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.
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%]
|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|