ECF27 ECF proteins

General description: Members of ECF27 are homologous to members of original ECF27 (90.2%) and ECF20 (0.06%), and are present in Actinobacteria (100%).

Anti-σ factor:  Position +1 contains a putative AS factor with one transmembrane helix (78.65%) and with a zinc-binding domain in ECF27s1 or non-conserved domains in other groups.

Genomic context conservation: As in the original group ECF27 (Staroń et al., 2009), the genetic context of members of ECF27 is extensively conserved. Position +2 encodes a pyridine nucleotide-disulfide oxidoreductase; position +3 encodes a thioredoxin; position +4 a N-acetylmuramoyl-L-alanine amidase with a peptidoglycan binding domain or an acetyltransferase of GNAT family (ECF27s1); position -1 contains a MviN-like protein (Pfam: MVIN) (-2 in ECF27s1 and ECF27s2) involved in flipping the lipid II peptidoglycan precursor to the periplasmic surface of the inner membrane in Salmonella typhimurium, E. coli and other gram-negative bacteria (Ling, Moore, Surette, & Woods, 2006). Furthermore, ECF27s1 contains a protein kinase in position +1, a sugar-specific transcription regulator TrmB in +5, an AAA domain-containing protein in +6, an rRNA small subunit methyltransferase G in +7, a KH domain-containing protein fused to a R3H domain in -8, possibly functioning as nucleic acid binding protein, a 60Kd inner membrane protein in +9, a polymerase A in charge of DNA repair and replacing Okazaki fragments with DNA in -4 and also conserved in ECF27s2 and ECF27s4, a major facilitator superfamily protein, and a PadR transcriptional regulator. There is a NUDIX domain protein in -3 of ECF27s5 and in ECF27s4.

Studied members: SigM, from Mycobacterium smegmatis (ECF27s4), is required for receiving DNA for conjugation (Clark et al., 2018). SigM is released from its membrane-bound AS factor upon detection of the donor cell and induces the expression of cell wall hydrolases, nucleases and the ESX-4 secretion apparatus (or type VII secretion system), in charge of connecting the donor and the acceptor cells to accomplish the DNA integration (Clark et al., 2018). The genetic context conservation of ECF27 agrees with this function, suggesting that other members of ECF27 have a similar function. Another member of ECF27, SigM from S. coelicolor (ECF27s1), plays a negative role in differentiation (Mao et al., 2009).

Promoter motif conservation: Promoter motifs are not conserved, indicating the lack of direct regulation of members of ECF27 over their expression. Indeed, this is the cases of SigM (Clark et al., 2018). The promoter motifs of original ECF27 (Staroń et al., 2009) are not observed in new ECF27, which agrees with the lack of activity of these promoters in a heterologous organism (Rhodius et al., 2013).

Summary: Due to the conservation of the proteins in the genetic neighborhood of members of ECF27, it is possible that ECF27 might be required for recipient cells during conjugation in Actinobacteria, as in the case of SigM in Mycobacterium smegmatis (ECF27s4).


 


Basic information

Number of representative ECFs: 1609

Number of non-redundant ECFs: 1674

Sequences with C-terminal extension: 30.59%

Sequences with N-terminal extension: 2.45%

Overrepresented class: Actinobacteria [99.94%]



Sample Neighborhood

Protein WP_012380077.1 of Assembly GCF_000010605.1 (Streptomyces griseus subsp. griseus NBRC 13350)


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 mviN homolog in Burkholderia pseudomallei is essential for viability and virulence. Canadian journal of microbiology 2006 J. Ling, R. Moore, M. Surette, D. Woods PubMed: 17110975 ECF27
The extracytoplasmic function-type sigma factor SigM of Corynebacterium glutamicum ATCC 13032 is involved in transcription of disulfide stress-related genes. Journal of bacteriology 2007 D. Nakunst, C. Larisch, A. Hüser, A. Tauch, A. Pühler, J. Kalinowski PubMed: 17483229 ECF27
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
Involvement of SigT and RstA in the differentiation of Streptomyces coelicolor. FEBS letters 2009 X. Mao, Z. Zhou, L. Cheng, X. Hou, W. Guan, Y. Li PubMed: 19755120 ECF27
The ECF sigma factor SigT regulates actinorhodin production in response to nitrogen stress in Streptomyces coelicolor. Applied microbiology and biotechnology 2011 W. Feng, X. Mao, Z. Liu, Y. Li PubMed: 22002068 ECF27
Dual positive feedback regulation of protein degradation of an extra-cytoplasmic function σ factor for cell differentiation in Streptomyces coelicolor. The Journal of biological chemistry 2013 X. Mao, N. Sun, F. Wang, S. Luo, Z. Zhou, W. Feng, F. Huang, Y. Li PubMed: 24014034 ECF27
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
Direct cell-cell contact activates SigM to express the ESX-4 secretion system in <i>Mycobacterium smegmatis</i>. Proceedings of the National Academy of Sciences of the United States of America 2018 R. Clark, J. Judd, E. Lasek-Nesselquist, S. Montgomery, J. Hoffmann, K. Derbyshire, T. Gray PubMed: 29941598 ECF27
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