Proteomics characterization of novel spore proteins of Bacillus subtilis

Kuwana, Ritsuko; Kasahara, Yasuhiro; Fujibayashi, Machiko; Takamatsu, Hiromu; Ogasawara, Nagahisa; Watabe, Kazuhito

doi:10.1099/00221287-148-12-3971

Cited by 125 publications

(144 citation statements)

References 36 publications

(30 reference statements)

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“…For example, no obvious phenotype was found for mutants deficient in the production of the s Egoverned CotJC Mn 2+ -type catalase (Henriques et al, 1995), but at least one other putative Mn 2+ -dependent catalase (encoded by yjqC) was found in the s K regulon (Supplementary Table S4). The present list of sporulationspecific genes will also assist proteomics-based studies aimed at the identification of spore proteins, proteins associated with certain spore structures (Kuwana et al, 2002;Lai et al, 2003), or proteins that may be present as complexes at specific stages in morphogenesis. It will serve as a basis for studies of sporulation-specific gene expression under different nutritional conditions or in undomesticated strains of B. subtilis (Duc et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

“…The finding of ripX, which encodes a site-specific integrase/recombinase involved in proper chromosome partitioning (Sciochetti et al, 1999), and yqhH, predicted to code for an SNF2-type helicase (Supplementary Table S1), suggests that their products may prepare the spore for the resumption of growth following germination and outgrowth. Several genes encode proteins that were found in the proteomics study of Kuwana et al (2002) to be under s F control and to encode spore components, including yfhE and yfhD, yhcM, ytfI and ytfJ (Supplementary Table S1). Detailed functional studies have not yet been reported for any of these genes.…”

Section: Differentiation Of the Compartment-specific Sporulation Regumentioning

confidence: 99%

“…Sporulation loci have also been identified by transposon mutagenesis or by the use of integrational plasmids for gene disruption, by reverse genetics, as encoding components of the spore or some of its structures (e.g. Donovan et al, 1987;Kuwana et al, 2002;Lai et al, 2003), or by expressionbased screens designed to find members of specific sporulation regulons (e.g. Beall et al, 1993).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilis

et al. 2005

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Temporal and compartment-specific control of gene expression during sporulation in Bacillus subtilis is governed by a cascade of four RNA polymerase subunits. s F in the prespore and s E in the mother cell control early stages of development, and are replaced at later stages by s G and s K , respectively. Ultimately, a comprehensive description of the molecular mechanisms underlying spore morphogenesis requires the knowledge of all the intervening genes and their assignment to specific regulons. Here, in an extension of earlier work, DNA macroarrays have been used, and members of the four compartment-specific sporulation regulons have been identified. Genes were identified and grouped based on: i) their temporal expression profile and ii) the use of mutants for each of the four sigma factors and a bofA allele, which allows s K activation in the absence of s G . As a further test, artificial production of active alleles of the sigma factors in non-sporulating cells was employed. A total of 439 genes were found, including previously characterized genes whose transcription is induced during sporulation: 55 in the s F regulon, 154 s E -governed genes, 113 s G -dependent genes, and 132 genes under s K control. The results strengthen the view that the activities of s F , s E , s G and s K are largely compartmentalized, both temporally as well as spatially, and that the major vegetative sigma factor (s A ) is active throughout sporulation. The results provide a dynamic picture of the changes in the overall pattern of gene expression in the two compartments of the sporulating cell, and offer insight into the roles of the prespore and the mother cell at different times of spore morphogenesis.

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Section: Discussionmentioning

confidence: 99%

Section: Differentiation Of the Compartment-specific Sporulation Regumentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilis

et al. 2005

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“…One of the unique structural features of the spore is the coat, the outermost layer of spores of many Bacillus species, including B. subtilis (5)(6)(7)(8). The B. subtilis spore coat is composed of several distinct layers and contains Ն30 proteins, almost all of which are spore-specific gene products (5)(6)(7)(8)(9)(10)(11)(12). There is extensive cross-linking of a number of proteins in the coats, at least in part by a transglutaminase and perhaps by the formation of dityrosine cross-links as well (13)(14)(15)(16)(17)(18).…”

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confidence: 99%

The Bacillus subtilis spore coat provides “eat resistance” during phagocytic predation by the protozoan Tetrahymena thermophila

Klobutcher

Ragkousi

Setlow

2005

Proc. Natl. Acad. Sci. U.S.A.

121

124

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Bacillus spores are highly resistant to many environmental stresses, owing in part to the presence of multiple ''extracellular'' layers. Although the role of some of these extracellular layers in resistance to particular stresses is known, the function of one of the outermost layers, the spore coat, is not completely understood. This study sought to determine whether the spore coat plays a role in resistance to predation by the ciliated protozoan Tetrahymena, which uses phagocytosis to ingest and degrade other microorganisms. Wild-type dormant spores of Bacillus subtilis were efficiently ingested by the protozoan Tetrahymena thermophila but were neither digested nor killed. However, spores with various coat defects were killed and digested, leaving only an outer shell termed a rind, and supporting the growth of Tetrahymena. A similar rind was generated when coat-defective spores were treated with lysozyme alone. The sensitivity of spores with different coat defects to predation by T. thermophila paralleled the spores' sensitivities to lysozyme. Spore killing by T. thermophila was by means of lytic enzymes within the protozoal phagosome, not by initial spore germination followed by killing. These findings suggest that a major function of the coat of spores of Bacillus species is to protect spores against predation. We also found that indigestible rinds were generated even from spores in which cross-linking of coat proteins was greatly reduced, implying the existence of a coat structure that is highly resistant to degradative enzymes.Bacillus spore ͉ phagocytosis ͉ spore resistance

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“…I n recent years, the bottom-up approach to proteomics has gained much notoriety in the scientific community [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15]. This approach begins with the proteolysis of a protein or mixture of proteins to generate an even more complex mixture of peptides.…”

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confidence: 99%

Factors that affect ion trap data-dependent MS/MS in proteomics

Wenner

Lynn

2004

J. Am. Soc. Mass Spectrom.

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Quadrupole ion trap scanning parameters for performing bottom-up proteomics in a datadependent fashion were evaluated on a Finnigan LCQ Deca mass spectrometer. Evaluation of parameters such as the number of averaged full scans, the number of averaged MS/MS scans, and ion injection times were necessary for acquiring high quality MS/MS spectra that yield favorable b and y ion coverage and high correlation to proteins using database searching algorithms. In this study, we demonstrated how the duty cycle of the mass spectrometer affects the number of peptides that can be successfully identified by SEQUEST using a model system of tryptic BSA peptides to mimic a typical complex mixture associated with bottom-up proteomics. The number of averaged scans and the duration of ion accumulation in the trap had a significant effect on the quality of acquired MS/MS spectra. For example, by increasing the ion injection time from 500 ms to 600 ms, peptide HLVDEPQNLIK improved from being improperly identified to being correctly identified with a SEQUEST cross-correlation score of 3.60. As a result of these experiments, we have devised the following set of ion trap parameters for performing bottom-up proteomics analysis in our laboratory: Three averaged full scans, five averaged MS/MS scans, and a maximum ion injection time of 600 ms. (J Am Soc Mass Spectrom 2004, 15, 150Ϫ157)

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Proteomics characterization of novel spore proteins of Bacillus subtilis

Cited by 125 publications

References 36 publications

Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilis

Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilis

The Bacillus subtilis spore coat provides “eat resistance” during phagocytic predation by the protozoan Tetrahymena thermophila

Factors that affect ion trap data-dependent MS/MS in proteomics

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