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Title: Comparison of the complete genome sequences of Pseudomonassyringae pv. syringae B728a and pv. tomato DC3000.

Abstract

The complete genomic sequence of Pseudomonas syringaepathovar syringae B728a (Pss B728a), has been determined and is comparedwith that of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Thesetwo pathovars of this economically important species of plant pathogenicbacteria differ in host range and apparent patterns of interaction withplants, with Pss having a more pronounced epiphytic stage of growth andhigher abiotic stress tolerance and Pst DC3000 having a more pronouncedapoplastic growth habitat. The Pss B728a genome (6.1 megabases) containsa circular chromosome and no plasmid, whereas the Pst DC3000 genome is6.5 mbp in size, composed of a circular chromosome and two plasmids.While a high degree of similarity exists between the two sequencedPseudomonads, 976 protein-encoding genes are unique to Pss B728a whencompared to Pst DC3000, including large genomic islands likely tocontribute to virulence and host specificity. Over 375 repetitiveextragenic palindromic sequences (REPs) unique to Pss B728a when comparedto Pst DC3000 are widely distributed throughout the chromosome except in14 genomic islands, which generally had lower GC content than the genomeas a whole. Content of the genomic islands vary, with one containing aprophage and another the plasmid pKLC102 of P. aeruginosa PAO1. Among the976 genes of Pss B728a with no counterpart in Pst DC3000 are thoseencoding formore » syringopeptin (SP), syringomycin (SR), indole acetic acidbiosynthesis, arginine degradation, and production of ice nuclei. Thegenomic comparison suggests that several unique genes for Pss B728a suchas ectoine synthase, DNA repair, and antibiotic production may contributeto epiphytic fitness and stress tolerance of this organism. Pseudomonassyringae, a member of the gamma subgroup of the Proteobacteria, is awidespread bacterial pathogen of many plant species. The species P.syringae is subdivided into approximately 50 pathovars based onpathogenicity and host range. P. syringae is capable of producing avariety of different symptoms depending on the host species and site ofinfection. For example, it causes leaf spot diseases that defoliateplants such as tomato, bean, soybean, trunk cankers, and so-called"blast" diseases on fruit, nut and ornamental species. Considerablevariation occurs both between and within different pathovars of P.syringae (1). Because of its importance as a plant pathogen, it has beenthe subject of much research, especially of its epidemiology andvirulence mechanisms (2). Pseudomonas syringae pv. syringae (Pss) strainB728a is typical of most strains of this pathovar in that it exhibits avery pronounced epiphytic phase on plants. Such strains achieve andmaintain large populations on healthy plants, where they are exposed tostressful conditions such as dryness and sunlight that are hostile tobacterial growth(2). Epiphytic Pss populations serve as inocula that cansubsequently invade plants and initiate disease. Pss strains are distinctfrom many P. syringae strains, such as P. syringae pv. tomato (Pst)strain DC3000, that poorly colonize the exterior of plants; these strainsmay be considered "endophytes" based on their ability to multiply mostlywithin the plant (3). True epiphytes such as Pss B728a often reachsurface populations of over 107 cells/g while strains such as Pst DC3000seldom exceed 105 cells/g (2, 3). Thus, these strains might be consideredto occupy different ends of the epiphytic/endophytic spectrum of plantcolonization as described by Beattie and Lindow (4). As a pathogen and anepiphyte, Pss B728a has evolved to exploit at least two distincthabitats: the leaf surface and apoplast. Because rapid changes intemperature, low water content, and incident solar radiation occur onleaf surfaces, it has been hypothesized that the epiphyte Pss B728aposseses more genes conferring environmental stress tolerance than theendophyte Pst DC3000 (4). Pss B728a also exhibits several traits such asice nucleation activity and SR production (2) that are lacking in manyother strains of P. syringae including Pst DC3000. As the most icenucleation active bacterial species, P. syringae is responsible forinciting frost injury to frost sensitive plants that can supercool andavoid damaging ice formation if not colonized by ice nucleation activebacteria (2,4). We present here a genomic comparison between strains PssB728a and Pst DC3000 of P. syringae pathovars as well as between thesestrains and P. aeruginosa and P. putida, two additional Pseudomonadsrecently sequenced. These genomic comparisons provide insights into theevolutionary history and diverse life styles of the pseudomonads,including their association with the environment, plant or mammalianhosts.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
Sponsoring Org.:
USDOE Director. Office of Science. Office of Biological andEnvironmental Research
OSTI Identifier:
877630
Report Number(s):
LBNL-58214
R&D Project: 626869; BnR: KP1103010
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
Proceedings of the National Academy ofSciences
Additional Journal Information:
Journal Volume: 102; Journal Issue: 31; Related Information: Journal Publication Date: Aug. 2, 2005
Country of Publication:
United States
Language:
English
Subject:
59; complete genome Pseudomonas syringae

Citation Formats

Feil, Helene, Feil, William S, Chain, Patrick, Larimer, Frank, DiBartolo, Genevieve, Copeland, Alex, Lykidis, Athanasios, Trong, Stephen, Nolan, Matt, Goltsman, Eugene, Thiel, James, Malfatti, Stephanie, Loper, Joyce E, Lapidus, Alla, Detter, John C, Land, Miriam, Richardson, Paul M, Kyrpides, Nikos C, Ivanova, Natalia, and Lindow, StevenE. Comparison of the complete genome sequences of Pseudomonassyringae pv. syringae B728a and pv. tomato DC3000.. United States: N. p., 2005. Web.
Feil, Helene, Feil, William S, Chain, Patrick, Larimer, Frank, DiBartolo, Genevieve, Copeland, Alex, Lykidis, Athanasios, Trong, Stephen, Nolan, Matt, Goltsman, Eugene, Thiel, James, Malfatti, Stephanie, Loper, Joyce E, Lapidus, Alla, Detter, John C, Land, Miriam, Richardson, Paul M, Kyrpides, Nikos C, Ivanova, Natalia, & Lindow, StevenE. Comparison of the complete genome sequences of Pseudomonassyringae pv. syringae B728a and pv. tomato DC3000.. United States.
Feil, Helene, Feil, William S, Chain, Patrick, Larimer, Frank, DiBartolo, Genevieve, Copeland, Alex, Lykidis, Athanasios, Trong, Stephen, Nolan, Matt, Goltsman, Eugene, Thiel, James, Malfatti, Stephanie, Loper, Joyce E, Lapidus, Alla, Detter, John C, Land, Miriam, Richardson, Paul M, Kyrpides, Nikos C, Ivanova, Natalia, and Lindow, StevenE. Fri . "Comparison of the complete genome sequences of Pseudomonassyringae pv. syringae B728a and pv. tomato DC3000.". United States. https://www.osti.gov/servlets/purl/877630.
@article{osti_877630,
title = {Comparison of the complete genome sequences of Pseudomonassyringae pv. syringae B728a and pv. tomato DC3000.},
author = {Feil, Helene and Feil, William S and Chain, Patrick and Larimer, Frank and DiBartolo, Genevieve and Copeland, Alex and Lykidis, Athanasios and Trong, Stephen and Nolan, Matt and Goltsman, Eugene and Thiel, James and Malfatti, Stephanie and Loper, Joyce E and Lapidus, Alla and Detter, John C and Land, Miriam and Richardson, Paul M and Kyrpides, Nikos C and Ivanova, Natalia and Lindow, StevenE},
abstractNote = {The complete genomic sequence of Pseudomonas syringaepathovar syringae B728a (Pss B728a), has been determined and is comparedwith that of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Thesetwo pathovars of this economically important species of plant pathogenicbacteria differ in host range and apparent patterns of interaction withplants, with Pss having a more pronounced epiphytic stage of growth andhigher abiotic stress tolerance and Pst DC3000 having a more pronouncedapoplastic growth habitat. The Pss B728a genome (6.1 megabases) containsa circular chromosome and no plasmid, whereas the Pst DC3000 genome is6.5 mbp in size, composed of a circular chromosome and two plasmids.While a high degree of similarity exists between the two sequencedPseudomonads, 976 protein-encoding genes are unique to Pss B728a whencompared to Pst DC3000, including large genomic islands likely tocontribute to virulence and host specificity. Over 375 repetitiveextragenic palindromic sequences (REPs) unique to Pss B728a when comparedto Pst DC3000 are widely distributed throughout the chromosome except in14 genomic islands, which generally had lower GC content than the genomeas a whole. Content of the genomic islands vary, with one containing aprophage and another the plasmid pKLC102 of P. aeruginosa PAO1. Among the976 genes of Pss B728a with no counterpart in Pst DC3000 are thoseencoding for syringopeptin (SP), syringomycin (SR), indole acetic acidbiosynthesis, arginine degradation, and production of ice nuclei. Thegenomic comparison suggests that several unique genes for Pss B728a suchas ectoine synthase, DNA repair, and antibiotic production may contributeto epiphytic fitness and stress tolerance of this organism. Pseudomonassyringae, a member of the gamma subgroup of the Proteobacteria, is awidespread bacterial pathogen of many plant species. The species P.syringae is subdivided into approximately 50 pathovars based onpathogenicity and host range. P. syringae is capable of producing avariety of different symptoms depending on the host species and site ofinfection. For example, it causes leaf spot diseases that defoliateplants such as tomato, bean, soybean, trunk cankers, and so-called"blast" diseases on fruit, nut and ornamental species. Considerablevariation occurs both between and within different pathovars of P.syringae (1). Because of its importance as a plant pathogen, it has beenthe subject of much research, especially of its epidemiology andvirulence mechanisms (2). Pseudomonas syringae pv. syringae (Pss) strainB728a is typical of most strains of this pathovar in that it exhibits avery pronounced epiphytic phase on plants. Such strains achieve andmaintain large populations on healthy plants, where they are exposed tostressful conditions such as dryness and sunlight that are hostile tobacterial growth(2). Epiphytic Pss populations serve as inocula that cansubsequently invade plants and initiate disease. Pss strains are distinctfrom many P. syringae strains, such as P. syringae pv. tomato (Pst)strain DC3000, that poorly colonize the exterior of plants; these strainsmay be considered "endophytes" based on their ability to multiply mostlywithin the plant (3). True epiphytes such as Pss B728a often reachsurface populations of over 107 cells/g while strains such as Pst DC3000seldom exceed 105 cells/g (2, 3). Thus, these strains might be consideredto occupy different ends of the epiphytic/endophytic spectrum of plantcolonization as described by Beattie and Lindow (4). As a pathogen and anepiphyte, Pss B728a has evolved to exploit at least two distincthabitats: the leaf surface and apoplast. Because rapid changes intemperature, low water content, and incident solar radiation occur onleaf surfaces, it has been hypothesized that the epiphyte Pss B728aposseses more genes conferring environmental stress tolerance than theendophyte Pst DC3000 (4). Pss B728a also exhibits several traits such asice nucleation activity and SR production (2) that are lacking in manyother strains of P. syringae including Pst DC3000. As the most icenucleation active bacterial species, P. syringae is responsible forinciting frost injury to frost sensitive plants that can supercool andavoid damaging ice formation if not colonized by ice nucleation activebacteria (2,4). We present here a genomic comparison between strains PssB728a and Pst DC3000 of P. syringae pathovars as well as between thesestrains and P. aeruginosa and P. putida, two additional Pseudomonadsrecently sequenced. These genomic comparisons provide insights into theevolutionary history and diverse life styles of the pseudomonads,including their association with the environment, plant or mammalianhosts.},
doi = {},
journal = {Proceedings of the National Academy ofSciences},
number = 31,
volume = 102,
place = {United States},
year = {2005},
month = {4}
}