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Paliwal D, Rabiey M, Mauchline TH, Hassani-Pak K, Nauen R, Wagstaff C, Andrews S, Bass C, Jackson RW. Multiple toxins and a protease contribute to the aphid-killing ability of Pseudomonas fluorescens PpR24. Environ Microbiol 2024; 26:e16604. [PMID: 38561900 DOI: 10.1111/1462-2920.16604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
Aphids are globally important pests causing damage to a broad range of crops. Due to insecticide resistance, there is an urgent need to develop alternative control strategies. In our previous work, we found Pseudomonas fluorescens PpR24 can orally infect and kill the insecticide-resistant green-peach aphid (Myzus persicae). However, the genetic basis of the insecticidal capability of PpR24 remains unclear. Genome sequencing of PpR24 confirmed the presence of various insecticidal toxins such as Tc (toxin complexes), Rhs (rearrangement hotspot) elements, and other insect-killing proteases. Upon aphids infection with PpR24, RNA-Seq analysis revealed 193 aphid genes were differentially expressed with down-regulation of 16 detoxification genes. In addition, 1325 PpR24 genes (542 were upregulated and 783 downregulated) were subject to differential expression, including genes responsible for secondary metabolite biosynthesis, the iron-restriction response, oxidative stress resistance, and virulence factors. Single and double deletion of candidate virulence genes encoding a secreted protease (AprX) and four toxin components (two TcA-like; one TcB-like; one TcC-like insecticidal toxins) showed that all five genes contribute significantly to aphid killing, particularly AprX. This comprehensive host-pathogen transcriptomic analysis provides novel insight into the molecular basis of bacteria-mediated aphid mortality and the potential of PpR24 as an effective biocontrol agent.
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Affiliation(s)
- Deepa Paliwal
- School of Biological Sciences, University of Reading, Reading, UK
| | - Mojgan Rabiey
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Tim H Mauchline
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | | | | | - Carol Wagstaff
- School of Chemistry, Food and Pharmacy, University of Reading, Reading, UK
| | - Simon Andrews
- School of Biological Sciences, University of Reading, Reading, UK
| | | | - Robert W Jackson
- School of Biological Sciences, University of Reading, Reading, UK
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham, UK
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2
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Kandel PP, Naumova M, Fautt C, Patel RR, Triplett LR, Hockett KL. Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae. Front Microbiol 2022; 12:815911. [PMID: 35095819 PMCID: PMC8790059 DOI: 10.3389/fmicb.2021.815911] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022] Open
Abstract
Bacterial toxin-antitoxin (TA) systems consist of two or more adjacent genes, encoding a toxin and an antitoxin. TA systems are implicated in evolutionary and physiological functions including genome maintenance, antibiotics persistence, phage defense, and virulence. Eight classes of TA systems have been described, based on the mechanism of toxin neutralization by the antitoxin. Although studied well in model species of clinical significance, little is known about the TA system abundance and diversity, and their potential roles in stress tolerance and virulence of plant pathogens. In this study, we screened the genomes of 339 strains representing the genetic and lifestyle diversity of the Pseudomonas syringae species complex for TA systems. Using bioinformatic search and prediction tools, including SLING, BLAST, HMMER, TADB2.0, and T1TAdb, we show that P. syringae strains encode 26 different families of TA systems targeting diverse cellular functions. TA systems in this species are almost exclusively type II. We predicted a median of 15 TA systems per genome, and we identified six type II TA families that are found in more than 80% of strains, while others are more sporadic. The majority of predicted TA genes are chromosomally encoded. Further functional characterization of the predicted TA systems could reveal how these widely prevalent gene modules potentially impact P. syringae ecology, virulence, and disease management practices.
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Affiliation(s)
- Prem P. Kandel
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States,*Correspondence: Prem P. kandel,
| | - Marina Naumova
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
| | - Chad Fautt
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
| | - Ravikumar R. Patel
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States
| | - Lindsay R. Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States
| | - Kevin L. Hockett
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States,Kevin L. Hockett,
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3
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Umasuthan N, Valderrama K, Vasquez I, Segovia C, Hossain A, Cao T, Gnanagobal H, Monk J, Boyce D, Santander J. A Novel Marine Pathogen Isolated from Wild Cunners ( Tautogolabrus adspersus): Comparative Genomics and Transcriptome Profiling of Pseudomonas sp. Strain J380. Microorganisms 2021; 9:812. [PMID: 33921528 PMCID: PMC8069873 DOI: 10.3390/microorganisms9040812] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
Cunner (Tautogolabrus adspersus) is a cleaner fish being considered for utilized in the North Atlantic salmon (Salmo salar) aquaculture industry to biocontrol sea lice infestations. However, bacterial diseases due to natural infections in wild cunners have yet to be described. This study reports the isolation of Pseudomonas sp. J380 from infected wild cunners and its phenotypic, genomic, and transcriptomic characterization. This Gram-negative motile rod-shaped bacterium showed a mesophilic (4-28 °C) and halotolerant growth. Under iron-limited conditions, Pseudomonas sp. J380 produced pyoverdine-type fluorescent siderophore. Koch's postulates were verified in wild cunners by intraperitoneally (i.p.) injecting Pseudomonas sp. J380 at 4 × 103, 4 × 105, and 4 × 107 colony forming units (CFU)/dose. Host-range and comparative virulence were also investigated in lumpfish and Atlantic salmon i.p. injected with ~106 CFU/dose. Lumpfish were more susceptible compared to cunners, and Atlantic salmon was resistant to Pseudomonas sp. J380 infection. Cunner tissues were heavily colonized by Pseudomonas sp. J380 compared to lumpfish and Atlantic salmon suggesting that it might be an opportunistic pathogen in cunners. The genome of Pseudomonas sp. J380 was 6.26 megabases (Mb) with a guanine-cytosine (GC) content of 59.7%. Biochemical profiles, as well as comparative and phylogenomic analyses, suggested that Pseudomonas sp. J380 belongs to the P. fluorescens species complex. Transcriptome profiling under iron-limited vs. iron-enriched conditions identified 1159 differentially expressed genes (DEGs). Cellular metabolic processes, such as ribosomal and energy production, and protein synthesis, were impeded by iron limitation. In contrast, genes involved in environmental adaptation mechanisms including two-component systems, histidine catabolism, and redox balance were transcriptionally up-regulated. Furthermore, iron limitation triggered the differential expression of genes encoding proteins associated with iron homeostasis. As the first report on a bacterial infection in cunners, the current study provides an overview of a new marine pathogen, Pseudomonas sp. J380.
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Affiliation(s)
- Navaneethaiyer Umasuthan
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (N.U.); (K.V.); (I.V.); (C.S.); (A.H.); (T.C.); (H.G.)
| | - Katherinne Valderrama
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (N.U.); (K.V.); (I.V.); (C.S.); (A.H.); (T.C.); (H.G.)
| | - Ignacio Vasquez
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (N.U.); (K.V.); (I.V.); (C.S.); (A.H.); (T.C.); (H.G.)
| | - Cristopher Segovia
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (N.U.); (K.V.); (I.V.); (C.S.); (A.H.); (T.C.); (H.G.)
| | - Ahmed Hossain
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (N.U.); (K.V.); (I.V.); (C.S.); (A.H.); (T.C.); (H.G.)
| | - Trung Cao
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (N.U.); (K.V.); (I.V.); (C.S.); (A.H.); (T.C.); (H.G.)
| | - Hajarooba Gnanagobal
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (N.U.); (K.V.); (I.V.); (C.S.); (A.H.); (T.C.); (H.G.)
| | - Jennifer Monk
- Dr. Joe Brown Aquatic Research Building (JBARB), Department of Ocean Sciences, Memorial University of Newfoundland, Logy Bay, NL A1C 5S7, Canada; (J.M.); (D.B.)
| | - Danny Boyce
- Dr. Joe Brown Aquatic Research Building (JBARB), Department of Ocean Sciences, Memorial University of Newfoundland, Logy Bay, NL A1C 5S7, Canada; (J.M.); (D.B.)
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (N.U.); (K.V.); (I.V.); (C.S.); (A.H.); (T.C.); (H.G.)
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4
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Xie Y, Liu W, Shao X, Zhang W, Deng X. Signal transduction schemes in Pseudomonas syringae. Comput Struct Biotechnol J 2020; 18:3415-3424. [PMID: 33294136 PMCID: PMC7691447 DOI: 10.1016/j.csbj.2020.10.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 11/11/2022] Open
Abstract
To cope with their continually fluctuating surroundings, pathovars of the unicellular phytopathogen Pseudomonas syringae have developed rapid and sophisticated signalling networks to sense extracellular stimuli, which allow them to adjust their cellular composition to survive and cause diseases in host plants. Comparative genomic analyses of P. syringae strains have identified various genes that encode several classes of signalling proteins, although how this bacterium directly perceives these environmental cues remains elusive. Recent work has revealed new mechanisms of a cluster of bacterial signal transduction systems that mainly include two-component systems (such as RhpRS, GacAS, CvsRS and AauRS), extracytoplasmic function sigma factors (such as HrpL and AlgU), nucleotide-based secondary messengers, methyl-accepting chemotaxis sensor proteins and several other intracellular surveillance systems. In this review, we compile a list of the signal transduction mechanisms that P. syringae uses to monitor and respond in a timely manner to intracellular and external conditions. Further understanding of these surveillance processes will provide new perspectives from which to combat P. syringae infections.
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Affiliation(s)
- Yingpeng Xie
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong 999077, Hong Kong Special Administrative Region
| | - Wenbao Liu
- College of Agricultural Sciences and Technology, Shandong Agriculture and Engineering University, Jinan 250100, China
| | - Xiaolong Shao
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong 999077, Hong Kong Special Administrative Region
| | - Weihua Zhang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong 999077, Hong Kong Special Administrative Region.,Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
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5
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Maunders EA, Triniman RC, Western J, Rahman T, Welch M. Global reprogramming of virulence and antibiotic resistance in Pseudomonas aeruginosa by a single nucleotide polymorphism in elongation factor, fusA1. J Biol Chem 2020; 295:16411-16426. [PMID: 32943550 DOI: 10.1074/jbc.ra119.012102] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 09/11/2020] [Indexed: 11/06/2022] Open
Abstract
Clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa from patients with cystic fibrosis (CF) frequently contain mutations in the gene encoding an elongation factor, FusA1. Recent work has shown that fusA1 mutants often display elevated aminoglycoside resistance due to increased expression of the efflux pump, MexXY. However, we wondered whether these mutants might also be affected in other virulence-associated phenotypes. Here, we isolated a spontaneous gentamicin-resistant fusA1 mutant (FusA1P443L) in which mexXY expression was increased. Proteomic and transcriptomic analyses revealed that the fusA1 mutant also exhibited discrete changes in the expression of key pathogenicity-associated genes. Most notably, the fusA1 mutant displayed greatly increased expression of the Type III secretion system (T3SS), widely considered to be the most potent virulence factor in the P. aeruginosa arsenal, and also elevated expression of the Type VI (T6) secretion machinery. This was unexpected because expression of the T3SS is usually reciprocally coordinated with T6 secretion system expression. The fusA1 mutant also displayed elevated exopolysaccharide production, dysregulated siderophore production, elevated ribosome synthesis, and transcriptomic signatures indicative of translational stress. Each of these phenotypes (and almost all of the transcriptomic and proteomic changes associated with the fusA1 mutation) were restored to levels comparable with that in the progenitor strain by expression of the WT fusA1 gene in trans, indicating that the mutant gene is recessive. Our data show that in addition to elevating antibiotic resistance through mexXY expression (and also additional contributory resistance mechanisms), mutations in fusA1 can lead to highly selective dysregulation of virulence gene expression.
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Affiliation(s)
- Eve A Maunders
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Rory C Triniman
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom; Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Joshua Western
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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6
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He Y, Yu S, Liu S, Tian H, Yu C, Tan W, Zhang J, Li Z, Jiang F, Duan L. Data-Independent Acquisition Proteomics Unravels the Effects of Iron Ions on Coronatine Synthesis in Pseudomonas syringae pv. tomato DC3000. Front Microbiol 2020; 11:1362. [PMID: 32793123 PMCID: PMC7385143 DOI: 10.3389/fmicb.2020.01362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/27/2020] [Indexed: 12/03/2022] Open
Abstract
Coronatine (COR) is a new type of plant growth regulator that is produced by Pseudomonas syringae pathovars and plays an important role in modulating plant growth, development, and tolerance to multiple stresses. However, the factors affecting COR production are not very clear. In this study, the effects of FeCl3 on COR production were researched. The data-independent acquisition (DIA) approach, which is a proteomic quantitative analysis method, was applied to quantitatively trace COR production and proteomic changes in P. syringae pv. tomato DC3000 under different FeCl3 culture conditions. The results showed that COR production increased with the addition of FeCl3 and that there was significant upregulation in the expression of proteins related to COR synthesis and regulation. In addition, FeCl3 also affected the expression of related proteins involved in various metabolic pathways such as glycolysis and the tricarboxylic acid cycle. Moreover, various precursors such as isoleucine and succinate semialdehyde, as well as other related proteins involved in the COR synthesis pathway, were significantly differentially expressed. Our findings revealed the dynamic regulation of COR production in response to FeCl3 at the protein level and showed the potential of using the DIA method to track the dynamic changes of the P. syringae pv. tomato DC3000 proteome during COR production, providing an important reference for future research on the regulatory mechanism of COR biosynthesis and theoretical support for COR fermentation production.
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Affiliation(s)
- Yan He
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Sha Yu
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Shaojin Liu
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Hao Tian
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Chunxin Yu
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Weiming Tan
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaohu Li
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Feng Jiang
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Horticulture, China Agricultural University, Beijing, China
| | - Liusheng Duan
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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7
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Nobori T, Wang Y, Wu J, Stolze SC, Tsuda Y, Finkemeier I, Nakagami H, Tsuda K. Multidimensional gene regulatory landscape of a bacterial pathogen in plants. NATURE PLANTS 2020; 6:883-896. [PMID: 32541952 DOI: 10.1038/s41477-020-0690-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/08/2020] [Indexed: 05/25/2023]
Abstract
Understanding the gene regulation of plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a bacterial pathogen in plants. We found a number of bacterial processes affected by plant immunity at the transcriptome and proteome levels. For instance, salicylic acid-mediated plant immunity suppressed the accumulation of proteins comprising the tip component of the bacterial type III secretion system. Interestingly, there were instances of concordant and discordant regulation of bacterial messenger RNAs and proteins. Gene co-expression analysis uncovered previously unknown gene regulatory modules underlying virulence. This study provides molecular insights into the multiple layers of gene regulation that contribute to bacterial growth in planta, and elucidates the role of plant immunity in affecting pathogen responses.
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Affiliation(s)
- Tatsuya Nobori
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- College of Plant Protection, Nanjing Agriculture University, Nanjing, China
| | - Jingni Wu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Sara Christina Stolze
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yayoi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Iris Finkemeier
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Plant Biology and Biotechnology, University of Muenster, Münster, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Liu J, Tian Y, Zhao Y, Zeng R, Chen B, Hu B, Walcott RR. Ferric Uptake Regulator (FurA) is Required for Acidovorax citrulli Virulence on Watermelon. PHYTOPATHOLOGY 2019; 109:1997-2008. [PMID: 31454303 DOI: 10.1094/phyto-05-19-0172-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Acidovorax citrulli is the causal agent of bacterial fruit blotch, a serious threat to commercial watermelon and melon crop production worldwide. Ferric uptake regulator (Fur) is a global transcription factor that affects a number of virulence-related functions in phytopathogenic bacteria; however, the role of furA has not been determined for A. citrulli. Hence, we constructed an furA deletion mutant and a corresponding complement in the background of A. citrulli strain xlj12 to investigate the role of the gene in siderophore production, concentration of intracellular Fe2+, bacterial sensitivity to hydrogen peroxide, biofilm formation, swimming motility, hypersensitive response induction, and virulence on melon seedlings. The A. citrulli furA deletion mutant displayed increased siderophore production, intracellular Fe2+ concentration, and increased sensitivity to hydrogen peroxide. In contrast, biofilm formation, swimming motility, and virulence on melon seedlings were significantly reduced in the furA mutant. As expected, complementation of the furA deletion mutant restored all phenotypes to wild-type levels. In accordance with the phenotypic results, the expression levels of bfrA and bfrB that encode bacterioferritin, sodB that encodes iron/manganese superoxide dismutase, fliS that encodes a flagellar protein, hrcN that encodes the type III secretion system (T3SS) ATPase, and hrcC that encodes the T3SS outer membrane ring protein were significantly downregulated in the A. citrulli furA deletion mutant. In addition, the expression of feo-related genes and feoA and feoB was significantly upregulated in the furA mutant. Overall, these results indicated that, in A. citrulli, FurA contributes to the regulation of the iron balance system, and affects a variety of virulence-related traits.
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Affiliation(s)
- Jun Liu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanli Tian
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuqiang Zhao
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
| | - Rong Zeng
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Baohui Chen
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Baishi Hu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Ron R Walcott
- Department of Plant Pathology, 4315 Miller Plant Sciences, the University of Georgia, Athens, GA 30602, U.S.A
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9
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Buscaill P, Chandrasekar B, Sanguankiattichai N, Kourelis J, Kaschani F, Thomas EL, Morimoto K, Kaiser M, Preston GM, Ichinose Y, van der Hoorn RAL. Glycosidase and glycan polymorphism control hydrolytic release of immunogenic flagellin peptides. Science 2019; 364:eaav0748. [PMID: 30975858 DOI: 10.1126/science.aav0748] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/12/2019] [Indexed: 11/02/2022]
Abstract
Plants and animals recognize conserved flagellin fragments as a signature of bacterial invasion. These immunogenic elicitor peptides are embedded in the flagellin polymer and require hydrolytic release before they can activate cell surface receptors. Although much of flagellin signaling is understood, little is known about the release of immunogenic fragments. We discovered that plant-secreted β-galactosidase 1 (BGAL1) of Nicotiana benthamiana promotes hydrolytic elicitor release and acts in immunity against pathogenic Pseudomonas syringae strains only when they carry a terminal modified viosamine (mVio) in the flagellin O-glycan. In counter defense, P. syringae pathovars evade host immunity by using BGAL1-resistant O-glycans or by producing a BGAL1 inhibitor. Polymorphic glycans on flagella are common to plant and animal pathogenic bacteria and represent an important determinant of host immunity to bacterial pathogens.
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Affiliation(s)
- Pierre Buscaill
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | | | | | - Farnusch Kaschani
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Emma L Thomas
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Kyoko Morimoto
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Markus Kaiser
- ZMB Chemical Biology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Yuki Ichinose
- The Graduate School of Environmental and Life Science, Okayama University, Japan
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10
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Prevention of Surface-Associated Calcium Phosphate by the Pseudomonas syringae Two-Component System CvsSR. J Bacteriol 2019; 201:JB.00584-18. [PMID: 30617243 DOI: 10.1128/jb.00584-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/03/2019] [Indexed: 12/21/2022] Open
Abstract
CvsSR is a Ca2+-induced two-component system (TCS) in the plant pathogen Pseudomonas syringae pv. tomato DC3000. Here, we discovered that CvsSR is induced by Fe3+, Zn2+, and Cd2+ However, only supplementation of Ca2+ to medium resulted in rugose, opaque colonies in ΔcvsS and ΔcvsR strains. This phenotype corresponded to formation of calcium phosphate precipitation on the surface of ΔcvsS and ΔcvsR colonies. CvsSR regulated swarming motility in P. syringae pv. tomato in a Ca2+-dependent manner, but swarming behavior was not influenced by Fe3+, Zn2+, or Cd2+ We hypothesized that reduced swarming displayed by ΔcvsS and ΔcvsR strains was due to precipitation of calcium phosphate on the surface of ΔcvsS and ΔcvsR cells grown on agar medium supplemented with Ca2+ By reducing the initial pH or adding glucose to the medium, calcium precipitation was inhibited, and swarming was restored to ΔcvsS and ΔcvsR strains, suggesting that calcium precipitation influences swarming ability. Constitutive expression of a CvsSR-regulated carbonic anhydrase and a CvsSR-regulated putative sulfate major facilitator superfamily transporter in ΔcvsS and ΔcvsR strains inhibited formation of calcium precipitates and restored the ability of ΔcvsS and ΔcvsR bacteria to swarm. Lastly, we found that glucose inhibited Ca2+-based induction of CvsSR. Hence, CvsSR is a key regulator that controls calcium precipitation on the surface of bacterial cells.IMPORTANCE Bacteria are capable of precipitating and dissolving minerals. We previously reported the characterization of the two-component system CvsSR in the plant-pathogenic bacterium Pseudomonas syringae CvsSR responds to the presence of calcium and is important for causing disease. Here, we show that CvsSR controls the ability of the bacterium to prevent calcium phosphate precipitation on the surface of cells. We also identified a carbonic anhydrase and transporter that modulate formation of surface-associated calcium precipitates. Furthermore, our results demonstrate that the ability of the bacterium to swarm is controlled by the formation and dissolution of calcium precipitates on the surface of cells. Our study describes new mechanisms for microbially induced mineralization and provides insights into the role of mineral deposits on bacterial physiology. The discoveries may lead to new technological and environmental applications.
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11
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Nobori T, Mine A, Tsuda K. Molecular networks in plant-pathogen holobiont. FEBS Lett 2018; 592:1937-1953. [PMID: 29714033 DOI: 10.1002/1873-3468.13071] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/13/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022]
Abstract
Plant immune receptors enable detection of a multitude of microbes including pathogens. The recognition of microbes activates various plant signaling pathways, such as those mediated by phytohormones. Over the course of coevolution with microbes, plants have expanded their repertoire of immune receptors and signaling components, resulting in highly interconnected plant immune networks. These immune networks enable plants to appropriately respond to different types of microbes and to coordinate immune responses with developmental programs and environmental stress responses. However, the interconnectivity in plant immune networks is exploited by microbial pathogens to promote pathogen fitness in plants. Analogous to plant immune networks, virulence-related pathways in bacterial pathogens are also interconnected. Accumulating evidence implies that some plant-derived compounds target bacterial virulence networks. Thus, the plant immune and bacterial virulence networks intimately interact with each other. Here, we highlight recent insights into the structures of the plant immune and bacterial virulence networks and the interactions between them. We propose that small molecules derived from plants and/or bacterial pathogens connect the two molecular networks, forming supernetworks in the plant-bacterial pathogen holobiont.
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Affiliation(s)
- Tatsuya Nobori
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Akira Mine
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Japan.,JST, PRESTO, Kawaguchi-shi, Japan
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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12
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Abstract
Plant pathogens can cause serious diseases that impact global agriculture. The plant innate immunity, when fully activated, can halt pathogen growth in plants. Despite extensive studies into the molecular and genetic bases of plant immunity against pathogens, the influence of plant immunity in global pathogen metabolism to restrict pathogen growth is poorly understood. Here, we developed RNA sequencing pipelines for analyzing bacterial transcriptomes in planta and determined high-resolution transcriptome patterns of the foliar bacterial pathogen Pseudomonas syringae in Arabidopsis thaliana with a total of 27 combinations of plant immunity mutants and bacterial strains. Bacterial transcriptomes were analyzed at 6 h post infection to capture early effects of plant immunity on bacterial processes and to avoid secondary effects caused by different bacterial population densities in planta We identified specific "immune-responsive" bacterial genes and processes, including those that are activated in susceptible plants and suppressed by plant immune activation. Expression patterns of immune-responsive bacterial genes at the early time point were tightly linked to later bacterial growth levels in different host genotypes. Moreover, we found that a bacterial iron acquisition pathway is commonly suppressed by multiple plant immune-signaling pathways. Overexpression of a P. syringae sigma factor gene involved in iron regulation and other processes partially countered bacterial growth restriction during the plant immune response triggered by AvrRpt2. Collectively, this study defines the effects of plant immunity on the transcriptome of a bacterial pathogen and sheds light on the enigmatic mechanisms of bacterial growth inhibition during the plant immune response.
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13
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Ca 2+-Induced Two-Component System CvsSR Regulates the Type III Secretion System and the Extracytoplasmic Function Sigma Factor AlgU in Pseudomonas syringae pv. tomato DC3000. J Bacteriol 2018; 200:JB.00538-17. [PMID: 29263098 DOI: 10.1128/jb.00538-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/12/2017] [Indexed: 11/20/2022] Open
Abstract
Two-component systems (TCSs) of bacteria regulate many different aspects of the bacterial life cycle, including pathogenesis. Most TCSs remain uncharacterized, with no information about the signal(s) or regulatory targets and/or role in bacterial pathogenesis. Here, we characterized a TCS in the plant-pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 composed of the histidine kinase CvsS and the response regulator CvsR. CvsSR is necessary for virulence of P. syringae pv. tomato DC3000, since ΔcvsS and ΔcvsR strains produced fewer symptoms than the wild type (WT) and demonstrated reduced growth on multiple hosts. We discovered that expression of cvsSR is induced by Ca2+ concentrations found in leaf apoplastic fluid. Thus, Ca2+ can be added to the list of signals that promote pathogenesis of P. syringae pv. tomato DC3000 during host colonization. Through chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) and global transcriptome analysis (RNA-seq), we discerned the CvsR regulon. CvsR directly activated expression of the type III secretion system regulators, hrpR and hrpS, that regulate P. syringae pv. tomato DC3000 virulence in a type III secretion system-dependent manner. CvsR also indirectly repressed transcription of the extracytoplasmic sigma factor algU and production of alginate. Phenotypic analysis determined that CvsSR inversely regulated biofilm formation, swarming motility, and cellulose production in a Ca2+-dependent manner. Overall, our results show that CvsSR is a key regulatory hub critical for interaction with host plants.IMPORTANCE Pathogenic bacteria must be able to react and respond to the surrounding environment, make use of available resources, and avert or counter host immune responses. Often, these abilities rely on two-component systems (TCSs) composed of interacting proteins that modulate gene expression. We identified a TCS in the plant-pathogenic bacterium Pseudomonas syringae that responds to the presence of calcium, which is an important signal during the plant defense response. We showed that when P. syringae is grown in the presence of calcium, this TCS regulates expression of factors contributing to disease. Overall, our results provide a better understanding of how bacterial pathogens respond to plant signals and control systems necessary for eliciting disease.
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Kraus CM, Mazo-Molina C, Smart CD, Martin GB. Pseudomonas syringae pv. tomato Strains from New York Exhibit Virulence Attributes Intermediate Between Typical Race 0 and Race 1 Strains. PLANT DISEASE 2017; 101:1442-1448. [PMID: 30678591 DOI: 10.1094/pdis-03-17-0330-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacterial speck disease, caused by Pseudomonas syringae pv. tomato, is a persistent problem for fresh-market tomato growers in New York. Race 0 strains of this pathogen express either or both of the type III effectors AvrPto or AvrPtoB, which are recognized by tomato varieties expressing the Pto resistance gene. Pto encodes a protein kinase that activates the host immune system, thereby inhibiting bacterial multiplication and preventing disease development. Race 1 P. syringae pv. tomato strains do not express these effectors and are virulent on tomato whether or not the variety expresses Pto. Very few fresh-market tomato varieties have the Pto gene. We collected six P. syringae pv. tomato strains from naturally infected tomato plants across New York in 2015 and characterized them for their virulence and for the presence of specific effectors. In experiments conducted in the greenhouse, all strains reached population sizes in Pto-expressing tomato leaves that were intermediate between typical race 0 and race 1 strains. This phenotype has not been observed previously and suggests that the strains are recognized by Pto but such recognition is compromised by another P. syringae pv. tomato factor. The strains were found to encode avrPto, which is transcribed and translated. They also express avrPtoB although, as reported for other P. syringae pv. tomato strains, protein expression for this effector was not detectable. Deletion of avrPto from a representative New York strain allowed it to reach high populations in Pto-expressing tomato varieties, without compromising its virulence on susceptible tomato plants. Collectively, our data suggest that introgression of the Pto gene into fresh-market tomato varieties could enhance protection against extant P. syringae pv. tomato strains.
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Affiliation(s)
- Christine M Kraus
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, and Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Carolina Mazo-Molina
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, and Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, and Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University
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15
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Chakravarthy S, Butcher BG, Liu Y, D'Amico K, Coster M, Filiatrault MJ. Virulence of Pseudomonas syringae pv. tomato DC3000 Is Influenced by the Catabolite Repression Control Protein Crc. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:283-294. [PMID: 28384054 DOI: 10.1094/mpmi-09-16-0196-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Pseudomonas syringae infects diverse plant species and is widely used as a model system in the study of effector function and the molecular basis of plant diseases. Although the relationship between bacterial metabolism, nutrient acquisition, and virulence has attracted increasing attention in bacterial pathology, it is largely unexplored in P. syringae. The Crc (catabolite repression control) protein is a putative RNA-binding protein that regulates carbon metabolism as well as a number of other factors in the pseudomonads. Here, we show that deletion of crc increased bacterial swarming motility and biofilm formation. The crc mutant showed reduced growth and symptoms in Arabidopsis and tomato when compared with the wild-type strain. We have evidence that the crc mutant shows delayed hypersensitive response (HR) when infiltrated into Nicotiana benthamiana and tobacco. Interestingly, the crc mutant was more susceptible to hydrogen peroxide, suggesting that, in planta, the mutant may be sensitive to reactive oxygen species generated during pathogen-associated molecular pattern-triggered immunity (PTI). Indeed, HR was further delayed when PTI-induced tissues were challenged with the crc mutant. The crc mutant did not elicit an altered PTI response in plants compared with the wild-type strain. We conclude that Crc plays an important role in growth and survival during infection.
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Affiliation(s)
- Suma Chakravarthy
- 1 School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A.; and
| | - Bronwyn G Butcher
- 1 School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A.; and
| | - Yingyu Liu
- 1 School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A.; and
| | - Katherine D'Amico
- 1 School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A.; and
- 2 Emerging Pests & Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, U.S.A
| | - Matthew Coster
- 1 School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A.; and
| | - Melanie J Filiatrault
- 1 School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A.; and
- 2 Emerging Pests & Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, U.S.A
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16
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O'Leary BM, Neale HC, Geilfus CM, Jackson RW, Arnold DL, Preston GM. Early changes in apoplast composition associated with defence and disease in interactions between Phaseolus vulgaris and the halo blight pathogen Pseudomonas syringae Pv. phaseolicola. PLANT, CELL & ENVIRONMENT 2016; 39:2172-84. [PMID: 27239727 PMCID: PMC5026161 DOI: 10.1111/pce.12770] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 05/23/2016] [Indexed: 05/19/2023]
Abstract
The apoplast is the arena in which endophytic pathogens such as Pseudomonas syringae grow and interact with plant cells. Using metabolomic and ion analysis techniques, this study shows how the composition of Phaseolus vulgaris leaf apoplastic fluid changes during the first six hours of compatible and incompatible interactions with two strains of P. syringae pv. phaseolicola (Pph) that differ in the presence of the genomic island PPHGI-1. Leaf inoculation with the avirulent island-carrying strain Pph 1302A elicited effector-triggered immunity (ETI) and resulted in specific changes in apoplast composition, including increases in conductivity, pH, citrate, γ-aminobutyrate (GABA) and K(+) , that are linked to the onset of plant defence responses. Other apoplastic changes, including increases in Ca(2+) , Fe(2/3+) Mg(2+) , sucrose, β-cyanoalanine and several amino acids, occurred to a relatively similar extent in interactions with both Pph 1302A and the virulent, island-less strain Pph RJ3. Metabolic footprinting experiments established that Pph preferentially metabolizes malate, glucose and glutamate, but excludes certain other abundant apoplastic metabolites, including citrate and GABA, until preferred metabolites are depleted. These results demonstrate that Pph is well-adapted to the leaf apoplast metabolic environment and that loss of PPHGI-1 enables Pph to avoid changes in apoplast composition linked to plant defences.
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Affiliation(s)
- Brendan M O'Leary
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, 6009, Australia
| | - Helen C Neale
- Faculty of Health and Applied Sciences, University of the West of England, Bristol, BS16 1QY, United Kingdom
| | - Christoph-Martin Geilfus
- Faculty of Agricultural and Nutritional Sciences, Institute of Plant Nutrition and Soil Science, Kiel University, Kiel, 24118, Germany
| | - Robert W Jackson
- School of Biological Sciences, University of Reading, Reading, RG6 6AH, UK
| | - Dawn L Arnold
- Faculty of Health and Applied Sciences, University of the West of England, Bristol, BS16 1QY, United Kingdom
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
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17
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Activity of Gallium Meso- and Protoporphyrin IX against Biofilms of Multidrug-Resistant Acinetobacter baumannii Isolates. Pharmaceuticals (Basel) 2016; 9:ph9010016. [PMID: 26999163 PMCID: PMC4812380 DOI: 10.3390/ph9010016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/12/2016] [Accepted: 03/15/2016] [Indexed: 11/17/2022] Open
Abstract
Acinetobacter baumannii is a challenging pathogen due to antimicrobial resistance and biofilm development. The role of iron in bacterial physiology has prompted the evaluation of iron-modulation as an antimicrobial strategy. The non-reducible iron analog gallium(III) nitrate, Ga(NO3)3, has been shown to inhibit A. baumannii planktonic growth; however, utilization of heme-iron by clinical isolates has been associated with development of tolerance. These observations prompted the evaluation of iron-heme sources on planktonic and biofilm growth, as well as antimicrobial activities of gallium meso- and protoporphyrin IX (Ga-MPIX and Ga-PPIX), metal heme derivatives against planktonic and biofilm bacteria of multidrug-resistant (MDR) clinical isolates of A. baumannii in vitro. Ga(NO3)3 was moderately effective at reducing planktonic bacteria (64 to 128 µM) with little activity against biofilms (≥512 µM). In contrast, Ga-MPIX and Ga-PPIX were highly active against planktonic bacteria (0.25 to 8 µM). Cytotoxic effects in human fibroblasts were observed following exposure to concentrations exceeding 128 µM of Ga-MPIX and Ga-PPIX. We observed that the gallium metal heme conjugates were more active against planktonic and biofilm bacteria, possibly due to utilization of heme-iron as demonstrated by the enhanced effects on bacterial growth and biofilm formation.
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18
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Sasnow SS, Wei H, Aristilde L. Bypasses in intracellular glucose metabolism in iron-limited Pseudomonas putida. Microbiologyopen 2015; 5:3-20. [PMID: 26377487 PMCID: PMC4767421 DOI: 10.1002/mbo3.287] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/07/2015] [Indexed: 12/30/2022] Open
Abstract
Decreased biomass growth in iron (Fe)-limited Pseudomonas is generally attributed to downregulated expression of Fe-requiring proteins accompanied by an increase in siderophore biosynthesis. Here, we applied a stable isotope-assisted metabolomics approach to explore the underlying carbon metabolism in glucose-grown Pseudomonas putida KT2440. Compared to Fe-replete cells, Fe-limited cells exhibited a sixfold reduction in growth rate but the glucose uptake rate was only halved, implying an imbalance between glucose uptake and biomass growth. This imbalance could not be explained by carbon loss via siderophore production, which accounted for only 10% of the carbon-equivalent glucose uptake. In lieu of the classic glycolytic pathway, the Entner-Doudoroff (ED) pathway in Pseudomonas is the principal route for glucose catabolism following glucose oxidation to gluconate. Remarkably, gluconate secretion represented 44% of the glucose uptake in Fe-limited cells but only 2% in Fe-replete cells. Metabolic (13) C flux analysis and intracellular metabolite levels under Fe limitation indicated a decrease in carbon fluxes through the ED pathway and through Fe-containing metabolic enzymes. The secreted siderophore was found to promote dissolution of Fe-bearing minerals to a greater extent than the high extracellular gluconate. In sum, bypasses in the Fe-limited glucose metabolism were achieved to promote Fe availability via siderophore secretion and to reroute excess carbon influx via enhanced gluconate secretion.
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Affiliation(s)
- Samantha S Sasnow
- Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, New York, 14853
| | - Hua Wei
- Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, New York, 14853
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, New York, 14853
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19
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Liu Y, Rainey PB, Zhang XX. Molecular mechanisms of xylose utilization by Pseudomonas fluorescens: overlapping genetic responses to xylose, xylulose, ribose and mannitol. Mol Microbiol 2015; 98:553-70. [PMID: 26194109 DOI: 10.1111/mmi.13142] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2015] [Indexed: 02/03/2023]
Abstract
Bacterial degradation of xylose is sequentially mediated by two enzymes - an isomerase (XutA) and a xylulokinase (XutB) - with xylulose as an intermediate. Pseudomonas fluorescens SBW25, though capable of growth on xylose as a sole carbon source, encodes only one degradative enzyme XutA at the xylose utilization (xut) locus. Here, using site-directed mutagenesis and transcriptional assays, we have identified two functional xylulokinase-encoding genes (xutB1 and xutB2) and further show that expression of xutB1 is specifically induced by xylose. Surprisingly, xylose-induced xutB1 expression is mediated by the mannitol-responsive regulator MtlR, using xylulose rather than xylose as the direct inducer. In contrast, expression of the xutA operon is regulated by XutR - a transcriptional activator of the AraC family - in a xylose-, xylulose- and ribose-dependent manner. Detailed genetic and biochemical analyses of XutR, including DNase I footprinting assays, suggest an unconventional model of XutR regulation that does not involve DNA-looping, a mechanism typically found for AraC-type regulators from enteric bacteria. XutR functions as a dimer and recognizes two inverted repeat sequences, but binding to one half site is weak thus requiring an inducer molecule such as xylose for activation.
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Affiliation(s)
- Yunhao Liu
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, 0745, New Zealand.,NZ Institute for Advanced Study, Massey University, Auckland, 0745, New Zealand
| | - Paul B Rainey
- NZ Institute for Advanced Study, Massey University, Auckland, 0745, New Zealand.,Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Xue-Xian Zhang
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, 0745, New Zealand
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20
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Chapelle E, Alunni B, Malfatti P, Solier L, Pédron J, Kraepiel Y, Van Gijsegem F. A straightforward and reliable method for bacterial in planta transcriptomics: application to the Dickeya dadantii/Arabidopsis thaliana pathosystem. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:352-62. [PMID: 25740271 DOI: 10.1111/tpj.12812] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/16/2015] [Accepted: 02/23/2015] [Indexed: 05/02/2023]
Abstract
Transcriptome analysis of bacterial pathogens is a powerful approach to identify and study the expression patterns of genes during host infection. However, analysis of the early stages of bacterial virulence at the genome scale is lacking with respect to understanding of plant-pathogen interactions and diseases, especially during foliar infection. This is mainly due to both the low ratio of bacterial cells to plant material at the beginning of infection, and the high contamination by chloroplastic material. Here we describe a reliable and straightforward method for bacterial cell purification from infected leaf tissues, effective even if only a small amount of bacteria is present relative to plant material. The efficiency of this method for transcriptomic analysis was validated by analysing the expression profiles of the phytopathogenic enterobacterium Dickeya dadantii, a soft rot disease-causing agent, during the first hours of infection of the model host plant Arabidopsis thaliana. Transcriptome profiles of epiphytic bacteria and bacteria colonizing host tissues were compared, allowing identification of approximately 100 differentially expressed genes. Requiring no specific equipment, cost-friendly and easily transferable to other pathosystems, this method should be of great interest for many other plant-bacteria interaction studies.
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Affiliation(s)
- Emilie Chapelle
- Institut National de la Recherche Agronomique, Universite Pierre et Marie Curie/Universite Paris 06, AgroParisTech, UMR217, Interactions Plantes-Pathogènes, F-75005, Paris, France
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21
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Lam HN, Chakravarthy S, Wei HL, BuiNguyen H, Stodghill PV, Collmer A, Swingle BM, Cartinhour SW. Global analysis of the HrpL regulon in the plant pathogen Pseudomonas syringae pv. tomato DC3000 reveals new regulon members with diverse functions. PLoS One 2014; 9:e106115. [PMID: 25170934 PMCID: PMC4149516 DOI: 10.1371/journal.pone.0106115] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/28/2014] [Indexed: 11/18/2022] Open
Abstract
The type III secretion system (T3SS) is required for virulence in the gram-negative plant pathogen Pseudomonas syringae pv. tomato DC3000. The alternative sigma factor HrpL directly regulates expression of T3SS genes via a promoter sequence, often designated as the "hrp promoter." Although the HrpL regulon has been extensively investigated in DC3000, it is not known whether additional regulon members remain to be found. To systematically search for HrpL-regulated genes, we used chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) and bulk mRNA sequencing (RNA-Seq) to identify HrpL-binding sites and likely hrp promoters. The analysis recovered 73 sites of interest, including 20 sites that represent new hrp promoters. The new promoters lie upstream of a diverse set of genes encoding potential regulators, enzymes and hypothetical proteins. PSPTO_5633 is the only new HrpL regulon member that is potentially an effector and is now designated HopBM1. Deletions in several other new regulon members, including PSPTO_5633, PSPTO_0371, PSPTO_2130, PSPTO_2691, PSPTO_2696, PSPTO_3331, and PSPTO_5240, in either DC3000 or ΔhopQ1-1 backgrounds, do not affect the hypersensitive response or in planta growth of the resulting strains. Many new HrpL regulon members appear to be unrelated to the T3SS, and orthologs for some of these can be identified in numerous non-pathogenic bacteria. With the identification of 20 new hrp promoters, the list of HrpL regulon members is approaching saturation and most likely includes all DC3000 effectors.
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Affiliation(s)
- Hanh N. Lam
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Suma Chakravarthy
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Hai-Lei Wei
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - HoangChuong BuiNguyen
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Paul V. Stodghill
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
| | - Alan Collmer
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Bryan M. Swingle
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
| | - Samuel W. Cartinhour
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
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22
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Park SH, Bao Z, Butcher BG, D'Amico K, Xu Y, Stodghill P, Schneider DJ, Cartinhour S, Filiatrault MJ. Analysis of the small RNA spf in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. MICROBIOLOGY-SGM 2014; 160:941-953. [PMID: 24600027 DOI: 10.1099/mic.0.076497-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bacteria contain small non-coding RNAs (ncRNAs) that are typically responsible for altering transcription, translation or mRNA stability. ncRNAs are important because they often regulate virulence factors and susceptibility to various stresses. Here, the regulation of a recently described ncRNA of Pseudomonas syringae DC3000, spot 42 (now referred to as spf), was investigated. A putative RpoE binding site was identified upstream of spf in strain DC3000. RpoE is shown to regulate the expression of spf. Also, deletion of spf results in increased sensitivity to hydrogen peroxide compared with the wild-type strain, suggesting that spf plays a role in susceptibility to oxidative stress. Furthermore, expression of alg8 is shown to be influenced by spf, suggesting that this ncRNA plays a role in alginate biosynthesis. Structural and comparative genomic analyses show this ncRNA is well conserved among the pseudomonads. The findings provide new information on the regulation and role of this ncRNA in P. syringae.
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Affiliation(s)
- So Hae Park
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zhongmeng Bao
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Bronwyn G Butcher
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Katherine D'Amico
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Yun Xu
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Paul Stodghill
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - David J Schneider
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Samuel Cartinhour
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - M J Filiatrault
- Plant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
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Fones H, Preston GM. The impact of transition metals on bacterial plant disease. FEMS Microbiol Rev 2013; 37:495-519. [DOI: 10.1111/1574-6976.12004] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 09/05/2012] [Accepted: 09/14/2012] [Indexed: 12/24/2022] Open
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González-Villanueva L, Arvizu-Gómez JL, Hernández-Morales A, Aguilera-Aguirre S, Álvarez-Morales A. The PhtL protein of Pseudomonas syringae pv. phaseolicola NPS3121 affects the expression of both phaseolotoxin cluster (Pht) and Non-Pht encoded genes. Microbiol Res 2013; 169:221-31. [PMID: 23806843 DOI: 10.1016/j.micres.2013.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/23/2013] [Accepted: 05/27/2013] [Indexed: 11/16/2022]
Abstract
Pseudomonas syringae pv. phaseolicola, the causal agent of halo blight disease in bean, produces a toxin known as phaseolotoxin, whose synthesis involves the products of some of the genes found within the Pht region. This region, considered a pathogenicity island, comprises 23 genes arranged in five transcriptional units: two single-gene units (argK, phtL) and three arranged as operons (phtA, phtD, phtM), most with unknown function. In P. syringae pv. phaseolicola, maximal expression of most of the genes encoded in the Pht region and the synthesis of phaseolotoxin require the product of the phtL gene, of unknown function but that has been proposed to have a regulatory role. In order to evaluate the role of phtL gene in P. syringae pv. phaseolicola, we performed a comparative transcriptional analysis with the wild type and a phtL(-) mutant strains using microarrays. The microarray data analysis showed that PhtL regulates the expression not only of genes within the Pht region, but also alters the expression of genomic genes outside it, indicating that this gene has been integrated into the regulatory machinery of the bacterium. The expression changes of many of those genes were confirmed by RT-PCR. This study also demonstrated the importance of the PhtL protein in the process of iron response, and suggests that the effect of PhtL on the expression of pathogenicity related, respiration and oxidative stress genes, observed in this study, appears to be indirect through its influence on the Fur protein expression.
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Affiliation(s)
- Luis González-Villanueva
- Departamento de Ingeniería Genética, CINVESTAV-IPN Unidad Irapuato, Apdo Postal 629, CP 36821 Irapuato, Gto, Mexico.
| | | | - Alejandro Hernández-Morales
- Universidad Autónoma de San Luis Potosí, Unidad Académica Multidisciplinaria Zona Huasteca, Romualdo del Campo 501, Fraccionamiento Rafael Curiel, C. P. 79060 Cd. Valles, San Luis Potosí, Mexico
| | - Selene Aguilera-Aguirre
- Departamento de Ingeniería Genética, CINVESTAV-IPN Unidad Irapuato, Apdo Postal 629, CP 36821 Irapuato, Gto, Mexico
| | - Ariel Álvarez-Morales
- Departamento de Ingeniería Genética, CINVESTAV-IPN Unidad Irapuato, Apdo Postal 629, CP 36821 Irapuato, Gto, Mexico.
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Varani AM, Monteiro-Vitorello CB, Nakaya HI, Van Sluys MA. The role of prophage in plant-pathogenic bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:429-451. [PMID: 23725471 DOI: 10.1146/annurev-phyto-081211-173010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A diverse set of phage lineages is associated with the bacterial plant-pathogen genomes sequenced to date. Analysis of 37 genomes revealed 5,169 potential genes (approximately 4.3 Mbp) of phage origin, and at least 50% had no function assigned or are nonessential to phage biology. Some phytopathogens have transcriptionally active prophage genes under conditions that mimic plant infection, suggesting an association between plant disease and prophage transcriptional modulation. The role of prophages within genomes for cell biology varies. For pathogens such as Pectobacterium, Pseudomonas, Ralstonia, and Streptomyces, involvement of prophage in disease symptoms has been demonstrated. In Xylella and Xanthomonas, prophage activity is associated with genome rearrangements and strain differentiation. For other pathogens, prophage roles are yet to be established. This review integrates available information in a unique interface ( http://propnav.esalq.usp.br ) that may be assessed to improve research in prophage biology and its association with genome evolution and pathogenicity.
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Affiliation(s)
- Alessandro M Varani
- Departamento de Genética (LGN), Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900 Piracicaba/SP, Brazil
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Arvizu-Gómez JL, Hernández-Morales A, Aguilar JRP, Álvarez-Morales A. Transcriptional profile of P. syringae pv. phaseolicola NPS3121 at low temperature: physiology of phytopathogenic bacteria. BMC Microbiol 2013; 13:81. [PMID: 23587016 PMCID: PMC3639832 DOI: 10.1186/1471-2180-13-81] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 04/08/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Low temperatures play key roles in the development of most plant diseases, mainly because of their influence on the expression of various virulence factors in phytopathogenic bacteria. Thus far, studies regarding this environmental parameter have focused on specific themes and little is known about phytopathogenic bacteria physiology under these conditions. To obtain a global view regarding phytopathogenic bacteria strategies in response to physiologically relevant temperature changes, we used DNA microarray technology to compare the gene expression profile of the model bacterial pathogen P. syringae pv. phaseolicola NPS3121 grown at 18°C and 28°C. RESULTS A total of 236 differentially regulated genes were identified, of which 133 were up-regulated and 103 were down-regulated at 18°C compared to 28°C. The majority of these genes are involved in pathogenicity and virulence processes. In general, the results of this study suggest that the expression profile obtained may be related to the fact that low temperatures induce oxidative stress in bacterial cells, which in turn influences the expression of iron metabolism genes. The expression also appears to be correlated with the profile expression obtained in genes related to motility, biofilm production, and the type III secretion system. CONCLUSIONS From the data obtained in this study, we can begin to understand the strategies used by this phytopathogen during low temperature growth, which can occur in host interactions and disease development.
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Affiliation(s)
| | - Alejandro Hernández-Morales
- Unidad Académica Multidisciplinaria Zona Huasteca, Universidad Autónoma de San Luis Potosí, Romualdo del Campo 501, Fraccionamiento Rafael Curiel, Cd. Valles, San Luis Potosí, CP 79060, Mexico
| | - Juan Ramiro Pacheco Aguilar
- Laboratorio de Plantas y Biotecnología Agrícola. Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las campanas S/N, CU. Col. Las Campanas, Querétaro Qro, CP 76010, Mexico
| | - Ariel Álvarez-Morales
- Departamento de Ingeniería Genética, CINVESTAV-IPN Unidad Irapuato, Apdo Postal 629, Irapuato, Gto, CP 36821, Mexico
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Andrews S, Norton I, Salunkhe AS, Goodluck H, Aly WSM, Mourad-Agha H, Cornelis P. Control of iron metabolism in bacteria. Met Ions Life Sci 2013; 12:203-39. [PMID: 23595674 DOI: 10.1007/978-94-007-5561-1_7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacteria depend upon iron as a vital cofactor that enables a wide range of key metabolic activities. Bacteria must therefore ensure a balanced supply of this essential metal. To do so, they invest considerable resourse into its acquisition and employ elaborate control mechanisms to eleviate both iron-induced toxitiy as well as iron deficiency. This chapter describes the processes that bacteria engage in maintaining iron homeostasis. The focus is Escherichia coli, as this bacterium provides a well studied example. A summary of the current status of understanding of iron management at the 'omics' level is also presented.
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Affiliation(s)
- Simon Andrews
- The School of Biological Sciences, The University of Reading, Whiteknights, Reading, RG6 6AJ, UK,
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28
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Worley JN, Russell AB, Wexler AG, Bronstein PA, Kvitko BH, Krasnoff SB, Munkvold KR, Swingle B, Gibson DM, Collmer A. Pseudomonas syringae pv. tomato DC3000 CmaL (PSPTO4723), a DUF1330 family member, is needed to produce L-allo-isoleucine, a precursor for the phytotoxin coronatine. J Bacteriol 2013; 195:287-96. [PMID: 23144243 PMCID: PMC3553850 DOI: 10.1128/jb.01352-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/30/2012] [Indexed: 01/12/2023] Open
Abstract
Pseudomonas syringae pv. tomato DC3000 produces the phytotoxin coronatine, a major determinant of the leaf chlorosis associated with DC3000 pathogenesis. The DC3000 PSPTO4723 (cmaL) gene is located in a genomic region encoding type III effectors; however, it promotes chlorosis in the model plant Nicotiana benthamiana in a manner independent of type III secretion. Coronatine is produced by the ligation of two moieties, coronafacic acid (CFA) and coronamic acid (CMA), which are produced by biosynthetic pathways encoded in separate operons. Cross-feeding experiments, performed in N. benthamiana with cfa, cma, and cmaL mutants, implicate CmaL in CMA production. Furthermore, analysis of bacterial supernatants under coronatine-inducing conditions revealed that mutants lacking either the cma operon or cmaL accumulate CFA rather than coronatine, supporting a role for CmaL in the regulation or biosynthesis of CMA. CmaL does not appear to regulate CMA production, since the expression of proteins with known roles in CMA production is unaltered in cmaL mutants. Rather, CmaL is needed for the first step in CMA synthesis, as evidenced by the fact that wild-type levels of coronatine production are restored to a ΔcmaL mutant when it is supplemented with 50 μg/ml l-allo-isoleucine, the starting unit for CMA production. cmaL is found in all other sequenced P. syringae strains with coronatine biosynthesis genes. This characterization of CmaL identifies a critical missing factor in coronatine production and provides a foundation for further investigation of a member of the widespread DUF1330 protein family.
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Affiliation(s)
- Jay N. Worley
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - Alistair B. Russell
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - Aaron G. Wexler
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - Philip A. Bronstein
- U.S. Department of Agriculture, Agricultural Research Service, Ithaca, New York, USA
| | - Brian H. Kvitko
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - Stuart B. Krasnoff
- U.S. Department of Agriculture, Agricultural Research Service, Ithaca, New York, USA
| | - Kathy R. Munkvold
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - Bryan Swingle
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
- U.S. Department of Agriculture, Agricultural Research Service, Ithaca, New York, USA
| | - Donna M. Gibson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
- U.S. Department of Agriculture, Agricultural Research Service, Ithaca, New York, USA
| | - Alan Collmer
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
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29
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Park SH, Butcher BG, Anderson Z, Pellegrini N, Bao Z, D’Amico K, Filiatrault MJ. Analysis of the small RNA P16/RgsA in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. MICROBIOLOGY-SGM 2012; 159:296-306. [PMID: 23258266 PMCID: PMC3709562 DOI: 10.1099/mic.0.063826-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Bacteria contain small non-coding RNAs (ncRNAs) that are responsible for altering transcription, translation or mRNA stability. ncRNAs are important because they regulate virulence factors and susceptibility to various stresses. Here, the regulation of a recently described ncRNA of Pseudomonas syringae pv. tomato DC3000, P16, was investigated. We determined that RpoS regulates the expression of P16. We found that deletion of P16 results in increased sensitivity to hydrogen peroxide compared to the wild-type strain, suggesting that P16 plays a role in the bacteria’s susceptibility to oxidative stress. Additionally the P16 mutant displayed enhanced resistance to heat stress. Our findings provide new information on the regulation and role of this ncRNA in P. syringae.
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Affiliation(s)
- So Hae Park
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Bronwyn G. Butcher
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zoe Anderson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nola Pellegrini
- Plant–Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Zhongmeng Bao
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Katherine D’Amico
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
- Plant–Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Melanie J. Filiatrault
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
- Plant–Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
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Regulons of three Pseudomonas syringae pv. tomato DC3000 iron starvation sigma factors. Appl Environ Microbiol 2012; 79:725-7. [PMID: 23124242 DOI: 10.1128/aem.02801-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas syringae pv. tomato DC3000 contains genes for 15 sigma factors. The majority are members of the extracytoplasmic function class of sigma factors, including five that belong to the iron starvation subgroup. In this study, we identified the genes controlled by three iron starvation sigma factors. Their regulons are composed of a small number of genes likely to be involved in iron uptake.
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31
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Stauber JL, Loginicheva E, Schechter LM. Carbon source and cell density-dependent regulation of type III secretion system gene expression in Pseudomonas syringae pathovar tomato DC3000. Res Microbiol 2012; 163:531-9. [PMID: 22944041 DOI: 10.1016/j.resmic.2012.08.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 08/13/2012] [Indexed: 01/07/2023]
Abstract
Pseudomonas syringae utilizes a type III secretion system (T3SS) encoded by the hrp/hrc genes to translocate virulence proteins called effectors into plant cells. To ensure that the T3SS functions at appropriate times during infection, hrp/hrc and effector gene expression is modulated by environmental conditions and a complex network of transcription factors. The sigma factor HrpL activates hrp/hrc and effector genes, while σ(54) and enhancer binding proteins HrpR and HrpS regulate hrpL. To better understand how environmental conditions control the T3SS regulatory cascade in P. syringae pathovar tomato strain DC3000, we tested the effects of various growth media and carbon sources on expression of the hrpRS operon, hrpL, and the effector avrPto. Fructose optimally induced hrpRS expression, while most other carbon sources had only mild stimulatory effects. In contrast, hrpL and avrPto were highly induced by several sugars and organic acids, yet expression decreased as cultures reached higher cell densities. This cell density-dependent regulation was not due to alteration of the pH of the medium, although involvement of a quorum sensing signal was also not apparent. Our findings may explain conflicting results from previous studies and additionally indicate that culture conditions should be considered carefully when examining T3SS gene expression.
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Affiliation(s)
- Jennifer L Stauber
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA.
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32
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Lim CK, Hassan KA, Tetu SG, Loper JE, Paulsen IT. The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5. PLoS One 2012; 7:e39139. [PMID: 22723948 PMCID: PMC3377617 DOI: 10.1371/journal.pone.0039139] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 05/18/2012] [Indexed: 11/18/2022] Open
Abstract
One of the most important micronutrients for bacterial growth is iron, whose bioavailability in soil is limited. Consequently, rhizospheric bacteria such as Pseudomonas fluorescens employ a range of mechanisms to acquire or compete for iron. We investigated the transcriptomic and proteomic effects of iron limitation on P. fluorescens Pf-5 by employing microarray and iTRAQ techniques, respectively. Analysis of this data revealed that genes encoding functions related to iron homeostasis, including pyoverdine and enantio-pyochelin biosynthesis, a number of TonB-dependent receptor systems, as well as some inner-membrane transporters, were significantly up-regulated in response to iron limitation. Transcription of a ribosomal protein L36-encoding gene was also highly up-regulated during iron limitation. Certain genes or proteins involved in biosynthesis of secondary metabolites such as 2,4-diacetylphloroglucinol (DAPG), orfamide A and pyrrolnitrin, as well as a chitinase, were over-expressed under iron-limited conditions. In contrast, we observed that expression of genes involved in hydrogen cyanide production and flagellar biosynthesis were down-regulated in an iron-depleted culture medium. Phenotypic tests revealed that Pf-5 had reduced swarming motility on semi-solid agar in response to iron limitation. Comparison of the transcriptomic data with the proteomic data suggested that iron acquisition is regulated at both the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Chee Kent Lim
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Karl A. Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Sasha G. Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Joyce E. Loper
- USDA-ARS Horticultural Crops Research Laboratory and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
- * E-mail:
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López G, Latorre M, Reyes-Jara A, Cambiazo V, González M. Transcriptomic response of Enterococcus faecalis to iron excess. Biometals 2012; 25:737-47. [DOI: 10.1007/s10534-012-9539-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 03/07/2012] [Indexed: 11/28/2022]
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Filiatrault MJ, Stodghill PV, Myers CR, Bronstein PA, Butcher BG, Lam H, Grills G, Schweitzer P, Wang W, Schneider DJ, Cartinhour SW. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS One 2011; 6:e29335. [PMID: 22216251 PMCID: PMC3247240 DOI: 10.1371/journal.pone.0029335] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 11/25/2011] [Indexed: 12/28/2022] Open
Abstract
RNA-Seq has provided valuable insights into global gene expression in a wide variety of organisms. Using a modified RNA-Seq approach and Illumina's high-throughput sequencing technology, we globally identified 5'-ends of transcripts for the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. A substantial fraction of 5'-ends obtained by this method were consistent with results obtained using global RNA-Seq and 5'RACE. As expected, many 5'-ends were positioned a short distance upstream of annotated genes. We also captured 5'-ends within intergenic regions, providing evidence for the expression of un-annotated genes and non-coding RNAs, and detected numerous examples of antisense transcription, suggesting additional levels of complexity in gene regulation in DC3000. Importantly, targeted searches for sequence patterns in the vicinity of 5'-ends revealed over 1200 putative promoters and other regulatory motifs, establishing a broad foundation for future investigations of regulation at the genomic and single gene levels.
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Affiliation(s)
- Melanie J Filiatrault
- lant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, New York, USA.
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Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000. J Bacteriol 2011; 193:4598-611. [PMID: 21784947 DOI: 10.1128/jb.00340-11] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plant pathogen Pseudomonas syringae pv. tomato DC3000 (DC3000) is found in a wide variety of environments and must monitor and respond to various environmental signals such as the availability of iron, an essential element for bacterial growth. An important regulator of iron homeostasis is Fur (ferric uptake regulator), and here we present the first study of the Fur regulon in DC3000. Using chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq), 312 chromosomal regions were highly enriched by coimmunoprecipitation with a C-terminally tagged Fur protein. Integration of these data with previous microarray and global transcriptome analyses allowed us to expand the putative DC3000 Fur regulon to include genes both repressed and activated in the presence of bioavailable iron. Using nonradioactive DNase I footprinting, we confirmed Fur binding in 41 regions, including upstream of 11 iron-repressed genes and the iron-activated genes encoding two bacterioferritins (PSPTO_0653 and PSPTO_4160), a ParA protein (PSPTO_0855), and a two-component system (TCS) (PSPTO_3382 to PSPTO_3380).
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36
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Jones AM, Wildermuth MC. The phytopathogen Pseudomonas syringae pv. tomato DC3000 has three high-affinity iron-scavenging systems functional under iron limitation conditions but dispensable for pathogenesis. J Bacteriol 2011; 193:2767-75. [PMID: 21441525 PMCID: PMC3133136 DOI: 10.1128/jb.00069-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 03/11/2011] [Indexed: 11/20/2022] Open
Abstract
High-affinity iron scavenging through the use of siderophores is a well-established virulence determinant in mammalian pathogenesis. However, few examples have been reported for plant pathogens. Here, we use a genetic approach to investigate the role of siderophores in Pseudomonas syringae pv. tomato DC3000 (DC3000) virulence in tomato. DC3000, an agronomically important pathogen, has two known siderophores for high-affinity iron scavenging, yersiniabactin and pyoverdin, and we uncover a third siderophore, citrate, required for growth when iron is limiting. Though growth of a DC3000 triple mutant unable to either synthesize or import these siderophores is severely restricted in iron-limited culture, it is fully pathogenic. One explanation for this phenotype is that the DC3000 triple mutant is able to directly pirate plant iron compounds such as heme/hemin or iron-nicotianamine, and our data indicate that DC3000 can import iron-nicotianamine with high affinity. However, an alternative explanation, supported by data from others, is that the pathogenic environment of DC3000 (i.e., leaf apoplast) is not iron limited but is iron replete, with available iron of >1 μM. Growth of the triple mutant in culture is restored to wild-type levels by supplementation with a variety of iron chelates at >1 μM, including iron(III) dicitrate, a dominant chelate of the leaf apoplast. This suggests that lower-affinity iron import would be sufficient for DC3000 iron nutrition in planta and is in sharp contrast to the high-affinity iron-scavenging mechanisms required in mammalian pathogenesis.
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Affiliation(s)
| | - Mary C. Wildermuth
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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37
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Small RNAs as regulators of primary and secondary metabolism in Pseudomonas species. Appl Microbiol Biotechnol 2011; 91:63-79. [PMID: 21607656 DOI: 10.1007/s00253-011-3332-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/11/2011] [Accepted: 04/11/2011] [Indexed: 10/18/2022]
Abstract
Small RNAs (sRNAs) exert important functions in pseudomonads. Classical sRNAs comprise the 4.5S, 6S, 10Sa and 10Sb RNAs, which are known in enteric bacteria as part of the signal recognition particle, a regulatory component of RNA polymerase, transfer-messenger RNA (tmRNA) and the RNA component of RNase P, respectively. Their homologues in pseudomonads are presumed to have analogous functions. Other sRNAs of pseudomonads generally have little or no sequence similarity with sRNAs of enteric bacteria. Numerous sRNAs repress or activate the translation of target mRNAs by a base-pairing mechanism. Examples of this group in Pseudomonas aeruginosa are the iron-repressible PrrF1 and PrrF2 sRNAs, which repress the translation of genes encoding iron-containing proteins, and PhrS, an anaerobically inducible sRNA, which activates the expression of PqsR, a regulator of the Pseudomonas quinolone signal. Other sRNAs sequester RNA-binding proteins that act as translational repressors. Examples of this group in P. aeruginosa include RsmY and RsmZ, which are central regulatory elements in the GacS/GacA signal transduction pathway, and CrcZ, which is a key regulator in the CbrA/CbrB signal transduction pathway. These pathways largely control the extracellular activities (including virulence traits) and the selection of the energetically most favourable carbon sources, respectively, in pseudomonads.
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Cunnac S, Chakravarthy S, Kvitko BH, Russell AB, Martin GB, Collmer A. Genetic disassembly and combinatorial reassembly identify a minimal functional repertoire of type III effectors in Pseudomonas syringae. Proc Natl Acad Sci U S A 2011; 108:2975-80. [PMID: 21282655 PMCID: PMC3041132 DOI: 10.1073/pnas.1013031108] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The virulence of Pseudomonas syringae and many other proteobacterial pathogens is dependent on complex repertoires of effector proteins injected into host cells by type III secretion systems. The 28 well-expressed effector genes in the repertoire of the model pathogen P. syringae pv. tomato DC3000 were deleted to produce polymutant DC3000D28E. Growth of DC3000D28E in Nicotiana benthamiana was symptomless and 4 logs lower than that of DC3000ΔhopQ1-1, which causes disease in this model plant. DC3000D28E seemed functionally effectorless but otherwise WT in diagnostic phenotypes relevant to plant interactions (for example, ability to inject the AvrPto-Cya reporter into N. benthamiana). Various effector genes were integrated by homologous recombination into native loci or by a programmable or random in vivo assembly shuttle (PRIVAS) system into the exchangeable effector locus in the Hrp pathogenicity island of DC3000D28E. The latter method exploited dual adapters and recombination in yeast for efficient assembly of PCR products into programmed or random combinations of multiple effector genes. Native and PRIVAS-mediated integrations were combined to identify a minimal functional repertoire of eight effector genes that restored much of the virulence of DC3000ΔhopQ1-1 in N. benthamiana, revealing a hierarchy in effector function: AvrPtoB acts with priority in suppressing immunity, enabling other effectors to promote further growth (HopM1 and HopE1), chlorosis (HopG1), lesion formation (HopAM1-1), and near full growth and symptom production (AvrE, HopAA1-1, and/or HopN1 functioning synergistically with the previous effectors). DC3000D28E, the PRIVAS method, and minimal functional repertoires provide new resources for probing the plant immune system.
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Affiliation(s)
- Sébastien Cunnac
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853; and
| | - Suma Chakravarthy
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853; and
| | - Brian H. Kvitko
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853; and
| | - Alistair B. Russell
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853; and
| | - Gregory B. Martin
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853; and
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853
| | - Alan Collmer
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853; and
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Rico A, McCraw SL, Preston GM. The metabolic interface between Pseudomonas syringae and plant cells. Curr Opin Microbiol 2011; 14:31-8. [PMID: 21236723 DOI: 10.1016/j.mib.2010.12.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 12/07/2010] [Accepted: 12/14/2010] [Indexed: 11/25/2022]
Abstract
The bacterial plant pathogen Pseudomonas syringae causes economically important diseases of a wide variety of plant species and is used as a model organism to understand the molecular basis of plant disease. Much existing research into P. syringae-plant interactions has focused on the molecular basis of plant disease resistance and the role of secreted effector proteins in the suppression of plant defences. However, researchers have speculated that the diverse array of effectors, toxins and hormones produced by this pathogen also play an important role in manipulating plant metabolism to promote infection. Recent advances in metabolomics, genomics, transcriptomics and metabolic modelling offer new opportunities to address this question and generate a system-level understanding of metabolic interactions at the host-pathogen interface.
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Affiliation(s)
- Arantza Rico
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
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Park DH, Mirabella R, Bronstein PA, Preston GM, Haring MA, Lim CK, Collmer A, Schuurink RC. Mutations in γ-aminobutyric acid (GABA) transaminase genes in plants or Pseudomonas syringae reduce bacterial virulence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:318-30. [PMID: 21070411 DOI: 10.1111/j.1365-313x.2010.04327.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Pseudomonas syringae pv. tomato DC3000 is a bacterial pathogen of Arabidopsis and tomato that grows in the apoplast. The non-protein amino acid γ-amino butyric acid (GABA) is produced by Arabidopsis and tomato and is the most abundant amino acid in the apoplastic fluid of tomato. The DC3000 genome harbors three genes annotated as gabT GABA transaminases. A DC3000 mutant lacking all three gabT genes was constructed and found to be unable to utilize GABA as a sole carbon and nitrogen source. In complete minimal media supplemented with GABA, the mutant grew less well than wild-type DC3000 and showed strongly reduced expression of hrpL and avrPto, which encode an alternative sigma factor and effector, respectively, associated with the type III secretion system. The growth of the gabT triple mutant was weakly reduced in Arabidopsis ecotype Landberg erecta (Ler) and strongly reduced in the Ler pop2-1 GABA transaminase-deficient mutant that accumulates higher levels of GABA. Much of the ability to grow on GABA-amended minimal media or in Arabidopsis pop2-1 leaves could be restored to the gabT triple mutant by expression in trans of just gabT2. The ability of DC3000 to elicit the hypersensitive response (HR) in tobacco leaves is dependent upon deployment of the type III secretion system, and the gabT triple mutant was less able than wild-type DC3000 to elicit this HR when bacteria were infiltrated along with GABA at levels of 1 mm or more. GABA may have multiple effects on P. syringae-plant interactions, with elevated levels increasing disease resistance.
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Affiliation(s)
- Duck Hwan Park
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
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41
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Soto-Suárez M, Bernal D, González C, Szurek B, Guyot R, Tohme J, Verdier V. In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1. BMC Microbiol 2010; 10:170. [PMID: 20540733 PMCID: PMC2893596 DOI: 10.1186/1471-2180-10-170] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 06/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial leaf blight causes significant yield losses in rice crops throughout Asia and Africa. Although both the Asian and African strains of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo), induce similar symptoms, they are nevertheless genetically different, with the African strains being more closely related to the Asian X. oryzae pv. oryzicola (Xoc). RESULTS Changes in gene expression of the African Xoo strain MAI1 in the susceptible rice cultivar Nipponbare were profiled, using an SSH Xoo DNA microarray. Microarray hybridization was performed comparing bacteria recovered from plant tissues at 1, 3, and 6 days after inoculation (dai) with bacteria grown in vitro. A total of 710 bacterial genes were found to be differentially expressed, with 407 up-regulated and 303 down-regulated. Expression profiling indicated that less than 20% of the 710 bacterial transcripts were induced in the first 24 h after inoculation, whereas 63% were differentially expressed at 6 dai. The 710 differentially expressed genes were one-end sequenced. 535 sequences were obtained from which 147 non-redundant sequences were identified. Differentially expressed genes were related to metabolism, secretion and transport, pathogen adherence to plant tissues, plant cell-wall degradation, IS elements, and virulence. In addition, various other genes encoding proteins with unknown function or showing no similarity to other proteins were also induced. The Xoo MAI1 non-redundant set of sequences was compared against several X. oryzae genomes, revealing a specific group of genes that was present only in MAI1. Numerous IS elements were also found to be differentially expressed. Quantitative real-time PCR confirmed 86% of the identified profile on a set of 14 genes selected according to the microarray analysis. CONCLUSIONS This is the first report to compare the expression of Xoo genes in planta across different time points during infection. This work shows that as-yet-unidentified and potentially new virulence factors are appearing in an emerging African pathogen. It also confirms that African Xoo strains do differ from their Asian counterparts, even at the transcriptional level.
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Affiliation(s)
- Mauricio Soto-Suárez
- UMR 5096 IRD-CNRS-Université de Perpignan, Laboratoire Génome et Développement des Plantes, Institut de Recherche pour le Développement, 911 Avenue Agropolis BP 64501, 34394 Montpellier Cedex 5, France
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42
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Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity. J Bacteriol 2010; 192:2359-72. [PMID: 20190049 DOI: 10.1128/jb.01445-09] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To fully understand how bacteria respond to their environment, it is essential to assess genome-wide transcriptional activity. New high-throughput sequencing technologies make it possible to query the transcriptome of an organism in an efficient unbiased manner. We applied a strand-specific method to sequence bacterial transcripts using Illumina's high-throughput sequencing technology. The resulting sequences were used to construct genome-wide transcriptional profiles. Novel bioinformatics analyses were developed and used in combination with proteomics data for the qualitative classification of transcriptional activity in defined regions. As expected, most transcriptional activity was consistent with predictions from the genome annotation. Importantly, we identified and confirmed transcriptional activity in areas of the genome inconsistent with the annotation and in unannotated regions. Further analyses revealed potential RpoN-dependent promoter sequences upstream of several noncoding RNAs (ncRNAs), suggesting a role for these ncRNAs in RpoN-dependent phenotypes. We were also able to validate a number of transcriptional start sites, many of which were consistent with predicted promoter motifs. Overall, our approach provides an efficient way to survey global transcriptional activity in bacteria and enables rapid discovery of specific areas in the genome that merit further investigation.
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Hassan KA, Johnson A, Shaffer BT, Ren Q, Kidarsa TA, Elbourne LDH, Hartney S, Duboy R, Goebel NC, Zabriskie TM, Paulsen IT, Loper JE. Inactivation of the GacA response regulator in Pseudomonas fluorescens Pf-5 has far-reaching transcriptomic consequences. Environ Microbiol 2010; 12:899-915. [PMID: 20089046 DOI: 10.1111/j.1462-2920.2009.02134.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The GacS/GacA signal transduction system is a central regulator in Pseudomonas spp., including the biological control strain P. fluorescens Pf-5, in which GacS/GacA controls the production of secondary metabolites and exoenzymes that suppress plant pathogens. A whole genome oligonucleotide microarray was developed for Pf-5 and used to assess the global transcriptomic consequences of a gacA mutation in P. fluorescens Pf-5. In cultures at the transition from exponential to stationary growth phase, GacA significantly influenced transcript levels of 635 genes, representing more than 10% of the 6147 annotated genes in the Pf-5 genome. Transcripts of genes involved in the production of hydrogen cyanide, the antibiotic pyoluteorin and the extracellular protease AprA were at a low level in the gacA mutant, whereas those functioning in siderophore production and other aspects of iron homeostasis were significantly higher in the gacA mutant than in wild-type Pf-5. Notable effects of gacA inactivation were also observed in the transcription of genes encoding components of a type VI secretion system and cytochrome c oxidase subunits. Two novel gene clusters expressed under the control of gacA were identified from transcriptome analysis, and we propose global-regulator-based genome mining as an approach to decipher the secondary metabolome of Pseudomonas spp.
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Affiliation(s)
- Karl A Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW, Australia
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Layton AN, Hudson DL, Thompson A, Hinton JCD, Stevens JM, Galyov EE, Stevens MP. Salicylidene acylhydrazide-mediated inhibition of type III secretion system-1 in Salmonella enterica serovar Typhimurium is associated with iron restriction and can be reversed by free iron. FEMS Microbiol Lett 2010; 302:114-22. [PMID: 20002188 DOI: 10.1111/j.1574-6968.2009.01847.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is an animal and zoonotic pathogen of worldwide importance. Intestinal colonization, induction of enteritis and systemic translocation by this bacterium requires type III protein secretion. Strategies that target this process have the potential to control infection, pathology and transmission. We defined the global transcriptional response of S. Typhimurium to INP0403, a member of a family of salicylidene acylhydrazides that inhibit type III secretion (T3S). INP0403 treatment was associated with reduced transcription of genes involved in T3S, but also increased transcription of genes associated with iron acquisition. We show that INP0403 restricts iron availability to Salmonella, and that inhibition of T3S system-1 by INP0403 is, at least in part, reversible by exogenous iron and independent of the iron response regulator Fur.
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Affiliation(s)
- Abigail N Layton
- Division of Microbiology, Institute for Animal Health, Compton, Berkshire, UK.
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45
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Ellison DW, Clark TR, Sturdevant DE, Virtaneva K, Hackstadt T. Limited transcriptional responses of Rickettsia rickettsii exposed to environmental stimuli. PLoS One 2009; 4:e5612. [PMID: 19440298 PMCID: PMC2680988 DOI: 10.1371/journal.pone.0005612] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 04/24/2009] [Indexed: 11/18/2022] Open
Abstract
Rickettsiae are strict obligate intracellular pathogens that alternate between arthropod and mammalian hosts in a zoonotic cycle. Typically, pathogenic bacteria that cycle between environmental sources and mammalian hosts adapt to the respective environments by coordinately regulating gene expression such that genes essential for survival and virulence are expressed only upon infection of mammals. Temperature is a common environmental signal for upregulation of virulence gene expression although other factors may also play a role. We examined the transcriptional responses of Rickettsia rickettsii, the agent of Rocky Mountain spotted fever, to a variety of environmental signals expected to be encountered during its life cycle. R. rickettsii exposed to differences in growth temperature (25 degrees C vs. 37 degrees C), iron limitation, and host cell species displayed nominal changes in gene expression under any of these conditions with only 0, 5, or 7 genes, respectively, changing more than 3-fold in expression levels. R. rickettsii is not totally devoid of ability to respond to temperature shifts as cold shock (37 degrees C vs. 4 degrees C) induced a change greater than 3-fold in up to 56 genes. Rickettsiae continuously occupy a relatively stable environment which is the cytosol of eukaryotic cells. Because of their obligate intracellular character, rickettsiae are believed to be undergoing reductive evolution to a minimal genome. We propose that their relatively constant environmental niche has led to a minimal requirement for R. rickettsii to respond to environmental changes with a consequent deletion of non-essential transcriptional response regulators. A minimal number of predicted transcriptional regulators in the R. rickettsii genome is consistent with this hypothesis.
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Affiliation(s)
- Damon W. Ellison
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infections Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Tina R. Clark
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infections Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Daniel E. Sturdevant
- Genomics Unit, Research Technology Section, Rocky Mountain Laboratories, National Institute of Allergy and Infections Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Kimmo Virtaneva
- Genomics Unit, Research Technology Section, Rocky Mountain Laboratories, National Institute of Allergy and Infections Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Ted Hackstadt
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infections Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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