ECF30 ECF proteins

General description: Proteins from ECF30 are homologous to original group ECF30 (94.68%) and are present in Firmicutes (99.86%).

Anti-σ factor and genomic context conservation: ECF30 is associated with single TMH AS factors with DUF4179 or DUF3298 fused or not to DUF4163 encoded in +1.

Genomic context conservation: The largest subgroup, ECF30s1, has an extensively conserved genetic context with the delta subunit of the DNA polymerase III in +2, the ribosomal protein S20 in +3, a metallo-beta-lactamase fused to a competence protein (DNA transport across the membrane) and a DUF4131, a germination protease and a cytidine and deoxycytidylate deaminase.

Studied members: Described members of ECF30 belong to ECF30s6 (SigV from Bacillus subtilis and SigV from Enterococcus faecalis), ECF30s11 (CsfT from Clostridium difficile), ECF30s48 (CsfV from Clostridium difficile) and ECF30s3 (SigW from Bacillus thuringiensis). SigV in critical for lysozyme resistance in both B. subtilis and E. feacalis due to its regulation of genes for the resistance to lysozyme, such as oatA, a gene located in +2 that encodes an O-acetylase that acetylates peptidoglycan (Lewerke, Kies, Müh, & Ellermeier, 2018; Woods & McBride, 2017). This protein is conserved in ECF30s6, where 80% of the proteins in ECF30s6 contain one acetyltransferase, but it is not conserved in other subgroups of ECF30. SigV from B. subtilis is activated when membrane proteins are delocalized (Omardien et al., 2018). The degradation of its AS factor, RsiV, occurs when it binds to lysozyme. This degradation is catalyzed by a signal peptidase as site-1 protease and RasP as site-2 protease (Helmann, 2016; Lewerke et al., 2018). The degradation is hampered in the absence of lysozyme by an amphipathic helix encoded in the position of DUF4179 (Lewerke et al., 2018). CsfT and CsfV play a role in antimicrobial resistance, and they are induced by bacitracin and lysozyme (Woods & McBride, 2017). The protease PrsW releases CsfT from its AS RsiT (Woods & McBride, 2017). In the case of CsfV, bacitracin binds directly to the AS factor RsiV (Woods & McBride, 2017). SigW from B. thuringiensis regulates the expression of the β-exotoxin I independently of the cry plasmid and it is encoded with its cognate AS factor (position +1) and EcfY (position +2), a negative regulator of the expression of SigW (Espinasse, Gohar, Lereclus, & Sanchis, 2004) conserved in the genetic context of members of ECF30s3.

Promoter motif conservation: Putative target promoters have small differences in different subgroups. They usually contain TGCAACA or TGAAACTTT in -35 and CGTC or CTCTAAT in -10. These motifs agree with the experimentally obtained auto-inducible target promoters of SigV in B. subtilis and SigW from B. thuringiensis (Espinasse et al., 2004; Helmann, 2016), and with original group ECF30 (Staroń et al., 2009).

Summary: ECF30 responds to cell wall damage caused by lysozyme or other antimicrobials. ECFs from ECF30 are regulated by AS factors that might be inactivated via RIP and protected from degradation by amphipathic helices since most of the AS factors contain a DUF4179, as in the case of some described members of this group. The final genes activated by the ECF might vary for different subgroups. ECFs from this group seem to auto-induce their expression.


 


Basic information

Number of representative ECFs: 2242

Number of non-redundant ECFs: 2840

Sequences with C-terminal extension: 1.30%

Sequences with N-terminal extension: 0.35%

Overrepresented phylum: Firmicutes [99.96%]



Sample Neighborhood

Protein WP_015594535.1 of Assembly GCF_000242895.2 (Bacillus sp. 1NLA3E)


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
An extracytoplasmic-function sigma factor is involved in a pathway controlling beta-exotoxin I production in Bacillus thuringiensis subsp. thuringiensis strain 407-1. Journal of bacteriology 2004 S. Espinasse, M. Gohar, D. Lereclus, V. Sanchis PubMed: 15126472 ECF30
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
Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope. Current opinion in microbiology 2016 J. Helmann PubMed: 26901131 ECF116, ECF30
Bacterial sensing: A putative amphipathic helix in RsiV is the switch for activating σV in response to lysozyme. PLoS genetics 2018 L. Lewerke, P. Kies, U. Müh, C. Ellermeier PubMed: 30020925 ECF30
Synthetic antimicrobial peptides delocalize membrane bound proteins thereby inducing a cell envelope stress response. Biochimica et biophysica acta. Biomembranes 2018 S. Omardien, J. Drijfhout, H. van Veen, S. Schachtschabel, M. Riool, L. Hamoen, S. Brul, S. Zaat PubMed: 29894683 ECF245, ECF30
Regulation of antimicrobial resistance by extracytoplasmic function (ECF) sigma factors. Microbes and infection 2019 E. Woods, S. McBride PubMed: 28153747 ECF02, ECF30
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