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.

 



This family belongs to the .

 

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.

Examples:

TC#NameOrganismal TypeExample
2.A.89.1.1The vacuolar Fe2+/Mn2+ uptake transporter, Ccc1YeastCcc1 of Saccharomyces cerevisiae (322 aas; P47818)
 
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

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

 
Examples:

TC#NameOrganismal TypeExample
2.A.89.2.1

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#NameOrganismal TypeExample
2.A.89.3.1

The bacterial VIT family homologue

Bacteria

VIT homologue of Burkholderia phytofirmans (376 aas; B2TCH9)

 
2.A.89.3.10The archaeal VIT family homologueArchaeaVIT 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#NameOrganismal TypeExample