ECF16 ECF proteins

General description: Members of ECF16 are present in Proteobacteria (96.5%), mainly Alphaproteobacteria, and ECF16s14 to Spirochaetes (2.67%). All the subgroups contain proteins with homology to original ECF16 (85.71%).

Anti-σ factor: Proteins from ECF16 are regulated by a putative AS factor with a conserved DUF1109 encoded in position +1. This protein contains six transmembrane helices (95.8%) and two conserved cysteine residues, as in the experimentally addressed AS factors of ECF16.

Genomic context conservation: Other conserved proteins in the genetic context of members of ECF16 are a DUF692-containing protein (ECF16s15 and ECF16s16) a DUF2282-containing protein (ECF16s15 and ECF16s16), a DoxX-domain containing protein (ECF16s15 and ECF16s16), an enoyl-CoA hydratase/isomerase (ECF16s2), a putative DNA-binding domain (ECF16s16), a cytochrome C biogenesis protein fused to a thioredoxin-like domain (ECF16s10), a AhpC/TSA family (ECF16s10), an outer membrane efflux protein (ECF16s2), a glutathione S-transferase (ECF16s19) and a protein from the AcrB/AcrD/AcrF family (ECF16s5).

Studied examples: Some members of ECF16, SigF from Caulobacter crescentus and Bradyrhizobium japonicum, have been functionally addressed. They are regulated by an AS factor (NrsF from C. crescentus and OsrA from B. japonicum) with six transmembrane helices and two cysteine residues facing the periplasm that are essential for sequestering their cognate ECF σ factor (Jogler et al., 2012).

Promoter motif conservation: Members of this group respond to heavy-metal stress (Jogler et al., 2012) or oxidative stress (Jogler et al., 2012). Both SigF from C. crescentus (ECF16s20) and B. japonicum (ECF16s2) self-induce their expression, and SigF from C. crescentus has the target promoter GTAACC-CGTA (Kohler et al., 2012; Masloboeva et al., 2012). These data do not agree with the predicted promoter elements (normally TTC in -35 and TAC or TAAC in -10).

Summary: Members of ECF16 are associated with DUF1109-containing AS factors with six transmembrane helices and conserved periplasmic cysteine residues. Their promoter motifs, although conserved, do not match experimental data. Members of ECF16 are involved in heavy metal and oxidative stress response.


 


Basic information

Number of representative ECFs: 1590

Number of non-redundant ECFs: 1715

Sequences with C-terminal extension: 0.12%

Sequences with N-terminal extension: 11.60%

Overrepresented phylum: Proteobacteria [97.80%]



Sample Neighborhood

Protein WP_043746511.1 of Assembly GCF_000768315.1 (Pseudooceanicola atlanticus)


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
A caulobacter crescentus extracytoplasmic function sigma factor mediating the response to oxidative stress in stationary phase. Journal of bacteriology 2006 C. Alvarez-Martinez, R. Baldini, S. Gomes PubMed: 16484194 ECF16
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
Reactive oxygen species-inducible ECF σ factors of Bradyrhizobium japonicum. PloS one 2012 N. Masloboeva, L. Reutimann, P. Stiefel, R. Follador, N. Leimer, H. Hennecke, S. Mesa, H. Fischer PubMed: 22916258 ECF16, ECF33
Extracytoplasmic function (ECF) sigma factor σF is involved in Caulobacter crescentus response to heavy metal stress. BMC microbiology 2012 C. Kohler, R. Lourenço, G. Avelar, S. Gomes PubMed: 22985357 ECF16
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