SporeWeb an interactive journey through thecomplete sporulation cycle of Bacillus subtilisRobyn T Eijlander12 Anne de Jong12 Antonina O Krawczyk12 Siger Holsappel2 and

Oscar P Kuipers2

1Top Institute Food and Nutrition (TIFN) Nieuwe Kanaal 9A 6709 PA Wageningen The Netherlands and2Department of Molecular Genetics Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of Groningen 9747 AG Groningen The Netherlands

Received July 26 2013 Revised and Accepted October 4 2013

ABSTRACT

Bacterial spores are a continuous problem for bothfood-based and health-related industries Decadesof scientific research dedicated towards under-standing molecular and gene regulatory aspects ofsporulation spore germination and spore propertieshave resulted in a wealth of data and informationTo facilitate obtaining a complete overview as wellas new insights concerning this complex and tightlyregulated process we have developed a database-driven knowledge platform called SporeWeb (httpsporewebmolgenrugnl) that focuses on generegulatory networks during sporulation in theGram-positive bacterium Bacillus subtilis Dynamicfeatures allow the user to navigate through allstages of sporulation with review-like descriptionsschematic overviews on transcriptional regulationand detailed information on all regulators and thegenes under their control The Web site supportsdata acquisition on sporulation genes and theirexpression regulon network interactions anddirect links to other knowledge platforms orrelevant literature The information found onSporeWeb (including figures and tables) can andwill be updated as new information becomes avail-able in the literature In this way SporeWeb offersa novel convenient and timely reference an infor-mation source and a data acquisition tool that willaid in the general understanding of the dynamicsof the complete sporulation cycle

INTRODUCTION

During adverse environmental conditions bacterial cellsadopt developmental strategies such as endospore

formation to ensure their survival Bacterial spores area continuous problem in food- and health-relatedindustries because of their persistence after treatmentsand their ability to revert to vegetative cells through theprocess of germination (12) For instance the disease ofanthrax can persevere through the ingestion of spores thatare able to survive the gastrointestinal tract and germinateto vegetative cells that produce lethal toxins (3) On theother hand use of bacterial spores in the form ofbioinsecticides (4) antigen delivery systems and vaccines(5) or probiotics (67) are upcoming fields that offer at-tractive applications Therefore a better understanding ofthe sporulation and germination processes the level ofheterogeneity therein all genes and proteins involved aswell as influential effects of environmental factors haveformed important fields of study for the past decades (8)and have provided a wealth of knowledge (9ndash12)Most of the work on sporulation has been performed

using the Gram-positive non-pathogenic organismBacillus subtilis The obtained data are extremelyvaluable and are often used as a reference model in sporu-lation research concerning other (pathogenic) bacteriaincluding Bacillus anthracis (1314) Bacillus cereus(1516) and various Clostridium species and strains thatare of both medical and industrial importance (includingClostridium difficile Clostridium perfringens andClostridium botulinum) (17ndash22) This results in even moredata and information with various theories and specula-tions on molecular mechanisms conservation of lsquocorersquosporulation genes and emergence of evolutionary founda-tions (2324) Sporulation of B subtilis is an extremelycomplex cellular developmental process (112526)New technological advances such as RNA sequencingidentification of small non-coding RNAs and increasedunderstanding of processes through mathematicalmodelling allow us to answer questions beyond previousexpectations (27ndash31) but simultaneously add to thecomplexity Newly sequenced bacterial genomes of other

To whom correspondence should be addressed Tel +31 50 3632190 Fax +31 50 363 2348 Email RTEijlanderrugnlCorrespondence may also be addressed to Oscar P Kuipers Tel +31 50 3632093 Fax +31 50 363 2348 Email OPKuipersrugnl

Published online 28 October 2013 Nucleic Acids Research 2014 Vol 42 Database issue D685ndashD691doi101093nargkt1007

The Author(s) 2013 Published by Oxford University PressThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (httpcreativecommonsorglicensesby-nc30) which permits non-commercial re-use distribution and reproduction in any medium provided the original work is properly cited For commercialre-use please contact journalspermissionsoupcom

Downloaded from httpsacademicoupcomnararticle-abstract42D1D6851041414by gueston 17 February 2018

spore-formers are increasingly available due to faster andcheaper methodologies and demand efficient analyses andreadily available databases for comparison purposes (32)Therefore a general overview on how spore formation isestablished (including which genes and regulatorypathways are involved) is very valuable to the field butdue to the complexity and dynamics increasingly difficultto obtainIn this work we describe a novel knowledge and data

acquisition platform called SporeWeb (httpsporewebmolgenrugnl) which focuses on all developmental stagesof sporulation of B subtilis from a gene regulatory pointof view Through an interactive web interface querying theSporeWeb database (details available in SupplementaryMaterial) it offers both a textual description and a graph-ical representation of the sequence of events throughoutspore development (Figure 1) Importantly it easily linksto more catalogued information present on other know-ledge Web sites such as SubtiWiki (httpsubtiwikiuni-goettingende) (33) This allows the reader to grasp whathappens inside the cell on the regulatory level with add-itional detailed information on key regulatory proteinsinvolved The database-driven SporeWeb Web site isdynamic and will be updated and extended when novelscientific data become available in the future We believethat SporeWeb will be a continuous valuable asset to theresearch field of bacterial sporulation and will aid in our

overall understanding of this complex developmentalprocess

An interactive journey through all stages of the bacterialsporulation process

Commitment to sporulation is characterized by asymmet-ric cell division and expression of dedicated gene sets (34)This expression is tightly regulated in various sequentialdevelopmental stages and governed by complex biochem-ical communication between the two compartments of thecell (11) SporeWeb offers an interactive review of thiscomplete process which is the result of an extensive lit-erature study The homepage serves as a starting point forany sporulation stage of interest which can be accessed byclicking on the homepage image or by selecting the lsquoStatersquoin the menu bar Subsequent pages offer both detaileddescriptions and schematic representations of develop-ment The figures are interactive and dynamic theycontain clickable items of interest and ensure updated in-formation as genes are added to or edited in the databaseLegends to the figures are described in the vertical grey baron the right of the web page whereas a review-likedescription of the sporulation state is shown below thefigure with direct links to relevant literature references

Sporulation-specific regulators and their regulons aredescribed on individual pages which can be accessed by

Figure 1 Graphical representation of the different levels in the SporeWeb Web site

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clicking on the item in the schematic figures or via themenu bar An example of such a page is shown inFigure 2 Genes under transcriptional control of aspecific regulator have been indicated in blue or redboxes for transcriptional activation or repression respect-ively Additionally there is a direct link to the SubtiWikilist of regulon members Lists and descriptions of all geneswithin the regulon can be downloaded in the form of up-datable Excel sheets by clicking on the coloured boxes orvia the Excel icon in the top right corner (Figure 2)

Graphic representations of regulon interactions definesubgroups of co-regulated genes

As sporulation progresses sporulation-specific sigmafactors are expressed and activated in a spatial andtemporal manner (1126) Together with secondary regu-lator proteins they control the timing sequence and levelof gene expression that are necessary for formationmaturation and release of the endospore Varioustranscriptomic studies in B subtilis have led to the identi-fication of genes controlled by these sigma factors and

other regulators to map the sporulation gene regulatorynetworks (35ndash42) In SporeWeb we have visualizedthese networks using Cytoscape-generated layouts forevery sporulation-specific stage (details available inSupplementary Material) (43) These layouts can beaccessed via the lsquoCytoscapersquo option in the menu bar orthe Cytoscape icon on the top of every State pageAn example of such a layout is shown in Figure 3A

This representation immediately shows which genes areunder single dual or even triple or quadruple controland which genes are co-regulated during a specific sporu-lation stage There is a zoom-in function that allows theuser to identify genes or regulators of interest The nameand direct links to the gene SubtiWiki and MicroScopeMaGe pages (httpwwwgenoscopecnsfragcmicroscopehome) are provided when the node is clickedFurthermore recently published spore-specific gene clas-sification of the minimal sporulation gene set by Galperinet al (24) has been integrated to immediately appreciatesimilarities and differences in regulation of functionalclasses of genes Additionally a visualization tool calledlsquoUser Subsetrsquo has been implemented in the Cytoscape

Figure 2 The lsquoSpoIIID during commitmentrsquo page on SporeWeb Detailed information on the role of a sporulation-specific regulator during anystage in sporulation can be found on such pages The schematic representation depicts its own regulation as well as the genes under its controlpositively regulated in a blue box negatively regulated in a red box A detailed list containing all genes within the regulon can be accessed using theSubtiWiki link or downloaded as an Excel file by clicking on the coloured boxes or the XLXS icon To see what happens to this regulator duringother stages in sporulation simply click on the link provided in the grey bar on the right

Nucleic Acids Research 2014 Vol 42 Database issue D687

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Figure 3 Cytoscape-generated layouts on gene regulatory networks (A) Active regulators during completion of engulfment are indicated by greensquares (proteins) or blue hexagons (sigma factors) Positive or negative effects on the transcription of genes (coloured circles) are indicated byconnecting blue and red lines respectively Important sporulation genes indicated as being part of the minimal sporulation gene set have been colour-coded according to their functional category as determined by Galperin et al (24) Genes unassigned to these functional categories are indicated asyellow circles These layouts are available on SporeWeb for five different stages during spore formation (B) A personal Cytoscape layout on specificgenes of interest can be generated using the lsquoUser Subsetrsquo option in the lsquoCytoscapersquo menu (indicated by a black arrow) Genes (separated by a comma

D688 Nucleic Acids Research 2014 Vol 42 Database issue

(continued)

Downloaded from httpsacademicoupcomnararticle-abstract42D1D6851041414by gueston 17 February 2018

Figure 4 Heatmap representation of gene expression values during the engulfment state of sporulation Tables like these are available on SporeWebfor five different stages in spore formation Expression value data were derived from Nicolas et al (45) Activation of gene expression is indicated aspositive values in blue boxes whereas downregulation is indicated as negative values in red boxes Genes are categorized in classes listed AndashLaccording to their documented regulation Expression values are shown throughout the complete sporulation process (t=0ndasht=8) and for three timepoints taken during spore germination (ger)

Figure 3 Continuedonly) should be typed in the white bar and will be organized in a graphical network via the lsquoAdd Cytoscapersquo option Coloured nodes (shapes) andedges (lines) represent genes and connections as described for Figure 3A Three-letter abbreviations at the edges indicate during which stage insporulation the particular regulation is relevant For Spo0A regulation thicker edges represent high-threshold genes whereas thin edges representlow-threshold genes (44)

Nucleic Acids Research 2014 Vol 42 Database issue D689

Downloaded from httpsacademicoupcomnararticle-abstract42D1D6851041414by gueston 17 February 2018

menu bar that will allow the users to generate their ownCytoscape interaction figure of specific sporulation genesof interest (Figure 3B)

Gene expression values during sporulation are visualizedin informative heatmaps

A large group of important sporulation genes has alreadybeen identified and characterized although many remainwhose function andor regulation is still unknown Tofurther visualize timing and co-regulation of gene expres-sion during sporulation we have displayed a recent sporu-lation-specific transcriptional dataset from Nicolas et al(45) in colour-coded heatmaps These heatmaps can beaccessed via the lsquoHeatmaprsquo option on the menu bar orvia the heatmap icon at the top of every State page Genesare categorized in classes based on their previously docu-mented regulation Their expression values during thecomplete course of sporulation as well as during threetime points of germination are shown in colour-codedboxes (Figure 4) In this way differences and similaritiesin expression between co-regulated genes are visible andcan provide clues about possible function andor regula-tion of uncharacterized genes The heatmaps can be down-loaded via the Excel icon on the top right of the page

Concluding remarks and perspectives

Knowledge on bacterial sporulation is rapidly growingpartly due to novel technological developments Thisprogress also reveals additional levels of complexity andmakes it increasingly difficult to obtain a general under-standing especially for non-specialists in the fieldFurthermore rapid advances in DNA and RNAsequencing technologies have enabled faster and cheaperaccess to genomic- and transcriptional data of a largenumber of bacterial species This leads to an expansionof our knowledge from laboratory-adapted modelbacteria such as B subtilis to more industrially or med-ically relevant species and strains The data reveal highlevels of conservation of certain genes or regulatorymodules on the one hand and highlight important differ-ences in gene presenceabsence and regulatory events onthe other which have significant implications for theoverall process of spore formation in specific groups ofbacteria (2324) The wealth of information that hasbeen generated over decades by research on bacterialmodel organisms is extremely useful and usable as refer-ence material for those bacterial species for which geneticmanipulation and in vivo validation is less straightforwardTo provide researchers from all disciplines and expertise

levels an accessible overview of the current state of know-ledge on B subtilis sporulation we have constructedan interactive and graphical knowledge platform calledSporeWeb We believe that the potential of SporeWeblies in the combination of a source of information on bac-terial sporulation an accessible starting point for furtherdetailed investigation and a dynamic platform that can beadjusted and supplemented as new relevant data becomeavailable in the future Moreover the user-friendly inter-face and intuitive organization provide comprehensibledata acquisition for both specialists and non-specialists

in the field Future perspectives for SporeWeb caninclude expansion to lsquosisterrsquo Web sites These cancontain similar content on sporulation from a proteomicspoint of view or of (for instance) members of the B cereusgroup (including B anthracis and Bacillus thuringiensis)andor Clostridium species which would be a constructiveaddition to the applications of SporeWeb and a valuablecontribution of knowledge to the entire field of sporula-tion research

SUPPLEMENTARY DATA

Supplementary Data are available at NAR Online

ACKNOWLEDGEMENTS

The authors are grateful for the time and dedication ofDr Adam Driks in thorough previewing of SporeWeb andthey also thank many others in the microbiological andbacterial sporulation community who have come forwardwith useful suggestions andor contributions

FUNDING

TI Food and Nutrition Wageningen The NetherlandsFunding for open access charge TI Food and Nutrition

Conflict of interest statement None declared

REFERENCES

1 EijlanderRT AbeeT and KuipersOP (2011) Bacterial sporesin food how phenotypic variability complicates prediction ofspore properties and bacterial behavior Curr Opin Biotechnol22 180ndash186

2 AugustinJC (2011) Challenges in risk assessment andpredictive microbiology of foodborne spore-forming bacteriaFood Microbiol 28 209ndash213

3 MockM and FouetA (2001) Anthrax Annu Rev Microbiol55 647ndash671

4 SchnepfE CrickmoreN Van RieJ LereclusD BaumJFeitelsonJ ZeiglerDR and DeanDH (1998) Bacillusthuringiensis and its pesticidal crystal proteins Microbiol MolBiol Rev 62 775ndash806

5 AmuguniH and TziporiS (2012) Bacillus subtilis a temperatureresistant and needle free delivery system of immunogens HumVaccin Immunother 8 979ndash986

6 BaderJ AlbinA and StahlU (2012) Spore-forming bacteriaand their utilisation as probiotics Benef Microbes 3 67ndash75

7 PermpoonpattanaP HongHA KhanejaR and CuttingSM(2012) Evaluation of Bacillus subtilis strains as probiotics andtheir potential as a food ingredient Benef Microbes 3 127ndash135

8 GouldGW (2006) History of sciencendashspores J Appl Microbiol101 507ndash513

9 HigginsD and DworkinJ (2012) Recent progress in Bacillussubtilis sporulation FEMS Microbiol Rev 36 131ndash148

10 ErringtonJ (2010) From spores to antibiotics via the cell cycleMicrobiology 156 1ndash13

11 HilbertDW and PiggotPJ (2004) Compartmentalization ofgene expression during Bacillus subtilis spore formationMicrobiol Mol Biol Rev 68 234ndash262

12 MoirA (2006) How do spores germinate J Appl Microbiol101 526ndash530

13 LiuH BergmanNH ThomasonB ShallomS HazenACrossnoJ RaskoDA RavelJ ReadTD PetersonSN et al(2004) Formation and composition of the Bacillus anthracisendospore J Bacteriol 186 164ndash178

D690 Nucleic Acids Research 2014 Vol 42 Database issue

Downloaded from httpsacademicoupcomnararticle-abstract42D1D6851041414by gueston 17 February 2018

Figure 4 Heatmap representation of gene expression values during the engulfment state of sporulation Tables like these are available on SporeWebfor five different stages in spore formation Expression value data were derived from Nicolas et al (45) Activation of gene expression is indicated aspositive values in blue boxes whereas downregulation is indicated as negative values in red boxes Genes are categorized in classes listed AndashLaccording to their documented regulation Expression values are shown throughout the complete sporulation process (t=0ndasht=8) and for three timepoints taken during spore germination (ger)

Figure 3 Continuedonly) should be typed in the white bar and will be organized in a graphical network via the lsquoAdd Cytoscapersquo option Coloured nodes (shapes) andedges (lines) represent genes and connections as described for Figure 3A Three-letter abbreviations at the edges indicate during which stage insporulation the particular regulation is relevant For Spo0A regulation thicker edges represent high-threshold genes whereas thin edges representlow-threshold genes (44)

Nucleic Acids Research 2014 Vol 42 Database issue D689

Downloaded from httpsacademicoupcomnararticle-abstract42D1D6851041414by gueston 17 February 2018

menu bar that will allow the users to generate their ownCytoscape interaction figure of specific sporulation genesof interest (Figure 3B)

Gene expression values during sporulation are visualizedin informative heatmaps

A large group of important sporulation genes has alreadybeen identified and characterized although many remainwhose function andor regulation is still unknown Tofurther visualize timing and co-regulation of gene expres-sion during sporulation we have displayed a recent sporu-lation-specific transcriptional dataset from Nicolas et al(45) in colour-coded heatmaps These heatmaps can beaccessed via the lsquoHeatmaprsquo option on the menu bar orvia the heatmap icon at the top of every State page Genesare categorized in classes based on their previously docu-mented regulation Their expression values during thecomplete course of sporulation as well as during threetime points of germination are shown in colour-codedboxes (Figure 4) In this way differences and similaritiesin expression between co-regulated genes are visible andcan provide clues about possible function andor regula-tion of uncharacterized genes The heatmaps can be down-loaded via the Excel icon on the top right of the page

Concluding remarks and perspectives

Knowledge on bacterial sporulation is rapidly growingpartly due to novel technological developments Thisprogress also reveals additional levels of complexity andmakes it increasingly difficult to obtain a general under-standing especially for non-specialists in the fieldFurthermore rapid advances in DNA and RNAsequencing technologies have enabled faster and cheaperaccess to genomic- and transcriptional data of a largenumber of bacterial species This leads to an expansionof our knowledge from laboratory-adapted modelbacteria such as B subtilis to more industrially or med-ically relevant species and strains The data reveal highlevels of conservation of certain genes or regulatorymodules on the one hand and highlight important differ-ences in gene presenceabsence and regulatory events onthe other which have significant implications for theoverall process of spore formation in specific groups ofbacteria (2324) The wealth of information that hasbeen generated over decades by research on bacterialmodel organisms is extremely useful and usable as refer-ence material for those bacterial species for which geneticmanipulation and in vivo validation is less straightforwardTo provide researchers from all disciplines and expertise

levels an accessible overview of the current state of know-ledge on B subtilis sporulation we have constructedan interactive and graphical knowledge platform calledSporeWeb We believe that the potential of SporeWeblies in the combination of a source of information on bac-terial sporulation an accessible starting point for furtherdetailed investigation and a dynamic platform that can beadjusted and supplemented as new relevant data becomeavailable in the future Moreover the user-friendly inter-face and intuitive organization provide comprehensibledata acquisition for both specialists and non-specialists

in the field Future perspectives for SporeWeb caninclude expansion to lsquosisterrsquo Web sites These cancontain similar content on sporulation from a proteomicspoint of view or of (for instance) members of the B cereusgroup (including B anthracis and Bacillus thuringiensis)andor Clostridium species which would be a constructiveaddition to the applications of SporeWeb and a valuablecontribution of knowledge to the entire field of sporula-tion research

SUPPLEMENTARY DATA

Supplementary Data are available at NAR Online

ACKNOWLEDGEMENTS

The authors are grateful for the time and dedication ofDr Adam Driks in thorough previewing of SporeWeb andthey also thank many others in the microbiological andbacterial sporulation community who have come forwardwith useful suggestions andor contributions

FUNDING

TI Food and Nutrition Wageningen The NetherlandsFunding for open access charge TI Food and Nutrition

Conflict of interest statement None declared

REFERENCES

1 EijlanderRT AbeeT and KuipersOP (2011) Bacterial sporesin food how phenotypic variability complicates prediction ofspore properties and bacterial behavior Curr Opin Biotechnol22 180ndash186

2 AugustinJC (2011) Challenges in risk assessment andpredictive microbiology of foodborne spore-forming bacteriaFood Microbiol 28 209ndash213

3 MockM and FouetA (2001) Anthrax Annu Rev Microbiol55 647ndash671

4 SchnepfE CrickmoreN Van RieJ LereclusD BaumJFeitelsonJ ZeiglerDR and DeanDH (1998) Bacillusthuringiensis and its pesticidal crystal proteins Microbiol MolBiol Rev 62 775ndash806

5 AmuguniH and TziporiS (2012) Bacillus subtilis a temperatureresistant and needle free delivery system of immunogens HumVaccin Immunother 8 979ndash986

6 BaderJ AlbinA and StahlU (2012) Spore-forming bacteriaand their utilisation as probiotics Benef Microbes 3 67ndash75

7 PermpoonpattanaP HongHA KhanejaR and CuttingSM(2012) Evaluation of Bacillus subtilis strains as probiotics andtheir potential as a food ingredient Benef Microbes 3 127ndash135

8 GouldGW (2006) History of sciencendashspores J Appl Microbiol101 507ndash513

9 HigginsD and DworkinJ (2012) Recent progress in Bacillussubtilis sporulation FEMS Microbiol Rev 36 131ndash148

10 ErringtonJ (2010) From spores to antibiotics via the cell cycleMicrobiology 156 1ndash13

11 HilbertDW and PiggotPJ (2004) Compartmentalization ofgene expression during Bacillus subtilis spore formationMicrobiol Mol Biol Rev 68 234ndash262

12 MoirA (2006) How do spores germinate J Appl Microbiol101 526ndash530

13 LiuH BergmanNH ThomasonB ShallomS HazenACrossnoJ RaskoDA RavelJ ReadTD PetersonSN et al(2004) Formation and composition of the Bacillus anthracisendospore J Bacteriol 186 164ndash178

D690 Nucleic Acids Research 2014 Vol 42 Database issue

Downloaded from httpsacademicoupcomnararticle-abstract42D1D6851041414by gueston 17 February 2018

menu bar that will allow the users to generate their ownCytoscape interaction figure of specific sporulation genesof interest (Figure 3B)

Gene expression values during sporulation are visualizedin informative heatmaps

A large group of important sporulation genes has alreadybeen identified and characterized although many remainwhose function andor regulation is still unknown Tofurther visualize timing and co-regulation of gene expres-sion during sporulation we have displayed a recent sporu-lation-specific transcriptional dataset from Nicolas et al(45) in colour-coded heatmaps These heatmaps can beaccessed via the lsquoHeatmaprsquo option on the menu bar orvia the heatmap icon at the top of every State page Genesare categorized in classes based on their previously docu-mented regulation Their expression values during thecomplete course of sporulation as well as during threetime points of germination are shown in colour-codedboxes (Figure 4) In this way differences and similaritiesin expression between co-regulated genes are visible andcan provide clues about possible function andor regula-tion of uncharacterized genes The heatmaps can be down-loaded via the Excel icon on the top right of the page

Concluding remarks and perspectives

Knowledge on bacterial sporulation is rapidly growingpartly due to novel technological developments Thisprogress also reveals additional levels of complexity andmakes it increasingly difficult to obtain a general under-standing especially for non-specialists in the fieldFurthermore rapid advances in DNA and RNAsequencing technologies have enabled faster and cheaperaccess to genomic- and transcriptional data of a largenumber of bacterial species This leads to an expansionof our knowledge from laboratory-adapted modelbacteria such as B subtilis to more industrially or med-ically relevant species and strains The data reveal highlevels of conservation of certain genes or regulatorymodules on the one hand and highlight important differ-ences in gene presenceabsence and regulatory events onthe other which have significant implications for theoverall process of spore formation in specific groups ofbacteria (2324) The wealth of information that hasbeen generated over decades by research on bacterialmodel organisms is extremely useful and usable as refer-ence material for those bacterial species for which geneticmanipulation and in vivo validation is less straightforwardTo provide researchers from all disciplines and expertise

levels an accessible overview of the current state of know-ledge on B subtilis sporulation we have constructedan interactive and graphical knowledge platform calledSporeWeb We believe that the potential of SporeWeblies in the combination of a source of information on bac-terial sporulation an accessible starting point for furtherdetailed investigation and a dynamic platform that can beadjusted and supplemented as new relevant data becomeavailable in the future Moreover the user-friendly inter-face and intuitive organization provide comprehensibledata acquisition for both specialists and non-specialists

in the field Future perspectives for SporeWeb caninclude expansion to lsquosisterrsquo Web sites These cancontain similar content on sporulation from a proteomicspoint of view or of (for instance) members of the B cereusgroup (including B anthracis and Bacillus thuringiensis)andor Clostridium species which would be a constructiveaddition to the applications of SporeWeb and a valuablecontribution of knowledge to the entire field of sporula-tion research

SUPPLEMENTARY DATA

Supplementary Data are available at NAR Online

ACKNOWLEDGEMENTS

The authors are grateful for the time and dedication ofDr Adam Driks in thorough previewing of SporeWeb andthey also thank many others in the microbiological andbacterial sporulation community who have come forwardwith useful suggestions andor contributions

FUNDING

TI Food and Nutrition Wageningen The NetherlandsFunding for open access charge TI Food and Nutrition

Conflict of interest statement None declared

REFERENCES

1 EijlanderRT AbeeT and KuipersOP (2011) Bacterial sporesin food how phenotypic variability complicates prediction ofspore properties and bacterial behavior Curr Opin Biotechnol22 180ndash186

2 AugustinJC (2011) Challenges in risk assessment andpredictive microbiology of foodborne spore-forming bacteriaFood Microbiol 28 209ndash213

3 MockM and FouetA (2001) Anthrax Annu Rev Microbiol55 647ndash671

4 SchnepfE CrickmoreN Van RieJ LereclusD BaumJFeitelsonJ ZeiglerDR and DeanDH (1998) Bacillusthuringiensis and its pesticidal crystal proteins Microbiol MolBiol Rev 62 775ndash806

5 AmuguniH and TziporiS (2012) Bacillus subtilis a temperatureresistant and needle free delivery system of immunogens HumVaccin Immunother 8 979ndash986

6 BaderJ AlbinA and StahlU (2012) Spore-forming bacteriaand their utilisation as probiotics Benef Microbes 3 67ndash75

7 PermpoonpattanaP HongHA KhanejaR and CuttingSM(2012) Evaluation of Bacillus subtilis strains as probiotics andtheir potential as a food ingredient Benef Microbes 3 127ndash135

8 GouldGW (2006) History of sciencendashspores J Appl Microbiol101 507ndash513

9 HigginsD and DworkinJ (2012) Recent progress in Bacillussubtilis sporulation FEMS Microbiol Rev 36 131ndash148

10 ErringtonJ (2010) From spores to antibiotics via the cell cycleMicrobiology 156 1ndash13

11 HilbertDW and PiggotPJ (2004) Compartmentalization ofgene expression during Bacillus subtilis spore formationMicrobiol Mol Biol Rev 68 234ndash262

12 MoirA (2006) How do spores germinate J Appl Microbiol101 526ndash530

13 LiuH BergmanNH ThomasonB ShallomS HazenACrossnoJ RaskoDA RavelJ ReadTD PetersonSN et al(2004) Formation and composition of the Bacillus anthracisendospore J Bacteriol 186 164ndash178

D690 Nucleic Acids Research 2014 Vol 42 Database issue

Downloaded from httpsacademicoupcomnararticle-abstract42D1D6851041414by gueston 17 February 2018

14 FisherN and HannaP (2005) Characterization of Bacillusanthracis germinant receptors in vitro J Bacteriol 187 8055ndash8062

15 van der VoortM GarcıaD MoezelaarR and AbeeT (2010)Germinant receptor diversity and germination responses of fourstrains of the Bacillus cereus group Int J Food Microbiol 139108ndash115

16 Vries deYP HornstraLM de VosWM and AbeeT (2004)Growth and sporulation of Bacillus cereus ATCC 14579 underdefined conditions temporal expression of genes for key sigmafactors Appl Environ Microbiol 70 2514ndash2519

17 XiaoY FranckeC AbeeT and Wells-BennikMH (2011)Clostridial spore germination versus bacilli genome mining andcurrent insights Food Microbiol 28 266ndash274

18 Paredes-SabjaD SetlowP and SarkerMR (2011) Germinationof spores of Bacillales and Clostridiales species mechanisms andproteins involved Trends Microbiol 19 85ndash94

19 SteinerE DagoAE YoungDI HeapJT MintonNPHochJA and YoungM (2011) Multiple orphan histidinekinases interact directly with Spo0A to control the initiation ofendospore formation in Clostridium acetobutylicum MolMicrobiol 80 641ndash654

20 BurnsDA and MintonNP (2011) Sporulation studies inClostridium difficile J Microbiol Methods 87 133ndash138

21 RosenbuschKE BakkerD KuijperEJ and SmitsWK (2012)C difficile 630erm Spo0A regulates sporulation but does notcontribute to toxin production by direct high-affinity binding totarget DNA PLoS One 7 e48608

22 LabbeRG and DurreP (2005) Sporulation of clostridiaIn DurreP (ed) Handbook on Clostridia CRC Press Taylor ampFrancis Group FL USA pp 647ndash669

23 de HoonMJL EichenbergerP and VitkupD (2010)Hierarchical evolution of the bacterial sporulation networkCurr Biol 20 R735ndashR745

24 GalperinMY MekhedovSL PuigboP SmirnovS WolfYIand RigdenDJ (2012) Genomic determinants of sporulation inBacilli and Clostridia towards the minimal set of sporulation-specific genes Environ Microbiol 11 2870ndash2890

25 StragierP and LosickR (1996) Molecular genetics of sporulationin Bacillus subtilis Annu Rev Genet 30 297ndash241

26 PiggotPJ and HilbertDW (2004) Sporulation of Bacillussubtilis Curr Opin Microbiol 7 579ndash586

27 SilvaggiJM PerkinsJB and LosickR (2006) Genes for smallnoncoding RNAs under sporulation control in Bacillus subtilisJ Bacteriol 188 532ndash541

28 SchmalischM MaiquesE NikolovL CampAH ChevreuxBMufflerA RodriguezS PerkinsJ and LosickR (2010) Smallgenes under sporulation control in the Bacillus subtilis genomeJ Bacteriol 192 5402ndash5412

29 LiebalUW MillatT De JongIG KuipersOP VolkerUand WolkenhauerO (2010) How mathematical modellingelucidates signalling in Bacillus subtilis Mol Microbiol 771083ndash1095

30 JabbariS HeapJT and KingJR (2011) Mathematicalmodelling of the sporulation-initiation network in Bacillus subtilisrevealing the dual role of the putative quorum-sensing signalmolecule PhrA Bull Math Biol 73 181ndash211

31 LevineJH FontesME DworkinJ and ElowitzMB (2012)Pulsed feedback defers cellular differentiation PLoS Biol 10e1001252

32 RottgerR RuckertU TaubertJ and BaumbachJ (2012) Howlittle do we actually know ndash on the size of gene regulatorynetworks IEEEACM Trans Comput Biol Bioinform 91293ndash1300

33 MaderU SchmeiskyAG FlorezLA and StulkeJ (2012)SubtiWikindasha comprehensive community resource for the modelorganism Bacillus subtilis Nucleic Acids Res 40 D1278ndashD1287

34 ParkerGF DanielRA and ErringtonJ (1996) Timing andgenetic regulation of commitment to sporulation in Bacillussubtilis Microbiology 142(Pt 12) 3445ndash3452

35 SteilL SerranoM HenriquesAO and VolkerU (2005)Genome-wide analysis of temporally regulated andcompartment-specific gene expression in sporulating cells ofBacillus subtilis Microbiology 151 399ndash420

36 CangianoG MazzoneA BaccigalupiL IsticatoREichenbergerP De FeliceM and RiccaE (2010) Direct andindirect control of late sporulation genes by GerR of Bacillussubtilis J Bacteriol 192 3406ndash3413

37 BrittonRA EichenbergerP Gonzalez-PastorJE FawcettPMonsonR LosickR and GrossmanAD (2002) Genome-wideanalysis of the stationary-phase sigma factor (sigma-H) regulonof Bacillus subtilis J Bacteriol 184 4881ndash4890

38 WangST SetlowB ConlonEM LyonJL ImamuraDSatoT SetlowP LosickR and EichenbergerP (2006) Theforespore line of gene expression in Bacillus subtilis J Mol Biol358 16ndash37

39 EichenbergerP FujitaM JensenST ConlonEMRudnerDZ WangST FergusonC HagaK SatoT LiuJSet al (2004) The program of gene transcription for a singledifferentiating cell type during sporulation in Bacillus subtilisPLoS Biol 2 e328

40 EichenbergerP JensenST ConlonEM van OoijCSilvaggiJ Gonzalez-PastorJE FujitaM Ben-YehudaSStragierP LiuJS et al (2003) The sigmaE regulon and theidentification of additional sporulation genes in Bacillus subtilisJ Mol Biol 327 945ndash972

41 MolleV FujitaM JensenST EichenbergerPGonzalez-PastorJE LiuJS and LosickR (2003) The Spo0Aregulon of Bacillus subtilis Mol Microbiol 50 1683ndash1701

42 FawcettP EichenbergerP LosickR and YoungmanP (2000)The transcriptional profile of early to middle sporulation inBacillus subtilis Proc Natl Acad Sci USA 97 8063ndash8068

43 SaitoR SmootME OnoK RuscheinskiJ WangPLLotiaS PicoAR BaderGD and IdekerT (2012) A travelguide to Cytoscape plugins Nat Methods 9 1069ndash1076

44 FujitaM Gonzalez-PastorJE and LosickR (2005) High- andlow-threshold genes of the Spo0A regulon of Bacillus subtilisJ Bacteriol 187 1357ndash1368

45 NicolasP MaderU DervynE RochatT LeducAPigeonneauN BidnenkoE MarchadierE HoebekeMAymerichS et al (2012) Condition-dependent transcriptomereveals high-level regulatory architecture in Bacillus subtilisScience 335 1103ndash1106

Nucleic Acids Research 2014 Vol 42 Database issue D691

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