ECF15

ECF subgroups

ECF15s1 1759 ECF15s2 205 ECF15s3 176 ECF15s4 61 ECF15s5 61 ECF15s6 48 ECF15s7 59 ECF15s8 41 ECF15s9 41 ECF15s10 33 ECF15s11 20 ECF15s12 18 ECF15s13 15 ECF15s14 1

ECF proteins

General description: Group ECF15 is mainly composed by members of original ECF15 (88.52%) with some members of original ECF26 (1.76%), and it is present in Proteobacteria (99.86%) and Cyanobacteria (0.14%). Original ECF15 is known to be regulated by a partner-switching mechanism (Sultana et al., 2004). The first identified example of partner-switching regulation was EcfG1 from Methylobactrium extorquens (Huang et al., 2015; Staroń et al., 2009). EcfG1 is an ECF negatively regulated by the anti-σ factor NepR. Apart from NepR, PhyR, a protein containing a receiver domain and a σ-like region, is encoded in the genomic context of EcfG1. PhyR acts as the response regulator of a two-component system and as an anti-anti-σ factor (AAS) under inducing conditions, titrating NepR and triggering the release of EcfG1 into its active form (Campagne et al., 2012; Francez-Charlot et al., 2009).

Special features: Indeed, we found that σ₂ domain (1.29 per ECF), σ₄ domain (1.91 per ECF) and the receiver domain of a response regulator (1.16 per ECF, usually in position -1) were conserved in the genetic context of members of ECF15. Moreover, histidine kinases are also in position +2 of ECF15s5 and ECF15s6, although when looking at all the members of ECF15 we only found an average of 0.56 histidine kinases per ECF. This suggests that in some instances the histidine kinase might be encoded somewhere else in the genome, as in the case of EcfG1 from Methylobactrium extorquens (Gaudion, Dawson, Davis, & Smollett, 2013), RpoE from Bradyrhizobium japonicum, RpoE from Rhodobacter sphaeroides (Huang et al., 2015) and RpoE2 from Sinorhizobium meliloti (Gaudion et al., 2013; Lee, Geiman, & Bishai, 2008). The anti-σ factors could be identified through a BLAST search using as a library the AS factors from the original ECF classification (Gaudion et al., 2013). Their position ranges from -2 to +2 in subgroups ECF15s1, ECF15s4, ECF15s5, ECF15s7 and ECF15s9. AS factors from ECF15 do not bear any PFAM domain and are cytoplasmic (90.32%).

Genomic context conservation: Genetic context conservation in ECF15s4 and ECF15s5, which share genetic context since they are transcribed consecutively, extends to a SecD/SecF GG motif and a protein-export membrane protein domain (PFAM: Sec_GG and SecD_SecF), which corresponds to the subunit of the SecDFYajC complex involved in the proton motive force-dependent steps of proteins translocation (Wecke et al., 2012). Subgroup ECF15s7 contains a conserved superoxide dismutase, in charge of detoxifying superoxide.

Studied members: Characterized members of ECF15 include SigT from Caulobacter crescentus (Goutam, Gupta, & Gopal, 2017), RpoE from Rhodobacter sphaeroides (Staroń et al., 2009), EcfG1 from Methylobactrium extorquens (Lee et al., 2012), RpoE from Bradyrhizobium japonicum (Souza et al., 2014), RpoE4 from Rhizobium etli (Hu, Kendall, Stoker, & Coates, 2004), RpoE2 from Sinorhizobium meliloti (Wecke et al., 2012) and EcfT from Rhodopseudomonas palustris (Goutam et al., 2017). Members of ECF15 are the main general stress response σ factor in most Alphaproteobacteria (Allen et al., 2015; Alvarez-Martinez et al., 2007; Francez-Charlot et al., 2009; Sauviac et al., 2007). However, in some cases, ECF15 members have more specialized functions in defense against membrane stress (Shukla et al., 2014).

Promoter motif conservation: The target promoters of members of ECF15 are conserved. The -35 region is usually GGAAC and the -10 CATT, which fits experimental data (Allen et al., 2015; Alvarez-Martinez et al., 2007; Gourion et al., 2009; Sauviac et al., 2007).

Summary: In summary, similarily to ECFs from original ECF15 (Jogler et al., 2012), members of ECF15 are regulated by parter-switching involving a response regulator that, when activated by its partner histidine kinase, acts as AAS factor, titrating the AS factor and releasing the active form of the ECF.