2.A.54 The Sideroflexin (SFXN) Family (formerly the Mitochondrial Tricarboxylate Carrier (MTC) Family)

The SFXN family (the (SLC56 family) consists of a limited number of homologues, all from eukaryotes. This sideroblastic-associated protein family was first identified in metazoans and was termed the sideroflexin (Sfxn) family. The metazoan Sfxn family comprises five groups of paralogous proteins, present in mitochondria and whose functions are in many cases uncertain. Using an in silico approach, several sideroflexin sequences from the genomes of different fungal species have been identified. An in-depth phylogenetic analysis of these fungal Sfxn sequences (termed Fsf1p) showed that they form a distinct clade within the metazoan Sfxn family. Hydrophobic cluster analysis and transmembrane topological mapping allowed comparison of conserved regions among Fsf1 and Sfxn proteins. The results indicate that Fsf1 probably belongs to an ancient, mitochondrial group of proteins, necessary to maintain the homeostasis of iron within this organelle (Miotto et al. 2007). Several members of the family have been partially functionally characterized. One is the tricarboxylate carrier from rat liver mitochondria. It is 357 amino acyl residues in length with 5 putative TMSs (Schmidt et al. 2018). It does not exhibit obvious internal repeats or show homology to proteins of the mitochondrial carrier family (TC #2.A.29). Homologues are found in Caenorhabditis elegans, Saccharomyces cerevisiae, Leishmania major and Homo sapiens. They are of 285-293 amino acyl residues with some exceptions, and are reported to possess 3-6 putative TMSs. the five sideroflexin genes in Xenopus show overlapping but nonsimilar expression patterns during Xenopus embryogenesis (Li et al. 2010).

The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. Trans-aconitate, α-ketoglutarate and malonate are not substrates. It presumably functions by a proton symport mechanism for the uptake of the variety of anionic substrates listed above (Schmidt et al. 2018). It is possible that it transports a citate-iron complex, explaining its effect on iron metabolism. Sideroflexins are highly conserved multi-spanning transmembrane proteins in the inner mitochondrial membrane in eukaryotes. Tifoun et al. 2021 reviewed sideroflexins, their presumed mitochondrial functions and the evidence linking sideroflexins to iron homeostasis and iron-sulfur cluster biogenesis. Members of this family have been reported to have the SLC56 fold (Ferrada and Superti-Furga 2022).

The generalized transport reaction catalyzed by the SSFXN protein of rat liver mitochondria is therefore probably:

anionic substrate (out) + nH+ (out)  anionic substrate (in) + nH+ (in)


 

References:

Acoba, M.G., E.S.S. Alpergin, S. Renuse, L. Fernández-Del-Río, Y.W. Lu, O. Khalimonchuk, C.F. Clarke, A. Pandey, M.J. Wolfgang, and S.M. Claypool. (2021). The mitochondrial carrier SFXN1 is critical for complex III integrity and cellular metabolism. Cell Rep 34: 108869.

Amorim, I.S., L.C. Graham, R.N. Carter, N.M. Morton, F. Hammachi, T. Kunath, G. Pennetta, S.M. Carpanini, J.C. Manson, D.J. Lamont, T.M. Wishart, and T.H. Gillingwater. (2017). Sideroflexin 3 is an α-synuclein-dependent mitochondrial protein that regulates synaptic morphology. J Cell Sci 130: 325-331.

Azzi, A., M. Glerum, R. Koller, W. Mertens and S. Spycher (1993). The mitochondrial tricarboxylate carrier. J. Bioenerg. Biomembr. 25: 515-524.

Ferrada, E. and G. Superti-Furga. (2022). A structure and evolutionary-based classification of solute carriers. iScience 25: 105096.

Gyimesi, G. and M.A. Hediger. (2020). Sequence Features of Mitochondrial Transporter Protein Families. Biomolecules 10:.

Hildick-Smith, G.J., J.D. Cooney, C. Garone, L.S. Kremer, T.B. Haack, J.N. Thon, N. Miyata, D.S. Lieber, S.E. Calvo, H.O. Akman, Y.Y. Yien, N.C. Huston, D.S. Branco, D.I. Shah, M.L. Freedman, C.M. Koehler, J.E. Italiano, Jr, A. Merkenschlager, S. Beblo, T.M. Strom, T. Meitinger, P. Freisinger, M.A. Donati, H. Prokisch, V.K. Mootha, S. DiMauro, and B.H. Paw. (2013). Macrocytic anemia and mitochondriopathy resulting from a defect in sideroflexin 4. Am J Hum Genet 93: 906-914.

Jackson, T.D., D.H. Hock, K.M. Fujihara, C.S. Palmer, A.E. Frazier, Y.C. Low, Y. Kang, C.S. Ang, N.J. Clemons, D.R. Thorburn, D.A. Stroud, and D. Stojanovski. (2021). The TIM22 complex mediates the import of sideroflexins and is required for efficient mitochondrial one-carbon metabolism. Mol. Biol. Cell 32: 475-491.

Kory, N., G.A. Wyant, G. Prakash, J. Uit de Bos, F. Bottanelli, M.E. Pacold, S.H. Chan, C.A. Lewis, T. Wang, H.R. Keys, Y.E. Guo, and D.M. Sabatini. (2018). SFXN1 is a mitochondrial serine transporter required for one-carbon metabolism. Science 362:.

Li, X., D. Han, R. Kin Ting Kam, X. Guo, M. Chen, Y. Yang, H. Zhao, and Y. Chen. (2010). Developmental expression of sideroflexin family genes in Xenopus embryos. Dev Dyn 239: 2742-2747.

Lockhart, P.J., B. Holtom, S. Lincoln, J. Hussey, A. Zimprich, T. Gasser, Z.K. Wszolek, J. Hardy, and M.J. Farrer. (2002). The human sideroflexin 5 (SFXN5) gene: sequence, expression analysis and exclusion as a candidate for PARK3. Gene 285: 229-237.

Miotto, G., S. Tessaro, G.A. Rotta, and D. Bonatto. (2007). In silico analyses of Fsf1 sequences, a new group of fungal proteins orthologous to the metazoan sideroblastic anemia-related sideroflexin family. Fungal Genet Biol 44: 740-753.

Mon, E.E., F.Y. Wei, R.N.R. Ahmad, T. Yamamoto, T. Moroishi, and K. Tomizawa. (2019). Regulation of mitochondrial iron homeostasis by sideroflexin 2. J. Physiol. Sci 69: 359-373.

Paul, B.T., L. Tesfay, C.R. Winkler, F.M. Torti, and S.V. Torti. (2019). Sideroflexin 4 affects Fe-S cluster biogenesis, iron metabolism, mitochondrial respiration and heme biosynthetic enzymes. Sci Rep 9: 19634.

Rivell, A., R.S. Petralia, Y.X. Wang, M.P. Mattson, and P.J. Yao. (2019). Sideroflexin 3 is a Mitochondrial Protein Enriched in Neuron.s. Neuromolecular Med 21: 314-321.

Schmidt, R.S., J.P. Macêdo, M.E. Steinmann, A.G. Salgado, P. Bütikofer, E. Sigel, D. Rentsch, and P. Mäser. (2018). Transporters of Trypanosoma brucei-phylogeny, physiology, pharmacology. FEBS J. 285: 1012-1023.

Tifoun, N., J.M. De Las Heras, A. Guillaume, S. Bouleau, B. Mignotte, and N. Le Floch. (2021). Insights into the Roles of the Sideroflexins/SLC56 Family in Iron Homeostasis and Iron-Sulfur Biogenesis. Biomedicines 9:.

Tifoun, N., M. Bekhouche, J.M. De Las Heras, A. Guillaume, S. Bouleau, I. Guénal, B. Mignotte, and N. Le Floch. (2022). A High-Throughput Search for SFXN1 Physical Partners Led to the Identification of ATAD3, HSD10 and TIM50. Biology (Basel) 11:.

Zheng, H., C. Ji, X. Zou, M. Wu, Z. Jin, G. Yin, J. Li, C. Feng, H. Cheng, S. Gu, Y. Xie, and Y. Mao. (2003). Molecular cloning and characterization of a novel human putative transmembrane protein homologous to mouse sideroflexin associated with sideroblastic anemia. DNA Seq 14: 369-373.

Examples:

TC#NameOrganismal TypeExample
2.A.54.1.1

Mitochondrial serine (and possibly cystine and alanine) carrier, Sideroflexin-1 (SFXN1; SLC56A1), of 322 aas and probably 5 TMSs (Kory et al. 2018). This system is believed to be required for one-carbon metabolism because serine is converted into glycine and formate in the mitochondrion. SFXN1, an integral inner mitochondrial membrane (IMM) protein with an uneven number of transmembrane domains, is a TIM22 complex substrate. An SFXN1 deficiency leads to mitochondrial respiratory chain impairments, the most detrimental being to complex III (CIII) biogenesis, activity, and assembly, compromising coenzyme Q levels (Acoba et al. 2021). The CIII dysfunction is independent of one-carbon metabolism, the known primary role for SFXN1 as a mitochondrial serine transporter. Instead, SFXN1 supports CIII function by participating in heme and alpha-ketoglutarate metabolism. Thus, SFXN1-based amino acid transport impacts mitochondrial and cellular metabolic efficiency in multiple ways. The TIM22 complex mediates the import of sideroflexins which transport L- and D-serine and other amino acids, and it is therefore required for efficient mitochondrial one-carbon metabolism (Jackson et al. 2021). SFXN1 interacts with ATAD3 and HSD10, both associated with neurological disorders (Tifoun et al. 2022).

Eukaryotes

SFXN1 of Homo sapiens

 
2.A.54.1.10

Sideroflexin-4 isoform X4 of 327 aas and 7 probable TMSs in a 1 + 2 + 2 + 2 TMS arrangement. Sideroflexin 4 affects Fe-S cluster biogenesis, iron metabolism, mitochondrial respiration and heme biosynthetic enzymes (Paul et al. 2019; Gyimesi and Hediger 2020).

SFXN4 of Pogona vitticeps

 
2.A.54.1.11

Uncharacterized protein of 331 aas and 6 putative TMSs in a 2 + 2 + 2 TMS arrangement.

UP of Peronospora effusa

 
2.A.54.1.12

Putative tricarboxylate/iron carrier of 332 aas and 5 or 6 TMSs in a 1 or 2 + 2 + 2 TMS arrangment.

UP of Glomus cerebriforme

 
2.A.54.1.13

Sideroflexin 5 of 310 aas and 5 TMSs in a 1 + 2 + 2 TMS arrangement.

SFXN5 of Chrysochromulina tobinii

 
2.A.54.1.2Hypothetical 36.7 KDa protein AH6.2 Eukaryotes AH6.2 of Caenorhabditis elegans
 
2.A.54.1.3

Sideroflexin-4 (Breast cancer resistance marker 1) or SFXN4 (SLC56A4) of 337 aas and 6 TMSs in a  2 +2 + 2 TMS arrangement. It has been found mutated in mice with siderocytic anemia (Zheng et al. 2003).

Animals

Sideroflexin-4 of Homo sapiens

 
2.A.54.1.4Probable mitochondrial transport protein FSF1 (Fungal sideroflexin-1)FungiFSF1 of Saccharomyces cerevisiae
 
2.A.54.1.5

Sideroflexin-5 (SFXN5; SLC56A5) of 342 aas and 5 TMSs in a 1 + 2 + 2 TMS arrangement. The identification and characterization of the human sideroflexin 5 gene, and its high expression in the brain have been reported (Lockhart et al. 2002). It does not appear to be a Parkinson disease protein but may be a citrate transporter. It is 99% identical to the human ortholog.

Animals

Sfxn5 of Mus musculus

 
2.A.54.1.6

Sideroflexin-3, Sfxn3 or SLC56A3, of 321 aas and 4 TMSs in a 2 + 2 TMS arrangement. It is an α-synuclein-dependent mitochondrial protein that regulates synaptic morphology (Amorim et al. 2017). It is highly expressed in mature neurons of the mouse, with expression developing as development occurs from birth to adulthood.  Within neurons, Sfxn3 localizes to mitochondria in all major neuronal compartments (Rivell et al. 2019). The human ortholog is 94% identical to the mouse protein.

Animals

Sfxn3 of Mus musculus

 
2.A.54.1.7

Tricarboxylic acid (TCA) transporter of 327 aas and 6 TMSs. Found to be essential for bloodstream-form Trypanosoma brucei through a genome-wide RNAi screen (Schmidt et al. 2018).

TCA carrier of Trypanosoma brucei

 
2.A.54.1.8

Sideroflexin 2, SFXN2, TMEM241 or SLC56A2, of 322 aas and 5 or 6 TMSs in a 1 or 2 + 2 + 2 TMS arrangement.  SFXN2 is involved in mitochondrial iron metabolism and is localized to the mitochondrial inner membrane (Mon et al. 2019). SFXN2-knockout (KO) cells have an increased mitochondrial iron content and decreases in the heme content and heme-dependent enzyme activities. By contrast, the activities of iron-sulfur cluster-dependent enzymes were unchanged. Abnormal iron metabolism impaired mitochondrial respiration in SFXN2-KO cells and accelerated iron-mediated death (Mon et al. 2019). It may exert its effects by alterning heme biosynthesis.

SFXN2 of Homo sapiens

 
2.A.54.1.9

Sideroflexin4, SFXN4, of 479 aas and possibly 7 TMSs in a 1 + 2 + 2 + 2 TMS arrangement, is important for mitochondrial function.  Macrocytic anemia and mitochondriopathy result from a defect in SFXN4in humans (Hildick-Smith et al. 2013).

 

SFXN4 of Sturnus vulgaris