RNA-seq Analysis Reveals That an ECF σ Factor, AcsS, Regulates Achromobactin Biosynthesis in Pseudomonas syringae pv. syringae B728a

Iron is an essential micronutrient for Pseudomonas syringae pv. syringae strain B728a and many other microorganisms; therefore, B728a has evolved methods of iron acquirement including the use of iron-chelating siderophores. In this study an extracytoplasmic function (ECF) sigma factor, AcsS, encoded within the achromobactin gene cluster is shown to be a major regulator of genes involved in the biosynthesis and secretion of this siderophore. However, production of achromobactin was not completely abrogated in the deletion mutant, implying that other regulators may be involved such as PvdS, the sigma factor that regulates pyoverdine biosynthesis. RNA-seq analysis identified 287 genes that are differentially expressed between the AcsS deletion mutant and the wild type strain. These genes are involved in iron response, secretion, extracellular polysaccharide production, and cell motility. Thus, the transcriptome analysis supports a role for AcsS in the regulation of achromobactin production and the potential activity of both AcsS and achromobactin in the plant-associated lifestyle of strain B728a.

[1]  D. Ackerley,et al.  Characterization of pyoverdine and achromobactin in Pseudomonas syringae pv. phaseolicola 1448a , 2011, BMC Microbiology.

[2]  Alexander M. Jones,et al.  The Phytopathogen Pseudomonas syringae pv. tomato DC3000 Has Three High-Affinity Iron-Scavenging Systems Functional under Iron Limitation Conditions but Dispensable for Pathogenesis , 2011, Journal of bacteriology.

[3]  D. Gross,et al.  Sensor Kinases RetS and LadS Regulate Pseudomonas syringae Type VI Secretion and Virulence Factors , 2010, Journal of bacteriology.

[4]  M. Ullrich,et al.  Impact of Siderophore Production by Pseudomonas syringae pv. syringae 22d/93 on Epiphytic Fitness and Biocontrol Activity against Pseudomonas syringae pv. glycinea 1a/96 , 2010, Applied and Environmental Microbiology.

[5]  Bronwyn G. Butcher,et al.  Transcriptome Analysis of Pseudomonas syringae Identifies New Genes, Noncoding RNAs, and Antisense Activity , 2010, Journal of bacteriology.

[6]  R. Sorek,et al.  Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity , 2010, Nature Reviews Genetics.

[7]  Xuegong Zhang,et al.  DEGseq: an R package for identifying differentially expressed genes from RNA-seq data , 2010, Bioinform..

[8]  Thomas M. Keane,et al.  A simple method for directional transcriptome sequencing using Illumina technology , 2009, Nucleic acids research.

[9]  Jessica M. A. Blair,et al.  Structure, function and inhibition of RND efflux pumps in Gram-negative bacteria: an update. , 2009, Current opinion in microbiology.

[10]  P. Cornelis,et al.  A survey of TonB-dependent receptors in fluorescent pseudomonads. , 2009, Environmental microbiology reports.

[11]  Samuel A. Assefa,et al.  A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi , 2009, PLoS genetics.

[12]  A. de Vicente,et al.  Contribution of mangotoxin to the virulence and epiphytic fitness of Pseudomonas syringae pv. syringae. , 2009, International microbiology : the official journal of the Spanish Society for Microbiology.

[13]  A. Berti,et al.  Analysis of Achromobactin Biosynthesis by Pseudomonas syringae pv. syringae B728a , 2009, Journal of bacteriology.

[14]  V. Beneš,et al.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. , 2009, Clinical chemistry.

[15]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[16]  D. K. Willis,et al.  Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation. , 2008, Journal of microbiological methods.

[17]  M. Stephens,et al.  RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.

[18]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[19]  M. Marahiel,et al.  Siderophore-Based Iron Acquisition and Pathogen Control , 2007, Microbiology and Molecular Biology Reviews.

[20]  G. Amoutzias,et al.  Siderophores in fluorescent pseudomonads: new tricks from an old dog. , 2007, Future microbiology.

[21]  M. Parsek,et al.  Pseudomonas aeruginosa Psl Is a Galactose- and Mannose-Rich Exopolysaccharide , 2007, Journal of bacteriology.

[22]  A. Berti,et al.  Identification of a Biosynthetic Gene Cluster and the Six Associated Lipopeptides Involved in Swarming Motility of Pseudomonas syringae pv. tomato DC3000 , 2007, Journal of bacteriology.

[23]  H. Ochman,et al.  Stepwise formation of the bacterial flagellar system , 2007, Proceedings of the National Academy of Sciences.

[24]  A. de Vicente,et al.  A nonribosomal peptide synthetase gene (mgoA) of Pseudomonas syringae pv. syringae is involved in mangotoxin biosynthesis and is required for full virulence. , 2007, Molecular plant-microbe interactions : MPMI.

[25]  M. Viljoen,et al.  Ferritin and ferritin isoforms I: Structure–function relationships, synthesis, degradation and secretion , 2007, Archives of physiology and biochemistry.

[26]  P. Visca,et al.  Pyoverdine siderophores: from biogenesis to biosignificance. , 2007, Trends in microbiology.

[27]  L. Ohno-Machado,et al.  Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates , 2007, BMC Genomics.

[28]  K. Weber,et al.  Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction , 2006, Nature Reviews Microbiology.

[29]  L. Piddock.  Multidrug-resistance efflux pumps ? not just for resistance , 2006, Nature Reviews Microbiology.

[30]  D. Wesenberg,et al.  TolC Is Involved in Enterobactin Efflux across the Outer Membrane of Escherichia coli , 2005, Journal of bacteriology.

[31]  D. Gross,et al.  Characterization of a Resistance-Nodulation-Cell Division Transporter System Associated with the syr-syp Genomic Island of Pseudomonas syringae pv. syringae , 2005, Applied and Environmental Microbiology.

[32]  E. Greenberg,et al.  Iron and Pseudomonas aeruginosa biofilm formation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Z. Chen,et al.  Oligonucleotide microarray analysis of the salA regulon controlling phytotoxin production by Pseudomonas syringae pv. syringae. , 2005, Molecular plant-microbe interactions : MPMI.

[34]  Matt Nolan,et al.  Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[35]  R A Irizarry,et al.  On the utility of pooling biological samples in microarray experiments. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[36]  D. Expert,et al.  Erwinia chrysanthemi requires a second iron transport route dependent of the siderophore achromobactin for extracellular growth and plant infection , 2004, Molecular microbiology.

[37]  R. Kolter,et al.  Two Genetic Loci Produce Distinct Carbohydrate-Rich Structural Components of the Pseudomonas aeruginosa Biofilm Matrix , 2004, Journal of bacteriology.

[38]  M. Parsek,et al.  Identification of psl, a Locus Encoding a Potential Exopolysaccharide That Is Essential for Pseudomonas aeruginosa PAO1 Biofilm Formation , 2004, Journal of bacteriology.

[39]  Stephen Lory,et al.  A four‐tiered transcriptional regulatory circuit controls flagellar biogenesis in Pseudomonas aeruginosa , 2003, Molecular microbiology.

[40]  Epiphytic Fitness of Pseudomonas syringae pv. syringae on Mango Trees is Increased by 62-Kb Plasmids , 2003 .

[41]  C. Andersen.  Channel-tunnels: outer membrane components of type I secretion systems and multidrug efflux pumps of Gram-negative bacteria. , 2003, Reviews of physiology, biochemistry and pharmacology.

[42]  Arnold J. Stromberg,et al.  Statistical implications of pooling RNA samples for microarray experiments , 2003, BMC Bioinform..

[43]  R. Sonti,et al.  Genetic Locus Encoding Functions Involved in Biosynthesis and Outer Membrane Localization of Xanthomonadin in Xanthomonas oryzae pv. oryzae , 2002, Journal of bacteriology.

[44]  N. Perna,et al.  hrp genes of Erwinia chrysanthemi 3937 are important virulence factors. , 2002, Molecular plant-microbe interactions : MPMI.

[45]  S. Lindow,et al.  Heterogeneity of iron bioavailability on plants assessed with a whole-cell GFP-based bacterial biosensor. , 2000, Microbiology.

[46]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[47]  R. Kolter,et al.  Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development , 1998, Molecular microbiology.

[48]  M. Guerinot.  Microbial iron transport. , 1994, Annual review of microbiology.

[49]  D. Cove,et al.  Development of an electro-transformation system for Escherichia coli DH10B , 1993 .

[50]  M. Couturier,et al.  Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. , 1992, Journal of molecular biology.

[51]  D. Hanahan,et al.  Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[52]  S. S. Hirano,et al.  Population Biology and Epidemiology of Pseudomonas Syringae , 1990 .

[53]  B. Staskawicz,et al.  Bacterial blight of soybean: regulation of a pathogen gene determining host cultivar specificity. , 1989, Science.

[54]  A. Landy.  Dynamic, structural, and regulatory aspects of lambda site-specific recombination. , 1989, Annual review of biochemistry.

[55]  G. Shand,et al.  Media for study of growth kinetics and envelope properties of iron-deprived bacteria , 1987, Journal of clinical microbiology.

[56]  S. Lindow,et al.  Lack of evidence for in situ fluorescent pigment production by Pseudomonas syringae pv. syringae on bean leaf surfaces , 1987 .

[57]  D. Gross.  Regulation of syringomycin synthesis in Pseudomonas syringae pv. syringae and defined conditions for its production. , 1985, The Journal of applied bacteriology.

[58]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[59]  G. Ditta,et al.  Heme biosynthesis in Rhizobium. Identification of a cloned gene coding for delta-aminolevulinic acid synthetase from Rhizobium meliloti. , 1982, The Journal of biological chemistry.

[60]  King Eo,et al.  Two simple media for the demonstration of pyocyanin and fluorescin. , 1954 .

[61]  E. King,et al.  Two simple media for the demonstration of pyocyanin and fluorescin. , 1954, The Journal of laboratory and clinical medicine.