ECF19 ECF proteins

General description: ECF19 is composed by a mixture of proteins from original groups ECF19 (56.46%), ECF18 (1%), ECF126 (3.66%) and ECF34 (2.72%). The taxonomic distribution of this group is diverse and subgroup-specific, with proteins coming from Actinobacteria (86.21%), Cyanobacteria (5.65%), Firmicutes (1.95%), Chloroflexi (0.51%), Proteobacteria (1.65%), Verrucomicrobia (0.51%), Deinococcus-Thermus (1.54%), Acidobacteria (1.03%) and Planctomycetes (0.62%) and Gemmatimonadetes (0.10%).

Regulation: The genetic context of ECF19 contains a conserved putative AS factor in position +1. Typically this AS factor has a RskA-like domain with or without a zinc-finger and one transmembrane helix (79.71%). In subgroup ECF19s19, the putative AS factor is a soluble protein with a ChrR-like CLD, as in members of ECF11. Moreover, the putative AS factor in subgroups ECF19s7 and ECF19s18 is a soluble protein with a putative zinc-finger fused to the N-terminal domain of a mycothiol maleylpyruvate isomerase. Interestingly, these two subgroups contain an anti-anti-σ (AAS) factor with a STAS domain in -1 (94.44% of the contexts in ECF19s7, 40% of ECF19s18). Only 21.82% of the ECFs from ECF19s4 contain putative AS factors, indicating that the cognate AS factors of the rest of the members of ECF19s4 are encoded somewhere else in the genome. Interestingly, subgroup ECF19s4 contains a MerR HTH family regulatory protein (64.15%) in position -1, which induces the transcription of the ECF LitS from S. coelicolor (ECF19s4) in response to light, leading to the transcription of the carotenoid biosynthesis pathway (Takano, Obitsu, Beppu, & Ueda, 2005).

Genomic context conservation: The rest of the proteins in the context of ECF19 are only conserved in a subgroup-specific manner. We could find several domains conserved within both ECF19s7 and ECF19s18, such as a bifunctional DNA primase/polymerase N-terminal domain, a protein with a conserved ACT domain fused to a formyltransferase domain. Other conserved proteins in include a mttA/Hcf106 protein (-1 of ECF19s27), a sortase (-1 of ECF19s5), a DUF4397 (-2 of ECF19s5), a SsgA protein involved in sporulation and cell division (-1 of ECF19s12), a FeoA Iron dependent repressor (+8 of ECF19s18), a SIS domain-containing protein (+9 of ECF19s18), a cytochrome C biogenesis protein (-2 of ECF19s9), a flavin-containing amine oxidoreductase (ECF19s4), an ABC transporter with a DUF4162 (ECF19s13) and a MbtH-like protein (ECF19s13).

Studied members: A member of ECF19, SigK (ECF19s2) from Mycobacterium spp., has been experimentally addressed. SigK regulon includes sigK, the antigens MPT70 and MPT83, and genes for the synthesis of lipids and oxidative stress response (Saïd-Salim, Mostowy, Kristof, & Behr, 2006; Sklar, Makinoshima, Schneider, & Glickman, 2010; Veyrier, Saïd-Salim, & Behr, 2008). Antigens MPT70 and MPT83 are induced when M. tuberculosis resides inside macrophages (Schnappinger et al., 2003). The AS factor of SigK, RskA, is dysfunctional in M. bovis, which makes the production of MPT70 and MPT83 higher in M. bovis resulting in a higher virulence of M. bovis respect to M. tuberculosis (Medina, Ryan, LaCourse, & North, 2006; Saïd-Salim, Mostowy, Kristof, & Behr, 2006). SigK is the first σ factor described to be dually activated by the dissociation of a disulfide bridge in σ4 domain due to reducing conditions (Shukla et al., 2014) and a signal that inactivates its AS factor via RIP mediated by the intramembrane protease Rip1 (Sklar, Makinoshima, Schneider, & Glickman, 2010). Even though this is the first group where the role of the two cysteines of the σ4 domain was described, this is not one of the defining features of ECF19 since it only appears in some subgroups (ECF19s1, ECF19s2, ECF19s6, ECF19s11, and ECF19s13).

Yet other members of ECF19 have been experimentally addressed, SigK from Rhodococcus hoagii (ECF19s2). This protein is upregulated during macrophage infection (Rahman, Parreira, & Prescott, 2005). Lastly, LitS from S. coelicolor (ECF19s4) is involved in the transcription of the carotenoid biosynthesis pathway when induced by LitR, a MerR-type transcriptional regulator encoded in -1, in response to light (Takano et al., 2005). LitS might also be regulated by a putative AS factor, LitB, encoded in position +2 and with a RskA domain (Takano et al., 2005). Indeed, 21.82% of the ECFs from ECF19s4 encode a RskA-like domain in their genetic context.

Promoter motif conservation: The predicted target promoter motif of members of ECF19 is only conserved at a subgroup level and among neighboring subgroups. A typical pattern is ATC in -35, and CG or TG in -10. The promoter motifs of LitS (GCATG -35 and CGGAAG -10 (Takano et al., 2005)) do not agree with the promoter predicted by our pipeline even though LitS is autoregulated (Takano et al., 2005), but agree with the motifs for SigK in Mycobacterium tuberculosis (Veyrier, Saïd-Salim, & Behr, 2008).

Summary: Members of ECF19 are regulated by putative AS factors, most of which contain one transmembrane helix and an RskA-like domain, as in the case of original ECF19 (Staroń et al., 2009). Some subgroups have soluble AS factors (ECF19s19, ECF19s18 and ECF19s7). Of those, ECF19s7 and ECF19s18, are associated with AAS factors encoded in -1 and contain a soluble ZAS fused to the N-terminal domain of a mycothiol maleylpyruvate isomerase. Since members of these groups have homology to original ECF126 and show a different mechanism that the rest of the members of ECF19, we consider ECF19s7 and ECF19s18 specialized members of ECF19. ECF19 illustrates how it is possible to unify different original groups from different taxonomic groups but with similar characteristics based on protein similarity.


Basic information

Number of representative ECFs: 3394

Number of non-redundant ECFs: 3388

Sequences with C-terminal extension: 0.74%

Sequences with N-terminal extension: 9.21%

Overrepresented phylum: Actinobacteria [91.99%]



Sample Neighborhood

Protein WP_021762532.1 of Assembly GCF_000469485.1 (Leifsonia aquatica ATCC 14665)


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
Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment. The Journal of experimental medicine 2003 D. Schnappinger, S. Ehrt, M. Voskuil, Y. Liu, J. Mangan, I. Monahan, G. Dolganov, B. Efron, P. Butcher, C. Nathan, G. Schoolnik PubMed: 12953091 ECF19
Light-induced carotenogenesis in Streptomyces coelicolor A3(2): identification of an extracytoplasmic function sigma factor that directs photodependent transcription of the carotenoid biosynthesis gene cluster. Journal of bacteriology 2005 H. Takano, S. Obitsu, T. Beppu, K. Ueda PubMed: 15716454 ECF19
Reduced expression of antigenic proteins MPB70 and MPB83 in Mycobacterium bovis BCG strains due to a start codon mutation in sigK. Molecular microbiology 2005 D. Charlet, S. Mostowy, D. Alexander, L. Sit, H. Wiker, M. Behr PubMed: 15882422 ECF19
In vitro and intra-macrophage gene expression by Rhodococcus equi strain 103. Veterinary microbiology 2005 M. Rahman, V. Parreira, J. Prescott PubMed: 16143469 ECF19
Superior virulence of Mycobacterium bovis over Mycobacterium tuberculosis (Mtb) for Mtb-resistant and Mtb-susceptible mice is manifest as an ability to cause extrapulmonary disease. Tuberculosis (Edinburgh, Scotland) 2006 E. Medina, L. Ryan, R. LaCourse, R. North PubMed: 16253563 ECF19
Mutations in Mycobacterium tuberculosis Rv0444c, the gene encoding anti-SigK, explain high level expression of MPB70 and MPB83 in Mycobacterium bovis. Molecular microbiology 2006 B. Saïd-Salim, S. Mostowy, A. Kristof, M. Behr PubMed: 17064366 ECF19
Evolution of the mycobacterial SigK regulon. Journal of bacteriology 2008 F. Veyrier, B. Saïd-Salim, M. Behr PubMed: 18203833 ECF19
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
M. tuberculosis intramembrane protease Rip1 controls transcription through three anti-sigma factor substrates. Molecular microbiology 2010 J. Sklar, H. Makinoshima, J. Schneider, M. Glickman PubMed: 20545848 ECF19
Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA σ-anti-σ complex. Acta crystallographica. Section D, Biological crystallography 2014 J. Shukla, R. Gupta, K. Thakur, R. Gokhale, B. Gopal PubMed: 24699647 ECF57, ECF19, ECF18, ECF288
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