Metabolic capacity of <i>Bacillus cereus</i> strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics

Mols, Maarten; Been, Mark de; Zwietering, Marcel H.; Moezelaar, Roy; Abee, Tjakko

doi:10.1111/j.1462-2920.2007.01404.x

Cited by 52 publications

(48 citation statements)

References 45 publications

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“…To test this idea, we employed a PM analysis to screen for phenotypes associated with the ⌬7ECF and ⌬MWX strains. PM analysis is a high-throughput approach to screen for novel phenotypic traits linked to genetic alterations (8,38,47). Our PM tests included 960 assays for carbon, nitrogen, phosphorus and sulfur source utilization, nutrient stimulation, and pH and osmotic stresses and 240 assays for chemical sensitivities.…”

Section: Resultsmentioning

confidence: 99%

Transcriptomic and Phenotypic Characterization of aBacillus subtilisStrain without Extracytoplasmic Function σ Factors

et al. 2010

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Bacillus subtilis encodes seven extracytoplasmic function (ECF) factors. Three ( M , W , and X ) mediate responses to cell envelope-active antibiotics. The functions of V , Y , Z , and YlaC remain largely unknown, and strong inducers of these factors and their regulons have yet to be defined. Here, we define transcriptomic and phenotypic differences under nonstress conditions between a strain carrying deletions in all seven ECF factor genes (the ⌬7ECF mutant), a ⌬MWX triple mutant, and the parental 168 strain. Our results identify >80 genes as at least partially dependent on ECF factors, and as expected, most of these are dependent on M , W , or X , which are active at a significant basal level during growth. Several genes, including the eps operon encoding enzymes for exopolysaccharide (EPS) production, were decreased in expression in the ⌬7ECF mutant but affected less in the ⌬MWX mutant. Consistent with this observation, the ⌬7ECF mutant (but not the ⌬MWX mutant) showed reduced biofilm formation. Extending previous observations, we also note that the ⌬MWX mutant is sensitive to a variety of antibiotics and the ⌬7ECF mutant is either as sensitive as, or slightly more sensitive than, the ⌬MWX strain to these stressors. These findings emphasize the overlapping nature of the seven ECF factor regulons in B. subtilis, confirm that three of these ( M , W , and X ) play the dominant role in conferring intrinsic resistance to antibiotics, and provide initial insights into the roles of the remaining ECF factors.

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Section: Resultsmentioning

confidence: 99%

Transcriptomic and Phenotypic Characterization of aBacillus subtilisStrain without Extracytoplasmic Function σ Factors

et al. 2010

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“…The genomic DNA sequences of Bacillus cereus strains ATCC 10987 and ATCC 14579 (nonpathogenic, biosafety level 1 strains) have been published (32). Genomic analysis indicated that B. cereus ATCC 10987 is more similar to Bacillus anthracis Ames than to B. cereus ATCC 14579 (19,29,32). In addition, nine more Bacillus cereus genomes of pathogenic and nonpathogenic strains have been sequenced (GenBank genome database).…”

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confidence: 99%

Characterization of Type II and III Restriction-Modification Systems from Bacillus cereus Strains ATCC 10987 and ATCC 14579

Nugent

Kasamkattil

et al. 2011

Journal of Bacteriology

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The genomes of two Bacillus cereus strains (ATCC 10987 and ATCC 14579) have been sequenced. Here, we report the specificities of type II/III restriction (R) and modification (M) enzymes. Found in the ATCC 10987 strain, BceSI is a restriction endonuclease (REase) with the recognition and cut site CGAAG 24-25/27-28. BceSII is an isoschizomer of AvaII (G/GWCC). BceSIII cleaves at ACGGC 12/14. The BceSIII C terminus resembles the catalytic domains of AlwI, MlyI, and Nt.BstNBI. BceSIV is composed of two subunits and cleaves on both sides of GCWGC. BceSIV activity is strongly stimulated by the addition of cofactor ATP or GTP. The large subunit (R1) of BceSIV contains conserved motifs of NTPases and DNA helicases. The R1 subunit has no endonuclease activity by itself; it strongly stimulates REase activity when in complex with the R2 subunit. BceSIV was demonstrated to hydrolyze GTP and ATP in vitro. BceSIV is similar to CglI (GCSGC), and homologs of R1 are found in 11 sequenced bacterial genomes, where they are paired with specificity subunits. In addition, homologs of the BceSIV R1-R2 fusion are found in many sequenced microbial genomes. An orphan methylase, M.BceSV, was found to modify GCNGC, GGCC, CCGG, GGN NCC, and GCGC sites. A ParB-methylase fusion protein appears to nick DNA nonspecifically. The ATCC 14579 genome encodes an active enzyme Bce14579I (GCWGC). BceSIV and Bce14579I belong to the phospholipase D (PLD) family of endonucleases that are widely distributed among Bacteria and Archaea. A survey of type II and III restriction-modification (R-M) system genes is presented from sequenced B. cereus, Bacillus anthracis, and Bacillus thuringiensis strains. Bacillus cereus is a Gram-positive, soil-dwelling, aerobic bacterium. Food contaminated with some B. cereus strains can cause nausea, vomiting, and diarrhea in humans. Certain B. cereus strains produce a pore-forming toxin called CytK (CytK-1 and CytK-2), which is hemolytic and toxic toward human intestinal Caco-2 cells and Vero cells (16). The genomic DNA sequences of Bacillus cereus strains ATCC 10987 and ATCC 14579 (nonpathogenic, biosafety level 1 strains) have been published (32). Genomic analysis indicated that B. cereus ATCC 10987 is more similar to Bacillus anthracis Ames than to B. cereus ATCC 14579 (19,29,32). In addition, nine more Bacillus cereus genomes of pathogenic and nonpathogenic strains have been sequenced (GenBank genome database). An additional 22 B. cereus strains have been sequenced by the shotgun sequencing method (GenBank). Bioinformatic analysis of the 11 fully sequenced genomes indicated that B. cereus strain ATCC 10987 harbors the most restriction-modification (R-M) systems among the B. cereus strains, with four predicted complete R-M systems, including one partially characterized type III R-M system, one orphan 5-cytosine methyltransferase (C5 methyltransferase [MTase]), and one ParB-methylase fusion (see the REBASE database) (34). Only one type II R-M system was predicted for the ATCC 14579 strain.The primary biological function of ...

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“…From this perspective, comparative transcriptomic analysis has been a powerful tool for exploring the metabolic variability in both eukaryotic and prokaryotic organisms (47). Recently, direct high-throughput assessment of phenotypes (phenome) using the Phenotype MicroArray (PM) system (Biolog) (9) has stirred much attention for molecular biology, genomic, and population studies of microorganisms (14,20,29,33,34,37,45,46).…”

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confidence: 99%

Metabolic Capacity of Sinorhizobium ( Ensifer ) meliloti Strains as Determined by Phenotype MicroArray Analysis

Biondi

Tatti

Comparini

et al. 2009

Appl Environ Microbiol

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Sinorhizobium meliloti is a soil bacterium that fixes atmospheric nitrogen in plant roots. The high genetic diversity of its natural populations has been the subject of extensive analysis. Recent genomic studies of several isolates revealed a high content of variable genes, suggesting a correspondingly large phenotypic differentiation among strains of S. meliloti. Here, using the Phenotype MicroArray (PM) system, hundreds of different growth conditions were tested in order to compare the metabolic capabilities of the laboratory reference strain Rm1021 with those of four natural S. meliloti isolates previously analyzed by comparative genomic hybridization (CGH). The results of PM analysis showed that most phenotypic differences involved carbon source utilization and tolerance to osmolytes and pH, while fewer differences were scored for nitrogen, phosphorus, and sulfur source utilization. Only the variability of the tested strain in tolerance to sodium nitrite and ammonium sulfate of pH 8 was hypothesized to be associated with the genetic polymorphisms detected by CGH analysis. Colony and cell morphologies and the ability to nodulate Medicago truncatula plants were also compared, revealing further phenotypic diversity. Overall, our results suggest that the study of functional (phenotypic) variability of S. meliloti populations is an important and complementary step in the investigation of genetic polymorphism of rhizobia and may help to elucidate rhizobial evolutionary dynamics, including adaptation to diverse environments.Sinorhizobium meliloti is a soil bacterium belonging to the Rhizobiales group of the Alphaproteobacteria subdivision, which includes pathogens, such as Bartonella and Brucella, and several plant-associated bacteria of relevant agricultural importance, such as Agrobacterium, Ochrobactrum, Bradyrhizobium, Mesorhizobium, and Rhizobium (21). S. meliloti forms nitrogenfixing nodules on the roots of leguminous plants of the genera Medicago, Melilotus, and Trigonella, and it is probably the beststudied model system for the rhizobium-legume symbiosis. S. meliloti is distributed worldwide and is present in many soil types, both in association with legumes and in free-living form (40). The ubiquitous occurrence of this species suggested a wide metabolic capability allowing adaptation to very different environmental and nutritional conditions. S. meliloti has been the subject of extensive genetic, biochemical, and metabolic research (25). The sequencing of the strain Rm1021 genome (4, 11, 17, 18) provided a solid foundation for a number of molecular studies of the genetic basis of plant-bacterium interactions and of the response of S. meliloti to environmental stimuli. Moreover, the genetic diversity of natural populations of S. meliloti has been the subject of extensive analyses (1-3, 8, 12, 24, 38, 42). These investigations showed that S. meliloti populations are very diverse and that S. meliloti strains harbor a high number of different mobile genetic elements, such as insertion sequences, transposons...

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Metabolic capacity of Bacillus cereus strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics

Cited by 52 publications

References 45 publications

Transcriptomic and Phenotypic Characterization of aBacillus subtilisStrain without Extracytoplasmic Function σ Factors

Transcriptomic and Phenotypic Characterization of aBacillus subtilisStrain without Extracytoplasmic Function σ Factors

Characterization of Type II and III Restriction-Modification Systems from Bacillus cereus Strains ATCC 10987 and ATCC 14579

Metabolic Capacity of Sinorhizobium ( Ensifer ) meliloti Strains as Determined by Phenotype MicroArray Analysis

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