ECF281 ECF proteins

General description: Proteins from ECF281 have homology to original groups ECF20 (10.45%) and ECF113 (0.85%), and are present in Firmicutes (41.44%), Actinobacteria (23.42%), Deinococcus-Thermus (18.92%) from genus Deinococcus and Proteobacteria (16.22%).

Anti-σ factor: Most of the subgroups contain putative AS factors with one TM helix (79.69%) and a zinc-finger encoded in +1. In subgroups ECF281s3 and ECF281s4, the putative AS factor could be fused to a DUF4349. Instead, subgroups ECF281s1, ECF281s5, ECF281s7 and ECF281s10 do not contain AS factors in their genomic context. It is likely that the AS factors of these subgroups are encoded somewhere else in the genome.

Genomic context conservation: Other proteins conserved are a heavy-metal resistance protein (+2 of ECF281s2), a tRNA-dihydrouridine synthase (-1 of ECF281s6), and a protein from family FUN14 (-1 of ECF281s5), which appears in Eubacteria, Archaea and Eukaryotes and is involved in mitophagy induced by hypoxia in mammalian cells (Liu et al., 2012).

Promoter motif conservation: Predicted target promoter motifs are conserved and contain GGAACTT in -35 and a less conserved GTCTAA in -10. This motif is similar, but not identical, to the target promoter motif in the original group ECF20 (Rhodius et al., 2013).

Summary: Members of ECF281 are regulated by zinc-finger AS factors with one transmembrane helix encoded in +1. Members of ECF281 could be involved in response to heavy metals and their detoxification. This function inherits from original ECF20 (Staroń et al., 2009), even though the only characterized member of original ECF20 is now classified against ECF291.


 


Basic information

Number of representative ECFs: 314

Number of non-redundant ECFs: 354

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 1.13%

Overrepresented phylum: Firmicutes [31.53%]



Sample Neighborhood

Protein WP_035854888.1 of Assembly GCF_000519045.1 (Dechloromonas agitata is5)


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
Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells. Nature cell biology 2012 L. Liu, D. Feng, G. Chen, M. Chen, Q. Zheng, P. Song, Q. Ma, C. Zhu, R. Wang, W. Qi, L. Huang, P. Xue, B. Li, X. Wang, H. Jin, J. Wang, F. Yang, P. Liu, Y. Zhu, S. Sui, Q. Chen PubMed: 22267086 ECF281
Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Molecular systems biology 2013 V. Rhodius, T. Segall-Shapiro, B. Sharon, A. Ghodasara, E. Orlova, H. Tabakh, D. Burkhardt, K. Clancy, T. Peterson, C. Gross, C. Voigt PubMed: 24169405 ECF22, ECF27, ECF03, ECF21, ECF39, ECF25, ECF26, ECF42, ECF38, ECF14, ECF29, ECF33, ECF281, ECF290, ECF291
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