The Genome Sequence of the Tomato-Pathogenic Actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 Reveals a Large Island Involved in Pathogenicity
Karl-Heinz Gartemann,Birte Abt,Thomas Bekel,Annette Burger,Jutta Engemann,Monika Flügel,Lars Gaigalat,Alexander Goesmann,Ines Gräfen,Jörn Kalinowski,Olaf Kaup,Oliver Kirchner,Lutz Krause,Burkhard Linke,Alice C. McHardy,Folker Meyer,Sandra Pohle,Christian Rückert,Susanne Schneiker,Eva-Maria Zellermann,Alfred Pühler,Rudolf Eichenlaub,Olaf Kaiser,Daniela Bartels +23 more
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The nucleotide sequence of the genome of strain NCPPB382 was determined as discussed by the authors, and the chromosome is circular, consists of 3.298 Mb, and has a high G+C content (72.6%).Abstract:
Clavibacter michiganensis subsp. michiganensis is a plant-pathogenic actinomycete that causes bacterial wilt and canker of tomato. The nucleotide sequence of the genome of strain NCPPB382 was determined. The chromosome is circular, consists of 3.298 Mb, and has a high G+C content (72.6%). Annotation revealed 3,080 putative protein-encoding sequences; only 26 pseudogenes were detected. Two rrn operons, 45 tRNAs, and three small stable RNA genes were found. The two circular plasmids, pCM1 (27.4 kbp) and pCM2 (70.0 kbp), which carry pathogenicity genes and thus are essential for virulence, have lower G+C contents (66.5 and 67.6%, respectively). In contrast to the genome of the closely related organism Clavibacter michiganensis subsp. sepedonicus, the genome of C. michiganensis subsp. michiganensis lacks complete insertion elements and transposons. The 129-kb chp/tomA region with a low G+C content near the chromosomal origin of replication was shown to be necessary for pathogenicity. This region contains numerous genes encoding proteins involved in uptake and metabolism of sugars and several serine proteases. There is evidence that single genes located in this region, especially genes encoding serine proteases, are required for efficient colonization of the host. Although C. michiganensis subsp. michiganensis grows mainly in the xylem of tomato plants, no evidence for pronounced genome reduction was found. C. michiganensis subsp. michiganensis seems to have as many transporters and regulators as typical soil-inhabiting bacteria. However, the apparent lack of a sulfate reduction pathway, which makes C. michiganensis subsp. michiganensis dependent on reduced sulfur compounds for growth, is probably the reason for the poor survival of C. michiganensis subsp. michiganensis in soil.read more
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The xylem as battleground for plant hosts and vascular wilt pathogens.
TL;DR: This review discusses the current knowledge on interactions of vascular wilt pathogens with their host plants, with emphasis on host defense responses against this group of pathogens.
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Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria
Beile Gao,Radhey S. Gupta +1 more
TL;DR: Large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades at various taxonomic levels enable the development of a stable and reliable phylogenetic framework for this phylum.
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The Gram-positive side of plant-microbe interactions.
Isolde M. Francis,Isolde M. Francis,Marcelle Holsters,Marcelle Holsters,Danny Vereecke,Danny Vereecke +5 more
TL;DR: The present knowledge of the beneficial and detrimental interactions of Gram-positive bacteria with plants is summarized to underline the importance of this particular group of bacteria.
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The Clavibacter michiganensis Subspecies: Molecular Investigation of Gram-Positive Bacterial Plant Pathogens
TL;DR: In the Clavibacter subspecies michiganensis and sepedonicus, infecting tomato and potato, respectively, essential factors for disease induction are plasmid encoded and loss of the virulence plasmids converts these biotrophic pathogens into endophytes.
Journal ArticleDOI
Mycothiol: synthesis, biosynthesis and biological functions of the major low molecular weight thiol in actinomycetes
TL;DR: This review covers progress that has so far been made in terms of its distribution, biosynthesis and metabolic functions, as well as chemical syntheses of mycothiol and alternative substrates and inhibitors of myCothiol biosynthetic and my cothiol-dependent enzymes.
References
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Book
Molecular Cloning: A Laboratory Manual
TL;DR: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years as mentioned in this paper and has been so popular, or so influential, that no other manual has been more widely used and influential.
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Journal ArticleDOI
Base-calling of automated sequencer traces using Phred. I. accuracy assessment
TL;DR: In this article, a base-calling program for automated sequencer traces, phred, with improved accuracy was proposed. But it was not shown to achieve a lower error rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.
Journal ArticleDOI
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Brent Ewing,Philip Green +1 more
TL;DR: The ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data, is developed and implemented in the base-calling program.