2.A.89 The Vacuolar Iron Transporter (VIT) Family Members of the VIT family (DUF125) have been characterized in yeast (Ccc1; TC #2.A.89.1.1) and plants (Vit1; TC #2.A.89.1.2) (Kim et al., 2006). The former transports Fe²⁺ and Mn²⁺ into the vacuole where Fe²⁺ is stored, while the latter has been shown to transport Fe²⁺. Mutants accumulate excess Fe²⁺ in the cytoplasm which can be toxic. Excess Fe²⁺ is taken up into the vacuole. Vacuolar iron storage is critical for seedling development, and so is Vit1. Vit2 and Ccc1 have 5 putative TMSs in a 2 + 2 + 1 arrangement. Homologues are found in eukaryotes, bacteria and archaea where they may have a 1 + 2 + 2 arrangement (e.g., TC #2.A.89.2.1 from Pyrococcus abyssi) or a 1 + 2 + 3 arrangement (e.g., TC #2.A.89.3.1 from Burkholderia phytofirmans). Other bacterial and archaeal homologues are about 250 aas in length. A 270 aa homologue EAN12646 from Frankia sp. has 5 TMSs in a 2 + 3 arrangement. A 399 residue homologue from Ustilago maydis (EAK82927) has 5 putative TMSs in a 2 + 3 arrangement with two less hydrophobic peaks between the 2 and 3 strongly hydrophobic peaks. Of the two pairs of 2 TMSs, the first peak is smaller than the second peak in both cases, suggesting that these proteins arose by an intragenic duplication followed by addition of other domains. The separation between the 2 pairs is variable (>100 aas to <20 aas). These proteins may have an extended hydrophilic N-terminus. Eukaryotic VIT family proteins probably function by an H⁺ antiport carrier-type mechanism accounting for vacuolar uptake. Ccc1/VIT1 homologs are widely distributed among organisms with the exception of animals. The recent elucidation of the crystal structure of a Ccc1/VIT1 plant ortholog has enabled the identification of both conserved and species-specific motifs required for metal transport. In Saccharomyces cerevisiae, multiple transcription factors including Yap5 and Msn2/Msn4 contribute to the expression of CCC1 under high-iron conditions. S. cerevisiae strains express a partially functional Ccc1 protein that renders them sensitive to iron. Different regulatory mechanisms have been described for non-Saccharomycetaceae Ccc1 homologs (Sorribes-Dauden et al. 2020).
References:
Becker, P., R. Hakenbeck, and B. Henrich. (2009). An ABC transporter of Streptococcus pneumoniae involved in susceptibility to vancoresmycin and bacitracin. Antimicrob. Agents Chemother. 53: 2034-2041.
Bhubhanil S., Chamsing J., Sittipo P., Chaoprasid P., Sukchawalit R. and Mongkolsuk S. (2014). Roles of Agrobacterium tumefaciens membrane-bound ferritin (MbfA) in iron transport and resistance to iron under acidic conditions. Microbiology. 160(Pt 5):863-71.
Gollhofer, J., C. Schläwicke, N. Jungnick, W. Schmidt, and T.J. Buckhout. (2011). Members of a small family of nodulin-like genes are regulated under iron deficiency in roots of Arabidopsis thaliana. Plant Physiol. Biochem 49: 557-564.
Kato, T., K. Kumazaki, M. Wada, R. Taniguchi, T. Nakane, K. Yamashita, K. Hirata, R. Ishitani, K. Ito, T. Nishizawa, and O. Nureki. (2019). Crystal structure of plant vacuolar iron transporter VIT1. Nat Plants. [Epub: Ahead of Print]
Kim, S.A., Punshon, T., Lanzirotti, A., Li, L., Alonso, J.M., Ecker, J.R., Kaplan, J., and Guerinot, M.L. (2006). Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1. Science 314: 1295-1298.
Li, L., O.S. Chen, D.M. Ward, and J. Kaplan. (2001). CCC1 is a transporter that mediates vacuolar iron storage in yeast. J. Biol. Chem. 276: 29515-29519.
Mohammad, A., Miranda-Rios, J., Navarrete, G.E., Quinto, C., Olivares, J.E., Garcia-Ponce, B., and Sanchez, F. (2004). Nodulin 22 from Phaseolus vulgaris protects Escherichia coli cells from oxidative stress. Planta 219: 993-1002.
Mydel, P., Takahashi, Y., Yumoto, H., Sztukowska, M., Kubica, M., Gibson, F.C., 3rd, Kurtz, D.M., Jr., Travis, J., Collins, L.V., Nguyen, K.A., Genco, C.A., and Potempa, J. (2006). Roles of the host oxidative immune response and bacterial antioxidant rubrerythrin during Porphyromonas gingivalis infection. PLoS Pathog. 2: e76.
Sorribes-Dauden, R., D. Peris, M.T. Martínez-Pastor, and S. Puig. (2020). Structure and function of the vacuolar Ccc1/VIT1 family of iron transporters and its regulation in fungi. Comput Struct Biotechnol J 18: 3712-3722.
Wunderlich, J., V. Kotov, L. Votborg-Novél, C. Ntalla, M. Geffken, S. Peine, S. Portugal, and J. Strauss. (2024). Iron transport pathways in the human malaria parasite revealed by RNA-sequencing. Front Cell Infect Microbiol 14: 1480076.
Examples:
TC#	Name	Organismal Type	Example
2.A.89.1.1	The vacuolar Fe²⁺/Mn²⁺ uptake transporter, Ccc1	Yeast	*Ccc1 of Saccharomyces cerevisiae* (322 aas; P47818)**

2.A.89.1.10	VIT family protein, partial, of 214 aas and 5 TMSs		VIT family protein of Lokiarchaeum sp. GC14_75 (marine sediment metagenome)

2.A.89.1.11	Uncharacterized VIT family protein of 222 aas and 5 TMSs in a 2 + 3 TMS arrangement.		UP of Candidatus Thorarchaeota archaeon AB_25 (marine sediment metagenome)

2.A.89.1.12	Uncharacterized protein of 203 aas and 5 TMSs in a 2 + 3 TMS arrangement.		UP of Candidatus Odinarchaeota archaeon LCB_4 (hot springs metagenome)

2.A.89.1.13	Vacuolar ferrous iron transporter, VIT, of 273 aas and 5 TMSs in a 2 + 3 TMS arrangement. A new model for parasite iron homeostasis, in which PfE140 is involved in iron uptake across the plasma membrane, PfMRS3 ensures non-redundant Fe²⁺ supply to the mitochondrion as the main site of iron utilization, PfVIT transports excess iron into cytoplasmic vesicles, and PfZIPCO exports Fe²⁺ from these organelles in case of iron scarcity (Wunderlich et al. 2024). Only VIT was available in NCBI at the time this discussion was enterred into TCDB. PfNRAMP/PfDMT1 and PfCRT have previously reported to efflux Fe²⁺ from the digestive vacuole (Wunderlich et al. 2024).		Iron transporter, VIT, of Plasmodium falciparum

2.A.89.1.2	The vacuolar Fe²⁺ uptake transporter, VIT1 of 250 aas and 5 putative TMSs (Gollhofer et al. 2011). The crystal structure of the orthogous VIT1 from rose gum, Eucalyptus grandis, which probably functions as a H⁺-dependent antiporter for Fe²⁺ and other transition metal ions, has been solved. VIT1 adopts a novel protein fold forming a dimer of five membrane-spanning domains, with an ion-translocating pathway constituted by the conserved methionine and carboxylate residues at the dimer interface. The second transmembrane helix protrudes from the lipid membrane by about 40 Å, and connects to a three-helical bundle, triangular, cytoplasmic domain, which binds to the substrate metal ions in preparation for their transport (Kato et al. 2019).	Plants	*VIT1 of Arabidopsis thaliana* (Q9ZUA5)**

2.A.89.1.3	Uncharacterized protein of 242 aas and 5 TMSs	Bacteroidetes	Uncharacterized protein of Marivirga tractuosa

2.A.89.1.4	Uncharacterized protein of 252 aas with 5 TMSs	Chlamidiae	Uncharacterized protein of Parachlamydia acanthamoebae

2.A.89.1.5	CCC1 (VIT) family protein of 248 aas and probably 5 TMSs in a 2 + 3 TMS arrangement.	Chlamydia	VIT family protein of Chlamydia trachomatis

2.A.89.1.6	Uncharacterized protein of 173 aas and 5 TMSs.		UP of Candidatus Sungbacteria bacterium

2.A.89.1.7	VIT family protein of 192 aas and 5 TMSs in a 2 + 3 TMS arrangement		*VIT protein of Methanobacterium* sp.**

2.A.89.1.8	Uncharacterized protein of 183 aas and 5 TMSs in a 2 + 3 TMS arrangement.		*UP of Sulfolobus* sp. A20**

2.A.89.1.9	Uncharacterized protein of 194 aas and 5 TMSs.	Proteobacteria	UP of Nitrosococcus halophilus

Examples:
TC#	Name	Organismal Type	Example
2.A.89.2.1	Member of rubrerythrin family of electron transporters; of 327 aas and 5 TMSs.	Proteobacteria	VIT family member of Rhizobium leguminosarum

2.A.89.2.2	Membrane-bound ferritin-like ferrous iron (Fe²⁺) exporter, MbfA, of the erythrin-vacuolar iron transport-1 (Er-VIT1) family of 327 aas. The protein has an N-terminal ferritin domain and a C-terminal VIT domain of 5 established TMSs (Bhubhanil et al. 2014).	Proteobacteria	MbfA of Agrobacterium tumefaciens

2.A.89.2.3	VIT family member of 2690 aas and 5 TMSs.	Proteobacteria	VIT of Bartonella clarridgeiae

Examples:
TC#	Name	Organismal Type	Example
2.A.89.3.1	The bacterial VIT family homologue	Bacteria	*VIT homologue of Burkholderia phytofirmans* (376 aas; B2TCH9)**

2.A.89.3.10	The archaeal VIT family homologue	Archaea	*VIT homologue of Pyrococcus abyssi* (364 aas; CAB50539)**

2.A.89.3.2	*VIT family member, Spr0814 (Becker et al., 2009).*	Bacteria	*Spr0814, VIT family member of Streptococcus pneumoniae* (E1H0W3)**

2.A.89.3.3	*Vacuolar Nodulin-like1 (At1g21140) Iron regulated (Gollhofer et al., 2011).*	Plants	*VIT homolog1 of Arabidopsis thaliana* (Q9LPU9)**

2.A.89.3.4	*Nodulin-like2 (At1g76800) Iron regulated (Gollhofer et al., 2011).*	Plants	*VIT homolog2 of Arabidopsis thaliana* (Q9SR03)**

2.A.89.3.5	*Nodulin-like2.1 (At3g25190) Iron regulated; involved in Fe homeostasis (Gollhofer et al., 2011).*	Plants	*VIT homolog2.1 of Arabidopsis thaliana* (Q9LSF6)**

2.A.89.3.6	*Nodulin-like3 (At3g43630) Not iron regulated; involved in Fe homeostasis (Gollhofer et al., 2011).*	Plants	*VIT3 of Arabidopsis thaliana* (Q9M2C3)**

2.A.89.3.7	*Nodulin-like4 (At3g43660) Not iron regulated (Gollhofer et al., 2011).*	Plants	*VIT4 of Arabidopsis thaliana* (Q9M2C0)**

2.A.89.3.8	Fe²⁺/Mn²⁺ transporter Pcl1 (Pombe ccc1-like protein 1)	Yeast	Pcl1 of Schizosaccharomyces pombe

2.A.89.3.9	VIT family protein of 413 aas with an N-terminal rubrerythrin-like (ferritin-like) domain and a C-terminal DUF125 (5 TMS) domain.	Verucomicrobia	VIT family protein of Methylacidiphilum infernorum (Methylokorus infernorum)

Examples:
TC#	Name	Organismal Type	Example