ECF116

ECF subgroups

ECF116s1 243 ECF116s2 178 ECF116s3 97 ECF116s4 51 ECF116s5 21 ECF116s6 20 ECF116s7 22 ECF116s8 15 ECF116s9 13 ECF116s10 14 ECF116s11 19 ECF116s12 13 ECF116s13 16 ECF116s14 12 ECF116s15 13 ECF116s16 15 ECF116s17 14 ECF116s18 13 ECF116s19 5

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.