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Hu Y, Zhang J, Zhang A. Genome-Wide Transcriptome Analysis of a Virulent sRNA, Trans217, in Xanthomonas oryzae pv. oryzae ( Xoo), the Causative Agent of Rice Bacterial Blight. Microorganisms 2024; 12:1684. [PMID: 39203526 PMCID: PMC11357379 DOI: 10.3390/microorganisms12081684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/10/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Small non-coding RNAs (sRNAs) act as post-transcriptional regulators to participate in many cellular processes. Among these, sRNA trans217 has been identified as a key virulent factor associated with pathogenicity in rice, triggering hypersensitive reactions in non-host tobacco and facilitating the secretion of the PthXo1 effector in Xanthomonas oryzae pv. oryzae (Xoo) strain PXO99A. Elucidating potential targets and downstream regulatory genes is crucial for understanding cellular networks governing pathogenicity and plant resistance. To explore the targets regulated by sRNA trans217, transcriptome sequencing was carried out to assess differential expression genes (DEGs) between the wild-type strain PXO99A and a mutant lacking the sRNA fragment under both virulence-inducing or normal growth conditions. DEG analysis revealed that sRNA trans217 was responsible for diverse functions, such as type III secretion system (T3SS), glutamate synthase activity, and oxidative stress response. Three genes were selected for further investigation due to their significant differential expression and biological relevance. Deletion of PXO_RS08490 attenuated the pathogenicity of Xoo in rice and reduced the tolerance level of PXO99A to hydrogen peroxide. These findings suggest a regulatory role of sRNA trans217 in modulating bacterial virulence through multiple gene targets, either directly or indirectly.
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Affiliation(s)
- Yiqun Hu
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China;
- Anhui Province Key Laboratory of Pesticide Resistance Management on Grain and Vegetable Pests, Hefei 230031, China
| | - Jianjian Zhang
- Department of science research University of Science and Technology of China, Hefei 230026, China;
| | - Aifang Zhang
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China;
- Anhui Province Key Laboratory of Pesticide Resistance Management on Grain and Vegetable Pests, Hefei 230031, China
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Frantsuzova E, Bogun A, Kopylova O, Vetrova A, Solyanikova I, Streletskii R, Delegan Y. Genomic, Phylogenetic and Physiological Characterization of the PAH-Degrading Strain Gordonia polyisoprenivorans 135. BIOLOGY 2024; 13:339. [PMID: 38785821 PMCID: PMC11117675 DOI: 10.3390/biology13050339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/07/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
The strain Gordonia polyisoprenivorans 135 is able to utilize a wide range of aromatic compounds. The aim of this work was to study the features of genetic organization and biotechnological potential of the strain G. polyisoprenivorans 135 as a degrader of aromatic compounds. The study of the genome of the strain 135 and the pangenome of the G. polyisoprenivorans species revealed that some genes, presumably involved in PAH catabolism, are atypical for Gordonia and belong to the pangenome of Actinobacteria. Analyzing the intergenic regions of strain 135 alongside the "panIGRome" of G. polyisoprenivorans showed that some intergenic regions in strain 135 also differ from those located between the same pairs of genes in related strains. The strain G. polyisoprenivorans 135 in our work utilized naphthalene (degradation degree 39.43%) and grew actively on salicylate. At present, this is the only known strain of G. polyisoprenivorans with experimentally confirmed ability to utilize these compounds.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Olga Kopylova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
- Pushchino Branch of Federal State Budgetary Educational Institution of Higher Education “Russian Biotechnology University (ROSBIOTECH)”, 142290 Pushchino, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Inna Solyanikova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
- Regional Microbiological Center, Belgorod State University, 308015 Belgorod, Russia
| | - Rostislav Streletskii
- Laboratory of Ecological Soil Science, Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
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Singh RN, Sani RK. Genome-Wide Computational Prediction and Analysis of Noncoding RNAs in Oleidesulfovibrio alaskensis G20. Microorganisms 2024; 12:960. [PMID: 38792789 PMCID: PMC11124144 DOI: 10.3390/microorganisms12050960] [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: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Noncoding RNAs (ncRNAs) play key roles in the regulation of important pathways, including cellular growth, stress management, signaling, and biofilm formation. Sulfate-reducing bacteria (SRB) contribute to huge economic losses causing microbial-induced corrosion through biofilms on metal surfaces. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation. This study aimed to identify ncRNAs in the genome of a model SRB, Oleidesulfovibrio alaskensis G20 (OA G20). Three in silico approaches revealed genome-wide distribution of 37 ncRNAs excluding tRNAs in the OA G20. These ncRNAs belonged to 18 different Rfam families. This study identified riboswitches, sRNAs, RNP, and SRP. The analysis revealed that these ncRNAs could play key roles in the regulation of several pathways of biosynthesis and transport involved in biofilm formation by OA G20. Three sRNAs, Pseudomonas P10, Hammerhead type II, and sX4, which were found in OA G20, are rare and their roles have not been determined in SRB. These results suggest that applying various computational methods could enrich the results and lead to the discovery of additional novel ncRNAs, which could lead to understanding the "rules of life of OA G20" during biofilm formation.
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Affiliation(s)
- Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota Mines, Rapid City, SD 57701, USA
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Pandey SS. The Role of Iron in Phytopathogenic Microbe-Plant Interactions: Insights into Virulence and Host Immune Response. PLANTS (BASEL, SWITZERLAND) 2023; 12:3173. [PMID: 37687419 PMCID: PMC10563075 DOI: 10.3390/plants12173173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
Iron is an essential element required for the growth and survival of nearly all forms of life. It serves as a catalytic component in multiple enzymatic reactions, such as photosynthesis, respiration, and DNA replication. However, the excessive accumulation of iron can result in cellular toxicity due to the production of reactive oxygen species (ROS) through the Fenton reaction. Therefore, to maintain iron homeostasis, organisms have developed a complex regulatory network at the molecular level. Besides catalyzing cellular redox reactions, iron also regulates virulence-associated functions in several microbial pathogens. Hosts and pathogens have evolved sophisticated strategies to compete against each other over iron resources. Although the role of iron in microbial pathogenesis in animals has been extensively studied, mechanistic insights into phytopathogenic microbe-plant associations remain poorly understood. Recent intensive research has provided intriguing insights into the role of iron in several plant-pathogen interactions. This review aims to describe the recent advances in understanding the role of iron in the lifestyle and virulence of phytopathogenic microbes, focusing on bacteria and host immune responses.
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Affiliation(s)
- Sheo Shankar Pandey
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati 781035, India; ; Tel.: +91-361-2270095 (ext. 216)
- Citrus Research and Education Center (CREC), Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, USA
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Jiang C, Li Z, Zheng L, Yu Y, Niu D. Small RNAs: Efficient and miraculous effectors that play key roles in plant-microbe interactions. MOLECULAR PLANT PATHOLOGY 2023; 24:999-1013. [PMID: 37026481 PMCID: PMC10346379 DOI: 10.1111/mpp.13329] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant-pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18-30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence-related sRNAs in the response to pathogens and our current understanding of their effects on plant-pathogen interactions. The main content of this review article includes the roles of sRNAs in plant-pathogen interactions, cross-kingdom sRNA trafficking between host and pathogen, and the application of RNA-based fungicides for plant disease control.
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Affiliation(s)
- Chun‐Hao Jiang
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Zi‐Jie Li
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Li‐Yu Zheng
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Yi‐Yang Yu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Dong‐Dong Niu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
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Forquet R, Jiang X, Nasser W, Hommais F, Reverchon S, Meyer S. Mapping the Complex Transcriptional Landscape of the Phytopathogenic Bacterium Dickeya dadantii. mBio 2022; 13:e0052422. [PMID: 35491820 PMCID: PMC9239193 DOI: 10.1128/mbio.00524-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Dickeya dadantii is a phytopathogenic bacterium that causes soft rot in a wide range of plant hosts worldwide and a model organism for studying virulence gene regulation. The present study provides a comprehensive and annotated transcriptomic map of D. dadantii obtained by a computational method combining five independent transcriptomic data sets: (i) paired-end RNA sequencing (RNA-seq) data for a precise reconstruction of the RNA landscape; (ii) DNA microarray data providing transcriptional responses to a broad variety of environmental conditions; (iii) long-read Nanopore native RNA-seq data for isoform-level transcriptome validation and determination of transcription termination sites; (iv) differential RNA sequencing (dRNA-seq) data for the precise mapping of transcription start sites; (v) in planta DNA microarray data for a comparison of gene expression profiles between in vitro experiments and the early stages of plant infection. Our results show that transcription units sometimes coincide with predicted operons but are generally longer, most of them comprising internal promoters and terminators that generate alternative transcripts of variable gene composition. We characterize the occurrence of transcriptional read-through at terminators, which might play a basal regulation role and explain the extent of transcription beyond the scale of operons. We finally highlight the presence of noncontiguous operons and excludons in the D. dadantii genome, novel genomic arrangements that might contribute to the basal coordination of transcription. The highlighted transcriptional organization may allow D. dadantii to finely adjust its gene expression program for a rapid adaptation to fast-changing environments. IMPORTANCE This is the first transcriptomic map of a Dickeya species. It may therefore significantly contribute to further progress in the field of phytopathogenicity. It is also one of the first reported applications of long-read Nanopore native RNA-seq in prokaryotes. Our findings yield insights into basal rules of coordination of transcription that might be valid for other bacteria and may raise interest in the field of microbiology in general. In particular, we demonstrate that gene expression is coordinated at the scale of transcription units rather than operons, which are larger functional genomic units capable of generating transcripts with variable gene composition for a fine-tuning of gene expression in response to environmental changes. In line with recent studies, our findings indicate that the canonical operon model is insufficient to explain the complexity of bacterial transcriptomes.
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Affiliation(s)
- Raphaël Forquet
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Xuejiao Jiang
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - William Nasser
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Florence Hommais
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Sylvie Reverchon
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Sam Meyer
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
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Boutet E, Djerroud S, Perreault J. Small RNAs beyond Model Organisms: Have We Only Scratched the Surface? Int J Mol Sci 2022; 23:ijms23084448. [PMID: 35457265 PMCID: PMC9029176 DOI: 10.3390/ijms23084448] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 01/27/2023] Open
Abstract
Small RNAs (sRNAs) are essential regulators in the adaptation of bacteria to environmental changes and act by binding targeted mRNAs through base complementarity. Approximately 550 distinct families of sRNAs have been identified since their initial characterization in the 1980s, accelerated by the emergence of RNA-sequencing. Small RNAs are found in a wide range of bacterial phyla, but they are more prominent in highly researched model organisms compared to the rest of the sequenced bacteria. Indeed, Escherichia coli and Salmonella enterica contain the highest number of sRNAs, with 98 and 118, respectively, with Enterobacteriaceae encoding 145 distinct sRNAs, while other bacteria families have only seven sRNAs on average. Although the past years brought major advances in research on sRNAs, we have perhaps only scratched the surface, even more so considering RNA annotations trail behind gene annotations. A distinctive trend can be observed for genes, whereby their number increases with genome size, but this is not observable for RNAs, although they would be expected to follow the same trend. In this perspective, we aimed at establishing a more accurate representation of the occurrence of sRNAs in bacteria, emphasizing the potential for novel sRNA discoveries.
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Roy S, Mittal P, Tayi L, Bondada S, Ray MK, Patel HK, Sonti RV. Xanthomonas oryzae pv. oryzae Exoribonuclease R Is Required for Complete Virulence in Rice, Optimal Motility, and Growth Under Stress. PHYTOPATHOLOGY 2022; 112:501-510. [PMID: 34384245 DOI: 10.1094/phyto-07-21-0310-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: 06/13/2023]
Abstract
Exoribonuclease R (RNase R) is a 3' hydrolytic exoribonuclease that can degrade structured RNA. Mutation in RNase R affects virulence of certain human pathogenic bacteria. The aim of this study was to determine whether RNase R is necessary for virulence of the phytopathogen that causes bacterial blight in rice, Xanthomonas oryzae pv. oryzae (Xoo). In silico analysis has indicated that RNase R is highly conserved among various xanthomonads. Amino acid sequence alignment of Xoo RNase R with RNase R from various taxa indicated that Xoo RNase R clustered with RNase R of order Xanthomonadales. To study its role in virulence, we generated a gene disruption mutant of Xoo RNase R. The Xoo rnr- mutant is moderately virulence deficient, and the complementing strain (rnr-/pHM1::rnr) rescued the virulence deficiency of the mutant. We investigated swimming and swarming motilities in both nutrient-deficient minimal media and nutrient-optimal media. We observed that RNase R mutation has adversely affected the swimming and swarming motilities of Xoo in optimal media. However, in nutrient-deficient media only swimming motility was noticeably affected. Growth curves in optimal media at suboptimal temperature (15°C cold stress) indicate that the Xoo rnr- mutant grows more slowly than the Xoo wild type and complementing strain (rnr-/pHM1::rnr). Given these findings, we report for the first time that RNase R function is necessary for complete virulence of Xoo in rice. It is also important for motility of Xoo in media and for growth of Xoo at suboptimal temperature.
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Affiliation(s)
- Sharmila Roy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Pragya Mittal
- MRC Human Genetics Unit, University of Edinburgh, Crewe Road South, Edinburgh, UK, EH4 2XU
| | - Lavanya Tayi
- Center for Plant Molecular Biology, Osmania University, Tarnaka, Hyderabad, Telangana State, India 500007
| | - Sahitya Bondada
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Malay K Ray
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Ramesh V Sonti
- Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh, India 517507
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Luneau JS, Cerutti A, Roux B, Carrère S, Jardinaud M, Gaillac A, Gris C, Lauber E, Berthomé R, Arlat M, Boulanger A, Noël LD. Xanthomonas transcriptome inside cauliflower hydathodes reveals bacterial virulence strategies and physiological adaptations at early infection stages. MOLECULAR PLANT PATHOLOGY 2022; 23:159-174. [PMID: 34837293 PMCID: PMC8743013 DOI: 10.1111/mpp.13117] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 06/01/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is a seed-transmitted vascular pathogen causing black rot disease on cultivated and wild Brassicaceae. Xcc enters the plant tissues preferentially via hydathodes, which are organs localized at leaf margins. To decipher both physiological and virulence strategies deployed by Xcc during early stages of infection, the transcriptomic profile of Xcc was analysed 3 days after entry into cauliflower hydathodes. Despite the absence of visible plant tissue alterations and despite a biotrophic lifestyle, 18% of Xcc genes were differentially expressed, including a striking repression of chemotaxis and motility functions. The Xcc full repertoire of virulence factors had not yet been activated but the expression of the HrpG regulon composed of 95 genes, including genes coding for the type III secretion machinery important for suppression of plant immunity, was induced. The expression of genes involved in metabolic adaptations such as catabolism of plant compounds, transport functions, sulphur and phosphate metabolism was upregulated while limited stress responses were observed 3 days postinfection. We confirmed experimentally that high-affinity phosphate transport is needed for bacterial fitness inside hydathodes. This analysis provides information about the nutritional and stress status of bacteria during the early biotrophic infection stages and helps to decipher the adaptive strategy of Xcc to the hydathode environment.
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Affiliation(s)
- Julien S. Luneau
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Aude Cerutti
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Brice Roux
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
- Present address:
Brice Roux, HalioDx, Luminy Biotech EntreprisesMarseille Cedex 9France
| | - Sébastien Carrère
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | | | - Antoine Gaillac
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Carine Gris
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Emmanuelle Lauber
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Richard Berthomé
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Matthieu Arlat
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Alice Boulanger
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Laurent D. Noël
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
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Comparative Genomics of Typical and Atypical Aeromonas salmonicida Complete Genomes Revealed New Insights into Pathogenesis Evolution. Microorganisms 2022; 10:microorganisms10010189. [PMID: 35056638 PMCID: PMC8780938 DOI: 10.3390/microorganisms10010189] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Aeromonas salmonicida is a global distributed Gram-negative teleost pathogen, affecting mainly salmonids in fresh and marine environments. A. salmonicida strains are classified as typical or atypical depending on their origin of isolation and phenotype. Five subspecies have been described, where A. salmonicida subsp. salmonicida is the only typical subspecies, and the subsp. achromogenes, masoucida, smithia, and pectinolytica are considered atypical. Genomic differences between A. salmonicida subsp. salmonicida isolates and their relationship with the current classification have not been explored. Here, we sequenced and compared the complete closed genomes of four virulent strains to elucidate their molecular diversity and pathogenic evolution using the more accurate genomic information so far. Phenotypes, biochemical, and enzymatic profiles were determined. PacBio and MiSeq sequencing platforms were utilized for genome sequencing. Comparative genomics showed that atypical strains belong to the subsp. salmonicida, with 99.55% ± 0.25% identity with each other, and are closely related to typical strains. The typical strain A. salmonicida J223 is closely related to typical strains, with 99.17% identity with the A. salmonicida A449. Genomic differences between atypical and typical strains are strictly related to insertion sequences (ISs) activity. The absence and presence of genes encoding for virulence factors, transcriptional regulators, and non-coding RNAs are the most significant differences between typical and atypical strains that affect their phenotypes. Plasmidome plays an important role in A. salmonicida virulence and genome plasticity. Here, we determined that typical strains harbor a larger number of plasmids and virulence-related genes that contribute to its acute virulence. In contrast, atypical strains harbor a single, large plasmid and a smaller number of virulence genes, reflected by their less acute virulence and chronic infection. The relationship between phenotype and A. salmonicida subspecies’ taxonomy is not evident. Comparative genomic analysis based on completed genomes revealed that the subspecies classification is more of a reflection of the ecological niche occupied by bacteria than their divergences at the genomic level except for their accessory genome.
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Osdaghi E, Jones JB, Sharma A, Goss EM, Abrahamian P, Newberry EA, Potnis N, Carvalho R, Choudhary M, Paret ML, Timilsina S, Vallad GE. A centenary for bacterial spot of tomato and pepper. MOLECULAR PLANT PATHOLOGY 2021; 22:1500-1519. [PMID: 34472193 PMCID: PMC8578828 DOI: 10.1111/mpp.13125] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 05/08/2023]
Abstract
DISEASE SYMPTOMS Symptoms include water-soaked areas surrounded by chlorosis turning into necrotic spots on all aerial parts of plants. On tomato fruits, small, water-soaked, or slightly raised pale-green spots with greenish-white halos are formed, ultimately becoming dark brown and slightly sunken with a scabby or wart-like surface. HOST RANGE Main and economically important hosts include different types of tomatoes and peppers. Alternative solanaceous and nonsolanaceous hosts include Datura spp., Hyoscyamus spp., Lycium spp., Nicotiana rustica, Physalis spp., Solanum spp., Amaranthus lividus, Emilia fosbergii, Euphorbia heterophylla, Nicandra physaloides, Physalis pubescens, Sida glomerata, and Solanum americanum. TAXONOMIC STATUS OF THE PATHOGEN Domain, Bacteria; phylum, Proteobacteria; class, Gammaproteobacteria; order, Xanthomonadales; family, Xanthomonadaceae; genus, Xanthomonas; species, X. euvesicatoria, X. hortorum, X. vesicatoria. SYNONYMS (NONPREFERRED SCIENTIFIC NAMES) Bacterium exitiosum, Bacterium vesicatorium, Phytomonas exitiosa, Phytomonas vesicatoria, Pseudomonas exitiosa, Pseudomonas gardneri, Pseudomonas vesicatoria, Xanthomonas axonopodis pv. vesicatoria, Xanthomonas campestris pv. vesicatoria, Xanthomonas cynarae pv. gardneri, Xanthomonas gardneri, Xanthomonas perforans. MICROBIOLOGICAL PROPERTIES Colonies are gram-negative, oxidase-negative, and catalase-positive and have oxidative metabolism. Pale-yellow domed circular colonies of 1-2 mm in diameter grow on general culture media. DISTRIBUTION The bacteria are widespread in Africa, Brazil, Canada and the USA, Australia, eastern Europe, and south-east Asia. Occurrence in western Europe is restricted. PHYTOSANITARY CATEGORIZATION A2 no. 157, EU Annex designation II/A2. EPPO CODES XANTEU, XANTGA, XANTPF, XANTVE.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Jeffrey B. Jones
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Anuj Sharma
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Erica M. Goss
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Peter Abrahamian
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
| | - Eric A. Newberry
- Department of Entomology and Plant PathologyAuburn UniversityAuburnAlabamaUSA
| | - Neha Potnis
- Department of Entomology and Plant PathologyAuburn UniversityAuburnAlabamaUSA
| | - Renato Carvalho
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Manoj Choudhary
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Mathews L. Paret
- Department of Plant PathologyNorth Florida Research and Education CenterUniversity of FloridaQuincyFloridaUSA
| | - Sujan Timilsina
- Plant Pathology DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Gary E. Vallad
- Gulf Coast Research and Education CenterUniversity of FloridaWimaumaFloridaUSA
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12
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Tang D, Chen X, Jia Y, Liang Y, He Y, Lu T, Zhu C, Han B, An S, Tang J. Genome-wide screen and functional analysis in Xanthomonas reveal a large number of mRNA-derived sRNAs, including the novel RsmA-sequester RsmU. MOLECULAR PLANT PATHOLOGY 2020; 21:1573-1590. [PMID: 32969159 PMCID: PMC7694677 DOI: 10.1111/mpp.12997] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/02/2020] [Accepted: 08/26/2020] [Indexed: 05/07/2023]
Abstract
Although bacterial small noncoding RNAs (sRNAs) are known to play a critical role in various cellular processes, including pathogenesis, the identity and action of such sRNAs are still poorly understood in many organisms. Here we have performed a genome-wide screen and functional analysis of the sRNAs in Xanthomonas campestris pv. campestris (Xcc), an important phytopathogen. The 50-500-nt RNA fragments isolated from the wild-type strain grown in a virulence gene-inducing condition were sequenced and a total of 612 sRNA candidates (SRCs) were identified. The majority (82%) of the SRCs were derived from mRNA, rather than specific sRNA genes. A representative panel of 121 SRCs were analysed by northern blotting; 117 SRCs were detected, supporting the contention that the overwhelming majority of the 612 SRCs identified are indeed sRNAs. Phenotypic analysis of strains overexpressing different candidates showed that a particular sRNA, RsmU, acts as a negative regulator of virulence, the hypersensitive response, and cell motility in Xcc. In vitro electrophoretic mobility shift assay and in vivo coimmunoprecipitation analyses indicated that RsmU interacted with the global posttranscriptional regulator RsmA, although sequence analysis displayed that RsmU is not a member of the sRNAs families known to antagonize RsmA. Northern blotting analyses demonstrated that RsmU has two isoforms that are processed from the 3'-untranslated region of the mRNA of XC1332 predicted to encode ComEA, a periplasmic protein required for DNA uptake in bacteria. This work uncovers an unexpected major sRNA biogenesis strategy in bacteria and a hidden layer of sRNA-mediated virulence regulation in Xcc.
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Affiliation(s)
- Dong‐Jie Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Xiao‐Lin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
- Present address:
Plant Protection Research InstituteGuangxi Academy of Agricultural Science174 Daxue RoadNanningGuangxi530007China
| | - Yu Jia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Yu‐Wei Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Yuan‐Ping He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Ting‐Ting Lu
- National Center for Gene Research & Institute of Plant Physiology and EcologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Chuan‐Rang Zhu
- National Center for Gene Research & Institute of Plant Physiology and EcologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Bin Han
- National Center for Gene Research & Institute of Plant Physiology and EcologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Shi‐Qi An
- National Biofilms Innovation CentreBiological SciencesUniversity of SouthamptonSouthamptonUK
| | - Ji‐Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
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13
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Cervantes-Rivera R, Puhar A. Whole-genome Identification of Transcriptional Start Sites by Differential RNA-seq in Bacteria. Bio Protoc 2020; 10:e3757. [PMID: 33659416 PMCID: PMC7842792 DOI: 10.21769/bioprotoc.3757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/25/2020] [Accepted: 07/23/2020] [Indexed: 11/02/2022] Open
Abstract
Gene transcription in bacteria often starts some nucleotides upstream of the start codon. Identifying the specific Transcriptional Start Site (TSS) is essential for genetic manipulation, as in many cases upstream of the start codon there are sequence elements that are involved in gene expression regulation. Taken into account the classical gene structure, we are able to identify two kinds of transcriptional start site: primary and secondary. A primary transcriptional start site is located some nucleotides upstream of the translational start site, while a secondary transcriptional start site is located within the gene encoding sequence. Here, we present a step by step protocol for genome-wide transcriptional start sites determination by differential RNA-sequencing (dRNA-seq) using the enteric pathogen Shigella flexneri serotype 5a strain M90T as model. However, this method can be employed in any other bacterial species of choice. In the first steps, total RNA is purified from bacterial cultures using the hot phenol method. Ribosomal RNA (rRNA) is specifically depleted via hybridization probes using a commercial kit. A 5'-monophosphate-dependent exonuclease (TEX)-treated RNA library enriched in primary transcripts is then prepared for comparison with a library that has not undergone TEX-treatment, followed by ligation of an RNA linker adaptor of known sequence allowing the determination of TSS with single nucleotide precision. Finally, the RNA is processed for Illumina sequencing library preparation and sequenced as purchased service. TSS are identified by in-house bioinformatic analysis. Our protocol is cost-effective as it minimizes the use of commercial kits and employs freely available software.
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Affiliation(s)
- Ramón Cervantes-Rivera
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, 90 187 Umeå, Sweden
- Department of Molecular Biology, Umeå University, 90 187 Umeå, Sweden
| | - Andrea Puhar
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, 90 187 Umeå, Sweden
- Department of Molecular Biology, Umeå University, 90 187 Umeå, Sweden
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14
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Botero D, Monk J, Rodríguez Cubillos MJ, Rodríguez Cubillos A, Restrepo M, Bernal-Galeano V, Reyes A, González Barrios A, Palsson BØ, Restrepo S, Bernal A. Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level. Front Genet 2020; 11:837. [PMID: 32849823 PMCID: PMC7432306 DOI: 10.3389/fgene.2020.00837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 07/10/2020] [Indexed: 01/05/2023] Open
Abstract
Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)+ balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species.
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Affiliation(s)
- David Botero
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Biología Computacional y Ecología Microbiana, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Jonathan Monk
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - María Juliana Rodríguez Cubillos
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | | | - Mariana Restrepo
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Vivian Bernal-Galeano
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Biología Computacional y Ecología Microbiana, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Bernhard Ø. Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Silvia Restrepo
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Adriana Bernal
- Laboratory of Molecular Interactions of Agricultural Microbes, LIMMA, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
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15
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Timilsina S, Potnis N, Newberry EA, Liyanapathiranage P, Iruegas-Bocardo F, White FF, Goss EM, Jones JB. Xanthomonas diversity, virulence and plant-pathogen interactions. Nat Rev Microbiol 2020; 18:415-427. [PMID: 32346148 DOI: 10.1038/s41579-020-0361-8] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 12/19/2022]
Abstract
Xanthomonas spp. encompass a wide range of plant pathogens that use numerous virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine recent insights into host-pathogen co-evolution, diversity in Xanthomonas populations and host specificity of Xanthomonas spp. that have substantially improved our fundamental understanding of pathogen biology. We emphasize the virulence factors in xanthomonads, such as type III secreted effectors including transcription activator-like effectors, type II secretion systems, diversity resulting in host specificity, evolution of emerging strains, activation of susceptibility genes and strategies of host evasion. We summarize the genomic diversity in several Xanthomonas spp. and implications for disease outbreaks, management strategies and breeding for disease resistance.
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Affiliation(s)
- Sujan Timilsina
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Neha Potnis
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Eric A Newberry
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | | | | | - Frank F White
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Erica M Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Jeffrey B Jones
- Plant Pathology Department, University of Florida, Gainesville, FL, USA.
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16
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Structure of a Core Promoter in Bifidobacterium longum NCC2705. J Bacteriol 2020; 202:JB.00540-19. [PMID: 31964699 DOI: 10.1128/jb.00540-19] [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: 08/21/2019] [Accepted: 01/14/2020] [Indexed: 01/04/2023] Open
Abstract
Bacterial promoters consist of core sequence motifs termed -35 and -10 boxes. The consensus motifs are TTGACA and TATAAT, respectively, which were identified from leading investigations on Escherichia coli However, the consensus sequences are not likely to fit genetically divergent bacteria. The sigma factor of the genus Bifidobacterium has a characteristic polar domain in the N terminus, suggesting the possibility of specific promoter recognition. We reevaluated the structure of Bifidobacterium longum NCC2705 promoters and compared them to other bacteria. Transcriptional start sites (TSSs) of the B. longum NCC2705 strain were identified using transcriptome sequencing (RNA-Seq) analysis to extract promoter regions. Conserved motifs of a bifidobacterial promoter were determined using regions upstream of TSSs and a hidden Markov model. As a result, consensus motifs of the -35 and -10 boxes were TTGTGC and TACAAT, respectively. To assess each base of both motifs, we constructed 37 plasmids based on pKO403-TPCTcon, including the hup promoter connected with a chloramphenicol acetyltransferase as a reporter gene. This reporter assay showed two optimal motifs of the -35 and -10 boxes, namely, TTGNNN and TANNNT, respectively. We further analyzed spacer lengths between the -35 and -10 boxes via a bioinformatics approach. The spacer lengths predominant in bacteria have been generally reported to be approximately 17 bp. In contrast, the predominant spacer lengths in the genus Bifidobacterium and related species were 11 bp, in addition to 17 bp. A reporter assay to assess the spacer lengths indicated that the 11-bp spacer length produced unusually high activity.IMPORTANCE The structures of sigma factors vary among bacterial strains, indicating that recognition rules may also vary. Therefore, we investigated the promoter structure of Bifidobacterium longum NCC2705 using a bioinformatics approach and wet analyses. The most frequent and optimal motifs were similar to other bacterial consensus motifs. The optimal spacer length between the two boxes was reported to be 17 bp. It is widely applied to a bioinformatics approach for other bacteria. Unexpectedly, conserved spacer lengths were 11 bp as well as 17 bp in the genus Bifidobacterium Moreover, the sigma factor of the genus Bifidobacterium has a characteristic domain in the N terminus which may contribute to the additional functions. Hence, it would be valuable to reevaluate the promoter in other organisms.
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17
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Slager J, Aprianto R, Veening JW. Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39. Nucleic Acids Res 2019; 46:9971-9989. [PMID: 30107613 PMCID: PMC6212727 DOI: 10.1093/nar/gky725] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/30/2018] [Indexed: 12/27/2022] Open
Abstract
A precise understanding of the genomic organization into transcriptional units and their regulation is essential for our comprehension of opportunistic human pathogens and how they cause disease. Using single-molecule real-time (PacBio) sequencing we unambiguously determined the genome sequence of Streptococcus pneumoniae strain D39 and revealed several inversions previously undetected by short-read sequencing. Significantly, a chromosomal inversion results in antigenic variation of PhtD, an important surface-exposed virulence factor. We generated a new genome annotation using automated tools, followed by manual curation, reflecting the current knowledge in the field. By combining sequence-driven terminator prediction, deep paired-end transcriptome sequencing and enrichment of primary transcripts by Cappable-Seq, we mapped 1015 transcriptional start sites and 748 termination sites. We show that the pneumococcal transcriptional landscape is complex and includes many secondary, antisense and internal promoters. Using this new genomic map, we identified several new small RNAs (sRNAs), RNA switches (including sixteen previously misidentified as sRNAs), and antisense RNAs. In total, we annotated 89 new protein-encoding genes, 34 sRNAs and 165 pseudogenes, bringing the S. pneumoniae D39 repertoire to 2146 genetic elements. We report operon structures and observed that 9% of operons are leaderless. The genome data are accessible in an online resource called PneumoBrowse (https://veeninglab.com/pneumobrowse) providing one of the most complete inventories of a bacterial genome to date. PneumoBrowse will accelerate pneumococcal research and the development of new prevention and treatment strategies.
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Affiliation(s)
- Jelle Slager
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Rieza Aprianto
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.,Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
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18
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Hausner J, Jordan M, Otten C, Marillonnet S, Büttner D. Modular Cloning of the Type III Secretion Gene Cluster from the Plant-Pathogenic Bacterium Xanthomonas euvesicatoria. ACS Synth Biol 2019; 8:532-547. [PMID: 30694661 DOI: 10.1021/acssynbio.8b00434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Type III secretion (T3S) systems are essential pathogenicity factors of most Gram-negative bacteria and translocate effector proteins into plant or animal cells. T3S systems can, therefore, be used as tools for protein delivery into eukaryotic cells, for instance after transfer of the T3S gene cluster into nonpathogenic recipient strains. Here, we report the modular cloning of the T3S gene cluster from the plant-pathogenic bacterium Xanthomonas euvesicatoria. The resulting multigene construct encoded a functional T3S system and delivered effector proteins into plant cells. The modular design of the T3S gene cluster allowed the efficient replacement and rearrangement of single genes or operons and the insertion of reporter genes for functional studies. In the present study, we used the modular T3S system to analyze the assembly of a fluorescent fusion of the predicted cytoplasmic ring protein HrcQ. Our studies demonstrate the use of the modular T3S gene cluster for functional analyses and mutant approaches in X. euvesicatoria. A potential application of the modular T3S system as protein delivery tool is discussed.
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Affiliation(s)
- Jens Hausner
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Saale, Germany
| | - Michael Jordan
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Saale, Germany
| | - Christian Otten
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Saale, Germany
| | | | - Daniela Büttner
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Saale, Germany
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19
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Carvalho Garcia A, Dos Santos VLP, Santos Cavalcanti TC, Collaço LM, Graf H. Bacterial Small RNAs in the Genus Herbaspirillum spp. Int J Mol Sci 2018; 20:ijms20010046. [PMID: 30583511 PMCID: PMC6337395 DOI: 10.3390/ijms20010046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 12/26/2022] Open
Abstract
The genus Herbaspirillum includes several strains isolated from different grasses. The identification of non-coding RNAs (ncRNAs) in the genus Herbaspirillum is an important stage studying the interaction of these molecules and the way they modulate physiological responses of different mechanisms, through RNA⁻RNA interaction or RNA⁻protein interaction. This interaction with their target occurs through the perfect pairing of short sequences (cis-encoded ncRNAs) or by the partial pairing of short sequences (trans-encoded ncRNAs). However, the companion Hfq can stabilize interactions in the trans-acting class. In addition, there are Riboswitches, located at the 5' end of mRNA and less often at the 3' end, which respond to environmental signals, high temperatures, or small binder molecules. Recently, CRISPR (clustered regularly interspaced palindromic repeats), in prokaryotes, have been described that consist of serial repeats of base sequences (spacer DNA) resulting from a previous exposure to exogenous plasmids or bacteriophages. We identified 285 ncRNAs in Herbaspirillum seropedicae (H. seropedicae) SmR1, expressed in different experimental conditions of RNA-seq material, classified as cis-encoded ncRNAs or trans-encoded ncRNAs and detected RNA riboswitch domains and CRISPR sequences. The results provide a better understanding of the participation of this type of RNA in the regulation of the metabolism of bacteria of the genus Herbaspirillum spp.
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Affiliation(s)
- Amanda Carvalho Garcia
- Department of Internal Medicine, Federal University of Paraná, Curitiba 80.060-240, Brazil.
| | | | | | - Luiz Martins Collaço
- Department of Pathology, Federal University of Paraná, PR, Curitiba 80.060-240, Brazil.
| | - Hans Graf
- Department of Internal Medicine, Federal University of Paraná, Curitiba 80.060-240, Brazil.
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20
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Hu Y, Zhang L, Wang X, Sun F, Kong X, Dong H, Xu H. Two virulent sRNAs identified by genomic sequencing target the type III secretion system in rice bacterial blight pathogen. BMC PLANT BIOLOGY 2018; 18:237. [PMID: 30326834 PMCID: PMC6192180 DOI: 10.1186/s12870-018-1470-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 10/05/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Small non-coding RNA (sRNA) short sequences regulate various biological processes in all organisms, including bacteria that are animal or plant pathogens. Virulent or pathogenicity-associated sRNAs have been increasingly elucidated in animal pathogens but little is known about similar category of sRNAs in plant-pathogenic bacteria. This is particularly true regarding rice bacterial blight pathogen Xanthomonas oryzae pathovar oryzae (Xoo) as studies on the virulent role of Xoo sRNAs is very limited at present. RESULTS The number and genomic distribution of sRNAs in Xoo were determined by bioinformatics analysis based on high throughput sequencing (sRNA-Seq) of the bacterial cultures from virulence-inducing and standard growth media, respectively. A total of 601 sRNAs were identified in the Xoo genome and ten virulent sRNA candidates were screened out based on significant differences of their expression levels between the culture conditions. In addition, trans3287 and trans3288 were also selected as candidates due to high expression levels in both media. The differential expression of 12 sRNAs evidenced by the sRNA-Seq data was confirmed by a convincing quantitative method. Based on genetic analysis of Xoo ΔsRNA mutants generated by deletion of the 12 single sRNAs, trans217 and trans3287 were characterized as virulent sRNAs. They are essential not only for the formation of bacterial blight in a susceptible rice variety Nipponbare but also for the induction of hypersensitive response (HR) in nonhost plant tobacco. Xoo Δtrans217 and Δtrans3287 mutants fail to induce bacterial blight in Nipponbare and also fail to induce the HR in tobacco, whereas, genetic complementation restores both mutants to the wild type in the virulent performance and HR induction. Similar effects of gene knockout and complementation were found in the expression of hrpG and hrpX genes, which encode regulatory proteins of the type III secretion system. Consistently, secretion of a type III effector, PthXo1, is blocked in Δtrans217 or Δtrans3287 bacterial cultures but retrieved by genetic complementation to both mutants. CONCLUSIONS The genetic analysis characterizes trans217 and trans3287 as pathogenicity-associated sRNAs essential for the bacterial virulence on the susceptible rice variety and for the HR elicitation in the nonhost plant. The molecular evidence suggests that both virulent sRNAs regulate the bacterial virulence by targeting the type III secretion system.
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Affiliation(s)
- Yiqun Hu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province China
| | - Liyuan Zhang
- State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 Jiangsu Province China
| | - Xuan Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province China
| | - Fengli Sun
- State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 Jiangsu Province China
- Current Address: Rural Work Bureau of Zhangpu Town, Suzhou, 215300 Jiangsu Province China
| | - Xiangxin Kong
- State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 Jiangsu Province China
| | - Hansong Dong
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province China
| | - Heng Xu
- State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 Jiangsu Province China
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21
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Choe D, Szubin R, Dahesh S, Cho S, Nizet V, Palsson B, Cho BK. Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance. Sci Rep 2018; 8:2215. [PMID: 29396540 PMCID: PMC5797083 DOI: 10.1038/s41598-018-20661-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/18/2018] [Indexed: 12/15/2022] Open
Abstract
Staphylococcus aureus infection is a rising public health care threat. S. aureus is believed to have elaborate regulatory networks that orchestrate its virulence. Despite its importance, the systematic understanding of the transcriptional landscape of S. aureus is limited. Here, we describe the primary transcriptome landscape of an epidemic USA300 isolate of community-acquired methicillin-resistant S. aureus. We experimentally determined 1,861 transcription start sites with their principal promoter elements, including well-conserved -35 and -10 elements and weakly conserved -16 element and 5' untranslated regions containing AG-rich Shine-Dalgarno sequence. In addition, we identified 225 genes whose transcription was initiated from multiple transcription start sites, suggesting potential regulatory functions at transcription level. Along with the transcription unit architecture derived by integrating the primary transcriptome analysis with operon prediction, the measurement of differential gene expression revealed the regulatory framework of the virulence regulator Agr, the SarA-family transcriptional regulators, and β-lactam resistance regulators. Interestingly, we observed a complex interplay between virulence regulation, β-lactam resistance, and metabolism, suggesting a possible tradeoff between pathogenesis and drug resistance in the USA300 strain. Our results provide platform resource for the location of transcription initiation and an in-depth understanding of transcriptional regulation of pathogenesis, virulence, and antibiotic resistance in S. aureus.
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Affiliation(s)
- Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, 92023, CA, USA
| | - Samira Dahesh
- University of California San Diego School of Medicine, La Jolla, 92023, CA, USA
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Victor Nizet
- University of California San Diego School of Medicine, La Jolla, 92023, CA, USA.
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, 92023, CA, USA.
- University of California San Diego School of Medicine, La Jolla, 92023, CA, USA.
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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22
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Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR. Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments. J Biotechnol 2017; 261:85-96. [DOI: 10.1016/j.jbiotec.2017.06.1203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 12/14/2022]
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23
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Xia Y, Fei B, He J, Zhou M, Zhang D, Pan L, Li S, Liang Y, Wang L, Zhu J, Li P, Zheng A. Transcriptome analysis reveals the host selection fitness mechanisms of the Rhizoctonia solani AG1IA pathogen. Sci Rep 2017; 7:10120. [PMID: 28860554 PMCID: PMC5579035 DOI: 10.1038/s41598-017-10804-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/15/2017] [Indexed: 11/12/2022] Open
Abstract
Rhizoctonia solani AG1IA is a major generalist pathogen that causes sheath blight. Its genome, which was the first to be sequenced from the Rhizoctonia genus, may serve as a model for studying pathogenic mechanisms. To explore the pathogen-host fitness mechanism of sheath-blight fungus, a comprehensive comparative transcriptome ecotype analysis of R. solani AG1IA isolated from rice, soybean and corn during infection was performed. Special characteristics in gene expression, gene ontology terms and expression of pathogenesis-associated genes, including genes encoding secreted proteins, candidate effectors, hydrolases, and proteins involved in secondary metabolite production and the MAPK pathway, were revealed. Furthermore, as an important means of pathogenic modulation, diverse alternative splicing of key pathogenic genes in Rhizoctonia solani AG1IA during infections of the abovementioned hosts was uncovered for the first time. These important findings of key factors in the pathogenicity of R. solani AG1IA ecotypes during infection of various hosts explain host preference and provide novel insights into the pathogenic mechanisms and host-pathogen selection. Furthermore, they provide information on the fitness of Rhizoctonia, a severe pathogen with a wide host range.
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Affiliation(s)
- Yuan Xia
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Binghong Fei
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiayu He
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Menglin Zhou
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Danhua Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linxiu Pan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuangcheng Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Southwest Corp Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yueyang Liang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Southwest Corp Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an, 625014, China
| | - Lingxia Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Southwest Corp Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an, 625014, China
| | - Jianqing Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Southwest Corp Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an, 625014, China
| | - Ping Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Southwest Corp Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an, 625014, China
| | - Aiping Zheng
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China.
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24
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Abendroth U, Adlung N, Otto A, Grüneisen B, Becher D, Bonas U. Identification of new protein-coding genes with a potential role in the virulence of the plant pathogen Xanthomonas euvesicatoria. BMC Genomics 2017; 18:625. [PMID: 28814272 PMCID: PMC5559785 DOI: 10.1186/s12864-017-4041-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 08/08/2017] [Indexed: 01/08/2023] Open
Abstract
Background Bacteria of the genus Xanthomonas are economically important plant pathogens. Pathogenicity of Xanthomonas spp. depends on the type III-secretion system and additional virulence determinants. The number of sequenced Xanthomonas genomes increases rapidly, however, accurate annotation of these genomes is difficult, because it relies on gene prediction programs. In this study, we used a mass-spectrometry (MS)-based approach to identify the proteome of Xanthomonas euvesicatoria (Xe) strain 85–10 also known as X. campestris pv. vesicatoria, a well-studied member of plant-pathogenic Xanthomonadaceae. Results Using different culture conditions, MS-datasets were searched against a six-frame-translated genome database of Xe. In total, we identified 2588 proteins covering 55% of the Xe genome, including 764 hitherto hypothetical proteins. Our proteogenomic approach identified 30 new protein-coding genes and allowed correction of the N-termini of 50 protein-coding genes. For five novel and two N-terminally corrected genes the corresponding proteins were confirmed by immunoblot. Furthermore, our data indicate that two putative type VI-secretion systems encoded in Xe play no role in bacterial virulence which was experimentally confirmed. Conclusions The discovery and re-annotation of numerous genes in the genome of Xe shows that also a well-annotated genome can be improved. Additionally, our proteogenomic analyses validates “hypothetical” proteins and will improve annotation of Xanthomonadaceae genomes, providing a solid basis for further studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4041-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ulrike Abendroth
- Institute for Biology, Department of Genetics, Martin-Luther-Universität Halle-Wittenberg, D-06099, Halle, Germany.
| | - Norman Adlung
- Institute for Biology, Department of Genetics, Martin-Luther-Universität Halle-Wittenberg, D-06099, Halle, Germany
| | - Andreas Otto
- Institute for Microbiology, Department of Mass Spectrometry, Ernst-Moritz-Arndt-Universität, D-17487, Greifswald, Germany
| | - Benjamin Grüneisen
- Institute for Biology, Department of Genetics, Martin-Luther-Universität Halle-Wittenberg, D-06099, Halle, Germany.,Department of Psychiatry and Psychotherapy, Martin-Luther-Universität Halle-Wittenberg, D-06097, Halle, Germany
| | - Dörte Becher
- Institute for Microbiology, Department of Mass Spectrometry, Ernst-Moritz-Arndt-Universität, D-17487, Greifswald, Germany
| | - Ulla Bonas
- Institute for Biology, Department of Genetics, Martin-Luther-Universität Halle-Wittenberg, D-06099, Halle, Germany.
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25
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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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26
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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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27
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Nawaz MZ, Jian H, He Y, Xiong L, Xiao X, Wang F. Genome-Wide Detection of Small Regulatory RNAs in Deep-Sea Bacterium Shewanella piezotolerans WP3. Front Microbiol 2017; 8:1093. [PMID: 28663744 PMCID: PMC5471319 DOI: 10.3389/fmicb.2017.01093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/30/2017] [Indexed: 11/13/2022] Open
Abstract
Shewanella are one of the most abundant Proteobacteria in the deep-sea and are renowned for their versatile electron accepting capacities. The molecular mechanisms involved in their adaptation to diverse and extreme environments are not well understood. Small non-coding RNAs (sRNAs) are known for modulating the gene expression at transcriptional and posttranscriptional levels, subsequently playing a key role in microbial adaptation. To understand the potential roles of sRNAs in the adaptation of Shewanella toward deep-sea environments, here an in silico approach was utilized to detect the sRNAs in the genome of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant deep-sea iron reducing bacterium. After scanning 3673 sets of 5' and 3' UTRs of orthologous genes, 209 sRNA candidates were identified with high confidence in S. piezotolerans WP3. About 92% (193 out of 209) of these putative sRNAs belong to the class trans-encoded RNAs, suggesting that trans-regulatory RNAs are the dominant class of sRNAs in S. piezotolerans WP3. The remaining 16 cis-regulatory RNAs were validated through quantitative polymerase chain reaction. Five cis-sRNAs were further shown to act as cold regulated sRNAs. Our study provided additional evidence at the transcriptional level to decipher the microbial adaptation mechanisms to extreme environmental conditions.
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Affiliation(s)
- Muhammad Z Nawaz
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | - Ying He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Lei Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong UniversityShanghai, China
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28
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Abstract
Biological processes such as defense mechanisms and microbial offense strategies are regulated through RNA induced interference in eukaryotes. Genetic mutations are modulated through biogenesis of small RNAs which directly impacts upon host development. Plant defense mechanisms are regulated and supported by a diversified group of small RNAs which are involved in streamlining several RNA interference pathways leading toward the initiation of pathogen gene silencing mechanisms. In the similar context, pathogens also utilize the support of small RNAs to launch their offensive attacks. Also there are strong evidences about the active involvement of these RNAs in symbiotic associations. Interestingly, small RNAs are not limited to the individuals in whom they are produced; they also show cross kingdom influences through variable interactions with other species thus leading toward the inter-organismic gene silencing. The phenomenon is understandable in the microbes which utilize these mechanisms to overcome host defense line. Understanding the mechanism of triggering host defense strategies can be a valuable step toward the generation of disease resistant host plants. We think that the cross kingdom trafficking of small RNA is an interesting insight that is needed to be explored for its vitality.
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Affiliation(s)
- Waqar Islam
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Saif Ul Islam
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Muhammad Qasim
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Liande Wang
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
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29
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Colgan AM, Cameron AD, Kröger C. If it transcribes, we can sequence it: mining the complexities of host-pathogen-environment interactions using RNA-seq. Curr Opin Microbiol 2017; 36:37-46. [PMID: 28189909 DOI: 10.1016/j.mib.2017.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 02/07/2023]
Abstract
Host-pathogen interactions are exceedingly complex because they involve multiple host tissues, often occur in the context of normal microflora, and can span diverse microenvironments. Although decades of gene expression studies have provided detailed insights into infection processes, technical challenges have restricted experiments to single pathogenic species or host tissues. RNA-sequencing (RNA-seq) has revolutionized the study of gene expression because in addition to quantifying transcriptional output, it allows detection and characterization of all transcripts in a genome. Here, we review how refined approaches to RNA-seq are used to map the transcriptional networks that control host-pathogen interactions. These enhanced techniques include dRNA-seq and term-seq for the fine-scale mapping of transcriptional start and termination sites, and dual RNA-seq for simultaneous sequencing of host and bacterial pathogen transcriptomes. Dual RNA-seq experiments are currently limited to in vitro infection systems that do not fully reflect the complexities of the in vivo environment, thus a challenge is to develop in vivo model systems and experimental approaches that address the biological heterogeneity of host environments, followed by the integration of RNA-seq with other genome-scale datasets to identify the transcriptional networks that mediate host-pathogen interactions.
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Affiliation(s)
- Aoife M Colgan
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Andrew Ds Cameron
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland.
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30
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Sundin GW, Wang N, Charkowski AO, Castiblanco LF, Jia H, Zhao Y. Perspectives on the Transition From Bacterial Phytopathogen Genomics Studies to Applications Enhancing Disease Management: From Promise to Practice. PHYTOPATHOLOGY 2016; 106:1071-1082. [PMID: 27183301 DOI: 10.1094/phyto-03-16-0117-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The advent of genomics has advanced science into a new era, providing a plethora of "toys" for researchers in many related and disparate fields. Genomics has also spawned many new fields, including proteomics and metabolomics, furthering our ability to gain a more comprehensive view of individual organisms and of interacting organisms. Genomic information of both bacterial pathogens and their hosts has provided the critical starting point in understanding the molecular bases of how pathogens disrupt host cells to cause disease. In addition, knowledge of the complete genome sequence of the pathogen provides a potentially broad slate of targets for the development of novel virulence inhibitors that are desperately needed for disease management. Regarding plant bacterial pathogens and disease management, the potential for utilizing genomics resources in the development of durable resistance is enhanced because of developing technologies that enable targeted modification of the host. Here, we summarize the role of genomics studies in furthering efforts to manage bacterial plant diseases and highlight novel genomics-enabled strategies heading down this path.
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Affiliation(s)
- George W Sundin
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
| | - Nian Wang
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
| | - Amy O Charkowski
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
| | - Luisa F Castiblanco
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
| | - Hongge Jia
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
| | - Youfu Zhao
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
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31
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Palma-Martínez I, Guerrero-Mandujano A, Ruiz-Ruiz MJ, Hernández-Cortez C, Molina-López J, Bocanegra-García V, Castro-Escarpulli G. Active Shiga-Like Toxin Produced by Some Aeromonas spp., Isolated in Mexico City. Front Microbiol 2016; 7:1552. [PMID: 27757103 PMCID: PMC5048074 DOI: 10.3389/fmicb.2016.01552] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/16/2016] [Indexed: 12/29/2022] Open
Abstract
RNA silencing is a conserved mechanism that utilizes small RNAs (sRNAs) to direct the regulation of gene expression at the transcriptional or post-transcriptional level. Plants utilizing RNA silencing machinery to defend pathogen infection was first identified in plant–virus interaction and later was observed in distinct plant–pathogen interactions. RNA silencing is not only responsible for suppressing RNA accumulation and movement of virus and viroid, but also facilitates plant immune responses against bacterial, oomycete, and fungal infection. Interestingly, even the same plant sRNA can perform different roles when encounters with different pathogens. On the other side, pathogens counteract by generating sRNAs that directly regulate pathogen gene expression to increase virulence or target host genes to facilitate pathogen infection. Here, we summarize the current knowledge of the characterization and biogenesis of host- and pathogen-derived sRNAs, as well as the different RNA silencing machineries that plants utilize to defend against different pathogens. The functions of these sRNAs in defense and counter-defense and their mechanisms for regulation during different plant–pathogen interactions are also discussed.
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Affiliation(s)
- Ingrid Palma-Martínez
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
| | - Andrea Guerrero-Mandujano
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
| | - Manuel J Ruiz-Ruiz
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico; Laboratorio Central de Análisis Clínicos Unidad Médica de Alta Especialidad Hospital de Pediatría "Silvestre Frenk Freund," Centro Médico Nacional Siglo XXIMexico City, Mexico
| | - Cecilia Hernández-Cortez
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico; Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico
| | - José Molina-López
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México Mexico City, Mexico
| | | | - Graciela Castro-Escarpulli
- Laboratorio de Bacteriología Médica, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
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32
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Jacques MA, Arlat M, Boulanger A, Boureau T, Carrère S, Cesbron S, Chen NWG, Cociancich S, Darrasse A, Denancé N, Fischer-Le Saux M, Gagnevin L, Koebnik R, Lauber E, Noël LD, Pieretti I, Portier P, Pruvost O, Rieux A, Robène I, Royer M, Szurek B, Verdier V, Vernière C. Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:163-87. [PMID: 27296145 DOI: 10.1146/annurev-phyto-080615-100147] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
How pathogens coevolve with and adapt to their hosts are critical to understanding how host jumps and/or acquisition of novel traits can lead to new disease emergences. The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria that collectively infect a broad range of crops and wild plant species. However, individual Xanthomonas strains usually cause disease on only a few plant species and are highly adapted to their hosts, making them pertinent models to study host specificity. This review summarizes our current understanding of the molecular basis of host specificity in the Xanthomonas genus, with a particular focus on the ecology, physiology, and pathogenicity of the bacterium. Despite our limited understanding of the basis of host specificity, type III effectors, microbe-associated molecular patterns, lipopolysaccharides, transcriptional regulators, and chemotactic sensors emerge as key determinants for shaping host specificity.
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Affiliation(s)
- Marie-Agnès Jacques
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Matthieu Arlat
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, F-31062 Toulouse, France
| | - Alice Boulanger
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, F-31062 Toulouse, France
| | - Tristan Boureau
- Université Angers, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France;
| | - Sébastien Carrère
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
| | - Sophie Cesbron
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Nicolas W G Chen
- Agrocampus Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France;
| | - Stéphane Cociancich
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Armelle Darrasse
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Nicolas Denancé
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Marion Fischer-Le Saux
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Lionel Gagnevin
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Ralf Koebnik
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Emmanuelle Lauber
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
| | - Laurent D Noël
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
| | - Isabelle Pieretti
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Perrine Portier
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Olivier Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Adrien Rieux
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Isabelle Robène
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Monique Royer
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Boris Szurek
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Valérie Verdier
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Christian Vernière
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
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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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D'Arrigo I, Bojanovič K, Yang X, Holm Rau M, Long KS. Genome-wide mapping of transcription start sites yields novel insights into the primary transcriptome ofPseudomonas putida. Environ Microbiol 2016; 18:3466-3481. [DOI: 10.1111/1462-2920.13326] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/01/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Isotta D'Arrigo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Klara Bojanovič
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Xiaochen Yang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Martin Holm Rau
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Katherine S. Long
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
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Cohen O, Doron S, Wurtzel O, Dar D, Edelheit S, Karunker I, Mick E, Sorek R. Comparative transcriptomics across the prokaryotic tree of life. Nucleic Acids Res 2016; 44:W46-53. [PMID: 27154273 PMCID: PMC4987935 DOI: 10.1093/nar/gkw394] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/28/2016] [Indexed: 12/23/2022] Open
Abstract
Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to ‘transcriptional noise’. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5′UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome.
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Affiliation(s)
- Ofir Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Shany Doron
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Omri Wurtzel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Daniel Dar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sarit Edelheit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Iris Karunker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Mick
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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Čuklina J, Hahn J, Imakaev M, Omasits U, Förstner KU, Ljubimov N, Goebel M, Pessi G, Fischer HM, Ahrens CH, Gelfand MS, Evguenieva-Hackenberg E. Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation. BMC Genomics 2016; 17:302. [PMID: 27107716 PMCID: PMC4842269 DOI: 10.1186/s12864-016-2602-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 03/25/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters. RESULTS A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file. CONCLUSIONS The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes.
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Affiliation(s)
- Jelena Čuklina
- />AA Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow, 127051 Russia
- />Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudnyy, Moscow region 141700 Russia
- />Present Address: Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard Hof 1, CH-8093 Zürich, Switzerland
| | - Julia Hahn
- />Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Maxim Imakaev
- />Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139 USA
| | - Ulrich Omasits
- />Agroscope, Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics and Bioinformatics & Swiss Institute of Bioinformatics (SIB), Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Konrad U. Förstner
- />Core Unit Systems Medicine, University of Würzburg, Josef-Schneider-Str. 2 Bau D15, D-97080 Würzburg, Germany
| | - Nikolay Ljubimov
- />Lomonosov Moscow State University, Faculty of Computational Mathematics and Cybernetics, Leninskie Gory, 2-nd educational building, Moscow, 119991 Russia
| | - Melanie Goebel
- />Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Gabriella Pessi
- />ETH, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
- />Present Address: Department of Plant and Microbial Biology University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | - Hans-Martin Fischer
- />ETH, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Christian H. Ahrens
- />Agroscope, Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics and Bioinformatics & Swiss Institute of Bioinformatics (SIB), Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Mikhail S. Gelfand
- />AA Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow, 127051 Russia
- />Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Vorobievy Gory 73-1, Moscow, 119991 Russia
| | - Elena Evguenieva-Hackenberg
- />Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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Gao R, Liu P, Yong Y, Wong SM. Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana. Sci Rep 2016; 6:24604. [PMID: 27086702 PMCID: PMC4834565 DOI: 10.1038/srep24604] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/01/2016] [Indexed: 11/16/2022] Open
Abstract
Turnip crinkle virus (TCV) is a carmovirus that infects many Arabidopsis ecotypes. Most studies mainly focused on discovery of resistance genes against TCV infection, and there is no Next Generation Sequencing based comparative genome wide transcriptome analysis reported. In this study, RNA-seq based transcriptome analysis revealed that 238 (155 up-regulated and 83 down-regulated) significant differentially expressed genes with at least 15-fold change were determined. Fifteen genes (including upregulated, unchanged and downregulated) were selected for RNA-seq data validation using quantitative real-time PCR, which showed consistencies between these two sets of data. GO enrichment analysis showed that numerous terms such as stress, immunity, defence and chemical stimulus were affected in TCV-infected plants. One putative plant defence related gene named WRKY61 was selected for further investigation. It showed that WRKY61 overexpression plants displayed reduced symptoms and less virus accumulation, as compared to wild type (WT) and WRKY61 deficient lines, suggesting that higher WRKY61 expression level reduced TCV viral accumulation. In conclusion, our transcriptome analysis showed that global gene expression was detected in TCV-infected Arabidopsis thaliana. WRKY61 gene was shown to be negatively correlated with TCV infection and viral symptoms, which may be connected to plant immunity pathways.
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Affiliation(s)
- Ruimin Gao
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Peng Liu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Yuhan Yong
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Singapore.,Temasek Life Sciences Laboratory, Singapore.,National University of Singapore Suzhou Research Institute, Suzhou Industrial Park, Jiangsu, China
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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: 28] [Impact Index Per Article: 3.5] [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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Tribelli PM, Solar Venero EC, Ricardi MM, Gómez-Lozano M, Raiger Iustman LJ, Molin S, López NI. Novel Essential Role of Ethanol Oxidation Genes at Low Temperature Revealed by Transcriptome Analysis in the Antarctic Bacterium Pseudomonas extremaustralis. PLoS One 2015; 10:e0145353. [PMID: 26671564 PMCID: PMC4686015 DOI: 10.1371/journal.pone.0145353] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/02/2015] [Indexed: 02/06/2023] Open
Abstract
Temperature is one of the most important factors for bacterial growth and development. Cold environments are widely distributed on earth, and psychrotolerant and psychrophilic microorganisms have developed different adaptation strategies to cope with the stress derived from low temperatures. Pseudomonas extremaustralis is an Antarctic bacterium able to grow under low temperatures and to produce high amounts of polyhydroxyalkanoates (PHAs). In this work, we analyzed the genome-wide transcriptome by RNA deep-sequencing technology of early exponential cultures of P. extremaustralis growing in LB (Luria Broth) supplemented with sodium octanoate to favor PHA accumulation at 8°C and 30°C. We found that genes involved in primary metabolism, including tricarboxylic acid cycle (TCA) related genes, as well as cytochromes and amino acid metabolism coding genes, were repressed at low temperature. Among up-regulated genes, those coding for transcriptional regulatory and signal transduction proteins were over-represented at cold conditions. Remarkably, we found that genes involved in ethanol oxidation, exaA, exaB and exaC, encoding a pyrroloquinoline quinone (PQQ)-dependent ethanol dehydrogenase, the cytochrome c550 and an aldehyde dehydrogenase respectively, were up-regulated. Along with RNA-seq experiments, analysis of mutant strains for pqqB (PQQ biosynthesis protein B) and exaA were carried out. We found that the exaA and pqqB genes are essential for growth under low temperature in LB supplemented with sodium octanoate. Additionally, p-rosaniline assay measurements showed the presence of alcohol dehydrogenase activity at both 8°C and 30°C, while the activity was abolished in a pqqB mutant strain. These results together with the detection of ethanol by gas chromatography in P. extremaustralis cultures grown at 8°C support the conclusion that this pathway is important under cold conditions. The obtained results have led to the identification of novel components involved in cold adaptation mechanisms in this bacterium, suggesting for the first time a role of the ethanol oxidation pathway for bacterial growth at low temperatures.
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Affiliation(s)
- Paula M. Tribelli
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Guiraldes 2160, C1428EGA Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
| | | | - Martiniano M. Ricardi
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Maria Gómez-Lozano
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Laura J. Raiger Iustman
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Guiraldes 2160, C1428EGA Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Nancy I. López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Guiraldes 2160, C1428EGA Buenos Aires, Argentina
- IQUIBICEN, CONICET, Buenos Aires, Argentina
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Potnis N, Timilsina S, Strayer A, Shantharaj D, Barak JD, Paret ML, Vallad GE, Jones JB. Bacterial spot of tomato and pepper: diverse Xanthomonas species with a wide variety of virulence factors posing a worldwide challenge. MOLECULAR PLANT PATHOLOGY 2015; 16:907-20. [PMID: 25649754 PMCID: PMC6638463 DOI: 10.1111/mpp.12244] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
TAXONOMIC STATUS Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species Xanthomonas euvesicatoria, Xanthomonas vesicatoria, Xanthomonas perforans and Xanthomonas gardneri. MICROBIOLOGICAL PROPERTIES Gram-negative, rod-shaped bacterium, aerobic, motile, single polar flagellum. HOST RANGE Causes bacterial spot disease on plants belonging to the Solanaceae family, primarily tomato (Solanum lycopersicum), pepper (Capsicum annuum) and chilli peppers (Capsicum frutescens). DISEASE SYMPTOMS Necrotic lesions on all above-ground plant parts. DISTRIBUTION Worldwide distribution of X. euvesicatoria and X. vesicatoria on tomato and pepper; X. perforans and X. gardneri increasingly being isolated from the USA, Canada, South America, Africa and Europe. A wide diversity within the bacterial spot disease complex, with an ability to cause disease at different temperatures, makes this pathogen group a worldwide threat to tomato and pepper production. Recent advances in genome analyses have revealed the evolution of the pathogen with a plethora of novel virulence factors. Current management strategies rely on the use of various chemical control strategies and sanitary measures to minimize pathogen spread through contaminated seed. Chemical control strategies have been a challenge because of resistance by the pathogen. Breeding programmes have been successful in developing commercial lines with hypersensitive and quantitative resistance. However, durability of resistance has been elusive. Recently, a transgenic approach has resulted in the development of tomato genotypes with significant levels of resistance and improved yield that hold promise. In this article, we discuss the current taxonomic status, distribution of the four species, knowledge of virulence factors, detection methods and strategies for disease control with possible directions for future research.
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Affiliation(s)
- Neha Potnis
- Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA
| | - Sujan Timilsina
- Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA
| | - Amanda Strayer
- Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA
| | - Deepak Shantharaj
- Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA
| | - Jeri D Barak
- Department of Plant Pathology, Russell Laboratories, University of Wisconsin, Madison, WI, 53706, USA
| | - Mathews L Paret
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA
| | - Gary E Vallad
- North Florida Research & Education Center, University of Florida, Quincy, FL, 32351-5677, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, Fifield Hall, University of Florida, Gainesville, FL, 32611, USA
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41
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Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome. BMC Genomics 2015; 16:975. [PMID: 26581393 PMCID: PMC4652430 DOI: 10.1186/s12864-015-2190-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/03/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf spot (pv. raphani). RESULTS In this study, we extended the genomic coverage of the species by sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome at the species level, the core type III effectome was limited to only three putative type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector proteins are injected inside the plant cells by the type III secretion system and contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins. CONCLUSIONS This dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.
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Fan B, Li L, Chao Y, Förstner K, Vogel J, Borriss R, Wu XQ. dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42. PLoS One 2015; 10:e0142002. [PMID: 26540162 PMCID: PMC4634765 DOI: 10.1371/journal.pone.0142002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/15/2015] [Indexed: 12/13/2022] Open
Abstract
Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments. In order to better understand the molecular mechanisms of bacteria-plant symbiosis, we have systematically analyzed the primary transcriptome of strain FZB42 grown under rhizosphere-mimicking conditions using differential RNA sequencing (dRNA-seq). Our analysis revealed 4,877 transcription start sites for protein-coding genes, identified genes differentially expressed under different growth conditions, and corrected many previously mis-annotated genes. We also identified a large number of riboswitches and cis-encoded antisense RNAs, as well as trans-encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus. Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.
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Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China
- * E-mail: (BF); (XW)
| | - Lei Li
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Yanjie Chao
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Konrad Förstner
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Rainer Borriss
- Fachgebiet Phytomedizin, Albrecht Daniel Thaer Institut für Agrar- und Gartenbauwissenschaften, Lebenswissenschaftliche Fakultät, Humboldt Universität zu Berlin, 14195 Berlin, Germany
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China
- * E-mail: (BF); (XW)
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Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape. PLoS Genet 2015; 11:e1005641. [PMID: 26536359 PMCID: PMC4633059 DOI: 10.1371/journal.pgen.1005641] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 10/10/2015] [Indexed: 11/19/2022] Open
Abstract
RNA-seq technologies have provided significant insight into the transcription networks of mycobacteria. However, such studies provide no definitive information on the translational landscape. Here, we use a combination of high-throughput transcriptome and proteome-profiling approaches to more rigorously understand protein expression in two mycobacterial species. RNA-seq and ribosome profiling in Mycobacterium smegmatis, and transcription start site (TSS) mapping and N-terminal peptide mass spectrometry in Mycobacterium tuberculosis, provide complementary, empirical datasets to examine the congruence of transcription and translation in the Mycobacterium genus. We find that nearly one-quarter of mycobacterial transcripts are leaderless, lacking a 5’ untranslated region (UTR) and Shine-Dalgarno ribosome-binding site. Our data indicate that leaderless translation is a major feature of mycobacterial genomes and is comparably robust to leadered initiation. Using translational reporters to systematically probe the cis-sequence requirements of leaderless translation initiation in mycobacteria, we find that an ATG or GTG at the mRNA 5’ end is both necessary and sufficient. This criterion, together with our ribosome occupancy data, suggests that mycobacteria encode hundreds of small, unannotated proteins at the 5’ ends of transcripts. The conservation of small proteins in both mycobacterial species tested suggests that some play important roles in mycobacterial physiology. Our translational-reporter system further indicates that mycobacterial leadered translation initiation requires a Shine Dalgarno site in the 5’ UTR and that ATG, GTG, TTG, and ATT codons can robustly initiate translation. Our combined approaches provide the first comprehensive view of mycobacterial gene structures and their non-canonical mechanisms of protein expression. The current paradigm for bacterial translation is based on an mRNA that includes an untranslated leader sequence containing the ribosome-binding site upstream of the initiation codon. We applied genome-scale approaches to map the protein-coding regions in the genomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We found that nearly one-quarter of mycobacterial transcripts are leaderless in mycobacterial species, thus indicating that ribosomes must recognize these mRNAs by a novel mechanism and suggesting that there are alternative modes of bacterial translation beyond the Escherichia coli paradigm. Our translational profiling showed that many mycobacterial proteins are mis-annotated, and also found many new genes encoding small proteins that had been previously overlooked, which are likely to play novel roles in diverse cellular processes. We also developed a new reporter system that provides mechanistic insights into translation initiation through deep sequencing. Our data show that leaderless translation is a robust process that is conserved in mycobacteria, that leaderless translation only requires that the mRNA begin with a start codon, and predict that mycobacteria encode hundreds of small proteins. This work will help us understand gene structure, genome organization and protein expression in bacteria, and how the translational machinery differs in different organisms.
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Stazic D, Voß B. The complexity of bacterial transcriptomes. J Biotechnol 2015; 232:69-78. [PMID: 26450562 DOI: 10.1016/j.jbiotec.2015.09.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/07/2015] [Accepted: 09/29/2015] [Indexed: 01/09/2023]
Abstract
For eukaryotes there seems to be no doubt that differences on the trancriptomic level substantially contribute to the process of species diversification, whereas for bacteria this is thought to be less important. Recent years saw a significant increase in full transcriptome studies for bacteria, which provided deep insight into the architecture of bacterial transcriptomes. Most notably, it became evident that, in contrast to previous scientific consensus, bacterial transcriptomes are quite complex. There exist a large number of cis-antisense RNAs, non-coding RNAs, overlapping transcripts and RNA elements that regulate transcription, such as riboswitches. Furthermore, processing and degradation of RNA has gained interest, because it has a significant impact on the composition of the transcriptome. In this review, we summarize recent findings and put them into a broader context with respect to the complexity of bacterial transcriptomes and its putative biological meanings.
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Affiliation(s)
- D Stazic
- University of Freiburg, Faculty of Biology, Computational Transcriptomics, Schänzlestr. 1, 79104 Freiburg, Germany.
| | - B Voß
- University of Freiburg, Faculty of Biology, Computational Transcriptomics, Schänzlestr. 1, 79104 Freiburg, Germany.
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Liu JJ, Sturrock RN, Sniezko RA, Williams H, Benton R, Zamany A. Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors. BMC Genomics 2015; 16:678. [PMID: 26338692 PMCID: PMC4559923 DOI: 10.1186/s12864-015-1861-1] [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: 03/09/2015] [Accepted: 08/18/2015] [Indexed: 12/21/2022] Open
Abstract
Background The fungus Cronartium ribicola (Cri) is an economically and ecologically important forest pathogen that causes white pine blister rust (WPBR) disease on five-needle pines. To cause stem cankers and kill white pine trees the fungus elaborates a life cycle with five stages of spore development on five-needle pines and the alternate host Ribes plants. To increase our understanding of molecular WP-BR interactions, here we report genome-wide transcriptional profile analysis of C. ribicola using RNA-seq. Results cDNA libraries were constructed from aeciospore, urediniospore, and western white pine (Pinus monticola) tissues post Cri infection. Over 200 million RNA-seq 100-bp paired-end (PE) reads from rust fungal spores were de novo assembled and a reference transcriptome was generated with 17,880 transcripts that were expressed from 13,629 unigenes. A total of 734 unique proteins were predicted as a part of the Cri secretome from complete open reading frames (ORFs), and 41 % of them were Cronartium-specific. This study further identified a repertoire of candidate effectors and other pathogenicity determinants. Differentially expressed genes (DEGs) were identified to gain an understanding of molecular events important during the WPBR fungus life cycle by comparing Cri transcriptomes at different infection stages. Large-scale changes of in planta gene expression profiles were observed, revealing that multiple fungal biosynthetic pathways were enhanced during mycelium growth inside infected pine stem tissues. Conversely, many fungal genes that were up-regulated at the urediniospore stage appeared to be signalling components and transporters. The secreted fungal protein genes that were up-regulated in pine needle tissues during early infection were primarily associated with cell wall modifications, possibly to mask the rust pathogen from plant defenses. Conclusion This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions. The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1861-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun-Jun Liu
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Rona N Sturrock
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Richard A Sniezko
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA.
| | - Holly Williams
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Ross Benton
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Arezoo Zamany
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
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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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Weiberg A, Jin H. Small RNAs--the secret agents in the plant-pathogen interactions. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:87-94. [PMID: 26123395 PMCID: PMC4573252 DOI: 10.1016/j.pbi.2015.05.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 05/15/2023]
Abstract
Eukaryotic regulatory small RNAs (sRNAs) that induce RNA interference (RNAi) are involved in a plethora of biological processes, including host immunity and pathogen virulence. In plants, diverse classes of sRNAs contribute to the regulation of host innate immunity. These immune-regulatory sRNAs operate through distinct RNAi pathways that trigger transcriptional or post-transcriptional gene silencing. Similarly, many pathogen-derived sRNAs also regulate pathogen virulence. Remarkably, the influence of regulatory sRNAs is not limited to the individual organism in which they are generated. It can sometimes extend to interacting species from even different kingdoms. There they trigger gene silencing in the interacting organism, a phenomenon called cross-kingdom RNAi. This is exhibited in advanced pathogens and parasites that produce sRNAs to suppress host immunity. Conversely, in host-induced gene silencing (HIGS), diverse plants are engineered to trigger RNAi against pathogens and pests to confer host resistance. Cross-kingdom RNAi opens up a vastly unexplored area of research on mobile sRNAs in the battlefield between hosts and pathogens.
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Affiliation(s)
- Arne Weiberg
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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Dequivre M, Diel B, Villard C, Sismeiro O, Durot M, Coppée JY, Nesme X, Vial L, Hommais F. Small RNA Deep-Sequencing Analyses Reveal a New Regulator of Virulence in Agrobacterium fabrum C58. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:580-589. [PMID: 26024442 DOI: 10.1094/mpmi-12-14-0380-fi] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Novel ways of regulating Ti plasmid functions were investigated by studying small RNAs (sRNAs) that are known to act as posttranscriptional regulators in plant pathogenic bacteria. sRNA-seq analyses of Agrobacterium fabrum C58 allowed us to identify 1,108 small transcripts expressed in several growth conditions that could be sRNAs. A quarter of them were confirmed by bioinformatics or by biological experiments. Antisense RNAs represent 24% of the candidates and they are over-represented on the pTi (with 62% of pTi sRNAs), suggesting differences in the regulatory mechanisms between the essential and accessory replicons. Moreover, a large number of these pTi antisense RNAs are transcribed opposite to those genes involved in virulence. Others are 5'- and 3'-untranslated region RNAs and trans-encoded RNAs. We have validated, by rapid amplification of cDNA ends polymerase chain reaction, the transcription of 14 trans-encoded RNAs, among which RNA1111 is expressed from the pTiC58. Its deletion decreased the aggressiveness of A. fabrum C58 on tomatoes, tobaccos, and kalanchoe, suggesting that this sRNA activates virulence. The identification of its putative target mRNAs (6b gene, virC2, virD3, and traA) suggests that this sRNA may coordinate two of the major pTi functions, the infection of plants and its dissemination among bacteria.
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Affiliation(s)
- M Dequivre
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
| | - B Diel
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
- 4CNRS, UMR 5557 Ecologie Microbienne, F-69622 Villeurbanne, France
- 5INRA, USC 1364 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - C Villard
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
| | - O Sismeiro
- 6Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur, 25 rue du Dr. Roux, F75015 Paris, France
| | - M Durot
- 7CEA/DSV/FAR/IG/Genoscope and CNRS UMR8030 Laboratoire d'Analyses Bioinformatiques en Métabolisme et Génomique, 2 rue Gaston Crémieux 91057 Evry cedex, France
- 8Total New Energies USA, 5858 Horton Street, Emeryville, CA 94608, U.S.A
| | - J Y Coppée
- 6Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur, 25 rue du Dr. Roux, F75015 Paris, France
| | - X Nesme
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 4CNRS, UMR 5557 Ecologie Microbienne, F-69622 Villeurbanne, France
- 5INRA, USC 1364 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - L Vial
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 4CNRS, UMR 5557 Ecologie Microbienne, F-69622 Villeurbanne, France
- 5INRA, USC 1364 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - F Hommais
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
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Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M, Dersch P. Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs. PLoS Genet 2015; 11:e1005087. [PMID: 25816203 PMCID: PMC4376681 DOI: 10.1371/journal.pgen.1005087] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/20/2015] [Indexed: 12/20/2022] Open
Abstract
One hallmark of pathogenic yersiniae is their ability to rapidly adjust their life-style and pathogenesis upon host entry. In order to capture the range, magnitude and complexity of the underlying gene control mechanisms we used comparative RNA-seq-based transcriptomic profiling of the enteric pathogen Y. pseudotuberculosis under environmental and infection-relevant conditions. We identified 1151 individual transcription start sites, multiple riboswitch-like RNA elements, and a global set of antisense RNAs and previously unrecognized trans-acting RNAs. Taking advantage of these data, we revealed a temperature-induced and growth phase-dependent reprogramming of a large set of catabolic/energy production genes and uncovered the existence of a thermo-regulated ‘acetate switch’, which appear to prime the bacteria for growth in the digestive tract. To elucidate the regulatory architecture linking nutritional status to virulence we also refined the CRP regulon. We identified a massive remodelling of the CRP-controlled network in response to temperature and discovered CRP as a transcriptional master regulator of numerous conserved and newly identified non-coding RNAs which participate in this process. This finding highlights a novel level of complexity of the regulatory network in which the concerted action of transcriptional regulators and multiple non-coding RNAs under control of CRP adjusts the control of Yersinia fitness and virulence to the requirements of their environmental and virulent life-styles. Many bacterial pathogens cycle between environmental sources and mammalian hosts. Adaptation to the different natural habitats and host niches is achieved through complex regulatory networks which adjust synthesis of the large repertoire of crucial virulence factors and fitness determinants. To uncover underlying control circuits, we determined the first in-depth single-nucleotide resolution transcriptome of Yersinia. This revealed important novel genetic information, such as global locations of transcriptional start sites, non-coding RNAs, potential riboswitches and provided a set of virulence-relevant expression profiles, which constitute a valuable tool for the research community. The analysis further uncovered a temperature-induced global reprogramming of central metabolic functions, likely to support intestinal colonization of the pathogen. This is accompanied by a major reorganization of the CRP regulon, which involves a multitude of regulatory RNAs. The primary consequence is a fine-tuned, coordinated control of metabolism and virulence through a plethora of environmentally controlled regulatory RNAs allowing rapid adaptation and high flexibility during life-style changes.
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Affiliation(s)
- Aaron M. Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ann Kathrin Heroven
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Barbara Waldmann
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jan Reinkensmeier
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Germany
| | - Michael Jarek
- Department of Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- * E-mail:
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50
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Irla M, Neshat A, Brautaset T, Rückert C, Kalinowski J, Wendisch VF. Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape. BMC Genomics 2015; 16:73. [PMID: 25758049 PMCID: PMC4342826 DOI: 10.1186/s12864-015-1239-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/12/2015] [Indexed: 01/27/2023] Open
Abstract
Background Bacillus methanolicus MGA3 is a thermophilic, facultative ribulose monophosphate (RuMP) cycle methylotroph. Together with its ability to produce high yields of amino acids, the relevance of this microorganism as a promising candidate for biotechnological applications is evident. The B. methanolicus MGA3 genome consists of a 3,337,035 nucleotides (nt) circular chromosome, the 19,174 nt plasmid pBM19 and the 68,999 nt plasmid pBM69. 3,218 protein-coding regions were annotated on the chromosome, 22 on pBM19 and 82 on pBM69. In the present study, the RNA-seq approach was used to comprehensively investigate the transcriptome of B. methanolicus MGA3 in order to improve the genome annotation, identify novel transcripts, analyze conserved sequence motifs involved in gene expression and reveal operon structures. For this aim, two different cDNA library preparation methods were applied: one which allows characterization of the whole transcriptome and another which includes enrichment of primary transcript 5′-ends. Results Analysis of the primary transcriptome data enabled the detection of 2,167 putative transcription start sites (TSSs) which were categorized into 1,642 TSSs located in the upstream region (5′-UTR) of known protein-coding genes and 525 TSSs of novel antisense, intragenic, or intergenic transcripts. Firstly, 14 wrongly annotated translation start sites (TLSs) were corrected based on primary transcriptome data. Further investigation of the identified 5′-UTRs resulted in the detailed characterization of their length distribution and the detection of 75 hitherto unknown cis-regulatory RNA elements. Moreover, the exact TSSs positions were utilized to define conserved sequence motifs for translation start sites, ribosome binding sites and promoters in B. methanolicus MGA3. Based on the whole transcriptome data set, novel transcripts, operon structures and mRNA abundances were determined. The analysis of the operon structures revealed that almost half of the genes are transcribed monocistronically (940), whereas 1,164 genes are organized in 381 operons. Several of the genes related to methylotrophy had highly abundant transcripts. Conclusion The extensive insights into the transcriptional landscape of B. methanolicus MGA3, gained in this study, represent a valuable foundation for further comparative quantitative transcriptome analyses and possibly also for the development of molecular biology tools which at present are very limited for this organism. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1239-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marta Irla
- Genetics of Prokaryotes, Faculty of Biology & Center for Biotechnology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
| | - Armin Neshat
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätstr. 27, 33615, Bielefeld, Germany.
| | - Trygve Brautaset
- Department of Molecular Biology, SINTEF Materials and Chemistry, Sem Selands vei 2, 7465, Trondheim, Norway. .,Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491, Trondheim, Norway.
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätstr. 27, 33615, Bielefeld, Germany. .,Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Universitätsstr. 27, 33615, Bielefeld, Germany.
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätstr. 27, 33615, Bielefeld, Germany. .,Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Universitätsstr. 27, 33615, Bielefeld, Germany.
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & Center for Biotechnology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
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