ECF14 ECF proteins

General description: Proteins from ECF14 have homology to original ECF14 (81.93%), which appears in subgrups from Actinobacteria (93.53%). ECF14 is also present in Proteobacteria (3.07%) (ECF14s5, ECF14s7, ECF14s9) and Armatimonadetes (0.65%) (ECF14s10).

Anti-σ factors: Proteins from ECF14 are regulated by a ZAS located in +1. The conservation observed for the N-termini of this AS factors does not extend to the transmembrane domain. Putative AS factors of ECF14 are soluble (47%) or with one transmembrane-helix membrane (52.14%).

Genomic context conservation: Proteins from ECF14s1, ECF14s3, and ECF14s4 (Actinobacteria) encode a conserved O-methyltransferase in -1, in agreement with previous findings in original ECF14 (Huang et al., 2015). The following proteins are conserved in the genomic context of members of ECF14:
The protein mtt/Hcf106 is located in +2 and +3, which is involved in a sec-independent translocation mechanism. A NUBPL iron-transfer P-loop NTPase (PFAM: ParA) fused to an iron-sulfur cluster assembly protein usually located in +4, domains present in ATPases involved in plasmid partitioning in prokaryotes and to a protein required for the biogenesis and export of ribosomal subunits in eukaryotes (Pfam), and a trypsin-like peptidase usually in position +2. Subgroup ECF14s6 is located in one of the outermost leaves of the tree of ECF14 and, even though it contains a ZAS encoded in +1, it lacks the rest of the proteins conserved in the genetic neighborhoods of rest of the subgroups.

Studied members: Described proteins from ECF14 include SigE from M. tuberculosis (ECF14s1), M. marinum (ECF14s1), C. glutamicum (ECF14s2) and C. pseudotuberculosis (ECF14s2). These proteins are involved in oxidative stress response and defense against cell envelope stress caused by SDS, vancomycin, and lysozyme. They might also be involved in fatty acid degradation (M. tuberculosis (Huang et al., 2015)), starvation, survival in stationary phase and thermal stress (Huang et al., 2015). In SigE from M. tuberculosis, the Ser/Thr protein kinase PknB is required to phosphorylate the AS factor RseA, which is degraded as a consequence (Huang et al., 2015).

Promoter motif conservation: Putative target promoter motifs contain CTACTGG in -35, similarly as original ECF14 (Huang et al., 2015), and a non-conserved -10 with a G-tract in some cases.

Summary: ECF14 is involved in response to a wide range of stresses, including oxidative stress, starvation, thermal shock, and cell envelope stress. The characteristics of new ECF14 match original ECF14 (Huang et al., 2015), where the response mechanisms involve a ZAS encoded in +1 and an O-methyltransferase encoded in -1. Since the functions of ECF14 are so broad, it could be possible that ECF14 modifies basic cellular processes in an attempt to respond to the stress agent.


 


Basic information

Number of representative ECFs: 2093

Number of non-redundant ECFs: 2037

Sequences with C-terminal extension: 1.96%

Sequences with N-terminal extension: 29.06%

Overrepresented phylum: Actinobacteria [94.79%]



Sample Neighborhood

Protein WP_017541832.1 of Assembly GCF_000341205.1 (Nocardiopsis baichengensis YIM 90130)


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
A mycobacterial extracytoplasmic function sigma factor involved in survival following stress. Journal of bacteriology 1997 Q. Wu, D. Kong, K. Lam, R. Husson PubMed: 9139909 ECF14
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
RseA, the SigE specific anti-sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis. Molecular microbiology 2009 S. Barik, K. Sureka, P. Mukherjee, J. Basu, M. Kundu PubMed: 20025669 ECF14
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
σ(ECF) factors of gram-positive bacteria: a focus on Bacillus subtilis and the CMNR group. Virulence 2014 B. Souza, T. Castro, R. Carvalho, N. Seyffert, A. Silva, A. Miyoshi, V. Azevedo PubMed: 24921931 ECF41, ECF14
Comparative Sigma Factor-mRNA Levels in Mycobacterium marinum under Stress Conditions and during Host Infection. PloS one 2015 B. Pettersson, S. Das, P. Behra, H. Jordan, M. Ramesh, A. Mallick, K. Root, M. Cheramie, I. de la Cruz Melara, P. Small, S. Dasgupta, D. Ennis, L. Kirsebom PubMed: 26445268 ECF14
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