ECF52 ECF proteins

General description: All the proteins from ECF52 could be classified against original ECF52 and are present in Actinobacteria.

Special features: Members of ECF52 have one to two transmembrane helices (except ECF52s8) in a C-terminal extension of up to ~400 amino acids that contains a zinc-finger and, in some cases, a carbohydrate-binding domain such as NPCBM/NEW2 domain (ECF52s1) or ricin-type beta-trefoil lectin-like domain (ECF52s4). Possible sensing of carbohydrates by members of original ECF52 has been speculated (Huang et al., 2015), although in our results it seems that this function might only be present in some subgroups. The σ4 domain is divergent in some members of ECF52.

Genomic context conservation: The genetic context conservation is only extended in ECF52s1 and ECF52s6. In ECF52s1, a conserved pyridine nucleotide-disulfide oxidoreductase is encoded in -2, potentially involved in oxidative stress response, a TetR repressor in -1, and a histidine kinase ATP-biding domain with a PAS fold and a SpoIIE domain in -3. In ECF52s6, ECFs are associated to a peptidase family S49, to a response regulator fused to a LytTr DNA-binding domain and a formamidopyrimidine-DNA glycosylase from the base excision repair system. The protease might release the ECF from the inhibition of the C-terminal extension and the whole signal transduction system could be responding to DNA damage.

Studied members: One member of ECF52, SCO4117 from Streptomyces coelicolor (ECF52s1), activates secondary metabolism, aerial mycelium differentiation, and sporulation (López-García, Yagüe, Gonzalez-Quiñonez, Rioseras, & Manteca, 2018).

Promoter motif conservation: The predicted target promoter motifs are not conserved among subgroups and, especially the -10 domains, have low information content. The promoter motif from the original group ECF52 (Huang et al., 2015) does not appear in any of the new subgroups. SCO4117 is self-induced, but its binding motifs differs from the one of its subgroup ECF52s1 and the original ECF52.

Summary: ECF52 inherits the same characteristics of original ECF52, except for the target promoter motifs, which could not be predicted. Some members of ECF52 might be involved in carbohydrate metabolism since their proteins contain a C-terminal extension periplasmic carbohydrate-binding domain. In general, the C-terminal extension of members of ECF52 could function as AS factors.


 


Basic information

Number of representative ECFs: 1231

Number of non-redundant ECFs: 1422

Sequences with C-terminal extension: 99.37%

Sequences with N-terminal extension: 33.97%

Overrepresented phylum: Actinobacteria [99.84%]



Sample Neighborhood

Protein ANZ37841.1 of Assembly GCA_001701025.1 (Lentzea guizhouensis)


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
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
The SCO4117 ECF Sigma Factor Pleiotropically Controls Secondary Metabolism and Morphogenesis in <i>Streptomyces coelicolor</i>. Frontiers in microbiology 2018 M. López-García, P. Yagüe, N. González-Quiñónez, B. Rioseras, A. Manteca PubMed: 29515563 ECF52
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