ECF235 ECF proteins

General description: ECF235 contains proteins with homology to several original groups – ECF124 (11.8%), ECF108 (10.79%), ECF110 (12.01%) and ECF40 (0.11%). All the proteins belong to Firmicutes (99.74%), mainly from genera Ruminococcus, Streptococcus and Bacillus, and 33.33% of ECF235s50 from Actinobacteria (0.26% of the total) from genus Slackia.

Anti-σ factor: Likewise original ECF124, ECF108 and ECF110 (Staroń et al., 2009), proteins from ECF235 encode AS factors in position +1. These AS factors contain the domains of ‘σ factor regulator’ (Pfam: Sigma_reg_N and Pfam: Sigma_reg_C) or a putative zinc-finger domain. AS factors of ECF235 typically contain one transmembrane helix (74.87%), although putative AS factors from ECF235s18 contain four (6.08%). In subgroup ECF235s15 we could not find any putative AS factor. Interestingly, members of ECF235s15 encode other σ factors in their genetic context (150% frequency of another protein with σ2 and σ4 domains), usually unclassified (64.29%), member of ECF235s15 (14.29%) or ECF235s42 (7.14%), or other non-ECF σ factors (14.29%).

Genomic context conservation: Apart from a DUF3139 in +2 of ECF235s18, the conservation in the genetic neighborhood of members of ECF235 does not extend beyond the ECF-AS pair.

Studied members: The only characterized proteins that belong to this group is YlaC (ECF235s6) from Bacillus subtilis. YlaC has overlapping functions with SigV, SigZ, and SigY in exopolysaccharide production as part of the biofilm formation, and in the resistance to cefuroxime, ciprofloxacin, and ofloxacin. YlaC is inhibited by the AS factor YlaD, which coordinates Zn2+ and releases it upon oxidation or excess of Mn2+, forming a disulfide bond and releasing the active YlaC (Kwak, Ryu, Song, Lee, & Kang, 2018). YlaC stimulates sporulation under oxidative stress and excess of Mn2+ since it upregulates SigH and ClpP (Kwak et al., 2018).

Promoter motif conservation: The predicted target promoter motifs of ECF235 contain a conserved TGTAAC in -35 and a subgroup-specific -10 element. YlaC is encoded in a four-gene operon regulated by YlaC (Kwak et al., 2018). The promoter that YlaC regulates (TTGAAC (-35) GCTGTCTA (-10) (Kwak et al., 2018)) is different from our predictions, raising the question of whether non-optimal promoter motifs regulate YlaC.

Summary: ECF235 is regulated by membrane-bound AS factors that respond to oxidative stress and/or metal stress. We fused several original minor groups (ECF108, ECF110, and ECF124) into a larger new group. ECF235 does not contain SigM from Bacillus subtilis as the original ECF124, which is now unclassified. The AS factor of some members of ECF235 is associated to a pair of cysteines that is sensitive to the redox state and the Mn concentration of the cell as described for YlaC of B. subtilis (Kwak et al., 2018).


 


Basic information

Number of representative ECFs: 1220

Number of non-redundant ECFs: 1890

Sequences with C-terminal extension: 0.37%

Sequences with N-terminal extension: 0.85%

Overrepresented phylum: Firmicutes [99.92%]



Sample Neighborhood

Protein EOS69634.1 of Assembly GCA_000403475.2 (Lachnospiraceae bacterium 3-2)


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
The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Molecular microbiology 2009 A. Staroń, H. Sofia, S. Dietrich, L. Ulrich, H. Liesegang, T. Mascher PubMed: 19737356 ECF103, ECF21, ECF123, ECF51, ECF39, ECF281, ECF102, ECF130, ECF122, ECF291, ECF15, ECF242, ECF22, ECF285, ECF106, ECF27, ECF31, ECF240, ECF114, ECF16, ECF38, ECF41, ECF105, ECF116, ECF111, ECF03, ECF239, ECF42, ECF294, ECF17, ECF11, ECF29, ECF235, ECF293, ECF118, ECF265, ECF30, ECF23, ECF14, ECF249, ECF18, ECF115, ECF290, ECF25, ECF121, ECF02, ECF120, ECF289, ECF28, ECF243, ECF19, ECF43, ECF107, ECF12, ECF32, ECF36, ECF292, ECF286, ECF271, ECF26, ECF40, ECF56, ECF33
Anti-σ factor YlaD regulates transcriptional activity of σ factor YlaC and sporulation via manganese-dependent redox-sensing molecular switch in <i>Bacillus subtilis</i>. The Biochemical journal 2018 M. Kwak, H. Ryu, S. Song, J. Lee, S. Kang PubMed: 29760236 ECF235
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