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).
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%]
|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||ECF114, ECF31, ECF22, ECF12, ECF27, ECF122, ECF121, ECF56, ECF03, ECF21, ECF23, ECF02, ECF41, ECF15, ECF107, ECF111, ECF39, ECF19, ECF25, ECF17, ECF26, ECF118, ECF11, ECF16, ECF42, ECF38, ECF103, ECF36, ECF28, ECF51, ECF115, ECF40, ECF14, ECF29, ECF123, ECF33, ECF102, ECF105, ECF106, ECF116, ECF130, ECF18, ECF235, ECF120, ECF239, ECF240, ECF242, ECF243, ECF249, ECF265, ECF271, ECF281, ECF285, ECF286, ECF289, ECF290, ECF291, ECF292, ECF293, ECF294, ECF30, ECF32, ECF43|
|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|