ECF25 ECF proteins

General description: Two subgroups of ECF25, ECF25s1 and ECF25s11, have homology to original ECF25 (30.6%) and ECF20 (0.19%). ECF25 is one of the most diverse ECF groups in terms of taxonomic origin of the sequences. Proteins from ECF25 are present mainly in Cyanobaceria (ECF25s1 and ECF25s11, 50%), but also in Firmicutes (11.88%), Deltaproteobacteria (15.84%), Spirochaetes (ECF25s3, 2.97%), Fibrobacteres (ECF25s13, 0.5%), Nitrospirae (ECF25s12, 0.5%), Deinococcus-Thermus (ECF25s5, 6.44%), Chloroflexi (ECF25s17, ECF25s18 and ECF25s19, 6.44%), Gemmatimonadetes (ECF25s4, 1%), Ignavibacteriae (ECF25s9, 1%), Acidobacteria (1%) , Bacteroidetes (1.98%), and Calditrichaeota (0.5%).

Anti-σ factor: Similarly to original ECF25 (Staroń et al., 2009), proteins from ECF25 contain a putative AS factor in position +1, which are mainly single membrane-pass (74.75%). Nevertheless, variants with two or three transmembrane helices are possible. For instance, putative AS factors from Firmicutes order Thermoanaerobacterales (ECF25s14), and Chloroflexi (ECF25s16, ECF25s18, ECF25s19) contain two transmembrane helices, and proteins ECF25s20 contain three transmembrane helices. These putative AS factors typically contain a zinc-binding domain and/or a DUF4384 or a DUF4349.

Genomic context conservation: Other proteins conserved in the genetic neighborhood of ECF25 are a transglycosylase SLT from phages, T2SS, T3SS or T4SS (ECF25s2), a DNA polymerase family A with 5'-3' exonuclease activity involved in DNA repair (ECF25s2), a dephospho-CoA kinase (ECF25s2), a DUF1800 (ECF25s5) and an iron-dependent repressor (ECF25s5).

Studied members: The only member of ECF25 experimentally addressed, SigG from Nostoc punctiforme (ECF25s1) is in charge of the defense against cell wall stress arising from external sources (EDTA, heat, lysozyme, cold) or cellular differentiation (Bell, Lee, & Summers, 2017). SigG is regulated by a single membrane pass AS factor SapG.

Promoter motif conservation: The predicted target promoter motifs of ECF25s1 and ECF25s2 are GGAAC in -35 and GTC in -10. This promoter motif is similar to the original group ECF25 (Rhodius et al., 2013) and the binding motif of SigG in N. punctiforme (Bell et al., 2017).

Summary: ECF25 is regulated by AS factors located in +1 and seem to be involved in cell wall homeostasis.


 


Basic information

Number of representative ECFs: 535

Number of non-redundant ECFs: 536

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 6.16%

Overrepresented phylum: Cyanobacteria [35.70%]



Sample Neighborhood

Protein AFZ23384.1 of Assembly GCA_000317535.1 (Cylindrospermum stagnale PCC 7417)


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
Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Molecular systems biology 2013 V. Rhodius, T. Segall-Shapiro, B. Sharon, A. Ghodasara, E. Orlova, H. Tabakh, D. Burkhardt, K. Clancy, T. Peterson, C. Gross, C. Voigt PubMed: 24169405 ECF22, ECF27, ECF03, ECF21, ECF39, ECF25, ECF26, ECF42, ECF38, ECF14, ECF29, ECF33, ECF281, ECF290, ECF291
Characterization and in vivo regulon determination of an ECF sigma factor and its cognate anti-sigma factor in Nostoc punctiforme. Molecular microbiology 2017 N. Bell, J. Lee, M. Summers PubMed: 28105698 ECF25
Cookies help us deliver our services. By using our services, you agree to our use of cookies. Learn more