ECF56 ECF proteins

General description: Proteins from ECF56 have homolog to original ECF56 (99.89%) and are present primary in Actinobacteria (96.15%), but also in Proteobacteria (2.86%), Chloroflexi (0.66%), Gemmatimonadetes (0.22%) and Acidobacteria (0.11%). Members of ECF56 contain a C-terminal extension of ~120 aa with a SnoaL-like domain (Pfam: snoaL_2). SnoaL is a small polyketide cyclase that catalyzes closure steps of the synthesis of polyketide antibiotics in Streptomyces spp. (Sultana et al., 2004). However, it has also been observed as part of ECF σ factors from original groups ECF56 and ECF41 (Huang et al., 2015; Staroń et al., 2009).

Genomic context conservation: The genomic context of members of ECF56 is not conserved beyond in the ECF in most of the cases. In ECF56s11 there is the N-terminal domain of a mycothiol maleylpyruvate isomerase (+1 of ECF56s11). The genetic context of ECF56s10 is conserved and includes an acyl-CoA dehydrogenase, a thiolase, an AMP-binding enzyme, a luciferase-like monooxygenase, a protein from the glyoxalase/bleomycin resistance protein/dioxygenase superfamily and a MlaE permease involved in maintaining the asymmetry of the outer membrane (Malinverni & Silhavy, 2009).

Studied members: One member of ECF56, SigG from M. tuberculosis (ECF56s1), is transcriptional induced by DNA damage from its RecA_NDp promoter as part of the RecA independent DNA damage response, which harnesses glyoxalases, type I estradiol dioxygenases and bleomycin resistance proteins to inactivate toxic compounds that damage DNA (Gaudion, Dawson, Davis, & Smollett, 2013). Indeed, one of these genes is part of the genetic context of ECF56s10.

Promoter motif conservation: The -10 promoter element predicted for original ECF56  (CGTC) (Huang et al., 2015) appears in ECF56s1 and ECF56s3, but the -35 element is subgroup-specific. The only described member of this group, SigG, is not autoregulated (Gaudion et al., 2013; Lee, Geiman, & Bishai, 2008). This might explain why the predicted target promoter motifs are not conserved and might indicate that most of the members of ECF56 are not autoregulated. However, the target promoter elements of SigG (CGATGA-GTCNNTA) (Gaudion et al., 2013) appear in some subgroups, suggesting that some members of ECF56 are autoregulated.

Summary: ECF56 might be regulated by a SnoaL C-terminal extension and, in the only described member of this group, it activates genes for the RecA-independent DNA damage response.


Basic information

Number of representative ECFs: 3052

Number of non-redundant ECFs: 3586

Sequences with C-terminal extension: 99.89%

Sequences with N-terminal extension: 3.85%

Overrepresented phylum: Actinobacteria [96.82%]



Sample Neighborhood

Protein WP_052311972.1 of Assembly GCF_000237145.1 (Actinoplanes sp. SE50/110)


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
Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation. The EMBO journal 2004 A. Sultana, P. Kallio, A. Jansson, J. Wang, J. Niemi, P. Mäntsälä, G. Schneider PubMed: 15071504 ECF56, ECF294
Role of stress response sigma factor SigG in Mycobacterium tuberculosis. Journal of bacteriology 2008 J. Lee, D. Geiman, W. Bishai PubMed: 18039768 ECF56
An ABC transport system that maintains lipid asymmetry in the gram-negative outer membrane. Proceedings of the National Academy of Sciences of the United States of America 2009 J. Malinverni, T. Silhavy PubMed: 19383799 ECF56
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
Characterisation of the Mycobacterium tuberculosis alternative sigma factor SigG: its operon and regulon. Tuberculosis (Edinburgh, Scotland) 2013 A. Gaudion, L. Dawson, E. Davis, K. Smollett PubMed: 23871545 ECF56
Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum. Journal of bacteriology 2015 X. Huang, D. Pinto, G. Fritz, T. Mascher PubMed: 25986905 ECF122, ECF56, ECF118, ECF128, ECF51, ECF52, ECF132, ECF53, ECF123, ECF125, ECF54, ECF130, ECF131, ECF218, ECF294, ECF48
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