A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528

Studholme, David J.; Ibanez, Selena Gimenez; MacLean, Daniel; Dangl, Jeffery L.; Chang, Jeff H.; Rathjen, John P.
January 2009
BMC Genomics;2009, Vol. 10, p395
Academic Journal
Background: Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is dependent on the type III secretion system, which secretes a suite of up to about thirty virulence 'effector' proteins into the host cytoplasm where they subvert the eukaryotic cell physiology and disrupt host defences. P. syringae pathovar tabaci naturally causes disease on wild tobacco, the model member of the Solanaceae, a family that includes many crop species as well as on soybean. Results: We used the 'next-generation' Illumina sequencing platform and the Velvet short-read assembly program to generate a 145X deep 6,077,921 nucleotide draft genome sequence for P. syringae pathovar tabaci strain 11528. From our draft assembly, we predicted 5,300 potential genes encoding proteins of at least 100 amino acids long, of which 303 (5.72%) had no significant sequence similarity to those encoded by the three previously fully sequenced P. syringae genomes. Of the core set of Hrp Outer Proteins that are conserved in three previously fully sequenced P. syringae strains, most were also conserved in strain 11528, including AvrE1, HopAH2, HopAJ2, HopAK1, HopAN1, HopI, HopJ1, HopX1, HrpK1 and HrpW1. However, the hrpZ1 gene is partially deleted and hopAF1 is completely absent in 11528. The draft genome of strain 11528 also encodes close homologues of HopO1, HopT1, HopAH1, HopR1, HopV1, HopAG1, HopAS1, HopAE1, HopAR1, HopF1, and HopW1 and a degenerate HopM1'. Using a functional screen, we confirmed that hopO1, hopT1, hopAH1, hopM1', hopAE1, hopAR1, and hopAI1' are part of the virulence-associated HrpL regulon, though the hopAI1' and hopM1' sequences were degenerate with premature stop codons. We also discovered two additional HrpL-regulated effector candidates and an HrpL-regulated distant homologue of avrPto1. Conclusion: The draft genome sequence facilitates the continued development of P. syringae pathovar tabaci on wild tobacco as an attractive model system for studying bacterial disease on plants. The catalogue of effectors sheds further light on the evolution of pathogenicity and host-specificity as well as providing a set of molecular tools for the study of plant defence mechanisms. We also discovered several large genomic regions in Pta 11528 that do not share detectable nucleotide sequence similarity with previously sequenced Pseudomonas genomes. These regions may include horizontally acquired islands that possibly contribute to pathogenicity or epiphytic fitness of Pta 11528.


Related Articles

  • A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks. Zhen Gao; Ruizhe Zhao; Jianhua Ruan // BMC Genomics;2013, Vol. 14 Issue Suppl 1, p1 

    Background: Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple method for cis-regulatory network discovery which aims to avoid some of the common problems of previous approaches. Results: Using promoter sequences and gene expression...

  • Boundaries in vertebrate genomes: different solutions to adequately insulate gene expression domains. Moltó, Eduardo; Fernández, Almudena; Montoliu, Lluis // Briefings in Functional Genomics & Proteomics;Jul2009, Vol. 8 Issue 4, p283 

    Gene expression domains are normally not arranged in vertebrate genomes according to their expression patterns. Instead, it is not unusual to find genes expressed in different cell types, or in different developmental stages, sharing a particular region of a chromosome. Therefore, the existence...

  • Stop codons in bacteria are not selectively equivalent. Povolotskaya, Inna S.; Kondrashov, Fyodor A.; Ledda, Alice; Vlasov, Peter K. // Biology Direct;2012, Vol. 7 Issue 1, p30 

    Background: The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes. Results: We show that in bacteria stop...

  • The functional landscape of mouse gene expression. Wen Zhang; Morris, Quaid D.; Chang, Richard; Shai, Ofer; Bakowski, Malina A.; Mitsakakis, Nicholas; Mohammad, Naveed; Robinson, Mark D.; Zirngibl, Ralph; Somogyi, Eszter; Laurin, Nancy; Eftekharpour, Eftekhar; Sat, Eric; Grigull, Jörg; Qun Pan; Wen-Tao Peng; Krogan, Nevan; Greenblatt, Jack; Fehlings, Michael; Van der Kooy, Derek // Journal of Biology;2004, Vol. 3, p21 

    Background: Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-specific expression is indicative...

  • Nourseothricin Acetyltransferease: A Positive Selectable Marker for Toxoplasma gondil. Van, Tam T.; Rooney, Peggy J.; Knoll, Laura J. // Journal of Parasitology;Jun2006, Vol. 92 Issue 3, p668 

    The article studies the use of nourseothricin acetyltransferease as a positive selectable marker for Toxoplasma gondii. The T. gondii genome is organized into a searchable database including ten times coverage of the genome, tags from serial analysis of gene expression, and expressed sequence...

  • Effect of CAR activation on selected metabolic pathways in normal and hyperlipidemic mouse livers. Režen, Tadeja; Tamasi, Viola; Lövgren-Sandblom, Anita; Björkhem, Ingemar; Meyer, Urs A.; Rozman, Damjana // BMC Genomics;2009, Vol. 10, p384 

    Background: The declining cost of DNA sequencing is making genome sequencing a feasible option for more organisms, including many of interest to ecologists and evolutionary biologists. While obtaining high-depth, completely assembled genome sequences for most non-model organisms remains...

  • A genetic signature of interspecies variations in gene expression. Tirosh, Itay; Weinberger, Adina; Carmi, Miri; Barkai, Naama // Nature Genetics;Jul2006, Vol. 38 Issue 7, p830 

    Phenotypic diversity is generated through changes in gene structure or gene regulation. The availability of full genomic sequences allows for the analysis of gene sequence evolution. In contrast, little is known about the principles driving the evolution of gene expression. Here we describe the...

  • Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. Kakaradov, Boyko; Xiong, Hui Yuan; Lee, Leo J.; Jojic, Nebojsa; Frey, Brendan J. // BMC Bioinformatics;2012 Supplement 6, Vol. 13 Issue Suppl 6, p1 

    Transcript quantification is a long-standing problem in genomics and estimating the relative abundance of alternatively-spliced isoforms from the same transcript is an important special case. Both problems have recently been illuminated by high-throughput RNA sequencing experiments which are...

  • Imprinting: Human genome gets full marks. Casci, Tanita // Nature Reviews Genetics;Jan2008, Vol. 9 Issue 1, p6 

    The article evaluates a research entitled "Computational and experimental identification of novel human imprinted genes," by P. P. Luedi and colleagues. The authors used the computational approach which involved teaching a computer to recognize the sequence features of imprinted genes by...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics