ECF292 ECF proteins

General description: Proteins from ECF292 appear in Actinobacteria, mainly in Micrococcales and Corynebacteriales.

Anti-σ factor: Genomic contexts of members of ECF292 contain an average of 2.08 soluble proteins (94.32%) from Asp23 family (Pfam: Asp23), which is one of the most abundant proteins S. aureus and is related with cell envelope homeostasis (Müller et al., 2014). The BLAST search recognizes proteins from the Asp23 family as AS factors since the ungrouped putative AS factor 1534 (YP_118547 from Nocardia farcinica) contains this domain in C-terminus (Staroń et al., 2009). Two different Asp23 proteins appear in our analysis, the ones with Asp23 domain and longer versions with an N-terminal extension whose length is subgroup-specific (~100 aa in ECF292s1 to ~20 in ECF292s2) and are encoded in position +1. Whether Asp23 family proteins are AS factors is unknown, but it could be possible since their deletion leads to upregulation of the cell envelope stress genes (Müller et al., 2014). Asp23 from S. aureus is attached to the membrane via DUF322 family protein (AmaP) (Müller et al., 2014). Interestingly, Asp23 proteins are also putative regulators of ECF286.

Genomic context conservation: In ECF292s4 there is also a conserved DUF2273-containing protein in -3.

Promoter motif conservation: Promoter motifs are not conserved.

Summary: ECF292 might be regulated by a new kind of soluble AS factor that belongs to the Asp23 family. This group could be involved in cell envelope stress response.


 


Basic information

Number of representative ECFs: 388

Number of non-redundant ECFs: 391

Sequences with C-terminal extension: 0.51%

Sequences with N-terminal extension: 7.42%

Overrepresented order: Micrococcales [56.96%]



Sample Neighborhood

Protein WP_056553112.1 of Assembly GCF_001426545.1 (Mycobacterium sp. Root135)


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 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
Deletion of membrane-associated Asp23 leads to upregulation of cell wall stress genes in Staphylococcus aureus. Molecular microbiology 2014 M. Müller, S. Reiß, R. Schlüter, U. Mäder, A. Beyer, W. Reiß, J. Marles-Wright, R. Lewis, H. Pförtner, U. Völker, K. Riedel, M. Hecker, S. Engelmann, J. Pané-Farré PubMed: 25074408 ECF286, ECF292
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