ECF proteins

General description: Proteins from ECF243 combine the non-ECF10 FecI-like groups of the original classification - ECF05 (45.1%), ECF07 (16.62%), ECF06 (6.67%), ECF09 (5.5%), ECF08 (3.14%), ECF10 (0.39%). Proteins from ECF243s172, ECF243s125 and ECF243s57 are fused to their FecR-like AS factor and, therefore, contain ~1 transmembrane helix. Some ECF243 subgroups contain short N-terminal (ECF243s134) or C-terminal (ECF243s62, ECF243s51, ECF243s1, ECF243s77, ECF243s66, ECF243s23, ECF243s59, ECF243s47, ECF243s134, ECF243s3, ECF243s38, ECF243s53) extension with a subgroup-dependent sequence. The region σ2.3 is not conserved in ECF243 and there are different possible types of linker between σ2 and σ4, some of them G-rich.

Anti-σ factor: Members of ECF243 contain a FecR-like AS factor (average of 1.14 per ECF) with one transmembrane helix (82.33%) in position +1 and a TonB-dependent receptor (average of 1.25 per ECF) in +2, as corresponds to the group of FecI from E. coli (ECF243s16). FecI is fused to a DUF4880 (average of 1.28 per ECF) and a DUF4974 (1 per ECF).

Genomic context conservation: Other proteins conserved in the genomic context of members of ECF243 include a heme-binding protein A (HasA) (+3 of ECF243s15), an protein from an ABC transporter (+4 of ECF243s15), a HlyD membrane-fusion protein of T1SS (+5 of ECF243s15), the beta domain of an autotransporter (+3 of ECF243s75), a beta-lactamase (-1 of ECF243s75), a carbohydrate phosphorylase (-2 of ECF243s75), an alpha amylase (-3 and -6 of ECF243s75), a nucleotidyl transferase (-4 of ECF243s75), a starch synthase (-5 of ECF243s75), a Glu-tRNAGln amidotransferase C subunit (ECF243s75), GatB (ECF243s75), an amidase (ECF243s75), a putative modulator of DNA gyrase (ECF243s24), a LysR regulator (ECF243s5 and ECF243s3), a FecCD transporter (ECF243s16), a periplasmic binding protein (ECF243s16), an amino acid permease (ECF243s2), a DUF454 (ECF243s2) and a heme oxygenase (ECF243s2).

Studied members: Proteins from ECF243 are involved in the uptake of iron-mediated by different siderophores, both synthesized by the same bacteria or by other organisms (siderophore piracy). This regulation can be made via the upregulation of the ferric-siderophore transporters or the synthesis machinery of the siderophore. FecI from E. coli (ECF243s16) participates in the uptake of iron-mediated by citrate via the activation of its transport system encoded in the fecABCDE operon. When cells are depleted of Fe2+, Fur releases its repression over the transcription of the operon fecIR. FecR is the membrane-bound AS factor of FecI. FecIR controls the expression of the operon fecABCDE, which encodes the proteins necessary for the uptake of ferric citrate. FecA is an outer membrane-bound TonB-dependent receptor that transports citrate loaded with Fe3+. Under the presence of ferric-citrate, the repression of FecR over FecI is released, and the complex formed by FecI and the N-terminal part of FecR directs RNAP to the transcription of the transport system fecABCDE (reviewed in (Braun & Mahren, 2005)). Other ECFs with a similar regulation belong to Pseudomonas syringae (Ecf5 (ECF243s5), Ecf6 (ECF243s73), AcsS (ECF243s9), PSPTO0444 (ECF243s44), PvdS (ECF243s1)) (Llamas, Imperi, Visca, & Lamont, 2014; Yu et al., 2014), Pseudomonas aeruginosa (FiuI (ECF243s1), FemI (ECF243s11), PA2050 (ECF243s20), PA2093 (ECF243s20), FoxI (ECF243s10), FecI (ECF243s5), PA4896 (ECF243s54), PA1300 (ECF243s80), HasI (ECF243s15), VreI (ECF243s56), PvdS (ECF243s1), FpvI (ECF243s40)) (Chevalier et al., 2018; Llamas et al., 2014; Marshall, Stintzi, Gilmour, Meyer, & Poole, 2009) and Pseudomonas putida (PfrI (ECF243s1), IutY (ECF243s57, TM helix), PP4611 (ECF243s5), PP0352 (ECF243s44), PP3577 (ECF243s9), PP3086 (ECF243s42), PP0162 (ECF243s69)) (Llamas et al., 2014), Serratia marcescens (HasI (ECF243s15)) (Biville et al., 2004), Burkholderia pseudomallei (BPSL1787 (ECF243s13)) (Alice, López, Lowe, Ledesma, & Crosa, 2006), Herbaspirillum seropedicae (PfrI (ECF243s129)) (Trovero et al., 2018), Bordetella pertussis (HurI (ECF243s11)) (Vanderpool & Armstrong, 2003),  among others. A special case is the FecI-like σ factor PrhI (ECF243s24), from Ralstonia solanacea, since it participates in plant infection, as discussed in (Braun & Mahren, 2005).

Paralogy: ECF43 is the most abundant and diverse ECF group, accounting for the importance of iron uptake, and yet it only appears in Proteobacteria. This system is not necessary for Gram-positive bacteria since they lack the outer membrane. Even in Gram-negative bacteria such as E. coli, FecA is not the only outer membrane protein able to transport iron – other ferric-siderophore complexes are transported through at least six TonB-dependent outer membrane transporters, of which only one, FecA, is regulating an ECF (reviewed in (Andrews, Robinson, & Rodríguez-Quiñones, 2003)). In general, the primary iron starvation regulators are Fur, or DtxR in high GC Gram-positive bacteria (reviewed in (Andrews et al., 2003)). Indeed, Fur is regulating the expression of fecIR in E. coli (Braun & Mahren, 2005). In general, FecIR-like systems seem the exception rather than the rule in iron scavenging - even within Proteobacteria: 88.38% of the representative/reference genomes do not contain any member of ECF243. Nevertheless, when present, there is usually more than one member of ECF243 per organism (average of 2.85 ECF243 per genome and a standard deviation of 3.25). These ECFs are usually from a different subgroup (94.01%). This notion raises the question of why some Proteobacteria has FecI-like systems if they do not seem essential from iron uptake. One possibility is that FecI-like systems provide bacteria with the ability to overexpress iron-import systems on demand. This is also congruent with the presence of several copies of ECF243 of different subgroups in the same organism. Since each copy could be regulating a different uptake system, the bacterium could upregulate only the systems that are currently in use. However, looking at the characterized members of ECF243, it does not seem that the same subgroup regulates the uptake of the same ferric-siderophore complex. For instance, members of ECF243s11 use as siderophores heme (HurI from B. pertussis (Vanderpool & Armstrong, 2003)) and mycobactin (FemI of P. aeruginosa (Chevalier et al., 2018)). Similarly, ECF243s9 uses achromobactin in P. syringae’s AcsS (Yu et al., 2014) and mycobactin in P. putida’s PP3577 (Llamas et al., 2014). More studies into the specificity of FecIR systems would shed light into the source of specificity of these systems given their paralogy in Proteobacterial genomes.

Promoter motif conservation: Predicted target promoter motifs are conserved in some subgroups, but they do not have a common pattern. These results agree with the data from original FecI-like groups, which are not autoregulated (Braun & Mahren, 2005; Staroń et al., 2009). Interestingly, some promoter regions contain conserved TAAT regions. These could be the binding site of Fur repressor, as discussed in (Andrews et al., 2003).

Summary: ECF243 is the largest and more diverse ECF group. It is a canonical FecI-like group that merges original groups ECF05-09. Members of this group are mainly, but not only, responsible for iron uptake, and are regulated by FecR-like AS factors and TonB-dependent receptors that sense and transport the loaded siderophore to the periplasm.


Basic information

Number of representative ECFs: 10152

Number of non-redundant ECFs: 12254

Sequences with C-terminal extension: 0.95%

Sequences with N-terminal extension: 1.51%

Overrepresented phylum: Proteobacteria [99.95%]

Sample Neighborhood

Protein WP_062746018.1 of Assembly GCF_001571305.1 (Erwinia persicina NBRC 102418)

Promoter Motif


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
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

Related publications

Title Journal Year Authors PubMed ECF groups
Heme-responsive transcriptional activation of Bordetella bhu genes. Journal of bacteriology 2003 C. Vanderpool, S. Armstrong PubMed: 12533466 ECF243
Bacterial iron homeostasis. FEMS microbiology reviews 2003 S. Andrews, A. Robinson, F. Rodríguez-Quiñones PubMed: 12829269 ECF243
Haemophore-mediated signalling in Serratia marcescens: a new mode of regulation for an extra cytoplasmic function (ECF) sigma factor involved in haem acquisition. Molecular microbiology 2004 F. Biville, H. Cwerman, S. Létoffé, M. Rossi, V. Drouet, J. Ghigo, C. Wandersman PubMed: 15306027 ECF243
Transmembrane transcriptional control (surface signalling) of the Escherichia coli Fec type. FEMS microbiology reviews 2004 V. Braun, S. Mahren PubMed: 16102597 ECF239, ECF243
Genetic and transcriptional analysis of the siderophore malleobactin biosynthesis and transport genes in the human pathogen Burkholderia pseudomallei K96243. Journal of bacteriology 2006 A. Alice, C. López, C. Lowe, M. Ledesma, J. Crosa PubMed: 16452439 ECF243
Citrate-mediated iron uptake in Pseudomonas aeruginosa: involvement of the citrate-inducible FecA receptor and the FeoB ferrous iron transporter. Microbiology (Reading, England) 2009 B. Marshall, A. Stintzi, C. Gilmour, J. Meyer, K. Poole PubMed: 19118371 ECF243
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 ECF114, ECF31, ECF22, ECF12, ECF27, ECF122, ECF121, ECF56, ECF03, ECF21, ECF23, ECF02, ECF41, ECF15, ECF107, ECF111, ECF39, ECF19, ECF25, ECF17, ECF26, ECF118, ECF11, ECF16, ECF42, ECF38, ECF103, ECF36, ECF28, ECF51, ECF115, ECF40, ECF14, ECF29, ECF123, ECF33, ECF102, ECF105, ECF106, ECF116, ECF130, ECF18, ECF235, ECF120, ECF239, ECF240, ECF242, ECF243, ECF249, ECF265, ECF271, ECF281, ECF285, ECF286, ECF289, ECF290, ECF291, ECF292, ECF293, ECF294, ECF30, ECF32, ECF43
Cell-surface signaling in Pseudomonas: stress responses, iron transport, and pathogenicity. FEMS microbiology reviews 2014 M. Llamas, F. Imperi, P. Visca, I. Lamont PubMed: 24923658 ECF02, ECF243
Transcriptional analysis of the global regulatory networks active in Pseudomonas syringae during leaf colonization. mBio 2014 X. Yu, S. Lund, J. Greenwald, A. Records, R. Scott, D. Nettleton, S. Lindow, D. Gross, G. Beattie PubMed: 25182327 ECF243, ECF32
<i>Herbaspirillum seropedicae</i> Differentially Expressed Genes in Response to Iron Availability. Frontiers in microbiology 2018 M. Trovero, P. Scavone, R. Platero, E. de Souza, E. Fabiano, F. Rosconi PubMed: 30018605 ECF243
Extracytoplasmic function sigma factors in Pseudomonas aeruginosa. Biochimica et biophysica acta. Gene regulatory mechanisms 2018 S. Chevalier, E. Bouffartigues, A. Bazire, A. Tahrioui, R. Duchesne, D. Tortuel, O. Maillot, T. Clamens, N. Orange, M. Feuilloley, O. Lesouhaitier, A. Dufour, P. Cornelis PubMed: 29729420 ECF02, ECF102, ECF243, ECF293, ECF35
Intrapulmonary percussive ventilation improves lung function in cystic fibrosis patients chronically colonized with Pseudomonas aeruginosa: a pilot cross-over study. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2018 J. Dingemans, H. Eyns, J. Willekens, P. Monsieurs, R. Van Houdt, P. Cornelis, A. Malfroot, A. Crabbé PubMed: 29560543 ECF243
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