ECF291 ECF proteins

General description: Members of ECF291 have homology against proteins from original ECF20 (33.76%) and appear in Proteobacteria (98.45%) and Cyanobacteria (1.55%).

Studied members: One member of ECF291, CnrH from Cupriavidus metallidurans (ECF291s9), has been experimentally addressed. CnrH is encoded as part of a metal resistance determinant that includes cnrYHX and cnrCBAT operons (Grass, Fricke, & Nies, 2005). CnrH is sequestered by the AS factor CnrY, encoded in -2 from the ECF (Maillard et al., 2014). CnrY is a type II AS factor since it only contains two transmembrane helices that wrap around the ECF protein (Maillard et al., 2014). CnrX, the transmembrane heavy metal resistance protein encoded in -1, serves as the periplasmic sensor of Ni2+ or Co2+ (Trepreau et al., 2011). Upon sensing of these metals, CnrY in inhibited by an unknown mechanism and CnrH (Maillard et al., 2014). CnrH then directs the RNAP towards the cnrYXH promoter and the cnrCBA efflux pump, which secretes heavy metals (Grass et al., 2005).

Genomic context conservation: Indeed, this metal resistance determinant is conserved in our analysis of the genetic neighborhood of members of ECF291. Proteins from ECF291 encode a multicopper oxidase in +2, a copper resistance protein B precursor (CopB) in +2, a heavy metal resistance protein in -1. Members of ECF291s1 and ECF291s4 also encode CopC in –3 and CopD in -4. The Pfam domain of CnrY is only conserved in ECF291s9 and ECF291s12. Nevertheless, it is known that AS factors of this type have a variable sequence (Maillard et al., 2014) and the proteins in -2 of the rest of the groups contain one transmembrane helix (81.4%), have homology to AS factors from the original classification (Staroń et al., 2009) and align well with the CnrY-like AS factors from ECF291s9 and ECF291s12. Other conserved proteins include a LuxR transcriptional regulator fused to a response regulator receiver domain (ECF291s1), a TonB dependent receptor (ECF291s4) and an E1-E2 ATPase.

Promoter motif conservation: Predicted target promoter motifs are only conserved in some subgroups such as ECF291s1, where there is TCTCC in -35 and TACGCA in -10. These motifs do not agree with the original group ECF20 (Rhodius et al., 2013). CnrH regulates the transcription of its operon, cnrYXH, in C. metallidurans (Grass et al., 2005).

Summary: Members of ECF291 are in charge of heavy metal resistance since they upregulate the expression of an efflux complex synthesized in coding sequences from +1 to +4. Members of this group are regulated by single-transmembrane helix AS factors encoded in -2 with homology to CnrY from C. metallidurans and a transmembrane protein with a heavy metal resistance domain encoded in -1 with homology to CnrX in C. metallidurans, which serves as a periplasmic sensor of the Ni2+ or Co2+.

 


 


Basic information

Number of representative ECFs: 566

Number of non-redundant ECFs: 388

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.00%

Overrepresented phylum: Proteobacteria [95.23%]



Sample Neighborhood

Protein WP_007013474.1 of Assembly GCF_000767465.1 (Novosphingobium pentaromativorans US6-1)


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
Control of expression of a periplasmic nickel efflux pump by periplasmic nickel concentrations. Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 2005 G. Grass, B. Fricke, D. Nies PubMed: 16158236 ECF291
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
Structural basis for metal sensing by CnrX. Journal of molecular biology 2011 J. Trepreau, E. Girard, A. Maillard, E. de Rosny, I. Petit-Haertlein, R. Kahn, J. Covès PubMed: 21414325 ECF291
Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Molecular systems biology 2013 V. Rhodius, T. Segall-Shapiro, B. Sharon, A. Ghodasara, E. Orlova, H. Tabakh, D. Burkhardt, K. Clancy, T. Peterson, C. Gross, C. Voigt PubMed: 24169405 ECF22, ECF27, ECF03, ECF21, ECF39, ECF25, ECF26, ECF42, ECF38, ECF14, ECF29, ECF33, ECF281, ECF290, ECF291
The crystal structure of the anti-σ factor CnrY in complex with the σ factor CnrH shows a new structural class of anti-σ factors targeting extracytoplasmic function σ factors. Journal of molecular biology 2014 A. Maillard, E. Girard, W. Ziani, I. Petit-Härtlein, R. Kahn, J. Covès PubMed: 24727125 ECF291
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