ECF245 ECF proteins

General description: Members of ECF245 appear in Firmicutes (100%) from order Bacillales and have homology to members of the original group ECF30 (1.78%) and ECF20 (2.53%).

Genomic context conservation: Members of ECF245 share a similar genetic context composed by a putative anti-σ factor with an N-terminal zinc-binding domain, one transmembrane helix (97.69%) and an extracytoplasmic bactofilin domain (Pfam: Bactofilin) (+1), a protein with the nucleotide-binding domain from a DisA bacterial checkpoint controller, which acts as a di-adenylate cyclase inhibited by stalled replication forks or recombination intermediates (source: Pfam) (+2), a YbbR-like protein (+3), and a phosphoglucomutase/phosphomannomutase (Pfam: PGM_PMM_IV) (+4). Other conserved proteins are a glutamine amidotransferase fused to an SIS domain, which binds to phosphor-carbohydrates (source: Pfam) (ECF245s2).

Studied members: One described member of this group is SigW from Bacillus subtilis (ECF245s1). SigW has overlapping functions to SigM and SigX (Mascher, Hachmann, & Helmann, 2007) and is involved in resistance to several antibiotics that inhibit cell wall synthesis during stationary phase (Cao, Bernat, Wang, Armstrong, & Helmann, 2001; Cao, Wang, Ye, & Helmann, 2002b). It is activated when cell membrane proteins are delocalized, and it regulates the fluidity of the cell membrane by changing the ratio between branched and linear fatty acids (Omardien et al., 2018). Genes controlled by SigW are involved both in detoxification of antibiotics and in the synthesis and transport of bacteriocins (Butcher & Helmann, 2006; Cao et al., 2002a).

Promoter motif conservation: Predicted target promoter motifs are conserved and contain TGAAAC in -35 and CGTAT in -10, suggesting that proteins from this group are autoregulated. Indeed, SigW is autoregulated, and the promoter that it controls is identical to the predicted in this study (Cao et al., 2001).

Summary: Members of ECF245 could coordinate cell-wall synthesis (bactofilin domain of putative AS factors encoded in +1) with the end of replication or recombination (DisA encoded in +2). The rest of the proteins encoded in the genetic context of members of ECF245, YbbR of unknown function and a soluble phosphoglucomutase/phosphomannomutase, could be involved in cell-wall biosynthesis. In agreement with this, the function of the only described member of ECF245, SigW from B. subtilis (ECF245s1), indicates that members of EC245 are part of the cell envelope stress response and regulate the fluidity of the cell membrane.


Basic information

Number of representative ECFs: 815

Number of non-redundant ECFs: 673

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.30%

Overrepresented order: Bacillales [99.88%]



Sample Neighborhood

Protein WP_039806395.1 of Assembly GCF_000818095.1 (Jeotgalibacillus malaysiensis)


Promoter Motif



Figures

Protein sequence length distribution

Gene neighbourhood conservation analysis


Overall Pfam domain distribution: Cumulative frequency of Pfam domains across the genetic neighborhoods. Frequency is expressed as number of Pfam domains per ECF sigma factor. Only domains present in more than 75% of the neighborhoods are shown. Genetic neighborhoods contain the proteins encoded in ±10 from the ECF coding sequence. Only the non-overlapping, highest scoring domains are considered positive. If a protein contains several copies of a domain, only one instance is further considered. In order to avoid sequence bias, only proteins from assemblies defined as "representative" or "reference" by NCBI are included (see https://www.ncbi.nlm.nih.gov/assembly/help/).
Pfam domain distribution per position: Frequency of Pfam domain architectures in the proteins encoded in ±10 (x-axis) from the ECF coding sequences. Frequency is expressed as number of times a certain domain architecture appears per ECF sigma factor. Only the highest scoring domains with no position overlap are considered in the domain architectures. Note that the order of the Pfam domains in domain architectures may differ from their name. When a protein contains several copies of a domain, only one instance is further considered. Only domain architectures present in more than 20% of the proteins encoded in any position are shown. In order to avoid sequence bias, only proteins from assemblies defined as "representative" or "reference" by NCBI are included (see https://www.ncbi.nlm.nih.gov/assembly/help/).

Related publications

Title Journal Year Authors PubMed ECF groups
FosB, a cysteine-dependent fosfomycin resistance protein under the control of sigma(W), an extracytoplasmic-function sigma factor in Bacillus subtilis. Journal of bacteriology 2001 M. Cao, B. Bernat, Z. Wang, R. Armstrong, J. Helmann PubMed: 11244082 ECF245
Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. Journal of molecular biology 2002 M. Cao, P. Kobel, M. Morshedi, M. Wu, C. Paddon, J. Helmann PubMed: 11866510 ECF245
Antibiotics that inhibit cell wall biosynthesis induce expression of the Bacillus subtilis sigma(W) and sigma(M) regulons. Molecular microbiology 2002 M. Cao, T. Wang, R. Ye, J. Helmann PubMed: 12207695 ECF245
Identification of Bacillus subtilis sigma-dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli. Molecular microbiology 2006 B. Butcher, J. Helmann PubMed: 16629676 ECF245
Regulatory overlap and functional redundancy among Bacillus subtilis extracytoplasmic function sigma factors. Journal of bacteriology 2007 T. Mascher, A. Hachmann, J. Helmann PubMed: 17675383 ECF116, ECF245
Synthetic antimicrobial peptides delocalize membrane bound proteins thereby inducing a cell envelope stress response. Biochimica et biophysica acta. Biomembranes 2018 S. Omardien, J. Drijfhout, H. van Veen, S. Schachtschabel, M. Riool, L. Hamoen, S. Brul, S. Zaat PubMed: 29894683 ECF245, ECF30
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