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.
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%]
|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|