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ComQXPA quorum sensing systems may not be unique to Bacillus subtilis: a census in prokaryotic genomes.

Dogsa I, Choudhary KS, Marsetic Z, Hudaiberdiev S, Vera R, Pongor S, Mandic-Mulec I - PLoS ONE (2014)

Bottom Line: Here we present results of a comprehensive census of comQXPA-like gene arrangements in 2620 complete and 6970 draft prokaryotic genomes (sequenced by the end of 2013).After manually checking the data for false-positive and false-negative hits, we found 39 novel com-like predictions.Pronounced sequence variability associated with the ComX peptide in B. subtilis clade is evident also in the non-B. subtilis clade suggesting grossly similar evolutionary constraints in the underlying quorum sensing systems.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.

ABSTRACT
The comQXPA locus of Bacillus subtilis encodes a quorum sensing (QS) system typical of Gram positive bacteria. It encodes four proteins, the ComQ isoprenyl transferase, the ComX pre-peptide signal, the ComP histidine kinase, and the ComA response regulator. These are encoded by four adjacent genes all situated on the same chromosome strand. Here we present results of a comprehensive census of comQXPA-like gene arrangements in 2620 complete and 6970 draft prokaryotic genomes (sequenced by the end of 2013). After manually checking the data for false-positive and false-negative hits, we found 39 novel com-like predictions. The census data show that in addition to B. subtilis and close relatives, 20 comQXPA-like loci are predicted to occur outside the B. subtilis clade. These include some species of Clostridiales order, but none outside the phylum Firmicutes. Characteristic gene-overlap patterns were observed in comQXPA loci, which were different for the B. subtilis-like and non-B. subtilis-like clades. Pronounced sequence variability associated with the ComX peptide in B. subtilis clade is evident also in the non-B. subtilis clade suggesting grossly similar evolutionary constraints in the underlying quorum sensing systems.

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Related in: MedlinePlus

Unusual comQXPA-like loci.(A) Non-canonical unusual com system is present in B. cereus VD102, B. cereus BAG4X12 1, B. cereus MSX A1 and L. fusiformis ZC1. Note that Lysinibacillus is the only genus whose two species have two com loci each: L. sphaericus C3 41 has two canonical loci while in L. fusiformis ZC1 one locus is canonical and the other one is non-canonical, shown here. (B) Canonical unusual com system present in Paenibacillus curdlanolyticus YK9 and B. coagulans 36D1.
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pone-0096122-g004: Unusual comQXPA-like loci.(A) Non-canonical unusual com system is present in B. cereus VD102, B. cereus BAG4X12 1, B. cereus MSX A1 and L. fusiformis ZC1. Note that Lysinibacillus is the only genus whose two species have two com loci each: L. sphaericus C3 41 has two canonical loci while in L. fusiformis ZC1 one locus is canonical and the other one is non-canonical, shown here. (B) Canonical unusual com system present in Paenibacillus curdlanolyticus YK9 and B. coagulans 36D1.

Mentions: A few com-like arrangements were found outside the Bacillus genus in which the comX sequence was of the right length and in the right position between comQ and comP, but showed no appreciable homology with the known comX sequences, except the tryptophan residue in the C-terminus. We term these reading frames as hypothetical comX, (Figure 4). In one of the groups the hypothetical comX gene is on the opposite strand (4A). Three strains (B. cereus VD102, B. cereus BAG4X12 1, B. cereus MSX A1) and L. fusiformis ZC1 have this arrangement. We note that Lysinibacillus is the only genus whose two species have two comQXPA loci each: L. sphaericus C3 41 has two canonical loci while in L. fusiformis ZC1 one locus is canonical and the other has the hypothetical comX gene on the opposite strand, shown in Figure 4A.


ComQXPA quorum sensing systems may not be unique to Bacillus subtilis: a census in prokaryotic genomes.

Dogsa I, Choudhary KS, Marsetic Z, Hudaiberdiev S, Vera R, Pongor S, Mandic-Mulec I - PLoS ONE (2014)

Unusual comQXPA-like loci.(A) Non-canonical unusual com system is present in B. cereus VD102, B. cereus BAG4X12 1, B. cereus MSX A1 and L. fusiformis ZC1. Note that Lysinibacillus is the only genus whose two species have two com loci each: L. sphaericus C3 41 has two canonical loci while in L. fusiformis ZC1 one locus is canonical and the other one is non-canonical, shown here. (B) Canonical unusual com system present in Paenibacillus curdlanolyticus YK9 and B. coagulans 36D1.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4008528&req=5

pone-0096122-g004: Unusual comQXPA-like loci.(A) Non-canonical unusual com system is present in B. cereus VD102, B. cereus BAG4X12 1, B. cereus MSX A1 and L. fusiformis ZC1. Note that Lysinibacillus is the only genus whose two species have two com loci each: L. sphaericus C3 41 has two canonical loci while in L. fusiformis ZC1 one locus is canonical and the other one is non-canonical, shown here. (B) Canonical unusual com system present in Paenibacillus curdlanolyticus YK9 and B. coagulans 36D1.
Mentions: A few com-like arrangements were found outside the Bacillus genus in which the comX sequence was of the right length and in the right position between comQ and comP, but showed no appreciable homology with the known comX sequences, except the tryptophan residue in the C-terminus. We term these reading frames as hypothetical comX, (Figure 4). In one of the groups the hypothetical comX gene is on the opposite strand (4A). Three strains (B. cereus VD102, B. cereus BAG4X12 1, B. cereus MSX A1) and L. fusiformis ZC1 have this arrangement. We note that Lysinibacillus is the only genus whose two species have two comQXPA loci each: L. sphaericus C3 41 has two canonical loci while in L. fusiformis ZC1 one locus is canonical and the other has the hypothetical comX gene on the opposite strand, shown in Figure 4A.

Bottom Line: Here we present results of a comprehensive census of comQXPA-like gene arrangements in 2620 complete and 6970 draft prokaryotic genomes (sequenced by the end of 2013).After manually checking the data for false-positive and false-negative hits, we found 39 novel com-like predictions.Pronounced sequence variability associated with the ComX peptide in B. subtilis clade is evident also in the non-B. subtilis clade suggesting grossly similar evolutionary constraints in the underlying quorum sensing systems.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.

ABSTRACT
The comQXPA locus of Bacillus subtilis encodes a quorum sensing (QS) system typical of Gram positive bacteria. It encodes four proteins, the ComQ isoprenyl transferase, the ComX pre-peptide signal, the ComP histidine kinase, and the ComA response regulator. These are encoded by four adjacent genes all situated on the same chromosome strand. Here we present results of a comprehensive census of comQXPA-like gene arrangements in 2620 complete and 6970 draft prokaryotic genomes (sequenced by the end of 2013). After manually checking the data for false-positive and false-negative hits, we found 39 novel com-like predictions. The census data show that in addition to B. subtilis and close relatives, 20 comQXPA-like loci are predicted to occur outside the B. subtilis clade. These include some species of Clostridiales order, but none outside the phylum Firmicutes. Characteristic gene-overlap patterns were observed in comQXPA loci, which were different for the B. subtilis-like and non-B. subtilis-like clades. Pronounced sequence variability associated with the ComX peptide in B. subtilis clade is evident also in the non-B. subtilis clade suggesting grossly similar evolutionary constraints in the underlying quorum sensing systems.

Show MeSH
Related in: MedlinePlus