ECF102 ECF proteins

General description: ECF122 have homology to proteins of original ECF102 (61.39%). The topology of this clade of the ECF σ factor tree follows the taxonomic origin of its proteins – members of ECF102 are present in Bacteroidetes (66.17%) (ECF102s2, ECF102s3, and ECF102s5) and Gammaproteobacteria (33.83%) (ECF102s1, ECF102s6).

Studied members: The only characterized member of ECF102 is SigX from P. aeruginosa (ECF102s1). SigX contributes to the composition of the cell membrane changing the membrane fluidity, antibiotic resistance (polymixin B and imipenem), iron uptake, virulence, motility and biofilm formation (Chevalier et al., 2018). This ECF is part of a 7-gene operon which includes a mechanosensitive ion channel (CmpX) encoded in -1, a putative AS factor (CfrX) encoded in -2 and an outer membrane porin (OprF) encoded in +1 (Chevalier et al., 2018). Even though original reports hypothesized that the regulation of SigX is carried out by CfrX, new findings argue a more complex regulatory mechanism involving a mechanosensing pathway in which CmpX, CfrX, and OprF might participate (reviewed in (Chevalier et al., 2018)). The functions of SigX are diverse. SigX contributes to the composition of the cell membrane changing the membrane fluidity, antibiotic resistance (polymixin B and imipenem), iron uptake, virulence, motility and biofilm formation (Chevalier et al., 2018).

Genomic context conservation: When looking at ECF102, we observed that subgroup ECF102s1 contains homologs of CmpX, CfrX, and OprF in its genomic context; the conservation extends to position -3 with a CorA-like Mg2+ transporter and to -4 with an aldolase as in the case of original ECF102 (Staroń et al., 2009). The mechanosensitive ion channel is conserved in subgroups ECF102s2 and ECF102s5, which indicates a similar regulation as members of ECF102s1. Other conserved domains are a kinase/pyrophosphorylase (ECF102s1) and a pyruvate phosphate dikinase (ECF102s1).

Promoter motif conservation: Predicted target promoter motifs are not conserved, indicating lack of autoregulation. Interestingly, SigX is autoregulated, but the SigX binding motifs were not found upstream of its coding sequence, indicating the presence of an intermediate regulator induced by SigX (Chevalier et al., 2018).

Summary: Activation of ECF102 might be triggered by mechanic stimuli transmitted to the ECF via a mechanosensor and a soluble molecule that could act as AS factor, as revealed by the genetic context of original ECF120 (Staroń et al., 2009) and by characterization of SigX from P. aeruginosa (Chevalier et al., 2018). ECF102 is likely autoregulated via an intermediate transcription factor.


 


Basic information

Number of representative ECFs: 704

Number of non-redundant ECFs: 562

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 2.49%

Overrepresented phylum: Proteobacteria [75.43%]



Sample Neighborhood

Protein WP_053102199.1 of Assembly GCF_001267175.1 (Oblitimonas alkaliphila)


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
Extracytoplasmic function sigma factors in Pseudomonas aeruginosa. Biochimica et biophysica acta. Gene regulatory mechanisms 2018 S. Chevalier, E. Bouffartigues, A. Bazire, A. Tahrioui, R. Duchesne, D. Tortuel, O. Maillot, T. Clamens, N. Orange, M. Feuilloley, O. Lesouhaitier, A. Dufour, P. Cornelis PubMed: 29729420 ECF02, ECF102, ECF243, ECF293, ECF35
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