Eukaryotic organisms, including microbial members such as protists and green algae, utilize suites of transporter proteins to move essential metabolites across cell organelle membranes. Amongst these different transporter families, the mitochondrial carrier family (MCF) is one of the most diverse, encompassing essential NAD+ and ADP/ATP translocators, as well as amino acid, sugar and cofactor transporters. They are typically associated with the mitochondrial inner membrane, but some display more dynamic localization. Here, we perform a census of predicted MCF domains in the genome of the model diatom alga Phaeodactylum tricornutum, identifying a new family of three proteins (termed here and elsewhere "MCFc") with strong internal sequence conservation but limited similarity to other MCF proteins encoded in its genome. Considering both phylogenetic data and experimental localization, we posit that MCFc is widespread across algae with complex red chloroplasts alongside some primary green algae, and contains multiple subfamilies targeted to diatom mitochondria, plastids, and endomembranes. Finally, using data from Tara Oceans, we identify putative roles for MCFc in diatom cells, including a possible association of the plastid-targeted Phatr3_J46742 subfamily in cellular nitrate assimilation. Our data provide insights into the evolutionary diversification of the membrane transport mechanisms associated with diatoms and other eukaryotic algae.

CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution FR2022 Tara Oceans GOSEE Paris France

Department of Computational Quantitative and Synthetic Biology CNRS INSERM Université Paris France

Faculty of Science University of South Bohemia České Budějovice Czech Republic

Guangzhou Marine Geological Survey China Geological Survey Guangzhou China

Imagerie Photonique Paris Seine Paris France

Institut de Biologie de L'ENS Département de Biologie École Normale Supérieure CNRS INSERM Université PSL Paris France

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budějovice Czech Republic

Zobrazit více v PubMed

Agrimi, G., A. Russo, C. L. Pierri, and F. Palmieri. 2012. “The Peroxisomal NAD+ Carrier of Arabidopsis thaliana Transports Coenzyme A and Its Derivatives.” Journal of Bioenergetics and Biomembranes 44, no. 3: 333–340.

Agrimi, G., A. Russo, P. Scarcia, and F. Palmieri. 2012. “The Human Gene SLC25A17 Encodes a Peroxisomal Transporter of Coenzyme A, FAD and NAD+.” Biochemical Journal 443, no. 1: 241–247.

Ait‐Mohamed, O., A. M. G. Novák Vanclová, N. Joli, et al. 2020. “PhaeoNet: A Holistic RNAseq‐Based Portrait of Transcriptional Coordination in the Model Diatom.” Frontiers in Plant Science 11: 590949.

Alipanah, L., J. Rohloff, P. Winge, A. M. Bones, and T. Brembu. 2015. “Whole‐Cell Response to Nitrogen Deprivation in the Diatom Phaeodactylum tricornutum.” Journal of Experimental Botany 66, no. 20: 6281–6296.

Ashworth, J., S. Turkarslan, M. Harris, M. V. Orellana, and N. S. Baliga. 2016. “Pan‐Transcriptomic Analysis Identifies Coordinated and Orthologous Functional Modules in the Diatoms Thalassiosira Pseudonana and Phaeodactylum tricornutum.” Marine Genomics 26: 21–28.

Ast, M., A. Gruber, S. Schmitz‐Esser, et al. 2009. “Diatom Plastids Depend on Nucleotide Import From the Cytosol.” Proceedings of the National Academy of Sciences of the United States of America 106, no. 9: 3621–3626.

Balamurugan, S., X. Wang, H. L. Wang, et al. 2017. “Occurrence of Plastidial Triacylglycerol Synthesis and the Potential Regulatory Role of AGPAT in the Model Diatom.” Biotechnology for Biofuels 10: 1–14.

Bendtsen, J. D., H. Nielsen, G. Von Heijne, and S. Brunak. 2004. “Improved Prediction of Signal Peptides: SignalP 3.0.” Journal of Molecular Biology 340, no. 4: 783–795.

Busseni, G., F. Rocha Jimenez Vieira, A. Amato, et al. 2019. “Meta‐Omics Reveals Genetic Flexibility of Diatom Nitrogen Transporters in Response to Environmental Changes.” Molecular Biology and Evolution 36, no. 11: 2522–2535.

Capella‐Gutiérrez, S., J. M. Silla‐Martínez, and T. Gabaldón. 2009. “trimAl: A Tool for Automated Alignment Trimming in Large‐Scale Phylogenetic Analyses.” Bioinformatics 25, no. 15: 1972–1973.

Dawson, P. A. 1973. “Observations on the Structure of Some Forms of GOMPHONEMA PARVULUM KÜTZ. Iii. Frustule FORMATION1.” Journal of Phycology 9, no. 4: 353–365.

Diekert, K., G. Kispal, B. Guiard, and R. Lill. 1999. “An Internal Targeting Signal Directing Proteins Into the Mitochondrial Intermembrane Space.” Proceedings of the National Academy of Sciences of the United States of America 96, no. 21: 11752–11757.

Edgar, R. C. 2004. “MUSCLE: Multiple Sequence Alignment With High Accuracy and High Throughput.” Nucleic Acids Research 32, no. 5: 1792–1797.

Falciatore, A., R. Casotti, C. Leblanc, C. Abrescia, and C. Bowler. 1999. “Transformation of Nonselectable Reporter Genes in Marine Diatoms.” Marine Biotechnology 1, no. 3: 239–251.

Fernie, A. R., J. H. F. Cavalcanti, and A. Nunes‐Nesi. 2020. “Metabolic Roles of Plant Mitochondrial Carriers.” Biomolecules 10, no. 7: 1013. https://doi.org/10.3390/biom10071013.

Fukasawa, Y., J. Tsuji, S. C. Fu, K. Tomii, P. Horton, and K. Imai. 2015. “MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites.” Molecular & Cellular Proteomics: MCP 14, no. 4: 1113–1126.

Gile, G. H., D. Moog, C. H. Slamovits, U. G. Maier, and J. M. Archibald. 2015. “Dual Organellar Targeting of Aminoacyl‐tRNA Synthetases in Diatoms and Cryptophytes.” Genome Biology and Evolution 7, no. 6: 1728–1742.

Giustini, C., D. Dal Bo, M. Storti, et al. 2025. A Mitochondrially Derived Plastidial Transporter Regulates Photosynthesis in the Diatom Phaeodactylum tricornutum. bioRxiv. https://doi.org/10.1101/2025.02.14.638225.

Grigoriev, I. V., R. D. Hayes, S. Calhoun, et al. 2021. “PhycoCosm, a Comparative Algal Genomics Resource.” Nucleic Acids Research 49, no. D1: D1004–D1011.

Gruber, A., C. McKay, G. Rocap, and M. Oborník. 2023. Comparison of Different Versions of SignalP and TargetP for Diatom Plastid Protein Predictions With ASAFind. arXiv (q‐bio.SC). https://doi.org/10.48550/ARXIV.2303.02509.

Gruber, A., G. Rocap, G. Rocap, P. G. Kroth, E. V. Armbrust, and T. Mock. 2015. “Plastid Proteome Prediction for Diatoms and Other Algae With Secondary Plastids of the Red Lineage.” Plant Journal: For Cell and Molecular Biology 81, no. 3: 519–528.

Gschloessl, B., Y. Guermeur, and J. M. Cock. 2008. “HECTAR: A Method to Predict Subcellular Targeting in Heterokonts.” BMC Bioinformatics 9: 393.

Hammond, M., R. G. Dorrell, D. Speijer, and J. Lukeš. 2022. “Eukaryotic Cellular Intricacies Shape Mitochondrial Proteomic Complexity.” BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology 44, no. 5: e2100258.

Huang, T., Y. Pan, E. Maréchal, and H. Hu. 2024. “Proteomes Reveal the Lipid Metabolic Network in the Complex Plastid of Phaeodactylum tricornutum.” Plant Journal: For Cell and Molecular Biology 117, no. 2: 385–403.

Huelsenbeck, J. P., and F. Ronquist. 2001. “MRBAYES: Bayesian Inference of Phylogenetic Trees.” Bioinformatics 17, no. 8: 754–755.

Ito, K., K. Matsukawa, and Y. Kato. 2006. “Functional Analysis of Skunk Cabbage SfUCPB, a Unique Uncoupling Protein Lacking the Fifth Transmembrane Domain, in Yeast Cells.” Biochemical and Biophysical Research Communications 349, no. 1: 383–390.

Jin, Z., Y. Sato, M. Kawashima, and M. Kanehisa. 2023. “KEGG Tools for Classification and Analysis of Viral Proteins.” Protein Science: A Publication of the Protein Society 32, no. 12: e4820.

Jumper, J., R. Evans, A. Pritzel, et al. 2021. “Highly Accurate Protein Structure Prediction With AlphaFold.” Nature 596, no. 7873: 583–589.

Kanehisa, M., M. Furumichi, Y. Sato, Y. Matsuura, and M. Ishiguro‐Watanabe. 2024. “KEGG: Biological Systems Database as a Model of the Real World.” Nucleic Acids Research 53: D672–D677. https://doi.org/10.1093/nar/gkae909.

Katoh, K., J. Rozewicki, and K. D. Yamada. 2019. “MAFFT Online Service: Multiple Sequence Alignment, Interactive Sequence Choice and Visualization.” Briefings in Bioinformatics 20, no. 4: 1160–1166.

Kearse, M., R. Moir, A. Wilson, et al. 2012. “Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data.” Bioinformatics 28, no. 12: 1647–1649.

Keeling, P. J., F. Burki, F. Burki, et al. 2014. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans Through Transcriptome Sequencing.” PLoS Biology 12, no. 6: e1001889.

Krogh, A., B. Larsson, G. Von Heijne, and E. L. L. Sonnhammer. 2001. “Predicting Transmembrane Protein Topology With a Hidden Markov Model: Application to Complete Genomes.” Journal of Molecular Biology 305, no. 3: 567–580.

Kroth, P. G., A. Chiovitti, A. Gruber, et al. 2008. “A Model for Carbohydrate Metabolism in the Diatom Phaeodactylum tricornutum Deduced From Comparative Whole Genome Analysis.” PLoS One 3, no. 1: e1426.

Kuan, J., and M. H. Saier Jr. 1993. “The Mitochondrial Carrier Family of Transport Proteins: Structural, Functional, and Evolutionary Relationships.” Critical Reviews in Biochemistry and Molecular Biology 28, no. 3: 209–233.

Kunji, E. R. S. 2004. “The Role and Structure of Mitochondrial Carriers.” FEBS Letters 564, no. 3: 239–244.

Lam, F., D. Cladière, D. Cladière, C. Guillaume, K. Wassmann, and S. Bolte. 2017. “Super‐Resolution for Everybody: An Image Processing Workflow to Obtain High‐Resolution Images With a Standard Confocal Microscope.” Methods 115: 17–27.

Lee, C. M., J. Sedman, W. Neupert, and R. A. Stuart. 1999. “The DNA Helicase, Hmi1p, Is Transported Into Mitochondria by a C‐Terminal Cleavable Targeting Signal.” Journal of Biological Chemistry 274, no. 30: 20937–20942.

Li, J., K. Zhang, L. Li, Y. Wang, and S. Lin. 2022. “Unsuspected Functions of Alkaline Phosphatase PhoD in the Diatom Phaeodactylum tricornutum.” Algal Research 68, no. 102873: 102873.

Liu, S., M. Storti, G. Finazzi, C. Bowler, and R. G. Dorrell. 2022. “A Metabolic, Phylogenomic and Environmental Atlas of Diatom Plastid Transporters From the Model Species.” Frontiers in Plant Science 13: 950467.

Liu, X., F. Hempel, S. Stork, et al. 2016. “Addressing Various Compartments of the Diatom Model Organism Phaeodactylum tricornutum via Sub‐Cellular Marker Proteins.” Algal Research 20: 249–257.

Mann, M., M. Serif, T. Wrobel, et al. 2020. “The Aureochrome Photoreceptor PtAUREO1a Is a Highly Effective Blue Light Switch in Diatoms.” iScience 23, no. 11: 101730.

McCarthy, J. K., S. R. Smith, M. C. JP, et al. 2017. “Nitrate Reductase Knockout Uncouples Nitrate Transport From Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom.” Plant Cell 29, no. 8: 2047–2070.

Miller, M. A., W. Pfeiffer, and T. Schwartz. 2010. “Creating the CIPRES Science Gateway for Inference of Large Phylogenetic Trees.” In Gateway Computing Environments Workshop (GCE). 2010 Gateway Computing Environments Workshop (GCE). IEEE. https://doi.org/10.1109/gce.2010.5676129.

Miyake, S.‐I., T. Yamashita, M. Taniguchi, M. Tamatani, K. Sato, and M. Tohyama. 2002. “Identification and Characterization of a Novel Mitochondrial Tricarboxylate Carrier.” Biochemical and Biophysical Research Communications 295, no. 2: 463–468.

Monné, M., and F. Palmieri. 2014. “Antiporters of the Mitochondrial Carrier Family.” Current Topics in Membranes 73: 289–320.

Moog, D., A. Nozawa, Y. Tozawa, and R. Kamikawa. 2020. “Substrate Specificity of Plastid Phosphate Transporters in a Non‐Photosynthetic Diatom and Its Implication in Evolution of Red Alga‐Derived Complex Plastids.” Scientific Reports 10, no. 1: 1167.

More, K. J., J. G. G. Kaufman, J. B. Dacks, and P. T. Manna. 2024. “Evolutionary Origins of the Lysosome‐Related Organelle Sorting Machinery Reveal Ancient Homology in Post‐Endosome Trafficking Pathways.” Proceedings of the National Academy of Sciences of the United States of America 121, no. 43: e2403601121.

Murik, O., L. Tirichine, J. Prihoda, et al. 2019. “Downregulation of Mitochondrial Alternative Oxidase Affects Chloroplast Function, Redox Status and Stress Response in a Marine Diatom.” New Phytologist 221, no. 3: 1303–1316.

Neckelmann, N., K. Li, R. P. Wade, R. Shuster, and D. C. Wallace. 1987. “cDNA Sequence of a Human Skeletal Muscle ADP/ATP Translocator: Lack of a Leader Peptide, Divergence From a Fibroblast Translocator cDNA, and Coevolution With Mitochondrial DNA Genes.” Proceedings of the National Academy of Sciences of the United States of America 84, no. 21: 7580–7584.

Novák Vanclová, A. M. G., and R. G. Dorrell. 2024. “Complex Plastids Across the Eukaryotes: An Overview of Inherited and Convergently Evolved Characters.” In Endosymbiotic Organelle Acquisition, 39–88. Springer International Publishing.

Nunes‐Nesi, A., J. H. F. Cavalcanti, and A. R. Fernie. 2020. “Characterization of In Vivo Function(s) of Members of the Plant Mitochondrial Carrier Family.” Biomolecules 10, no. 9: 1226.

Palmieri, F. 2004. “The Mitochondrial Transporter Family (SLC25): Physiological and Pathological Implications.” Pflügers Archiv/European Journal of Physiology 447, no. 5: 689–709.

Palmieri, F., C. L. Pierri, A. De Grassi, A. Nunes‐Nesi, and A. R. Fernie. 2011. “Evolution, Structure and Function of Mitochondrial Carriers: A Review With New Insights.” Plant Journal: For Cell and Molecular Biology 66, no. 1: 161–181.

Palmieri, F., B. Rieder, A. Ventrella, et al. 2009. “Molecular Identification and Functional Characterization of Arabidopsis thaliana Mitochondrial and Chloroplastic NAD+ Carrier Proteins.” Journal of Biological Chemistry 284, no. 45: 31249–31259.

Palmieri, L., H. Rottensteiner, W. Girzalsky, P. Scarcia, F. Palmieri, and R. Erdmann. 2001. “Identification and Functional Reconstitution of the Yeast Peroxisomal Adenine Nucleotide Transporter.” EMBO Journal 20, no. 18: 5049–5059.

Penot‐Raquin, M., M. Sivia, M. Fafoumi, R. Larson, R. G. Dorrell, and J. B. Dacks. 2025. Prevalence and Environmental Abundance of the Elusive Membrane Trafficking Complex TSET in Five Cosmopolitan Eukaryotic Groups. bioRxiv. https://doi.org/10.1101/2024.06.15.599112.

Pesant, S., F. Not, M. Picheral, et al. 2015. “Open Science Resources for the Discovery and Analysis of Tara Oceans Data.” Scientific Data 2: 150023.

Remmers, I. M., S. D'Adamo, D. E. Martens, et al. 2018. “Orchestration of Transcriptome, Proteome and Metabolome in the Diatom Phaeodactylum tricornutum During Nitrogen Limitation.” Algal Research 35: 33–49.

Richards, T. A., L. Eme, J. M. Archibald, et al. 2024. “Reconstructing the Last Common Ancestor of all Eukaryotes.” PLoS Biology 22, no. 11: e3002917.

Ruprecht, J. J., and E. R. S. Kunji. 2020. “The SLC25 Mitochondrial Carrier Family: Structure and Mechanism.” Trends in Biochemical Sciences 45, no. 3: 244–258.

Russo, M. T., R. Annunziata, R. Sanges, M. I. Ferrante, and A. Falciatore. 2015. “The Upstream Regulatory Sequence of the Light Harvesting Complex Lhcf2 Gene of the Marine Diatom Phaeodactylum tricornutum Enhances Transcription in an Orientation‐ and Distance‐Independent Fashion.” Marine Genomics 24, no. Pt 1: 69–79.

Saier, M. H., Jr., C. V. Tran, and R. D. Barabote. 2006. “TCDB: The Transporter Classification Database for Membrane Transport Protein Analyses and Information.” Nucleic Acids Research 34: D181–D186.

Schober, A. F., C. Rïo Bïrtulos, A. Bischoff, B. Lepetit, A. Gruber, and P. G. Kroth. 2019. “Organelle Studies and Proteome Analyses of Mitochondria and Plastids Fractions From the Diatom Thalassiosira pseudonana.” Plant & Cell Physiology 60, no. 8: 1811–1828.

Serôdio, J., and J. Lavaud. 2020. “Diatoms and Their Ecological Importance.” In Encyclopedia of the UN Sustainable Development Goals, 1–9. Springer International Publishing.

Shu, H., Y. You, H. Wang, et al. 2022. “Transcriptomic‐Guided Phosphonate Utilization Analysis Unveils Evidence of Clathrin‐Mediated Endocytosis and Phospholipid Synthesis in the Model Diatom.” mSystems 7, no. 6: e0056322.

Siaut, M., M. Heijde, M. Mangogna, et al. 2007. “Molecular Toolbox for Studying Diatom Biology in Phaeodactylum tricornutum.” Gene 406, no. 1‐2: 23–35.

Smith, S. R., C. L. Dupont, M. C. JK, et al. 2019. “Evolution and Regulation of Nitrogen Flux Through Compartmentalized Metabolic Networks in a Marine Diatom.” Nature Communications 10, no. 1: 4552.

Stamatakis, A. 2014. “RAxML Version 8: A Tool for Phylogenetic Analysis and Post‐Analysis of Large Phylogenies.” Bioinformatics 30, no. 9: 1312–1313.

Suzek, B. E., Y. Wang, H. Huang, M. G. PB, and C. H. Wu. 2015. “UniRef Clusters: A Comprehensive and Scalable Alternative for Improving Sequence Similarity Searches.” Bioinformatics 31, no. 6: 926–932.

Tanaka, A., A. de Martino, A. Amato, et al. 2015. “Ultrastructure and Membrane Traffic During Cell Division in the Marine Pennate Diatom Phaeodactylum tricornutum.” Protist 166, no. 5: 506–521.

Toleco, M. R., T. Naake, Y. Zhang, J. L. Heazlewood, and A. R. Fernie. 2020. “Plant Mitochondrial Carriers: Molecular Gatekeepers That Help to Regulate Plant Central Carbon Metabolism.” Plants 9, no. 1: 117. https://doi.org/10.3390/plants9010117.

Ustick, L. J., A. A. Larkin, C. A. Garcia, et al. 2021. “Metagenomic Analysis Reveals Global‐Scale Patterns of Ocean Nutrient Limitation.” Science 372: 287–291.

Uwizeye, C., J. Decelle, P. H. Jouneau, et al. 2021. “Morphological Bases of Phytoplankton Energy Management and Physiological Responses Unveiled by 3D Subcellular Imaging.” Nature Communications 12, no. 1: 1049.

Villar, E., N. Zweig, P. Vincens, et al. 2025. “DiatOmicBase: A Versatile Gene‐Centered Platform for Mining Functional Omics Data in Diatom Research.” Plant Journal: For Cell and Molecular Biology 121, no. 6: e70061.