ECF18

ECF subgroups

ECF18s1 299 ECF18s2 133 ECF18s3 197 ECF18s4 138 ECF18s5 185 ECF18s6 89 ECF18s7 138 ECF18s8 99 ECF18s9 110 ECF18s10 117 ECF18s11 140 ECF18s12 77 ECF18s13 60 ECF18s14 54 ECF18s15 60 ECF18s16 31 ECF18s17 72 ECF18s18 20 ECF18s19 34 ECF18s20 32 ECF18s21 34 ECF18s22 33 ECF18s23 41 ECF18s24 21 ECF18s25 25 ECF18s26 22 ECF18s27 23 ECF18s28 25 ECF18s29 20 ECF18s30 18 ECF18s31 20 ECF18s32 16 ECF18s33 15 ECF18s34 17 ECF18s35 18 ECF18s36 16 ECF18s37 12 ECF18s38 11 ECF18s39 12 ECF18s40 8 ECF18s41 5 ECF18s42 10 ECF18s43 13

ECF proteins

General description: This group is almost exclusively composed of proteins of original group ECF18 (95.33%). Proteins from ECF18 belong exclusively to Proteobacteria and have two highly conserved cysteine residues in the σ₄ domain.

Special features: Like ECF214, members of ECF18 are associated with RskA-like putative AS factors encoded in position +1. These putative AS factors contain one transmembrane helix (96.64%) and a putative zinc-finger in some cases.

Genomic context conservation: Other than the AS factor, the only conserved proteins encoded in the genetic context of several groups are a DUF4394-containing protein (-1 of ECF18s15 and ECF18s12) and a fasciclin domain-containing protein (-1 of ECF18s2 and +2 of ECF18s3 and ECF18s11). Faciclin domain-containing proteins are usually transmembrane or cell-surface proteins involved in cell adhesion (Moody & Williamson, 2013). Other conserved domains include a SelR domain (+2 of ECF18s11), a DUF4331 (+2 of ECF18s13), a DUF3455 (-1 of ECF18s1), a flagellar FliJ protein (-1 of ECF18s9), an ATP synthase (-2 of ECF18s9), a response regulator with a transcription regulator (-3 of ECF18s9), a mycolic acid cyclopropane synthetase (ECF18s14), a CheR methyltransferase (ECF18s9), a protein from FHIPEP family (ECF18s9), a haloacid dehalogenase (ECF18s11), an amino acid kinase (ECF18s11) and a 50S ribosome-binding GTPase (ECF18s11).

Studied members: RpoT from Pseudomonas putida (ECF18s1) is involved in resistance to organic solvents since it regulates an efflux pump (Duque et al., 2007). Another characterized member of this group, Rsph17029_3536 (ECF18s7) from Rhodobacter sphaeroides, induces the expression of the alanine synthetase hemT in response to two inputs. First, changes in reducing conditions sensed by the two cysteine residues in σ₄ domain release the ECF from the inhibition of it's AS factor, similarly as SigK from M. tuberculosis (Shukla et al., 2014); second, C₄-dicarboxylic acids inactivate its AS factor (Coulianos, 2018). The third characterized member of ECF18, LitS from Burkholderia multivorans (ECF18s6), is responsible for the light-dependent activation of genes for the biosynthesis cyclopropane-fatty-acyl-phospholipid and the photolyase PhrB2 for DNA repair (Sumi, Shiratori-Takano, Ueda, & Takano, 2018). Lastly, RpoP from C. metallidurans (ECF18s4) plays a role in nickel and cobalt resistance (Grosse et al., 2019).

Promoter motif conservation: In general, the target promoter motifs of ECF18 agree with the prediction for original ECF18 (Staroń et al., 2009), this is TGCATCTT in -35 and CGTA in -10. In general, the -35 elements are more conserved. Some promoter motifs correspond to the target of housekeeping σ factors (for example ECF18s24). The putative promoter motif of Rsph17029_3536 does not agree with the prediction for subgroup ECF18s7 since this ECF is not autoregulated (Coulianos, 2018). Nevertheless, genes regulated by LitS in B. multivorans contain the same motif as predicted for ECF18 (Sumi et al., 2018). This motif is not conserved in ECF18s6, the subgroup of LitS, indicating that even though LitS might not be autoregulated, the target promoter motif still matches the predictions of the most conserved motif of ECF18.

Summary: ECF18 has several regulatory layers - on the one hand it is regulated by a single transmembrane AS factor similar to RskA from M. tuberculosis and original ECF18 (Staroń et al., 2009); on the other hand the two cysteines in its σ₄ domain may form a disulfide bridge that unbinds under reducing conditions, releasing the ECF from its AS factor as in the case of SigK and its AS factor RskA (Shukla et al., 2014). Not all the ECFs from ECF18 are auto-induced.