ECF15 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.


 


Basic information

Number of representative ECFs: 2538

Number of non-redundant ECFs: 2108

Sequences with C-terminal extension: 1.52%

Sequences with N-terminal extension: 14.47%

Overrepresented phylum: Proteobacteria [99.41%]



Sample Neighborhood

Protein AKI00422.1 of Assembly GCA_001011155.1 (Hoeflea sp. IMCC20628)


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
An extracytoplasmic function sigma factor acts as a general stress response regulator in Sinorhizobium meliloti. Journal of bacteriology 2007 L. Sauviac, H. Philippe, K. Phok, C. Bruand PubMed: 17400745 ECF15
The ECF sigma factor sigma(T) is involved in osmotic and oxidative stress responses in Caulobacter crescentus. Molecular microbiology 2007 C. Alvarez-Martinez, R. Lourenço, R. Baldini, M. Laub, S. Gomes PubMed: 17986185 ECF15
Sigma factor mimicry involved in regulation of general stress response. Proceedings of the National Academy of Sciences of the United States of America 2009 A. Francez-Charlot, J. Frunzke, C. Reichen, J. Ebneter, B. Gourion, J. Vorholt PubMed: 19218445 ECF15
Role of the extracytoplasmic function sigma factor RpoE4 in oxidative and osmotic stress responses in Rhizobium etli. Journal of bacteriology 2009 J. Martínez-Salazar, E. Salazar, S. Encarnación, M. Ramírez-Romero, J. Rivera PubMed: 19376852 ECF15
The PhyR-sigma(EcfG) signalling cascade is involved in stress response and symbiotic efficiency in Bradyrhizobium japonicum. Molecular microbiology 2009 B. Gourion, S. Sulser, J. Frunzke, A. Francez-Charlot, P. Stiefel, G. Pessi, J. Vorholt, H. Fischer PubMed: 19555458 ECF15
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 membrane component SecDF that enhances protein export. Nature 2011 T. Tsukazaki, H. Mori, Y. Echizen, R. Ishitani, S. Fukai, T. Tanaka, A. Perederina, D. Vassylyev, T. Kohno, A. Maturana, K. Ito, O. Nureki PubMed: 21562494 ECF15
Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria. Proceedings of the National Academy of Sciences of the United States of America 2012 S. Campagne, F. Damberger, A. Kaczmarczyk, A. Francez-Charlot, F. Allain, J. Vorholt PubMed: 22550171 ECF15
Rhodopseudomonas palustris CGA010 Proteome Implicates Extracytoplasmic Function Sigma Factor in Stress Response. Journal of proteome research 2015 M. Allen, G. Hurst, T. Lu, L. Perry, C. Pan, P. Lankford, D. Pelletier PubMed: 25853567 ECF15
The PhyR homolog RSP_1274 of Rhodobacter sphaeroides is involved in defense of membrane stress and has a moderate effect on RpoE (RSP_1092) activity. BMC microbiology 2018 Q. Li, T. Peng, G. Klug PubMed: 29486719 ECF15
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