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Publication in Mol Biol Evol: DNA repeats in the Bacillus cereus group.
In this publication we have performed a comprehensive bioinformatic analysis of 18 sets of short (100−400 bp) interspersed repeated DNA elements, bcr1−bcr18, in 36 B. cereus group genomes. We show that these repeated elements form three distinct groups with different evolutionary and functional patterns. Group A repeats (bcr1−bcr3) exhibit highly variable copy numbers and non−conserved chromosomal distributions between strains, and display features of mobile elements. Group B repeats (bcr4−bcr6) are associated with strain−specific genes and genome rearrangements and/or horizontal gene transfer events. Group C repeats (bcr7−bcr18) have a conserved chromosomal location, and several of them exhibit a conserved secondary structure and/or overlap previously characterized riboswitches, possibly indicating that they could represent functional RNAs, novel riboswitches, and/or constitute other types of regulatory elements. The analysis suggests that the numerous repeated elements in the B. cereus group promote genome dynamics and plasticity, and could contribute to the flexible and adaptive life style of these bacteria.
For details, please see: "Interspersed DNA repeats bcr1−bcr18 of Bacillus cereus group bacteria form three distinct groups with different evolutionary and functional patterns". Kristoffersen SM, Tourasse NJ, Kolstø AB, Økstad OA. (2010). MOLECULAR BIOLOGY AND EVOLUTION, in press


Publication in Food Microbiol: Global view of the Bacillus cereus group population.
In this publication we have conducted a global phylogenetic analysis of the Bacillus cereus group population using the data and tools from the HyperCAT database that we recently developed. The analysis combined data from multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP), and multilocus enzyme electrophoresis (MLEE) genotyping techniques, and incorporated more than 2000 isolates, including 450 from food and dairy products. The main results include the detection of phylogenetically separated groups of isolates possibly representing novel evolutionary lineages within the B. cereus group, a putative new branch of B. anthracis, as well as new groups of related strains containing both environmental and clinical isolates. In addition, the multi−datatype analysis indicated that food−borne isolates can share identical genotyping profiles with strains from various other origins.
For details, please see: "Extended and global phylogenetic view of the Bacillus cereus group population by combination of MLST, AFLP, and MLEE genotyping data". Tourasse NJ, Helgason E, Klevan A, Sylvestre P, Moya M, Haustant M, Økstad OA, Fouet A, Mock M, Kolstø AB. (2010). FOOD MICROBIOLOGY, in press


Publication in DATABASE: Bacillus cereus group MLST+AFLP+MLEE database.
In our second database publication we have extended the multi−scheme multilocus sequence typing (MLST) database SuperCAT we developed previously into a new database, HyperCAT. This database compiles and integrates data from MLST and the other, different, typing methods amplified fragment length polymorphism (AFLP) and multilocus enzyme electrophoresis (MLEE). The database is accessible here or by following the MLST/AFLP/MLEE database link in the left−hand toolbar. In addition to supertree techniques that were used to combine the phylogenetic information coming from analysis of all three typing methods, a tree−independent clustering algorithm was designed to build superclusters of isolates sharing identical genotyping data. The database currently contains strain information, sequences, and phylogenetic data for more than 2000 isolates, and thus provides the most comprehensive genetic and phylogenetic snapshot of the B. cereus group population to date.
For details, please see: "HyperCAT: an extension of the SuperCAT database for global multi−scheme and multi−datatype phylogenetic analysis of the Bacillus cereus group population". Tourasse NJ, Økstad OA, Kolstø AB. (2010). DATABASE, baq017


Publication in New Biotechnol: Group II introns with an unusual 3' extension.
In this review article we summarize the results of the research on group II introns that harbor an unusual extension of 53/56 nt at the 3' end. Currently, 15 such introns have been identified, all in the Bacillus cereus group of bacteria. Their 3' extensions are conserved in structure and partially in sequence. Phylogenetic analyses of these introns revealed that they belong to two evolutionary subgroups and gave evidence that some introns are mobile with their extension. Furthermore, functional analyses showed that the 3' extension has a differential effect on the self−splicing reactions in vitro for introns of the two subgroups. The unusual introns have provided new insights into the structural and functional evolution of group II ribozymes.
For details, please see: "Structural and functional evolution of group II intron ribozymes: insights from unusual elements carrying a 3' extension". Tourasse NJ, Stabell FB, Kolstø AB. (2010). NEW BIOTECHNOLOGY, 27 (3): 204-211


Publication in Annu Rev Microbiol: What sets B. anthracis apart from other Bacillus species?
In this review article we summarize the genomic, phylogenetic, and functional data that differentiate B. anthracis from closely related species of the B. cereus group. B. anthracis, the cause of anthrax, forms a highly monomorphic lineage within the B. cereus group. During the past five years B. cereus strains that contain the pXO1 virulence plasmid encoding the anthrax toxin genes were discovered, and strains with both pXO1 and pXO2 (which encode a protective capsule) have been isolated. Therefore, the presence of pXO1 and pXO2 plasmids no longer principally separates B. anthracis from other Bacilli. The B. anthracis lineage carries a specific mutation in the global regulator PlcR, which controls the transcription of secreted virulence factors in B. cereus and B. thuringiensis. In summary, the B. anthracis−specific characteristics are: (a) Being part of a clonal lineage, (b) having a specific mutation in PlcR, and (c) having a full set of 4 chromosomal prophages.
For details, please see: "What sets B. anthracis apart from other Bacillus species?". Kolstø AB, Tourasse NJ, Økstad OA. (2009). ANNUAL REVIEWS OF MICROBIOLOGY, 63: 451-476


Publication in Nucl Acids Res: New group II introns with an unusual 3' extension.
In this publication we report the discovery of four additional group II introns in Bacillus thuringiensis kurstaki 4D1 that harbor a 53/54−nt 3' extension similar to that of the unusual B.c.I4 intron we previously found in B. cereus ATCC 10987. Phylogenetic analyses revealed that the introns are only 47−61% identical to each other. Strikingly, they do not form a single evolutionary lineage even though they belong to the same class. The extension of these introns is predicted to form a conserved two−stem−loop structure. Mutational analysis in vitro showed that the smaller stem S1 is not critical for self-splicing, whereas the larger stem S2 is important for efficient exon ligation and lariat release in presence of the extension. This study clearly demonstrates that the previously reported B.c.I4 intron is not a single example of a specialized intron, but forms a new functional class with an unusual mode that ensures proper positioning of the 3' splice site.
For details, please see: "A conserved 3' extension in unusual group II introns is important for efficient second−step splicing". Stabell FB, Tourasse NJ, Kolstø AB. (2009). NUCLEIC ACIDS RESEARCH, 37 (10): 3202-3214


Publication in Lett Appl Microbiol: A new DNA binding protein from Bacillus cereus phage.
In this publication we report the functional characterization of ORF 2 encoded by the bacteriophage−related autonomously replicating linear genetic element pBClin15 carried by the Bacillus cereus type strain, ATCC 14579. The protein was isolated and identified during a search for DNA−binding proteins with affinity for the mobile chromosomal repeat element bcr1 in B. cereus group bacteria. A biotinylated bcr1 element was immobilized to streptavidin−coated magnetic beads and used to pull out a 20 kDa DNA−binding protein from a whole cell protein extract of B. cereus ATCC 14579. The protein was identified as the product of ORF 2 of pBClin15. ORF 2 thus encodes a DNA−binding protein. DNA binding was not bcr1−specific. Northern blotting showed that ORF 2 is co−transcribed with its upstream gene ORF 1, and in a subset of the transcripts also with the downstream gene ORF 3 through alternative transcription termination.
For details, please see: "ORF 2 from the Bacillus cereus linear plasmid pBClin15 encodes a DNA binding protein". Stabell FB, Egge−Jacobsen W, Risøen PA, Kolstø AB, Økstad OA. (2009). LETTERS IN APPLIED MICROBIOLOGY, 48 (1): 51-57


Publication in PLoS ONE: The PlcR virulence regulon of Bacillus cereus.
In this publication, made in collaboration with INRA, France, we present an analysis of the set of genes controlled by PlcR, an important Bacillus cereus transcriptional regulator, which activates gene expression by binding to a nucleotidic sequence called the "PlcR box". To build a list of all genes included in the PlcR regulon, a consensus sequence was identified by directed mutagenesis. PlcR control of these genes was confirmed by comparing gene expression in the B. cereus type strain, ATCC 14579, and its isogenic strain deleted of PlcR using DNA microarrays, lacZ fusions and proteomics methods. The resulting list included 45 genes. Forty of the PlcR controlled proteins were exported. The functions of these proteins were related to food supply, cell protection and environment-sensing. Four genes coded for cytoplasmic regulators. The PlcR regulon appears to integrate a large range of environmental signals, including food deprivation and self cell-density, and regulate the transcription of genes designed to overcome obstacles that hinder B. cereus growth within the host: food supply, host barriers, host immune defenses, and competition with other bacterial species. PlcR appears to be a key component in the efficient adaptation of B. cereus to its host environment.
For details, please see: "The PlcR virulence regulon of Bacillus cereus". Gohar M, Fægri K, Perchat S, Ravnum S, Økstad OA, Gominet M, Kolstø AB, Lereclus D. (2008). PLoS ONE, 3 (7): e2793


Publication in Nucl Acids Res: Group I and group II introns in the Bacillus cereus group.
In this genomics publication we present a comprehensive review of group I and group II introns in the B. cereus group. Group I and group II introns are different catalytic self-splicing and mobile RNA elements that contribute to genome dynamics. We have analyzed the distribution and evolution of 150 introns in 29 sequenced genomes from the B. cereus group. Introns were of different structural classes and evolutionary origins, and a large number of nearly identical elements are shared between multiple strains of different sources. While group I introns are inserted in essential genes from the chromosome or newly described prophages, and are spread among strains by bacteriophages, group II introns are found within a diverse set of chromosomal and plasmidic genes and are mainly disseminated via plasmids.
For details, please see: "Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution". Tourasse NJ, Kolstø AB. (2008). NUCLEIC ACIDS RESEARCH, 36 (14): 4529-4548


Publication in Nucl Acids Res: Bacillus cereus group supertree MLST database.
In our first database publication we have developed a new database that compiles and integrates data from all five schemes used for multilocus sequence typing (MLST) of the B. cereus group. The database is accessible here or by following the MLST/AFLP/MLEE databases link in the left−hand toolbar. Supertree techniques were used to combine the phylogenetic information from analysis of all schemes and datasets, in order to produce an integrated view of the B. cereus group population. The database currently contains strain information, sequences, and phylogenetic data for more than 1000 isolates and 26 housekeeping gene fragments. Besides analysis of the available data, the user has the possibility to enter her/his own sequences and compare them to the database and/or include them into the supertree reconstructions.
For details, please see: "SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis)". Tourasse NJ, Kolstø AB. (2008). NUCLEIC ACIDS RESEARCH, 36 (Database issue):D461-468


Bacillus group: Two of most highly cited Norwegian papers during last 10 years
In a comprehensive analysis of international biology journals from the last 10 years, published in the Journal of the Norwegian Biochemical Society (NBS), issue 3, 2005, the Kolstø B. cereus research group is listed with 2 of the most highly cited Norwegian papers from the last 10−year period: