ECF114 ECF proteins

General description: Members of ECF114 are homologous to members of original ECF114 (36.83%) and are present in Bacteroidetes (99.11%).

Genomic context conservation: The only conserved protein in the genomic context of members of ECF114 is a GDP-mannose 4,6 dehydratase (ECF114s6). One of the smallest subgroups of ECF114, ECF114s11, composed by only three proteins from representative organisms from the gut microbiota (Bacteroides uniformis ATCC 8492, Bacteroides thetaiotaomicron and Bacteroides stercoris ATC 43183), encodes proteins needed for carbohydrate catabolism (phosphoglycerate mutase, fructose-bisphosphate aldolase, 6-phosphofructokinase, methylglyoxal synthase) and anabolism (alpha-glucan phosphorylase), urea cycle (arginase), a Na+/H+ antiporter, a MarC-like protein of unknown function, a heat-shock protein and two copies of ferritin. Since iron can catalyze the synthesis of ROS in aerobic conditions, ferritin sequesters Fe2+ into an insoluble core as Fe3+, and releases it in a controlled manner (Orino et al., 2001). The two copies of ferritin in this region of the genome of B. uniformis and B. thetaiotaomicron are speculated to be required as iron storage to protect against ROS damage or/and as competitive advantage against other gastrointestinal bacteria (Rocha & Smith, 2013). Indeed, the expression of the ferritin in iron-replete media increases 10-fold in anaerobic media over aerobic culture (Rocha & Smith, 2013).

Studied members: SigH, from the oral cavity dweller Porphyromonas gingivalis, belongs to ECF114s4 and plays a role in aerotolerance (Yanamandra, Sarrafee, Anaya-Bergman, Jones, & Lewis, 2012). SigH is induced upon exposure to O2, and its deletion mutant is downregulated in genes involved in oxidative stress protection (ferritin is the gene downregulated in a greater fold) and hemin uptake (Yanamandra et al., 2012).

Promoter motif conservation: Promoter motifs are not conserved, potentially due to the lack of autoregulation of members of ECF114 as it is the case for SigH from P. gingivalis (Yanamandra et al., 2012).

Summary: It is likely that ECF114 proteins play a role in aerotolerance of anaerobic Bacteroidetes and might participate in carbohydrate metabolism. We did not find any putative AS factor or potential modulator of members of ECF114, as in the case of original ECF114 (Staroń et al., 2009).


 


Basic information

Number of representative ECFs: 843

Number of non-redundant ECFs: 687

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.58%

Overrepresented phylum: Bacteroidetes [99.41%]



Sample Neighborhood

Protein WP_047448458.1 of Assembly GCF_000798815.1 (Alistipes sp. ZOR0009)


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
Ferritin and the response to oxidative stress. The Biochemical journal 2001 K. Orino, L. Lehman, Y. Tsuji, H. Ayaki, S. Torti, F. Torti PubMed: 11415455 ECF114
The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Molecular microbiology 2009 A. StaroĊ„, 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
Role of the Porphyromonas gingivalis extracytoplasmic function sigma factor, SigH. Molecular oral microbiology 2012 S. Yanamandra, S. Sarrafee, C. Anaya-Bergman, K. Jones, J. Lewis PubMed: 22520389 ECF114
Ferritin-like family proteins in the anaerobe Bacteroides fragilis: when an oxygen storm is coming, take your iron to the shelter. Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 2013 E. Rocha, C. Smith PubMed: 23842847 ECF114
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