Conservation and dynamics of the agr cell-to-cell communication system across firmicutes

Reference:
Arthur Wuster and M. Madan Babu (2007) Conservation and dynamics of the agr cell-to-cell communication system across firmicutes

gene identifiers

all gene identifiers of potential agrBDCA homologues used in the paper, with species information

same list, in Excel format

alignments

AgrB protein alignment
concatenated agr locus protein alignment
AgrD alignment (as figure agrd_aln in printed text)
alignment of unidentified agr associated protein

Coloured alignments in HTML format were created using Jalview. Shades of purple refer to percentage identity.

phylogenies

tree of AgrB sequences as a GIF image
TXT

tree of AgrB sequences in Newick format
GIF

tree of concatenated Agr sequences as a GIF image
TXT

tree of concatenated Agr sequences in Newick format
TXT

tree of ribosomal sequences of firmicutes in Newick format (as figure agr_tree in printed text)

differentially expressed genes

GIs and log₂ expression ratios of genes differentially expressed in Staphylococcus aureus N315
TXT

Pfam assignments of genes differentially expressed in Staphylococcus aureus N315
TXT

GIs and log₂ expression ratios of genes differentially expressed in Enterococcus faecalis
TXT

Pfam assignments of genes differentially expressed in Enterococcus faecalis
TXT

GIs and log₂ expression ratios of genes differentially expressed in Lactobacillus plantarum
TXT

Pfam assignments of genes differentially expressed in Lactobacillus plantarum
TXT

GIs and log₂ expression ratios of genes differentially expressed in Staphylococcus epidermidis
TXT

Pfam assignments of genes differentially expressed in Staphylococcus epidermidis

All Pfam assignments have an E-value cutoff of 0.001.

BLAST results

PSI-BLAST results for searching against the non-redundant NCBI protein sequence database as of 09 May 2007.
Numbers refer to GI identifiers of the query sequence. All searches were iterated until saturation.

Searching AgrB homologues:
TXT   20515553 (Thermoanaerobacter tengcongensis)
TXT   13701830 (Staphylococcus aureus N315)
TXT   29343827 (Enterococcus faecalis V583)
TXT   16409407 (Listeria monocytogenes)

Searching AgrD homologues:
TXT   13701831 (Staphylococcus aureus N315)
TXT   46879544 (Listeria monocytogenes)
TXT   110674548 (Clostridium perfringens ATCC 13124)
TXT   10176097 (Bacillus halodurans C-125)
TXT   28272731 (Lactobacillus plantarum WCFS1)

Searching for the agr associated protein (also see figure S1):
TXT 110683450 (Clostridium perfringens SM101)

figures

Figure S1. Transmembrane topology of a protein which is encoded in close proximity to the agr locus in many Clostridia. Highly conserved residues in grey. Also see alignment.

Figure S2. Some of the interactions surrounding the agr system in Staphylococcus aureus, as reported in the literature. Negative interactions in red. Positive interactions in black. Secreted components have a yellow background. Components encoded at the agr locus have a green background.

Figure S3. Comparison of gene expression experiments comparing wildtype strains to strains with a non-functional agr-like locus. In all cases, data from the late logarithmic growth phase/early stationary phase transition was used. Genes which are downregulated are in brackets.

TXT Full list of orthologous clusters between the genomes of Staphylococcus aureus N315, Staphylococcus epidermidis, Enterococcus faecalis and Lactobacillus plantarum.

TXT Distribution of orthologous clusters between the genomes of Staphylococcus aureus N315, Staphylococcus epidermidis, Enterococcus faecalis and Lactobacillus plantarum.

Last update: 19 September 2007