Genome Sequence of the Bacillus subtilis Biofilm-Forming Transformable Strain PS216

Durrett, Richard; Miras, Mathieu; Mirouze, Nicolas; Narechania, Apurva; Mandić-Mulec, Ines; Dubnau, David

doi:10.1128/genomea.00288-13

Cited by 18 publications

(21 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…To find these alternative mechanisms, we repeated the genetic screen in a different strain background: PS-216, a strain with high genome similarity to NCIB 3610 [34, 35], yet the two form a partial boundary (see Figure 7B below). We recovered one kin recognition mutant that contained an insertion in the epsI gene (Figure 4C), part of the biosynthetic operon that produces the polysaccharide component of the extracellular matrix [36].…”

Section: Resultsmentioning

confidence: 99%

“…Here we tested a much more closely related pair: NCIB 3610 and PS-216, whose major difference is the lack of SPβ in the latter [34] (Figure 7A), and in particular the major lantibiotic sublancin [29], encoded by the sunA gene. Deletion of sunA in NCIB 3610 virtually eliminated the boundary with PS-216 (Figure 7B), indicating sublancin is the primary factor distinguishing these strains as non-kin.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

A Combinatorial Kin Discrimination System in Bacillus subtilis

et al. 2016

Self Cite

View full text Add to dashboard Cite

SUMMARY Multicellularity inherently involves a number of cooperative behaviors that are potentially susceptible to exploitation but can be protected by mechanisms such as kin discrimination. Discrimination of kin from non-kin has been observed in swarms of the bacterium Bacillus subtilis, but the underlying molecular mechanism has been unknown. We used genetic, transcriptomic, and bioinformatic analyses to uncover kin recognition factors in this organism. Our results identified many molecules involved in cell surface modification and antimicrobial production and response. These genes varied significantly in expression level and mutation phenotype among B. subtilis strains, suggesting interstrain variation in the exact kin discrimination mechanism used. Genome analyses revealed a substantial diversity of antimicrobial genes present in unique combinations in different strains, with many likely acquired by horizontal gene transfer. The dynamic combinatorial effect derived from this plethora of kin discrimination genes creates a tight relatedness cutoff for cooperation that has likely led to rapid diversification within the species. Our data suggest that genes likely originally selected for competitive purposes also generate preferential interactions among kin, thus stabilizing multicellular lifestyles.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

A Combinatorial Kin Discrimination System in Bacillus subtilis

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…subtilis RO-OO-2 and RO-FF-1 strains, the B. subtilis subsp. spizizenii RO-E-2 [all three isolated in the Mojave desert (Cohan et al, 1991)], the commonly used model strain 3610 (Branda et al, 2006; McLoon et al, 2011) and B. subtilis PS216, isolated in Slovenia (Durrett et al, 2013). Throughout this study we have used comI mutants of 3610.…”

Section: Resultsmentioning

confidence: 99%

“…The backgrounds used for all experiments were either IS75, a derivative of strain 168, PS216 (an undomesticated strain of B. subtilis isolated in Slovenia and kindly provided by Inés Mandic-Mulec) (Durrett et al, 2013), 3610△ comI or 3610 comI Q12L (both gifts from Dan Kearns). The comI Q12L mutation abolishes ComI activity (Konkol et al, 2013), removing a block in DNA uptake.…”

Section: Methodsmentioning

confidence: 99%

A DegU-P and DegQ-Dependent Regulatory Pathway for the K-state in Bacillus subtilis

Miras

Dubnau

2016

Front. Microbiol.

Self Cite

View full text Add to dashboard Cite

The K-state in the model bacterium Bacillus subtilis is associated with transformability (competence) as well as with growth arrest and tolerance for antibiotics. Entry into the K-state is determined by the stochastic activation of the transcription factor ComK and occurs in about ∼15% of the population in domesticated strains. Although the upstream mechanisms that regulate the K-state have been intensively studied and are well understood, it has remained unexplained why undomesticated isolates of B. subtilis are poorly transformable compared to their domesticated counterparts. We show here that this is because fewer cells enter the K-state, suggesting that a regulatory pathway limiting entry to the K-state is missing in domesticated strains. We find that loss of this limitation is largely due to an inactivating point mutation in the promoter of degQ. The resulting low level of DegQ decreases the concentration of phosphorylated DegU, which leads to the de-repression of the srfA operon and ultimately to the stabilization of ComK. As a result, more cells reach the threshold concentration of ComK needed to activate the auto-regulatory loop at the comK promoter. In addition, we demonstrate that the activation of srfA transcription in undomesticated strains is transient, turning off abruptly as cells enter the stationary phase. Thus, the K-state and transformability are more transient and less frequently expressed in the undomesticated strains. This limitation is more extreme than appreciated from studies of domesticated strains. Selection has apparently limited both the frequency and the duration of the bistably expressed K-state in wild strains, likely because of the high cost of growth arrest associated with the K-state. Future modeling of K-state regulation and of the fitness advantages and costs of the K-state must take these features into account.

show abstract

“…This plasmid is not found in other isolates of B. subtilis subsp. subtilis (27), but a highly homologous plasmid, pLS32, which is found in a more distant strain of B. subtilis subsp. natto, has been analyzed and sequenced (28).…”

mentioning

confidence: 99%

The RapP-PhrP Quorum-Sensing System of Bacillus subtilis Strain NCIB3610 Affects Biofilm Formation through Multiple Targets, Due to an Atypical Signal-Insensitive Allele of RapP

et al. 2014

View full text Add to dashboard Cite

The genome of Bacillus subtilis 168 encodes eight rap-phr quorum-sensing pairs. Rap proteins of all characterized Rap-Phr pairs inhibit the function of one or several important response regulators: ComA, Spo0F, or DegU. This inhibition is relieved upon binding of the peptide encoded by the cognate phr gene. Bacillus subtilis strain NCIB3610, the biofilm-proficient ancestor of strain 168, encodes, in addition, the rapP-phrP pair on the plasmid pBS32. RapP was shown to dephosphorylate Spo0F and to regulate biofilm formation, but unlike other Rap-Phr pairs, RapP does not interact with PhrP. In this work we extend the analysis of the RapP pathway by reexamining its transcriptional regulation, its effect on downstream targets, and its interaction with PhrP. At the transcriptional level, we show that rapP and phrP regulation is similar to that of other rap-phr pairs. We further find that RapP has an Spo0F-independent negative effect on biofilm-related genes, which is mediated by the response regulator ComA. Finally, we find that the insensitivity of RapP to PhrP is due to a substitution of a highly conserved residue in the peptide binding domain of the rapP allele of strain NCIB3610. Reversing this substitution to the consensus amino acid restores the PhrP dependence of RapP activity and eliminates the effects of the rapP-phrP locus on ComA activity and biofilm formation. Taken together, our results suggest that RapP strongly represses biofilm formation through multiple targets and that PhrP does not counteract RapP due to a rare mutation in rapP.T he behavior of bacterial communities is often regulated by quorum-sensing (QS) signaling pathways. In these pathways, a secreted molecular signal accumulates in the environment and activates a cognate receptor at sufficiently high concentrations. Gram-positive bacteria frequently utilize peptides as QS signals (1-3), thereby eliciting a variety of behaviors, including the secretion of various molecules (e.g., enzymes, antibiotics, surfactants, and exopolysaccharides [4]), the initiation of developmental processes (such as sporulation and biofilm formation), and horizontal gene transfer through transformation or conjugation (5-7).Members of the Rap-Phr family of QS systems in the Grampositive model Bacillus subtilis are involved in the regulation of competence, sporulation, and biofilm formation. The chromosome of strain B. subtilis 168 encodes eight full receptor signal systems and three orphan receptors from this family (6,8). In each of the full systems, the phr gene encodes a prepeptide, which is secreted through the major secretory system and then further processed outside the cell, resulting in the formation of a mature penta-or hexapeptide signal (9). The mature peptide is transported into the cell by the oligopeptide-permease (Opp) complex, where it interacts with its Rap targets within the cytoplasm (10). All characterized Rap proteins contain two domains (10-12), a tricopeptide repeat (TPR) domain that interacts with the signaling peptide and a second domain that f...

show abstract

Genome Sequence of the Bacillus subtilis Biofilm-Forming Transformable Strain PS216

Abstract: Bacillus subtilis PS216, a strain isolated in Slovenia, has been sequenced. PS216 is transformable and forms robust biofilms, making it useful for the study of competence regulation in an undomesticated bacterium.

Cited by 18 publications

References 12 publications

A Combinatorial Kin Discrimination System in Bacillus subtilis

A Combinatorial Kin Discrimination System in Bacillus subtilis

A DegU-P and DegQ-Dependent Regulatory Pathway for the K-state in Bacillus subtilis

The RapP-PhrP Quorum-Sensing System of Bacillus subtilis Strain NCIB3610 Affects Biofilm Formation through Multiple Targets, Due to an Atypical Signal-Insensitive Allele of RapP

Contact Info

Product

Resources

About