ECF26 ECF proteins

General description: Proteins from ECF26 have homology to proteins from the original group ECF26 (94.35%). Group ECF26 is present in Proteobacteria (99.87%), mainly Alpha- and Betaproteobacteria, and Bacteroidetes (0.13%) from genus Bacteroides.

Anti-σ factor: Members of ECF26 contain a putative AS factor in position +1, as described for the original group ECF26 (Staroń et al., 2009). Putative AS factors of ECF26 contain one TM helix (85.83%) and a zinc finger.

Genomic context conservation: Position -1 is usually conserved, and its specific function depends on the position of the subgroup in the phylogenetic tree of ECF26; we could find catalases (ECF26s1), subtilases (ECF26s10, ECF26s4, ECF26s27 and ECF26s14), chitin-binding proteins (ECF26s2), enoyl-(acyl carrier protein) reductases involved in fatty acid biosynthesis (ECF26s12), and a conserved protein with a secreted repeat domain (ECF26s6, ECF26s16, ECF26s17 and ECF26s9). Other domains conserved in the context of members of ECF26 are the SsrA-system RNA-binding protein SmpB (ECF26s9), the domain of the inhibitor of apoptosis-promoting Bax1 involved in calcium leakage across the membrane (ECF26s7 and ECF26s22), the prokaryotic cytochrome b561 from the electron transport chain (ECF26s1), a LysR-like transcription regulator (ECF26s8), the small subunit of an acetolactate synthase (ECF26s6), the beta subunit of the nitrile hydratase (ECF26s6), an aldo/keto reductase (ECF26s6), an UvrD-like helicase (ECF26s6), a LysE type translocator (ECF26s6), a DUF1194-containing protein (ECF26s12), a 17 kDa outer membrane surface antigen (ECF26s12), a pyridoxine 5'-phosphate oxidase (ECF26s12), a histidine phosphatase (ECF26s12), a chorismate synthase  (ECF26s12), a DnaJ-like protein (ECF26s12), an ubiquitin from the RnfH family (ECF26s9), an IMP dehydrogenase/GMP reductase (ECF26s9) and a polyketide cyclase/dehydrase (ECF26s9).

Studied members: SigE from Starkella novella (ECF26s28) regulates the expression of sorAB, located in +2 and +3, which encode a soluble sulfite:cytochrome c oxidoreductase involved in thiosulfate oxidation independent of a membrane-associated thiosulfate-oxidizing complex during chemolithotrophy (Kappler, Friedrich, Trüper, & Dahl, 2001). The protein encoded downstream of SigE has been proposed to be a membrane-bound AS factor with a short cytoplasmic region (Kappler et al., 2001). PrtI (ECF26s1), present in Pseudomonas spp., regulates the temperature-dependent production of a protease in P. fluorescens WH6 (Okrent et al., 2014). Sinorhizobium meliloti encodes four members of ECF26, RpoE1 (ECF26s6), RpoE3 (ECF26s29), RpoE4 (ECF26s34) and RpoE6 (ECF26s14). RpoE1 and RpoE4 are involved in detoxification of disulfide compounds, and all are regulated by one transmembrane helix AS factors encoded in +1 (Lang et al., 2018)., and all are regulated by one transmembrane helix AS factors encoded in +1 (Lang et al., 2018).

Promoter motif conservation: The promoter motifs are diverse but usually follow the pattern GGAATAAA in -35 and GTT in -10 in agreement with previous reports (Rhodius et al., 2013). This conservation indicates the autoregulatory role of members of ECF26. Indeed, SigE from S. novella is self-induced, although its described promoter motif (Kappler et al., 2001) does not entirely agree with the predicted target promoter of ECF26. ECFs from group ECF26 in S. meliloti are autoregulated (except RpoE3), and their binding motif agrees with the predictions for ECF26, although the specific predicted target promoter motifs of their subgroups might vary (Lang et al., 2018).


 


Basic information

Number of representative ECFs: 3801

Number of non-redundant ECFs: 4141

Sequences with C-terminal extension: 0.75%

Sequences with N-terminal extension: 0.56%

Overrepresented phylum: Proteobacteria [99.58%]



Sample Neighborhood

Protein WP_048465985.1 of Assembly GCF_001043915.1 (Methylobacterium aquaticum)


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
Evidence for two pathways of thiosulfate oxidation in Starkeya novella (formerly Thiobacillus novellus). Archives of microbiology 2001 U. Kappler, C. Friedrich, H. Trüper, C. Dahl PubMed: 11285738 ECF26
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
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
Negative regulation of germination-arrest factor production in Pseudomonas fluorescens WH6 by a putative extracytoplasmic function sigma factor. Microbiology (Reading, England) 2014 R. Okrent, A. Halgren, M. Azevedo, J. Chang, D. Mills, M. Maselko, D. Armstrong, G. Banowetz, K. Trippe PubMed: 25165126 ECF26
Most <i>Sinorhizobium meliloti</i> Extracytoplasmic Function Sigma Factors Control Accessory Functions. mSphere 2018 C. Lang, M. Barnett, R. Fisher, L. Smith, M. Diodati, S. Long PubMed: 30305320 ECF26
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