ECF128 ECF proteins

General description: Members of this group are only present in Actinobacteria and have homology to proteins from the original group ECF128 (91.59%).

Anti-σ factor: Members of ECF128 contain a transmembrane protein in +1 of both ECF128s1 and ECF128s2 (ECF128s1: 72.73%, ECF128s2: 75%). These proteins contain a conserved cytoplasmic N-terminal region with no Pfam domain that could serve as AS domain. These putative AS factors bear several extracytoplasmic Pfam domains in ECF128s2, such as a BNR/Asp-box repeat, sortilin and/or YCF48 photosynthesis system II assembly factor, which could serve as sensing domains. Since the BNR/Asp-box is present in neuraminidases, it is possible that putative AS factors of ECF128s2 are sensing degradation products of the cell wall and, therefore, responding to cell wall stress.

Genomic context conservation: Aside from the transmembrane putative AS factor encoded in +1, likewise members of original ECF128, members of new ECF128 contain a membrane protein in -2 and a sortase in -1 of ECF128s1 (87.5%) (Staroń et al., 2009). The transmembrane protein in -2 is present in 75% of the ECFs of ECF128s1, but this value reduces to 16.67% in ECF128s2. Transmembrane proteins encoded in -2 of ECF128s1 are mainly extracytoplasmic, with a short cytoplasmic region in C-terminal unlikely to contain an AS domain. Other conserved domains of members of ECF128 include an ATP-grasp domain in +2 of ECF128s2.

Studied members: One protein of this group, SCO3736 from S. coelicolor (ECF128s1), is the most upregulated protein in a deletion mutant of ppm1, which encodes the donor sugar polyprenol phosphate mannose (PPM), which provides sugars for the extracytoplasmic glycosyltransferases (Huang et al., 2015). ppm1 deletion mutant is more sensitive to antibiotics that target the biosynthesis of the cell wall (Huang et al., 2015). SCO3736 is co-transcribed with the sortase encoded in -1 and the transmembrane protein encoded in -2 (Huang et al., 2015). It is speculated that the sortase attaches to the transmembrane protein to the cell wall (Huang et al., 2015).

Promoter motif conservation: Predicted target promoter motifs are only conserved in ECF128s2, with CCAACC in -35 and GGCGTC in -10.

Summary: In conclusion, ECF128 could be regulated by CAS encoded in +1, which may respond to extracytoplasmic signals related to the synthesis of the cell wall and/or the process of glycosyl transfer.


Basic information

Number of representative ECFs: 251

Number of non-redundant ECFs: 214

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.00%

Overrepresented order: Streptomycetales [90.84%]



Sample Neighborhood

Protein WP_027748803.1 of Assembly GCF_000424825.1 (Streptomyces sp. CNH287)


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
Streptomyces coelicolor strains lacking polyprenol phosphate mannose synthase and protein O-mannosyl transferase are hyper-susceptible to multiple antibiotics. Microbiology (Reading, England) 2018 R. Howlett, N. Read, A. Varghese, C. Kershaw, Y. Hancock, M. Smith PubMed: 29458553 ECF128
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