gijsegem F. A straightforward and reliable method for bacterial in planta transcriptomics: application to the Dickeya dadantii/Arabidopsis thaliana pathosystem. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:352-62. [PMID: 25740271 DOI: 10.1111/tpj.12812] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/16/2015] [Accepted: 02/23/2015] [Indexed: 05/02/2023]
Abstract
Transcriptome analysis of bacterial pathogens is a powerful approach to identify and study the expression patterns of genes during host infection. However, analysis of the early stages of bacterial virulence at the genome scale is lacking with respect to understanding of plant-pathogen interactions and diseases, especially during foliar infection. This is mainly due to both the low ratio of bacterial cells to plant material at the beginning of infection, and the high contamination by chloroplastic material. Here we describe a reliable and straightforward method for bacterial cell purification from infected leaf tissues, effective even if only a small amount of bacteria is present relative to plant material. The efficiency of this method for transcriptomic analysis was validated by analysing the expression profiles of the phytopathogenic enterobacterium Dickeya dadantii, a soft rot disease-causing agent, during the first hours of infection of the model host plant Arabidopsis thaliana. Transcriptome profiles of epiphytic bacteria and bacteria colonizing host tissues were compared, allowing identification of approximately 100 differentially expressed genes. Requiring no specific equipment, cost-friendly and easily transferable to other pathosystems, this method should be of great interest for many other plant-bacteria interaction studies.
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Affiliation(s)
- Emilie Chapelle
- Institut National de la Recherche Agronomique, Universite Pierre et Marie Curie/Universite Paris 06, AgroParisTech, UMR217, Interactions Plantes-Pathogènes, F-75005, Paris, France
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Messerschmidt SJ, Kemter FS, Schindler D, Waldminghaus T. Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae. Biotechnol J 2014; 10:302-14. [PMID: 25359671 DOI: 10.1002/biot.201400031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 10/02/2014] [Accepted: 10/30/2014] [Indexed: 01/25/2023]
Abstract
Recent developments in DNA-assembly methods make the synthesis of synthetic chromosomes a reachable goal. However, the redesign of primary chromosomes bears high risks and still requires enormous resources. An alternative approach is the addition of synthetic chromosomes to the cell. The natural secondary chromosome of Vibrio cholerae could potentially serve as template for a synthetic secondary chromosome in Escherichia coli. To test this assumption we constructed a replicon named synVicII based on the replication module of V. cholerae chromosome II (oriII). A new assay for the assessment of replicon stability was developed based on flow-cytometric analysis of unstable GFP variants. Application of this assay to cells carrying synVicII revealed an improved stability compared to a secondary replicon based on E. coli oriC. Cell cycle analysis and determination of cellular copy numbers of synVicII indicate that replication timing of the synthetic replicon in E. coli is comparable to the natural chromosome II (ChrII) in V. cholerae. The presented synthetic biology work provides the basis to use secondary chromosomes in E. coli to answer basic research questions as well as for several biotechnological applications.
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Affiliation(s)
- Sonja J Messerschmidt
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Germany
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20
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Dugé de Bernonville T, Noël LD, SanCristobal M, Danoun S, Becker A, Soreau P, Arlat M, Lauber E. Transcriptional reprogramming and phenotypical changes associated with growth ofXanthomonas campestrispv.campestrisin cabbage xylem sap. FEMS Microbiol Ecol 2014; 89:527-41. [DOI: 10.1111/1574-6941.12345] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/22/2014] [Accepted: 04/22/2014] [Indexed: 11/27/2022] Open
Affiliation(s)
- Thomas Dugé de Bernonville
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 441; INRA; Castanet-Tolosan France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 2594; CNRS; Castanet-Tolosan France
| | - Laurent D. Noël
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 441; INRA; Castanet-Tolosan France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 2594; CNRS; Castanet-Tolosan France
| | - Magali SanCristobal
- UMR 1388 Génétique, Physiologie et Systèmes d'Elevage; INRA; Castanet-Tolosan France
- UMR 1388 Génétique, Physiologie et Systèmes d'Elevage; Université de Toulouse INPT ENSAT; Castanet-Tolosan France
- UMR 1388 Génétique, Physiologie et Systèmes d'Elevage; Université de Toulouse INPT ENVT; Toulouse France
| | - Saida Danoun
- Laboratoire de Recherches en Sciences Végétales (LRSV); UMR 5546; Université de Toulouse, UPS; Castanet-Tolosan France
- Laboratoire de Recherches en Sciences Végétales (LRSV); UMR 5546; CNRS; Castanet-Tolosan France
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology; Philipps-Universität Marburg; Marburg Germany
| | - Paul Soreau
- CEA Cadarache; IBEB-SBVME; Research Group in Applied Phytotechnics; UMR 6191 CNRS-CEA; Aix-Marseille University; Saint-Paul-lez-Durance Cedex France
| | - Matthieu Arlat
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 441; INRA; Castanet-Tolosan France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 2594; CNRS; Castanet-Tolosan France
- Université de Toulouse, UPS; Toulouse France
| | - Emmanuelle Lauber
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 441; INRA; Castanet-Tolosan France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 2594; CNRS; Castanet-Tolosan France
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21
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Characterization of the pyrophosphate-dependent 6-phosphofructokinase from Xanthomonas campestris pv. campestris. Arch Biochem Biophys 2014; 546:53-63. [DOI: 10.1016/j.abb.2014.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 01/23/2014] [Accepted: 01/26/2014] [Indexed: 01/01/2023]
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Schmidtke C, Abendroth U, Brock J, Serrania J, Becker A, Bonas U. Small RNA sX13: a multifaceted regulator of virulence in the plant pathogen Xanthomonas. PLoS Pathog 2013; 9:e1003626. [PMID: 24068933 PMCID: PMC3771888 DOI: 10.1371/journal.ppat.1003626] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 08/01/2013] [Indexed: 01/12/2023] Open
Abstract
Small noncoding RNAs (sRNAs) are ubiquitous posttranscriptional regulators of gene expression. Using the model plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv), we investigated the highly expressed and conserved sRNA sX13 in detail. Deletion of sX13 impinged on Xcv virulence and the expression of genes encoding components and substrates of the Hrp type III secretion (T3S) system. qRT-PCR analyses revealed that sX13 promotes mRNA accumulation of HrpX, a key regulator of the T3S system, whereas the mRNA level of the master regulator HrpG was unaffected. Complementation studies suggest that sX13 acts upstream of HrpG. Microarray analyses identified 63 sX13-regulated genes, which are involved in signal transduction, motility, transcriptional and posttranscriptional regulation and virulence. Structure analyses of in vitro transcribed sX13 revealed a structure with three stable stems and three apical C-rich loops. A computational search for putative regulatory motifs revealed that sX13-repressed mRNAs predominantly harbor G-rich motifs in proximity of translation start sites. Mutation of sX13 loops differentially affected Xcv virulence and the mRNA abundance of putative targets. Using a GFP-based reporter system, we demonstrated that sX13-mediated repression of protein synthesis requires both the C-rich motifs in sX13 and G-rich motifs in potential target mRNAs. Although the RNA-binding protein Hfq was dispensable for sX13 activity, the hfq mRNA and Hfq::GFP abundance were negatively regulated by sX13. In addition, we found that G-rich motifs in sX13-repressed mRNAs can serve as translational enhancers and are located at the ribosome-binding site in 5% of all protein-coding Xcv genes. Our study revealed that sX13 represents a novel class of virulence regulators and provides insights into sRNA-mediated modulation of adaptive processes in the plant pathogen Xanthomonas. Since the discovery of the first regulatory RNA in 1981, hundreds of small RNAs (sRNAs) have been identified in bacteria. Although sRNA-mediated control of virulence was demonstrated for numerous animal- and human-pathogenic bacteria, sRNAs and their functions in plant-pathogenic bacteria have been enigmatic. We discovered that the sRNA sX13 is a novel virulence regulator of Xanthomonas campestris pv. vesicatoria (Xcv), which causes bacterial spot disease on pepper and tomato. sX13 contributes to the Xcv-plant interaction by promoting the synthesis of an essential pathogenicity factor of Xcv, i. e., the type III secretion system. Thus, in addition to transcriptional regulation, sRNA-mediated posttranscriptional regulation contributes to virulence of plant-pathogenic xanthomonads. To repress target mRNAs carrying G-rich motifs, sX13 employs C-rich loops. Hence, sX13 exhibits striking structural similarity to sRNAs in distantly related human pathogens, e. g., Staphylococcus aureus and Helicobacter pylori, suggesting that structure-driven target regulation via C-rich motifs represents a conserved feature of sRNA-mediated posttranscriptional regulation. Furthermore, sX13 is the first sRNA shown to control the mRNA level of hfq, which encodes a conserved RNA-binding protein required for sRNA activity and virulence in many enteric bacteria.
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Affiliation(s)
- Cornelius Schmidtke
- Institute for Biology, Department of Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
- * E-mail: (CS); (UB)
| | - Ulrike Abendroth
- Institute for Biology, Department of Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Juliane Brock
- Institute for Biology, Department of Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Javier Serrania
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Ulla Bonas
- Institute for Biology, Department of Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
- * E-mail: (CS); (UB)
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Pini F, Frage B, Ferri L, De Nisco NJ, Mohapatra SS, Taddei L, Fioravanti A, Dewitte F, Galardini M, Brilli M, Villeret V, Bazzicalupo M, Mengoni A, Walker GC, Becker A, Biondi EG. The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti. Mol Microbiol 2013; 90:54-71. [PMID: 23909720 DOI: 10.1111/mmi.12347] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2013] [Indexed: 01/09/2023]
Abstract
Sinorhizobium meliloti is a soil bacterium that invades the root nodules it induces on Medicago sativa, whereupon it undergoes an alteration of its cell cycle and differentiates into nitrogen-fixing, elongated and polyploid bacteroid with higher membrane permeability. In Caulobacter crescentus, a related alphaproteobacterium, the principal cell cycle regulator, CtrA, is inhibited by the phosphorylated response regulator DivK. The phosphorylation of DivK depends on the histidine kinase DivJ, while PleC is the principal phosphatase for DivK. Despite the importance of the DivJ in C. crescentus, the mechanistic role of this kinase has never been elucidated in other Alphaproteobacteria. We show here that the histidine kinases DivJ together with CbrA and PleC participate in a complex phosphorylation system of the essential response regulator DivK in S. meliloti. In particular, DivJ and CbrA are involved in DivK phosphorylation and in turn CtrA inactivation, thereby controlling correct cell cycle progression and the integrity of the cell envelope. In contrast, the essential PleC presumably acts as a phosphatase of DivK. Interestingly, we found that a DivJ mutant is able to elicit nodules and enter plant cells, but fails to establish an effective symbiosis suggesting that proper envelope and/or low CtrA levels are required for symbiosis.
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Affiliation(s)
- Francesco Pini
- Interdisciplinary Research Institute USR3078, CNRS-Université Lille Nord de France, 50 avenue de Halley, Villeneuve d'Ascq Cedex, France
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Establishment, in silico analysis, and experimental verification of a large-scale metabolic network of the xanthan producing Xanthomonas campestris pv. campestris strain B100. J Biotechnol 2013; 167:123-34. [DOI: 10.1016/j.jbiotec.2013.01.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/28/2013] [Accepted: 01/28/2013] [Indexed: 11/20/2022]
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Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates. BMC Microbiol 2012; 12:116. [PMID: 22720735 PMCID: PMC3438084 DOI: 10.1186/1471-2180-12-116] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 05/31/2012] [Indexed: 11/21/2022] Open
Abstract
Background Plant root exudates have been shown to play an important role in mediating interactions between plant growth-promoting rhizobacteria (PGPR) and their host plants. Most investigations were performed on Gram-negative rhizobacteria, while much less is known about Gram-positive rhizobacteria. To elucidate early responses of PGPR to root exudates, we investigated changes in the transcriptome of a Gram-positive PGPR to plant root exudates. Results Bacillus amyloliquefaciens FZB42 is a well-studied Gram-positive PGPR. To obtain a comprehensive overview of FZB42 gene expression in response to maize root exudates, microarray experiments were performed. A total of 302 genes representing 8.2% of the FZB42 transcriptome showed significantly altered expression levels in the presence of root exudates. The majority of the genes (261) was up-regulated after incubation of FZB42 with root exudates, whereas only 41 genes were down-regulated. Several groups of the genes which were strongly induced by the root exudates are involved in metabolic pathways relating to nutrient utilization, bacterial chemotaxis and motility, and non-ribosomal synthesis of antimicrobial peptides and polyketides. Conclusions Here we present a transcriptome analysis of the root-colonizing bacterium Bacillus amyloliquefaciens FZB42 in response to maize root exudates. The 302 genes identified as being differentially transcribed are proposed to be involved in interactions of Gram-positive bacteria with plants.
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Flügel M, Becker A, Gartemann KH, Eichenlaub R. Analysis of the interaction of Clavibacter michiganensis subsp. michiganensis with its host plant tomato by genome-wide expression profiling. J Biotechnol 2012; 160:42-54. [PMID: 22326627 DOI: 10.1016/j.jbiotec.2012.01.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 01/12/2012] [Accepted: 01/24/2012] [Indexed: 11/26/2022]
Abstract
Genome-wide expression profiles of the phytopathogenic actinomycete Clavibacter michiganensis subsp. michiganensis (Cmm) strain NCPPB382 were analyzed using a 70mer oligonucleotide microarray. Cmm causes bacterial wilt and canker of tomato, a systemic disease leading to substantial economic losses worldwide. Global gene expression was monitored in vitro after long- and short-term incubation with tomato homogenate to simulate conditions in planta and in vivo ten days after inoculation of tomatoes. Surprisingly, both in the presence of tomato homogenate and in planta known virulence genes (celA, chpC, ppaA/C) were down-regulated indicating that the encoded extracellular enzymes are dispensable in late infection stages where plant tissue has already been heavily destroyed. In contrast, some genes of the tomA-region which are involved in sugar metabolism showed an enhanced RNA-level after permanent growth in supplemented medium. Therefore, these genes may be important for utilization of plant derived nutrients. In the plant Cmm exhibited an expression profile completely different from that in vitro. Especially, the strong expression of genes of the wco-cluster (extracellular polysaccharide II), 10 genes encoding surface or pilus assembly proteins, and CMM_2382, coding for a putative perforin suggest a possible role of these genes in the plant-pathogenic interaction.
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Affiliation(s)
- Monika Flügel
- Lehrstuhl für Gentechnologie/Mikrobiologie, Fakultät für Biologie, Universität Bielefeld, Universitätsstraße 25, Bielefeld, Germany
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Insights into the genome of the xanthan-producing phytopathogen Xanthomonas arboricola pv. pruni 109 by comparative genomic hybridization. J Biotechnol 2011; 155:40-9. [DOI: 10.1016/j.jbiotec.2011.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 04/05/2011] [Accepted: 04/18/2011] [Indexed: 11/20/2022]
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Krol E, Becker A. ppGpp in Sinorhizobium meliloti: biosynthesis in response to sudden nutritional downshifts and modulation of the transcriptome. Mol Microbiol 2011; 81:1233-54. [PMID: 21696469 DOI: 10.1111/j.1365-2958.2011.07752.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sinorhizobium meliloti Rm2011 responds to sudden shifts to nitrogen or carbon starvation conditions by an accumulation of the stringent response alarmone ppGpp and remodelling of the transcriptome. The gene product of relA, Rel(Sm) , responsible for synthesis of ppGpp, shows functional similarities to E. coli SpoT. Using promoter-egfp gene fusions, we showed that in Rm2011 relA is expressed at a low rate, as a readthrough from the rpoZ promoter and from its own weak promoter. The low level of relA expression is physiologically relevant, since overexpression of Rel(Sm) inhibits ppGpp accumulation. The N-terminal portion of Rel(Sm) is required for ppGpp degradation in nutrient-sufficient cells and might be involved in regulation of the ppGpp synthase and hydrolase activities of the protein. Expression profiling of S. meliloti subjected to sudden nitrogen or carbon downshifts revealed that repression of 'house-keeping' genes is largely dependent on relA whereas activation of gene targets of the stress sigma factor RpoE2 occurred independently of relA. The regulatory genes nifA, ntrB, aniA and sinR, as well as genes related to modulation of protein biosynthesis and nucleotide catabolism, were induced in a relA-dependent manner. dksA was required for the majority of the relA-dependent regulations.
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Affiliation(s)
- Elizaveta Krol
- Faculty of Biology and Center for Systems Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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Haag AF, Wehmeier S, Muszyński A, Kerscher B, Fletcher V, Berry SH, Hold GL, Carlson RW, Ferguson GP. Biochemical characterization of Sinorhizobium meliloti mutants reveals gene products involved in the biosynthesis of the unusual lipid A very long-chain fatty acid. J Biol Chem 2011; 286:17455-66. [PMID: 21454518 PMCID: PMC3093819 DOI: 10.1074/jbc.m111.236356] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 03/25/2011] [Indexed: 11/06/2022] Open
Abstract
Sinorhizobium meliloti forms a symbiosis with the legume alfalfa, whereby it differentiates into a nitrogen-fixing bacteroid. The lipid A species of S. meliloti are modified with very long-chain fatty acids (VLCFAs), which play a central role in bacteroid development. A six-gene cluster was hypothesized to be essential for the biosynthesis of VLCFA-modified lipid A. Previously, two cluster gene products, AcpXL and LpxXL, were found to be essential for S. meliloti lipid A VLCFA biosynthesis. In this paper, we show that the remaining four cluster genes are all involved in lipid A VLCFA biosynthesis. Therefore, we have identified novel gene products involved in the biosynthesis of these unusual lipid modifications. By physiological characterization of the cluster mutant strains, we demonstrate the importance of this gene cluster in the legume symbiosis and for growth in the absence of salt. Bacterial LPS species modified with VLCFAs are substantially less immunogenic than Escherichia coli LPS species, which lack VLCFAs. However, we show that the VLCFA modifications do not suppress the immunogenicity of S. meliloti LPS or affect the ability of S. meliloti to induce fluorescent plant defense molecules within the legume. Because VLCFA-modified lipids are produced by other rhizobia and mammalian pathogens, these findings will also be important in understanding the function and biosynthesis of these unusual fatty acids in diverse bacterial species.
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Affiliation(s)
- Andreas F. Haag
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
| | - Silvia Wehmeier
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
| | - Artur Muszyński
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | | | - Vivien Fletcher
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
| | - Susan H. Berry
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
| | - Georgina L. Hold
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
| | - Russell W. Carlson
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Gail P. Ferguson
- From the School of Medicine and Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom and
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Insights into the extracytoplasmic stress response of Xanthomonas campestris pv. campestris: role and regulation of {sigma}E-dependent activity. J Bacteriol 2010; 193:246-64. [PMID: 20971899 DOI: 10.1128/jb.00884-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Xanthomonas campestris pv. campestris is an epiphytic bacterium that can become a vascular pathogen responsible for black rot disease of crucifers. To adapt gene expression in response to ever-changing habitats, phytopathogenic bacteria have evolved signal transduction regulatory pathways, such as extracytoplasmic function (ECF) σ factors. The alternative sigma factor σ(E), encoded by rpoE, is crucial for envelope stress response and plays a role in the pathogenicity of many bacterial species. Here, we combine different approaches to investigate the role and mechanism of σ(E)-dependent activation in X. campestris pv. campestris. We show that the rpoE gene is organized as a single transcription unit with the anti-σ gene rseA and the protease gene mucD and that rpoE transcription is autoregulated. rseA and mucD transcription is also controlled by a highly conserved σ(E)-dependent promoter within the σ(E) gene sequence. The σ(E)-mediated stress response is required for stationary-phase survival, resistance to cadmium, and adaptation to membrane-perturbing stresses (elevated temperature and ethanol). Using microarray technology, we started to define the σ(E) regulon of X. campestris pv. campestris. These genes encode proteins belonging to different classes, including periplasmic or membrane proteins, biosynthetic enzymes, classical heat shock proteins, and the heat stress σ factor σ(H). The consensus sequence for the predicted σ(E)-regulated promoter elements is GGAACTN(15-17)GTCNNA. Determination of the rpoH transcription start site revealed that rpoH was directly regulated by σ(E) under both normal and heat stress conditions. Finally, σ(E) activity is regulated by the putative regulated intramembrane proteolysis (RIP) proteases RseP and DegS, as previously described in many other bacteria. However, our data suggest that RseP and DegS are not only dedicated to RseA cleavage and that the proteolytic cascade of RseA could involve other proteases.
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Soto-Suárez M, Bernal D, González C, Szurek B, Guyot R, Tohme J, Verdier V. In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1. BMC Microbiol 2010; 10:170. [PMID: 20540733 PMCID: PMC2893596 DOI: 10.1186/1471-2180-10-170] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 06/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial leaf blight causes significant yield losses in rice crops throughout Asia and Africa. Although both the Asian and African strains of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo), induce similar symptoms, they are nevertheless genetically different, with the African strains being more closely related to the Asian X. oryzae pv. oryzicola (Xoc). RESULTS Changes in gene expression of the African Xoo strain MAI1 in the susceptible rice cultivar Nipponbare were profiled, using an SSH Xoo DNA microarray. Microarray hybridization was performed comparing bacteria recovered from plant tissues at 1, 3, and 6 days after inoculation (dai) with bacteria grown in vitro. A total of 710 bacterial genes were found to be differentially expressed, with 407 up-regulated and 303 down-regulated. Expression profiling indicated that less than 20% of the 710 bacterial transcripts were induced in the first 24 h after inoculation, whereas 63% were differentially expressed at 6 dai. The 710 differentially expressed genes were one-end sequenced. 535 sequences were obtained from which 147 non-redundant sequences were identified. Differentially expressed genes were related to metabolism, secretion and transport, pathogen adherence to plant tissues, plant cell-wall degradation, IS elements, and virulence. In addition, various other genes encoding proteins with unknown function or showing no similarity to other proteins were also induced. The Xoo MAI1 non-redundant set of sequences was compared against several X. oryzae genomes, revealing a specific group of genes that was present only in MAI1. Numerous IS elements were also found to be differentially expressed. Quantitative real-time PCR confirmed 86% of the identified profile on a set of 14 genes selected according to the microarray analysis. CONCLUSIONS This is the first report to compare the expression of Xoo genes in planta across different time points during infection. This work shows that as-yet-unidentified and potentially new virulence factors are appearing in an emerging African pathogen. It also confirms that African Xoo strains do differ from their Asian counterparts, even at the transcriptional level.
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Affiliation(s)
- Mauricio Soto-Suárez
- UMR 5096 IRD-CNRS-Université de Perpignan, Laboratoire Génome et Développement des Plantes, Institut de Recherche pour le Développement, 911 Avenue Agropolis BP 64501, 34394 Montpellier Cedex 5, France
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Schlüter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jänicke S, Becker JD, Giegerich R, Becker A. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics 2010; 11:245. [PMID: 20398411 PMCID: PMC2873474 DOI: 10.1186/1471-2164-11-245] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 04/17/2010] [Indexed: 12/03/2022] Open
Abstract
Background Small untranslated RNAs (sRNAs) are widespread regulators of gene expression in bacteria. This study reports on a comprehensive screen for sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti applying deep sequencing of cDNAs and microarray hybridizations. Results A total of 1,125 sRNA candidates that were classified as trans-encoded sRNAs (173), cis-encoded antisense sRNAs (117), mRNA leader transcripts (379), and sense sRNAs overlapping coding regions (456) were identified in a size range of 50 to 348 nucleotides. Among these were transcripts corresponding to 82 previously reported sRNA candidates. Enrichment for RNAs with primary 5'-ends prior to sequencing of cDNAs suggested transcriptional start sites corresponding to 466 predicted sRNA regions. The consensus σ70 promoter motif CTTGAC-N17-CTATAT was found upstream of 101 sRNA candidates. Expression patterns derived from microarray hybridizations provided further information on conditions of expression of a number of sRNA candidates. Furthermore, GenBank, EMBL, DDBJ, PDB, and Rfam databases were searched for homologs of the sRNA candidates identified in this study. Searching Rfam family models with over 1,000 sRNA candidates, re-discovered only those sequences from S. meliloti already known and stored in Rfam, whereas BLAST searches suggested a number of homologs in related alpha-proteobacteria. Conclusions The screening data suggests that in S. meliloti about 3% of the genes encode trans-encoded sRNAs and about 2% antisense transcripts. Thus, this first comprehensive screen for sRNAs applying deep sequencing in an alpha-proteobacterium shows that sRNAs also occur in high number in this group of bacteria.
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Affiliation(s)
- Jan-Philip Schlüter
- Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany
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Dondrup M, Albaum SP, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Küster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Pühler A, Goesmann A. EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 2009; 10:50. [PMID: 19200358 PMCID: PMC2645365 DOI: 10.1186/1471-2105-10-50] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Accepted: 02/06/2009] [Indexed: 11/10/2022] Open
Abstract
Background Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.
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Affiliation(s)
- Michael Dondrup
- Computational Genomics, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany.
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Valverde C, Livny J, Schlüter JP, Reinkensmeier J, Becker A, Parisi G. Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics 2008; 9:416. [PMID: 18793445 PMCID: PMC2573895 DOI: 10.1186/1471-2164-9-416] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Accepted: 09/16/2008] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Small non-coding RNAs (sRNAs) have emerged as ubiquitous regulatory elements in bacteria and other life domains. However, few sRNAs have been identified outside several well-studied species of gamma-proteobacteria and thus relatively little is known about the role of RNA-mediated regulation in most other bacterial genera. Here we have conducted a computational prediction of putative sRNA genes in intergenic regions (IgRs) of the symbiotic alpha-proteobacterium S. meliloti 1021 and experimentally confirmed the expression of dozens of these candidate loci in the closely related strain S. meliloti 2011. RESULTS Our first sRNA candidate compilation was based mainly on the output of the sRNAPredictHT algorithm. A thorough manual sequence analysis of the curated list rendered an initial set of 18 IgRs of interest, from which 14 candidates were detected in strain 2011 by Northern blot and/or microarray analysis. Interestingly, the intracellular transcript levels varied in response to various stress conditions. We developed an alternative computational method to more sensitively predict sRNA-encoding genes and score these predicted genes based on several features to allow identification of the strongest candidates. With this novel strategy, we predicted 60 chromosomal independent transcriptional units that, according to our annotation, represent strong candidates for sRNA-encoding genes, including most of the sRNAs experimentally verified in this work and in two other contemporary studies. Additionally, we predicted numerous candidate sRNA genes encoded in megaplasmids pSymA and pSymB. A significant proportion of the chromosomal- and megaplasmid-borne putative sRNA genes were validated by microarray analysis in strain 2011. CONCLUSION Our data extend the number of experimentally detected S. meliloti sRNAs and significantly expand the list of putative sRNA-encoding IgRs in this and closely related alpha-proteobacteria. In addition, we have developed a computational method that proved useful to predict sRNA-encoding genes in S. meliloti. We anticipate that this predictive approach can be flexibly implemented in many other bacterial species.
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Affiliation(s)
- Claudio Valverde
- Programa Interacciones Biológicas, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, Buenos Aires, B1876BXD, Argentina.
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Towards systems metabolic engineering of microorganisms for amino acid production. Curr Opin Biotechnol 2008; 19:454-60. [PMID: 18760356 DOI: 10.1016/j.copbio.2008.08.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 07/23/2008] [Accepted: 08/01/2008] [Indexed: 11/23/2022]
Abstract
Microorganisms capable of efficient production of amino acids have traditionally been developed by random mutation and selection method, which might cause unwanted physiological changes in cellular metabolism. Rational genome-wide metabolic engineering based on systems and synthetic biology tools, which is termed 'systems metabolic engineering', is rising as an alternative to overcome these problems. Recently, several amino acid producers have been successfully developed by systems metabolic engineering, where the metabolic engineering procedures were performed within a systems biology framework, and entire metabolic networks, including complex regulatory circuits, were engineered in an integrated manner. Here we review the current status of systems metabolic engineering successfully applied for developing amino acid producing strains and discuss future prospects.
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