ECF214 ECF proteins

General description: ECF214 contains proteins with homology to the sequences of original ECF10 (1.03%). ECF214 is present in Firmicutes (24.16%) and Bacteroidetes (75.56%).

Anti-σ factor: Proteins from this group are associated with RskA-like AS factors in +1. In subgroups from Firmicutes, AS factors are fused to a putative zinc-finger; instead, this domain is not conserved in Bacteroidetes. RskA is the AS factor of SigK from Mycobacterium tuberculosis (ECF19s2). RskA is degraded by regulated intramembrane proteolysis (RIP), has one transmembrane helix and contains a non-zinc-binding class I ASD, composed of four alpha helices (Schumacher et al., 2018). Most of the proteins in position +1 of ECF214 contain only one transmembrane helix (94.33%), supporting the idea that proteins in position +1 are RskA-like AS factors that could be regulated RIP, as in the case of RskA.

Genomic context conservation: The presence of a conserved aspartyl-protease in position -3 of ECF214s10, ECF214s18 and ECF214s6 suggests that this enzyme could be in charge of the first step of the degradation by RIP of the AS factors – 79.31% of the proteins in position -3 in these subgroups contain a signal peptide according to TopCons (Tsirigos, Peters, Shu, Käll, & Elofsson, 2015), a prerequisite for a site-1 protease. The aspartyl protease also contains a PDZ domain (PFAM: PDZ or PDZ_2) in ECF214s18. The PDZ domain of the site-1 protease DegS binds unfolded periplasmic proteins, changing the conformation of DegS and allowing for the proteolysis of the anti-σ factor RseA, thereby activating the RpoE-dependent transcription (Hasselblatt et al., 2007; Sohn, Grant, & Sauer, 2007). This suggests a potential activation of members of ECF214s18 by periplasmic unfolded proteins.

Other proteins conserved in the genetic context of the members of ECF214 are UDP-N-acetylenolpyruvoylglucosamine reductase (-1 of ECF214s10, ECF214s18 and ECF214s6), an aminotransferase class I and II (-2 of ECF214s10, ECF214s18 and ECF214s6), an aspartyl protease (-3 of ECF214s10 and ECF214s6) fused to a PDZ domain in ECF214s18, a DUF1573-containing protein (-4 of ECF214s10, ECF214s18 and ECF214s6), a tRNA synthetase (-5 of ECF214s10, ECF214s18 and ECF214s6), a extracellular solute-biding protein (ECF214s4), a secreted repeat of unknown function (-1 of ECF214s4), an ECF from ECF245s2 (+3 of ECF214s10), a radical SAM superfamily protein (+4 of ECF214s10), a glyceraldehyde 3-phosphate dehydrogenase (ECF214s18, ECF214s6 and +5 of ECF214s10), an histidine kinase from a 2CS fused to a receiver domain (+6 of ECF214s10), a tetraacyldisaccharide-1-P 4'-kinase (ECF214s18, ECF214s6 and +7 of ECF214s10), NIF3 (+8 of ECF214s10), a C4-type zinc ribbon domain (+9 of ECF214s10), a penicillin-binding protein (ECF214s18), a MreB/MbI protein (ECF214s18), a DUF4331 (ECF214s1), a pyridine nucleotide-disulphide oxidoreductase (-1 of ECF214s11), an enoyl-(Acyl carrier protein) reductase (ECF214s11), a beta-eliminating lyase (ECF214s11), a DUF2721 (ECF214s11), a fasciclin domain containing protein (ECF214s2).

Promoter motif conservation: The promoter motifs are diverse across subgroups so that a consensus could not be defined. Some groups have TATATACG in -35 and a more variable GGATG in -10 (ECF214s20, ECF214s10, ECF214s18, ECF214s6 and ECF214s2).

Summary: Members of ECF214 are regulated by a RskA-like AS factors that can contain a zinc-finger. In subgroup ECF214s18, ECF214s10 and ECF214s6 these AS factors seem to be degraded by RIP induced by an extracytoplasmic aspartyl protease encoded in position -3, which contains a PDZ domain (in >75% of the proteins only in ECF214s18), in charge of sensing unfolded peptides in the periplasm in DegS from E. coli (Hasselblatt et al., 2007; Sohn et al., 2007).


 


Basic information

Number of representative ECFs: 1015

Number of non-redundant ECFs: 1069

Sequences with C-terminal extension: 0.09%

Sequences with N-terminal extension: 0.84%

Overrepresented phylum: Bacteroidetes [70.05%]



Sample Neighborhood

Protein WP_045113114.1 of Assembly GCF_000169175.1 (Microscilla marina ATCC 23134)


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
Regulation of the sigmaE stress response by DegS: how the PDZ domain keeps the protease inactive in the resting state and allows integration of different OMP-derived stress signals upon folding stress. Genes & development 2007 H. Hasselblatt, R. Kurzbauer, C. Wilken, T. Krojer, J. Sawa, J. Kurt, R. Kirk, S. Hasenbein, M. Ehrmann, T. Clausen PubMed: 17938245 ECF02, ECF214, ECF273
Allosteric activation of DegS, a stress sensor PDZ protease. Cell 2007 J. Sohn, R. Grant, R. Sauer PubMed: 17981123 ECF214
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic acids research 2015 K. Tsirigos, C. Peters, N. Shu, L. Käll, A. Elofsson PubMed: 25969446 ECF214
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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