ECF12 ECF proteins

General description: Members of ECF12 are homologous to proteins from original ECF12 (86.15%) and ECF26 (3.5%). Members of ECF12 are mainly present in Actinobacteria (88.76%), but also in Bacteroidetes (6.91%),  Proteobacteria (1.75%), Chlorobi (1.24%), Ignavibacteriae (0.31%), Planctomycetes (0.21%), Firmicutes (0.10%) and Calditrichaeota (0.10%).

Regulation: As in the original group ECF12 (Staroń et al., 2009), the genetic neighborhood of most of the members of new ECF12 contain a putative AS factor in position +1. These putative AS factors contain a zinc-finger and are soluble (96.05%), except in the case of subgroup ECF12s19, where the putative AS factors are transmembrane.

Special features: No putative AS factor is present for some of the smaller subgroups, which could be encoded somewhere else in the genome. One of these subgroups is ECF12s9. It contains an ECF from ECF12s2 in +1 in three out of four proteins from representative genomes. Interestingly, none of the ECFs from ECF12s9 has a putative AS associated, they are transcribed convergently, and their 3’ ends are overlapping, which could indicate that these ECFs are mutually exclusive and only one can be expressed at a time. Regulation by transcriptional interference caused by convergent, overlapping transcripts has been shown to resolve in RNAP collision, truncated RNA (Shearwin, Callen, & Egan, 2005) and was used to generate bistable switch that responds to a signaling molecule in Streptomyces coelicolor (Chatterjee et al., 2011). If this is a regulatory mechanism for members of ECF12s9 and some members of ECF12s2, it remains unclear what triggers the switch towards the opposite ECF and what are the differences in the response mediated by these two ECFs, given their high sequence similarity. Subgroup ECF12s22, with a single sequence from representative/reference genomes, contains a σ factor in position +1 and lacks an evident putative AS factor. Nevertheless, the two σ factors are encoded in tandem, non-overlapping configuration, discarding a transcriptional interference mechanism in this subgroup.

Genomic context conservation: Other domains conserved in some ECF12 groups are a guanylate kinase (+2 of ECF12s6), a cytidylyltransferase-like protein (ECF12s6) and an EPSP synthase (ECF12s1).

Studied members: One of the members of ECF12, σR from Streptomyces coelicolor (ECF12s1), responds to thiol-oxidative stress by inducing thioredoxin, mycothiol metabolism, proteases, among others (Kim, Hahn, Cho, Cho, & Roe, 2009). σR is activated when its AS factor, RsrA, forms disulfide bonds within its zinc-binding domain under exposure to oxidation agents and disulfide stress (Paget et al., 2001; Zdanowski et al., 2006). Upon stress exposure, σR induces its expression from an earlier promoter that produces a variant of σR ) 55aa longer and more prone to be degraded by the also upregulated ClpP1/P2 proteases (Kim et al., 2009). It is not clear whether this promoter-shift mechanism is present in other members of ECF12.

SigH from M. tuberculosis (ECF12s1) is induced by heat, oxidative and nitric oxide stresses and it activates the expression of a broad set of genes involved in DNA repair, sulfur metabolism and translation recovery (Sharp et al., 2016). The AS factor of SigH, RshA, is located in position +2, coordinates a [2Fe-2S] cluster and binds SigH using salt bridges (Kumar et al., 2012). Apart from oxidants, RshA is also inhibited by the eukaryotic-like Ser/Thr kinase PnkB (Park, Kang, & Husson, 2008), which illustrates the integration of different sensing pathways in bacteria. Members of ECF12s1 do not usually contain AS factors in position +2.

Promoter motif conservation: SigH from C. glutamicum (ECF12s2) binds to the same motif a the prediction for its subgroup – GGAAT in -35 and GTT in -10 (Pátek et al., 2018). The target promoter of SigH (GGAAYR-(N17-18)-GTT) (Sharp et al., 2016) does not match the motif observed for subgroup ECF12s1, but ECF12s2. In general, predicted promoter motifs for the subgroups of  ECF12 are not conserved.

Summary: Members of ECF12 are related to oxidative and disulfide stress response. The soluble AS factors associated to this group coordinate metals that serve to sense oxidative stress and release the inhibition over the ECF. The nature of the metal might differ, even within the same subgroup. Moreover, the putative AS factor is lacking in some subgroups, raising the possibility of another regulatory mechanism such as transcriptional interference in subgroup ECF12s9. Nevertheless, it is possible that their AS factor is encoded somewhere else in the genome.


 


Basic information

Number of representative ECFs: 3293

Number of non-redundant ECFs: 3228

Sequences with C-terminal extension: 1.27%

Sequences with N-terminal extension: 27.91%

Overrepresented phylum: Actinobacteria [89.68%]



Sample Neighborhood

Protein WP_011895524.1 of Assembly GCF_000184435.1 (Mycolicibacterium gilvum Spyr1)


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
Regulation of motility behavior in Myxococcus xanthus may require an extracytoplasmic-function sigma factor. Journal of bacteriology 1998 M. Ward, H. Lew, A. Treuner-Lange, D. Zusman PubMed: 9791117 ECF12
Mutational analysis of RsrA, a zinc-binding anti-sigma factor with a thiol-disulphide redox switch. Molecular microbiology 2001 M. Paget, J. Bae, M. Hahn, W. Li, C. Kleanthous, J. Roe, M. Buttner PubMed: 11251822 ECF12
Transcriptional interference--a crash course. Trends in genetics : TIG 2005 K. Shearwin, B. Callen, J. Egan PubMed: 15922833 ECF12
Assignment of the zinc ligands in RsrA, a redox-sensing ZAS protein from Streptomyces coelicolor. Biochemistry 2006 K. Zdanowski, P. Doughty, P. Jakimowicz, L. O'Hara, M. Buttner, M. Paget, C. Kleanthous PubMed: 16819828 ECF12, ECF11
Regulation of the SigH stress response regulon by an essential protein kinase in Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America 2008 S. Park, C. Kang, R. Husson PubMed: 18728196 ECF12
Positive and negative feedback regulatory loops of thiol-oxidative stress response mediated by an unstable isoform of sigmaR in actinomycetes. Molecular microbiology 2009 M. Kim, M. Hahn, Y. Cho, S. Cho, J. Roe PubMed: 19682253 ECF12
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
Convergent transcription in the butyrolactone regulon in Streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis. PloS one 2011 A. Chatterjee, L. Drews, S. Mehra, E. Takano, Y. Kaznessis, W. Hu PubMed: 21765930 ECF12
Interaction of Mycobacterium tuberculosis RshA and SigH is mediated by salt bridges. PloS one 2012 S. Kumar, S. Badireddy, K. Pal, S. Sharma, C. Arora, S. Garg, M. Alam, P. Agrawal, G. Anand, K. Swaminathan PubMed: 22937074 ECF12
Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses. PloS one 2016 J. Sharp, A. Singh, S. Park, A. Lyubetskaya, M. Peterson, A. Gomes, L. Potluri, S. Raman, J. Galagan, R. Husson PubMed: 27003599 ECF12
The anti-sigma factor RsrA responds to oxidative stress by reburying its hydrophobic core. Nature communications 2016 K. Rajasekar, K. Zdanowski, J. Yan, J. Hopper, M. Francis, C. Seepersad, C. Sharp, L. Pecqueur, J. Werner, C. Robinson, S. Mohammed, J. Potts, C. Kleanthous PubMed: 27432510 ECF12
Overlap of Promoter Recognition Specificity of Stress Response Sigma Factors SigD and SigH in <i>Corynebacterium glutamicum</i> ATCC 13032. Frontiers in microbiology 2018 H. Dostálová, T. Busche, J. Holátko, L. Rucká, V. Štěpánek, I. Barvík, J. Nešvera, J. Kalinowski, M. Pátek PubMed: 30687273 ECF12, ECF40
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