ECF243

ECF subgroups

ECF243s1 396 ECF243s2 372 ECF243s3 325 ECF243s4 329 ECF243s5 249 ECF243s6 311 ECF243s7 228 ECF243s8 271 ECF243s9 264 ECF243s10 243 ECF243s11 232 ECF243s12 192 ECF243s13 119 ECF243s14 122 ECF243s15 160 ECF243s16 104 ECF243s17 114 ECF243s18 103 ECF243s19 63 ECF243s20 120 ECF243s21 159 ECF243s22 71 ECF243s23 78 ECF243s24 46 ECF243s25 112 ECF243s26 93 ECF243s27 73 ECF243s28 72 ECF243s29 71 ECF243s30 52 ECF243s31 73 ECF243s32 63 ECF243s33 40 ECF243s34 74 ECF243s35 75 ECF243s36 58 ECF243s37 68 ECF243s38 105 ECF243s39 74 ECF243s40 56 ECF243s41 55 ECF243s42 66 ECF243s43 65 ECF243s44 56 ECF243s45 45 ECF243s46 49 ECF243s47 71 ECF243s48 32 ECF243s49 69 ECF243s50 36 ECF243s51 60 ECF243s52 46 ECF243s53 59 ECF243s54 49 ECF243s55 64 ECF243s56 85 ECF243s57 48 ECF243s58 45 ECF243s59 45 ECF243s60 11 ECF243s61 46 ECF243s62 55 ECF243s63 19 ECF243s64 41 ECF243s65 27 ECF243s66 8 ECF243s67 29 ECF243s68 24 ECF243s69 45 ECF243s70 29 ECF243s71 36 ECF243s72 37 ECF243s73 27 ECF243s74 37 ECF243s75 45 ECF243s76 6 ECF243s77 40 ECF243s78 6 ECF243s79 14 ECF243s80 38 ECF243s81 32 ECF243s82 27 ECF243s83 38 ECF243s84 29 ECF243s85 23 ECF243s86 34 ECF243s87 9 ECF243s88 22 ECF243s89 23 ECF243s90 18 ECF243s91 40 ECF243s92 14 ECF243s93 22 ECF243s94 22 ECF243s95 30 ECF243s96 18 ECF243s97 31 ECF243s98 10 ECF243s99 26 ECF243s100 20 ECF243s101 16 ECF243s102 28 ECF243s103 28 ECF243s104 22 ECF243s105 22 ECF243s106 6 ECF243s107 18 ECF243s108 23 ECF243s109 27 ECF243s110 32 ECF243s111 16 ECF243s112 16 ECF243s113 12 ECF243s114 15 ECF243s115 17 ECF243s116 27 ECF243s117 18 ECF243s118 36 ECF243s119 20 ECF243s120 19 ECF243s121 15 ECF243s122 26 ECF243s123 18 ECF243s124 19 ECF243s125 15 ECF243s126 24 ECF243s127 22 ECF243s128 35 ECF243s129 21 ECF243s130 31 ECF243s131 21 ECF243s132 17 ECF243s133 17 ECF243s134 19 ECF243s135 2 ECF243s136 13 ECF243s137 23 ECF243s138 14 ECF243s139 25 ECF243s140 34 ECF243s141 22 ECF243s142 27 ECF243s143 5 ECF243s144 10 ECF243s145 8 ECF243s146 12 ECF243s147 14 ECF243s148 25 ECF243s149 18 ECF243s150 13 ECF243s151 19 ECF243s152 28 ECF243s153 23 ECF243s154 16 ECF243s155 17 ECF243s156 15 ECF243s157 15 ECF243s158 15 ECF243s159 3 ECF243s160 13 ECF243s161 6 ECF243s162 11 ECF243s163 10 ECF243s164 12 ECF243s165 18 ECF243s166 17 ECF243s167 17 ECF243s168 12 ECF243s169 16 ECF243s170 15 ECF243s171 15 ECF243s172 12 ECF243s173 13 ECF243s174 12 ECF243s175 17 ECF243s176 13 ECF243s177 13 ECF243s178 18 ECF243s179 11 ECF243s180 10 ECF243s181 15 ECF243s182 13 ECF243s183 6 ECF243s184 11 ECF243s185 13 ECF243s186 6 ECF243s187 12 ECF243s188 14 ECF243s189 9 ECF243s190 4 ECF243s191 8 ECF243s192 7 ECF243s193 17 ECF243s194 10 ECF243s195 10 ECF243s196 12 ECF243s197 1 ECF243s198 8 ECF243s199 16 ECF243s200 13 ECF243s201 14 ECF243s202 15 ECF243s203 5 ECF243s204 14 ECF243s205 12 ECF243s206 8 ECF243s207 12 ECF243s208 11 ECF243s209 17 ECF243s210 7 ECF243s211 20 ECF243s212 13 ECF243s213 10 ECF243s214 12 ECF243s215 10 ECF243s216 13 ECF243s217 5 ECF243s218 4 ECF243s219 11 ECF243s220 11 ECF243s221 11 ECF243s222 13 ECF243s223 4 ECF243s224 14 ECF243s225 9 ECF243s226 11 ECF243s227 3 ECF243s228 9 ECF243s229 10 ECF243s230 4 ECF243s231 10 ECF243s232 9 ECF243s233 10 ECF243s234 10 ECF243s235 8 ECF243s236 5 ECF243s237 9 ECF243s238 8 ECF243s239 7 ECF243s240 15 ECF243s241 1 ECF243s242 12 ECF243s243 10 ECF243s244 13 ECF243s245 10 ECF243s246 11 ECF243s247 9 ECF243s248 3 ECF243s249 9 ECF243s250 10 ECF243s251 10 ECF243s252 13 ECF243s253 6 ECF243s254 7 ECF243s255 7 ECF243s256 8 ECF243s257 4 ECF243s258 3

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 σ_2.3 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.