ECF116 ECF proteins

General description: Members of ECF116 have homology to original ECF116 (25.24%) and belong to Firmicutes from the order Bacillales.

Anti-σ factors: Proteins from ECF116 contain AS factors in +1 as original ECF116 (Staroń et al., 2009). In subgroups ECF116s1 and ECF116s2, AS factors are fused to GerM-like sporulation and spore germination domains. By their function as periplasmic-sensing AS factors, proteins encoded in +1 of members of ECF116 contain one transmembrane helix in most of the cases (71.37%). Interestingly, some putative AS factors have a SpoIIP domain (4.38%), specially from subgroups ECF116s7 (100%), ECF116s14 (40%) and ECF116s12 (20%). SpoIIP is a cell wall hydrolase required for the dissolution of the septal cell wall (Chastanet & Losick, 2007). The N-terminus of these SpoIIP proteins aligns well with the rest of the putative AS factors of ECF116, indicating that they are indeed real AS factors.

Genomic context conservation: Other than the AS factor, subgroups ECF116s1 and ECF116s2 are associated with two-component systems typically encoded in -1 (sensor histidine kinase with PAS and HAMP domains) and -2 (response regulator fused to a transcriptional regulator) (frequency of response regulators: 73.77% and 91.12%, respectively; frequency of histidine kinase: 72.13% and 88.24%, respectively). Other conserved genes encoded in the context of members of ECF116 include a ferredoxin I (ECF116s1), a transcriptional regulator fused to a response regulator (ECF116s2), an ECF transporter (ECF116s2) and an RNA pseudouridylate synthase (ECF116s2).

Studied members: The only characterized protein of ECF116 is SigX (ECF116s1), from B. subtilis. SigX is involved in resistance against cationic antimicrobial peptides, and its function is overlapping with SigM and SigV (Cao & Helmann, 2004; Helmann, 2016; Mascher, Hachmann, & Helmann, 2007). SigX is regulated by the single transmembrane pass AS factor RsiX, encoded in +1 (Brutsche & Braun, 1997; Yoshimura, Asai, Sadaie, & Yoshikawa, 2004) and with an extracytoplasmic sporulation and spore germination domain, as predicted for members of ECF116s1. SigX is also regulated by glucose-induced acetylation of the DEAD-box of the RNA-helicase CshA, which induces its expression (Ogura & Asai, 2016).

Promoter motif conservation: Predicted target promoter motifs are conserved and share TGAAAC in -35 and a less conserved CGTCTAAT in -10. Indeed, the promoter motifs of SigX agree in -35 but not in -10 (Cao & Helmann, 2004).

Summary: In conclusion, ECF116 seems to be regulated by a membrane-bound AS factor encoded in +1, as in the case of SigX from B. subtilis. These AS factors are commonly fused to sporulation, spore germination and SpoIIP domains, which might indicate that members of ECF116 are involved in these processes. The conserved proteins encoded in the genetic context of ECF116 indicate a function in oxidative stress response. Nevertheless, the only characterized member of this group, SigX from B. subtilis, is involved in the resistance against cationic microbial peptides.


 


Basic information

Number of representative ECFs: 794

Number of non-redundant ECFs: 824

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.36%

Overrepresented family: Bacillaceae [84.38%]



Sample Neighborhood

Protein KQL19710.1 of Assembly GCA_001420595.1 (Bacillus solani)


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
SigX of Bacillus subtilis replaces the ECF sigma factor fecI of Escherichia coli and is inhibited by RsiX. Molecular & general genetics : MGG 1997 S. Brutsche, V. Braun PubMed: 9393439 ECF116
The Bacillus subtilis extracytoplasmic-function sigmaX factor regulates modification of the cell envelope and resistance to cationic antimicrobial peptides. Journal of bacteriology 2004 M. Cao, J. Helmann PubMed: 14762009 ECF116
Interaction of Bacillus subtilis extracytoplasmic function (ECF) sigma factors with the N-terminal regions of their potential anti-sigma factors. Microbiology (Reading, England) 2004 M. Yoshimura, K. Asai, Y. Sadaie, H. Yoshikawa PubMed: 14993308 ECF116
Engulfment during sporulation in Bacillus subtilis is governed by a multi-protein complex containing tandemly acting autolysins. Molecular microbiology 2007 A. Chastanet, R. Losick PubMed: 17376078 ECF116
Regulatory overlap and functional redundancy among Bacillus subtilis extracytoplasmic function sigma factors. Journal of bacteriology 2007 T. Mascher, A. Hachmann, J. Helmann PubMed: 17675383 ECF116, ECF245
The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Molecular microbiology 2009 A. StaroĊ„, 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
Glucose Induces ECF Sigma Factor Genes, <i>sigX</i> and <i>sigM</i>, Independent of Cognate Anti-sigma Factors through Acetylation of CshA in <i>Bacillus subtilis</i>. Frontiers in microbiology 2016 M. Ogura, K. Asai PubMed: 27965645 ECF116
Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope. Current opinion in microbiology 2016 J. Helmann PubMed: 26901131 ECF116, ECF30
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