ECF17 ECF proteins

General description: Group ECF17 is composed of 85.82% of proteins with homology to the original group ECF17. All the proteins are present in Actinobacteria.

Anti-σ factors: Members of ECF17 might be regulated by putative AS factors with a zinc-finger and one transmembrane helix (83.33%). Putative AS factors are encoded in position +1, except in ECF17s1, where it is located mainly in position +2. Subgroups ECF17s18 and ECF17s19 lack of putative AS factors in their genetic context. Indeed, previous studies identified this protein as an AS factor previous studies (Gordon et al., 2008; Hahn, Raman, Anaya, & Husson, 2005; Staroń et al., 2009).

Genomic context conservation: Aside from the AS factor, the remaining conserved proteins are subgroup-specific. ECF17s1 contains a conserved protein with a bacterial capsule synthesis protein PGA_cap (Pfam: PGA_cap) in position -1, a conserved formamidopyrimidine-DNA glycosylase, a universal stress protein, and a sortase. ECF17s2 and ECF17s11 contain a conserved protein from the Major Facilitator Superfamily (MFS). Consequent with this conserved genomic context, the only described member of ECF17s2, SigU from Streptomyces coelicolor is involved in response to envelope stress and morphological differentiation (Xu & Min, 2011). ECF17s4 contains a conserved metallopeptidase from family M24 in position -1, an adenylate kinase in position -2, a SecY translocase in position -3 and ~2 copies of a leucine carboxyl methyltransferase. Lastly, ECF17s11 encodes a secreted protein in position -1 and members of ECF17s18 encode a conserved N-acetylmuramoyl-L-alanine amidase in their genetic context.

Studied members: The genetic context of ECF17s4 agrees with the function of its only characterized member, SigL from M. tuberculosis, which is involved in the synthesis of envelope lipids, extracytoplasmic protein modification, and pathogenesis, although none of the genes in its genetic neighborhood are regulated by SigL (Jogler et al., 2012).

Promoter motif conservation: Promoter motifs are conserved, with the consensus TGAACC in -35 and CGT in -10, although other variations are possible in some subgroups. These consensus promoter motifs agree with reports of original ECF17 (Staroń et al., 2009) and with experimental data from SigL (Hahn, Raman, Anaya, & Husson, 2005) and SigU (Gordon et al., 2008).

Summary: ECF17 is regulated by anti-σ factors. The conservation of the promoter motifs indicates that it auto-induces its expression in most of the cases. Indeed, this is the case for SigL (Hahn et al., 2005) and SigU (Gordon et al., 2008). It is possible that proteases encoded near ECFs from ECF17 are in charge of the degradation of their cognate anti-σ factor. The functions of members of ECF17 are diverse, and it does seem to be the main factor that contributes to their sequence similarity.


 


Basic information

Number of representative ECFs: 2635

Number of non-redundant ECFs: 2328

Sequences with C-terminal extension: 0.30%

Sequences with N-terminal extension: 5.24%

Overrepresented phylum: Actinobacteria [99.96%]



Sample Neighborhood

Protein AFC45517.1 of Assembly GCA_000277125.1 (Mycobacterium intracellulare ATCC 13950)


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 Mycobacterium tuberculosis extracytoplasmic-function sigma factor SigL regulates polyketide synthases and secreted or membrane proteins and is required for virulence. Journal of bacteriology 2005 M. Hahn, S. Raman, M. Anaya, R. Husson PubMed: 16199577 ECF17
Secreted-protein response to sigmaU activity in Streptomyces coelicolor. Journal of bacteriology 2007 N. Gordon, G. Ottaviano, S. Connell, G. Tobkin, C. Son, S. Shterental, A. Gehring PubMed: 18065550 ECF17
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
Structural and biochemical bases for the redox sensitivity of Mycobacterium tuberculosis RslA. Journal of molecular biology 2010 K. Thakur, T. Praveena, B. Gopal PubMed: 20184899 ECF17, ECF36
Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of σ-factor activity by proteolysis. Nucleic acids research 2013 R. Jaiswal, T. Prabha, G. Manjeera, B. Gopal PubMed: 23314154 ECF17, ECF40
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