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.
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%]
|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|