ECF11 ECF proteins

General description: ECF11 is mainly composed of proteins with homology to original ECF11 (83.58%). Members of this group are present in Proteobacteria (Gamma and Alphaproteobacteria).

Anti-σ factor: Members of ECF11 are regulated by putative AS factors with a ChrR cupin-like domain (CLD) encoded in position +1, as in the case of members of original ECF11 (Staroń et al., 2009). This protein may contain a zinc finger, and it is absent in ECF11s6, where it could be encoded elsewhere in the genome. Putative AS factors of members of ECF11 are soluble proteins (100%), as expected from the AS of original ECF11 (Staroń et al., 2009).

Genomic context conservation: Members of ECF11 contain an average of about one flavin-containing amino oxidoreductase per genomic context. This protein is encoded in position -4, -3 or -1 and is part of the set of domains that appears in several subgroups of ECF11, among which we also found the substrate-binding domain of LON ATP-dependent protease (position -1), a SnoaL-like domain-containing protein (positions -2 or -1), a short chain dehydrogenase (position -3 or -2), a DUF1365-containing protein (position -5, -4 or -2) and a mycolic acid cyclopropane synthetase.

Studied members: The most studied member of this group, σE from Rhodobacter sphaeroides (ECF11s1), is inhibited by its anti-σ factor, ChrR (Campbell et al., 2007). ChrR is a soluble zinc-finger AS factor with a C-terminal CLD, which also binds a zinc atom but with less affinity than the zinc-finger in the AS factor domain (Greenwell, Nam, & Donohue, 2011). The CLD senses the presence of oxidative stress from singlet oxygen or tert-butyl hydroperoxide (Campbell et al., 2007; Greenwell et al., 2011). Another member of this group, SigW from Pseudomonas syringae (ECF11s4), responds to the same kind of stresses and is regulated by a ChrR type AS factor (Butcher et al., 2017).

Promoter motif conservation: The predicted target promoter motifs found upstream of the ECF11 coding sequences are conserved and have a consensus of GTGATC for -35 and CGTA for -10. This promoter matches previous predictions (Staroń et al., 2009) and experimental data (Butcher et al., 2017; Newman, Falkowski, Schilke, Anthony, & Donohue, 1999). The coherent prediction of the promoter motifs within and across subgroups reflects the autoregulatory role of ECF11 (Butcher et al., 2017; Newman et al., 1999) and the conservation of its members.

Summary: Members of ECF11 are associated with soluble AS factors with a cupin-like domain (CLD) involved in the sensing of oxidative stress induced by singlet oxygen or an organic peroxide. The association of ECF11 with soluble zinc-binding AS factors and their involvement in oxidative stress response reminds of ECF12. However, ECF12 has a different target promoter sequence, is present in more taxonomic groups, and usually responds to disulfide stress rather than oxidative stress per se.


 


Basic information

Number of representative ECFs: 1390

Number of non-redundant ECFs: 1602

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 18.98%

Overrepresented class: Alphaproteobacteria [49.71%]



Sample Neighborhood

Protein WP_040787400.1 of Assembly GCF_000169395.1 (Rhodobacteraceae bacterium HTCC2150)


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 Rhodobacter sphaeroides ECF sigma factor, sigma(E), and the target promoters cycA P3 and rpoE P1. Journal of molecular biology 1999 J. Newman, M. Falkowski, B. Schilke, L. Anthony, T. Donohue PubMed: 10610760 ECF11
Crystal structure of Escherichia coli sigmaE with the cytoplasmic domain of its anti-sigma RseA. Molecular cell 2003 E. Campbell, J. Tupy, T. Gruber, S. Wang, M. Sharp, C. Gross, S. Darst PubMed: 12718891 ECF11
Assignment of the zinc ligands in RsrA, a redox-sensing ZAS protein from Streptomyces coelicolor. Biochemistry 2006 K. Zdanowski, P. Doughty, P. Jakimowicz, L. O'Hara, M. Buttner, M. Paget, C. Kleanthous PubMed: 16819828 ECF12, ECF11
A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria. Molecular cell 2007 E. Campbell, R. Greenwell, J. Anthony, S. Wang, L. Lim, K. Das, H. Sofia, T. Donohue, S. Darst PubMed: 17803943 ECF11
Organization and evolution of the biological response to singlet oxygen stress. Journal of molecular biology 2008 Y. Dufour, R. Landick, T. Donohue PubMed: 18723027 ECF11
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
Features of Rhodobacter sphaeroides ChrR required for stimuli to promote the dissociation of σ(E)/ChrR complexes. Journal of molecular biology 2011 R. Greenwell, T. Nam, T. Donohue PubMed: 21295582 ECF11
The ECF sigma factor, PSPTO_1043, in Pseudomonas syringae pv. tomato DC3000 is induced by oxidative stress and regulates genes involved in oxidative stress response. PloS one 2017 B. Butcher, Z. Bao, J. Wilson, P. Stodghill, B. Swingle, M. Filiatrault, D. Schneider, S. Cartinhour PubMed: 28700608 ECF11
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