ECF121 ECF proteins

General description: Members of ECF121 share homology to the original group ECF121 (73.36%) and are present in Actinobacteria (100%). Members of ECF121 are associated with subgroup-dependent N-terminal extensions, whose length ranges from ~30 aa in ECF121s5 to ~130 aa in ECF121s5.

Anti-σ factor: Members of ECF121 might be regulated by a putative AS factor encoded in position +1 (except ECF121s7). The N-terminal part of these putative AS factors is conserved. These AS factors contain one transmembrane helix (27.17% of the ECFs according to TopCons, ~100% when looking at the MSA.)

Genomic context conservation: The conservation of the genetic context of members of ECF121 is extensive and includes an acyltransferase (ECF121s3, ECF121s5 and ECF121s2, +2 of ECF121s1 and ECF121s4), a NAD dependent epimerase/dehydratase (+3 of ECF121s1 and ECF121s4), a protein with an helix-turn-helix domain (ECF121s2, ECF121s3, ECF121s5 and +4 of ECF121s1 and ECF121s4), a haloacid dehalogenase-like hydrolase (-1 of ECF121s4 and ECF121s1, +2 of ECF121s2 and ECF121s5), an antibiotic biosynthesis monooxygenase (-1 of ECF121s5), an AMP-binding enzyme (-1 of ECF121s2, -2 of ECF121s4), a glutaredoxin-like domain (DUF836) (-3 of ECF121s4, -2 of ECF121s3, ECF121s1, ECF121s5 and ECF121s2), a putative DNA-binding protein with a CoA binding domain (ECF121s3, -3 of ECF121s1 and ECF121s5), a glutamyl-tRNAGlu reductase (ECF121s2, ECF121s3, ECF121s4, -4 of ECF121s1 and ECF121s5), a porphobilinogen deaminase (hemC) (-5 of ECF121s1 and ECF121s5), an uroporphyrinogen-III synthase HemD (ECF121s2, ECF121s3, ECF121s4, -6 of ECF121s1 and ECF121s5), a delta-aminolevulinic acid dehydratase (HemB) (ECF121s1, ECF121s2, ECF121s3 and -7 of ECF121s5), the N-terminal domain of a bifunctional DNA primase/polymerase (-8 of ECF121s5), a pyrroline-5-carboxylate reductase (ECF121s4 and ECF121s2), a phosphatase (ECF121s1 and ECF121s5), a histone deacetylase (ECF121s1 and ECF121s5), a NAD dependent epimerase/dehydratase (ECF121s5).

Studied members: One member of ECF121, BldN from Streptomyces coelicolor and Streptomyces venezuelae (ECF121s1), has been functionally addressed. In S. venezuelae, BldN regulates aerial mycelium formation as it activates the transcription of chaplin and rodlin genes (Bibb & Buttner, 2003). Moreover, BldN induces the transcription of its single-pass transmembrane AS factor RsbN, which is encoded in +1 and consists in three helices structurally distinct for other AS domain, the so-called class III ASD (Schumacher et al., 2018). BldN from S. coelicolor contains a ~86 amino acid N-terminal extension proteolytically processed into a mature BldN (Bibb & Buttner, 2003). The processing of the pro-BldN seems to be typical of members of ECF121 since all of them contain an N-terminal extension.

Promoter motif conservation: Predicted target promoter motifs of members of ECF121 are not conserved among different subgroups. Indeed, target promoter motifs of S. venezuelae’s BldN differs, and it is not autoregulated (Staroń et al., 2009).

Summary: Members of ECF112 are regulated by an AS encoded in +1 and by an N-terminal extension, as in the case of BldN from S. coelicolor (Liu, Pinto, & Mascher, 2018). Moreover, members of ECF121 contain an extensively conserved genetic context, which encodes proteins for the synthesis of protoporphyrin-IX.


 


Basic information

Number of representative ECFs: 1032

Number of non-redundant ECFs: 882

Sequences with C-terminal extension: 0.11%

Sequences with N-terminal extension: 92.06%

Overrepresented class: Actinobacteria [99.90%]



Sample Neighborhood

Protein WP_027764609.1 of Assembly GCF_000426325.1 (Streptomyces sp. CNS606)


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
The Streptomyces coelicolor developmental transcription factor sigmaBldN is synthesized as a proprotein. Journal of bacteriology 2003 M. Bibb, M. Buttner PubMed: 12644505 ECF121
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
Expression of the chaplin and rodlin hydrophobic sheath proteins in Streptomyces venezuelae is controlled by σ(BldN) and a cognate anti-sigma factor, RsbN. Molecular microbiology 2012 M. Bibb, A. Domonkos, G. Chandra, M. Buttner PubMed: 22582857 ECF121
The crystal structure of the RsbN-σBldN complex from Streptomyces venezuelae defines a new structural class of anti-σ factor. Nucleic acids research 2018 M. Schumacher, M. Bush, M. Bibb, F. Ramos-León, G. Chandra, W. Zeng, M. Buttner PubMed: 29905823 ECF121, ECF214
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