ECF52

ECF subgroups

ECF52s1 438 ECF52s2 290 ECF52s3 154 ECF52s4 104 ECF52s5 52 ECF52s6 46 ECF52s7 41 ECF52s8 27 ECF52s9 16 ECF52s10 17 ECF52s11 17 ECF52s12 8 ECF52s13 10 ECF52s14 11

ECF proteins

General description: All the proteins from ECF52 could be classified against original ECF52 and are present in Actinobacteria.

Special features: Members of ECF52 have one to two transmembrane helices (except ECF52s8) in a C-terminal extension of up to ~400 amino acids that contains a zinc-finger and, in some cases, a carbohydrate-binding domain such as NPCBM/NEW2 domain (ECF52s1) or ricin-type beta-trefoil lectin-like domain (ECF52s4). Possible sensing of carbohydrates by members of original ECF52 has been speculated (Huang et al., 2015), although in our results it seems that this function might only be present in some subgroups. The σ₄ domain is divergent in some members of ECF52.

Genomic context conservation: The genetic context conservation is only extended in ECF52s1 and ECF52s6. In ECF52s1, a conserved pyridine nucleotide-disulfide oxidoreductase is encoded in -2, potentially involved in oxidative stress response, a TetR repressor in -1, and a histidine kinase ATP-biding domain with a PAS fold and a SpoIIE domain in -3. In ECF52s6, ECFs are associated to a peptidase family S49, to a response regulator fused to a LytTr DNA-binding domain and a formamidopyrimidine-DNA glycosylase from the base excision repair system. The protease might release the ECF from the inhibition of the C-terminal extension and the whole signal transduction system could be responding to DNA damage.

Studied members: One member of ECF52, SCO4117 from Streptomyces coelicolor (ECF52s1), activates secondary metabolism, aerial mycelium differentiation, and sporulation (López-García, Yagüe, Gonzalez-Quiñonez, Rioseras, & Manteca, 2018).

Promoter motif conservation: The predicted target promoter motifs are not conserved among subgroups and, especially the -10 domains, have low information content. The promoter motif from the original group ECF52 (Huang et al., 2015) does not appear in any of the new subgroups. SCO4117 is self-induced, but its binding motifs differs from the one of its subgroup ECF52s1 and the original ECF52.

Summary: ECF52 inherits the same characteristics of original ECF52, except for the target promoter motifs, which could not be predicted. Some members of ECF52 might be involved in carbohydrate metabolism since their proteins contain a C-terminal extension periplasmic carbohydrate-binding domain. In general, the C-terminal extension of members of ECF52 could function as AS factors.