ECF42 ECF proteins

General description: ECF42 is homologous to original ECF42 (99.9%) and one of the largest groups, with 10,294 unique protein sequences. ECF42 is present in a broad range of bacteria, mainly in Actinobacteria (70.66%) and Proteobacteria (22.49%). Members of ECF42 contain a C-terminal extension of ~200 aa with a tetratricopeptide repeat. This C-terminus is essential for the activity of members of ECF42 (Liu, Pinto, & Mascher, 2018).

Genomic context conservation: As previously described, members of ECF42 encode a protein with a YCII-related domain in -1 (Staroń et al., 2009). Other conserved domains encoded in the genetic context of members of ECF42 include a MurR protein (ECF42s15), an acetylmuramoyl-L-alanine amidase (ECF42s15), a MraW methylase (ECF42s15), a penicillin-binding protein (ECF42s15), about two copies of a mycolic acid cyclopropane synthetase (ECF42s10) and a MaoC dehydratase (ECF42s10). Therefore, ECF42 seems to be involved in peptidoglycan synthesis and cell-wall stress resistance.

Studied members: A described members of ECF42, ECF-10 from Pseudomonas putida (ECF42s7), controls a small sigmulon of about twelve coding sequences that mediates resistance to antibiotics such as beta-lactams, sulfonamides, and chloramphenicol, and is involved in biofilm formation (Tettmann, Dötsch, Armant, Fjell, & Overhage, 2014). Both these functions are related to the overexpression of the efflux pump encoded by ttgGHI. Instead, the targets of the proteins encoded by sven_0747 (ECF42s2) and sven_4377 (ECF42s3) from Streptomyces venezuelae are exclusively the YCII genes sitting directly upstream of their coding sequences (Liu et al., 2018).

Promoter motif conservation: Promoter motifs of ECF42 share a TGTCGAT in -35 and CGTC in -10, in agreement with the original classification (Staroń et al., 2009) and the target sequences of sven_0747 and sven_4377 (Liu et al., 2018).

Summary: ECF42 has been expanded to over 10,000 unique sequences with the same C-terminal extension, genetic context conservation, and target promoter as original ECF42 (Staroń et al., 2009). Given the absence of putative AS factors in the genetic context of members of ECF42, the regulation could be carried out by the transmembrane helix, found to be essential for the activity of members of ECF42 (Liu et al., 2018).


 


Basic information

Number of representative ECFs: 8622

Number of non-redundant ECFs: 10294

Sequences with C-terminal extension: 99.90%

Sequences with N-terminal extension: 0.24%

Overrepresented phylum: Actinobacteria [65.75%]



Sample Neighborhood

Protein WP_020406937.1 of Assembly GCF_000376785.1 (Hahella ganghwensis DSM 17046)


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 tetratricopeptide repeat: a structural motif mediating protein-protein interactions. BioEssays : news and reviews in molecular, cellular and developmental biology 1999 G. Blatch, M. Lässle PubMed: 10517866 ECF42
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
Knockout of extracytoplasmic function sigma factor ECF-10 affects stress resistance and biofilm formation in Pseudomonas putida KT2440. Applied and environmental microbiology 2014 B. Tettmann, A. Dötsch, O. Armant, C. Fjell, J. Overhage PubMed: 24907323 ECF42
Characterization of the Widely Distributed Novel ECF42 Group of Extracytoplasmic Function σ Factors in Streptomyces venezuelae. Journal of bacteriology 2018 Q. Liu, D. Pinto, T. Mascher PubMed: 30126941 ECF42
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