ECF18 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.


 


Basic information

Number of representative ECFs: 2520

Number of non-redundant ECFs: 2826

Sequences with C-terminal extension: 0.04%

Sequences with N-terminal extension: 8.85%

Overrepresented phylum: Proteobacteria [99.80%]



Sample Neighborhood

Protein WP_012205632.1 of Assembly GCF_000018665.1 (Delftia acidovorans SPH-1)


Promoter Motif



Figures

Protein sequence length distribution

Gene neighbourhood conservation analysis


Overall Pfam domain distribution: Cumulative frequency of Pfam domains across the genetic neighborhoods. Frequency is expressed as number of Pfam domains per ECF sigma factor. Only domains present in more than 75% of the neighborhoods are shown. Genetic neighborhoods contain the proteins encoded in ±10 from the ECF coding sequence. Only the non-overlapping, highest scoring domains are considered positive. If a protein contains several copies of a domain, only one instance is further considered. In order to avoid sequence bias, only proteins from assemblies defined as "representative" or "reference" by NCBI are included (see https://www.ncbi.nlm.nih.gov/assembly/help/).
Pfam domain distribution per position: Frequency of Pfam domain architectures in the proteins encoded in ±10 (x-axis) from the ECF coding sequences. Frequency is expressed as number of times a certain domain architecture appears per ECF sigma factor. Only the highest scoring domains with no position overlap are considered in the domain architectures. Note that the order of the Pfam domains in domain architectures may differ from their name. When a protein contains several copies of a domain, only one instance is further considered. Only domain architectures present in more than 20% of the proteins encoded in any position are shown. In order to avoid sequence bias, only proteins from assemblies defined as "representative" or "reference" by NCBI are included (see https://www.ncbi.nlm.nih.gov/assembly/help/).

Related publications

Title Journal Year Authors PubMed ECF groups
The RpoT regulon of Pseudomonas putida DOT-T1E and its role in stress endurance against solvents. Journal of bacteriology 2006 E. Duque, J. Rodríguez-Herva, J. de la Torre, P. Domínguez-Cuevas, J. Muñoz-Rojas, J. Ramos PubMed: 17071759 ECF18
The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Molecular microbiology 2009 A. Staroń, H. Sofia, S. Dietrich, L. Ulrich, H. Liesegang, T. Mascher PubMed: 19737356 ECF103, ECF21, ECF123, ECF51, ECF39, ECF281, ECF102, ECF130, ECF122, ECF291, ECF15, ECF242, ECF22, ECF285, ECF106, ECF27, ECF31, ECF240, ECF114, ECF16, ECF38, ECF41, ECF105, ECF116, ECF111, ECF03, ECF239, ECF42, ECF294, ECF17, ECF11, ECF29, ECF235, ECF293, ECF118, ECF265, ECF30, ECF23, ECF14, ECF249, ECF18, ECF115, ECF290, ECF25, ECF121, ECF02, ECF120, ECF289, ECF28, ECF243, ECF19, ECF43, ECF107, ECF12, ECF32, ECF36, ECF292, ECF286, ECF271, ECF26, ECF40, ECF56, ECF33
Structure and function of a bacterial Fasciclin I Domain Protein elucidates function of related cell adhesion proteins such as TGFBIp and periostin. FEBS open bio 2013 R. Moody, M. Williamson PubMed: 23772377 ECF18
Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA σ-anti-σ complex. Acta crystallographica. Section D, Biological crystallography 2014 J. Shukla, R. Gupta, K. Thakur, R. Gokhale, B. Gopal PubMed: 24699647 ECF57, ECF19, ECF18, ECF288
Role and Function of Class III LitR, a Photosensor Homolog from Burkholderia multivorans. Journal of bacteriology 2018 S. Sumi, H. Shiratori-Takano, K. Ueda, H. Takano PubMed: 30249707 ECF18
The third pillar of metal homeostasis in Cupriavidus metallidurans CH34: preferences are controlled by extracytoplasmic function sigma factors. Metallomics : integrated biometal science 2019 C. Große, A. Poehlein, K. Blank, C. Schwarzenberger, G. Schleuder, M. Herzberg, D. Nies PubMed: 30681120 ECF18, ECF290
Cookies help us deliver our services. By using our services, you agree to our use of cookies. Learn more