ECF16

ECF subgroups

ECF16s1 346 ECF16s2 108 ECF16s3 142 ECF16s4 18 ECF16s5 88 ECF16s6 66 ECF16s7 78 ECF16s8 99 ECF16s9 104 ECF16s10 47 ECF16s11 63 ECF16s12 41 ECF16s13 48 ECF16s14 16 ECF16s15 38 ECF16s16 31 ECF16s17 28 ECF16s18 48 ECF16s19 49 ECF16s20 29 ECF16s21 13 ECF16s22 20 ECF16s23 20 ECF16s24 17 ECF16s25 14 ECF16s26 10 ECF16s27 9

ECF proteins

General description: Members of ECF16 are present in Proteobacteria (96.5%), mainly Alphaproteobacteria, and ECF16s14 to Spirochaetes (2.67%). All the subgroups contain proteins with homology to original ECF16 (85.71%).

Anti-σ factor: Proteins from ECF16 are regulated by a putative AS factor with a conserved DUF1109 encoded in position +1. This protein contains six transmembrane helices (95.8%) and two conserved cysteine residues, as in the experimentally addressed AS factors of ECF16.

Genomic context conservation: Other conserved proteins in the genetic context of members of ECF16 are a DUF692-containing protein (ECF16s15 and ECF16s16) a DUF2282-containing protein (ECF16s15 and ECF16s16), a DoxX-domain containing protein (ECF16s15 and ECF16s16), an enoyl-CoA hydratase/isomerase (ECF16s2), a putative DNA-binding domain (ECF16s16), a cytochrome C biogenesis protein fused to a thioredoxin-like domain (ECF16s10), a AhpC/TSA family (ECF16s10), an outer membrane efflux protein (ECF16s2), a glutathione S-transferase (ECF16s19) and a protein from the AcrB/AcrD/AcrF family (ECF16s5).

Studied examples: Some members of ECF16, SigF from Caulobacter crescentus and Bradyrhizobium japonicum, have been functionally addressed. They are regulated by an AS factor (NrsF from C. crescentus and OsrA from B. japonicum) with six transmembrane helices and two cysteine residues facing the periplasm that are essential for sequestering their cognate ECF σ factor (Jogler et al., 2012).

Promoter motif conservation: Members of this group respond to heavy-metal stress (Jogler et al., 2012) or oxidative stress (Jogler et al., 2012). Both SigF from C. crescentus (ECF16s20) and B. japonicum (ECF16s2) self-induce their expression, and SigF from C. crescentus has the target promoter GTAACC-CGTA (Kohler et al., 2012; Masloboeva et al., 2012). These data do not agree with the predicted promoter elements (normally TTC in -35 and TAC or TAAC in -10).

Summary: Members of ECF16 are associated with DUF1109-containing AS factors with six transmembrane helices and conserved periplasmic cysteine residues. Their promoter motifs, although conserved, do not match experimental data. Members of ECF16 are involved in heavy metal and oxidative stress response.