Dr Rémi Zallot

Dr. Rémi Zallot profile picture

Dr Rémi Zallot FHEA

Lecturer

Leveraging a multidisciplinary approach to deepen understanding of microbes for enhancing human health

My profile

Biography

Trained as a biologist at the Université de Bordeaux, France, I specialised in Biochemistry during my Licence in Biology, further delving into Plant Biology and Biotechnology during my Master’s degree. My academic journey culminated in a PhD from the Laboratoire de Biogenèse Membranaire, where I defended my thesis on “Identification and characterization of a lipase expressed during Arabidopsis thaliana reserves hydrolysis” in 2011.

Drawn by the investigative power of comparative genomics, I joined the Microbiology and Cell Science Department at the University of Florida, USA. Here, I contributed to characterising genes involved in B vitamin metabolism and tRNA modification metabolism in plants and microbes until 2016.

To further my bioinformatics skills, I joined the Enzyme Function Initiative team at the Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign. There, we enhanced the capabilities of the Enzyme Function Initiative webtools and provided training to biologists, facilitating hypothesis generation. My research concentrated on characterising genes from the gut microbiome until 2019.

Securing a Marie Skłodowska-Curie Individual Fellowship, funded by the European Commission’s Horizon 2020 program, I returned to Europe to conduct the deCrYPtion action (ID 839116) at Swansea University Medical School, UK. This project, titled “Decrypting Mycobacterium cytochrome P450 (CYP) physiological functions”, utilized large-scale comparative genomics analysis. Concurrently, I completed the Teaching in Higher Education Postgraduate Certification programme at Swansea, becoming a Fellow of the Higher Academy Education (FHEA).

In the subsequent years, I expanded my experience as a Research Associate at the Manchester Institute of Biotechnology (MIB), an affiliate of The University of Manchester, until 2023.

Since June 2023, I have been serving as a lecturer in the Department of Life Sciences at MMU, nurturing the next generation of scientists and researchers.

Interests and expertise

My work focuses on deepening our understanding of microbes with the ultimate goal of enhancing human health.

I employ a multidisciplinary approach that merges bioinformatics — specifically, comparative genomics and genomic enzymology — with experimental validation techniques drawn from various disciplines such as microbiology, genetics, and biochemistry. The strategy I use allows me to identify and decipher the biological function of uncharacterised genes, enzymes, and transporters that are important for health improvement.

I also contribute to the advancement of bioinformatics tools and provide support for their effective use. This aims to empower researchers to generate meaningful hypotheses easily.

As an educator, I strive for effective learning. I aim to foster an environment that stimulates intellectual curiosity, deep understanding, and skill development. I’m committed to equipping my students with the necessary tools and knowledge to become the professionals they aspire to be.

Get in touch

John Dalton Building

Research outputs

Publications

25     EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools.

Oberg N, Zallot R, Gerlt JA.

Journal of Molecular Biology. 2023 Feb 17:168018.

24    Mechanistic and Structural Insights into the Specificity and Biological Function of Bacterial Sulfoglycosidases

Zhang Z, Dong M, Zallot R, Ruan S, Blackburn GM, Wang N, Wang C, Chen L, Baumann P, Wu Z, Wang Z, Fan H, Roth C, Jin Y, He Y. Co-first author.

ACS Catalysis 2022,13, 1, 824–836

23    Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme

Li Q, Zallot R, MacTavish BS, Montoya A, Payan DJ, Hu Y, Gerlt JA, Angerhofer A, de Crécy-Lagard, Bruner SD.

Biochemistry 2021 60 (42), 3152–3161

22    Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools

Zallot R, N Oberg, Gerlt JA. First author.

Current Opinion in Biotechnology 2021 69, 77–90

21     The Enzyme Function Initiative (EFI) suite of genomic enzymology web tools: Leveraging protein, genome, and metagenome databases to discover novel enzymes and metabolic pathways

Zallot R, Oberg NO, Gerlt JA. First author.

Biochemistry. 2019 58(41), 4169–4182

20     Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens

Yuan Y, Zallot R, Grove TL, Payan DJ, Martin-Verstrate I, Šepić S, Balamkundu S, Neelakandan R, Gadi VK, Liu C-F, Swairjo MA, Dedon PC, Almo SC, Gerlt JA and de Crécy-Lagard V. Co-first author.

PNAS. 2019 116(38), 19126–19135

19     ‘Democratized’ genomic enzymology web tools for functional assignment.

Zallot R, Oberg NO, Gerlt JA. First author.

Curr Opin Chem Bio. 2018 47, 77–85

18     Functional assignment of multiple catabolic pathways for D-apiose.

Carter MS, Zhang X, Huang H, Bouvier JT, San Francisco B, Vetting MW, Al-Obaidi N, Bonanno JB, Ghosh A, Zallot R, Andersen HM, Almo SC, Gerlt JA.

Nat Chem Biol. 2018 14, 696–705

17     Gene Graphics: a genomic neighborhood data visualization web application.

Harrison KJ, de Crécy-Lagard V, Zallot R. Corresponding author

Bioinformatics. 2018 34(8), 1406–1408

16     The Escherichia coli COG1738 member YhhQ is involved in 7-Cyanodeazaguanine (preQ₀) transport.

Zallot R, Yuan Y, de Crécy-Lagard V. Corresponding author

Biomolecules. 2017 7(1), pii: E12

15     Identification of a novel epoxyqueuosine reductase family by comparative genomics.

Zallot R, Ross R, Chen WH, Bruner SD, Limbach PA, de Crécy-Lagard V. Corresponding author

ACS Chem Biol. 2017 12(3), 844–851

14     Arabidopsis TH2 encodes the orphan enzyme thiamin monophosphate phosphatase.

Mimura M, Zallot R, Niehaus TD, Hasnain G, Gidda SK, Nguyen TN, Anderson EM, Mullen RT, Brown G, Yakunin AF, de Crécy-Lagard V, Gregory JF 3rd, McCarty DR, Hanson AD. Co-first author.

Plant Cell. 2016 28(10), 2683–2696

13     Functional Annotations of Paralogs: A Blessing and a Curse.

Zallot R, Harrison KJ, Kolaczkowski B, de Crécy-Lagard V. Corresponding author

Life (Basel). 2016 6(3)

12     Systematic identification and analysis of frequent gene fusion events in metabolic pathways.

Henry CS, Lerma-Ortiz C, Gerdes SY, Mullen JD, Colasanti R, Zhukov A, Frelin O, Thiaville JJ, Zallot R, Niehaus TD, Hasnain G, Conrad N, Hanson AD, de Crécy-Lagard V. 

BMC Genomics. 2016 17, 473

11     A family of metal-dependent phosphatases implicated in metabolite damage-control.

Huang L, Khusnutdinova A, Nocek B, Brown G, Xu X, Cui H, Petit P, Flick R, Zallot R, Balmant K, Ziemak MJ, Shanklin J, de Crécy-Lagard V, Fiehn O, Gregory JF 3rd, Joachimiak A, Savchenko A, Yakunin AF, Hanson AD.

Nat Chem Biol. 2016 12(8), 621–627

10     Bacterial and plant HAD enzymes catalyse a missing phosphatase step in thiamin diphosphate biosynthesis.

Hasnain G, Roje S, Sa N, Zallot R, Ziemak MJ, de Crécy-Lagard V, Gregory JF 3rd, Hanson AD.

Biochem J. 2016 473(2), 157–166

9      Functional diversity of haloacid dehalogenase superfamily phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

Kuznetsova E, Nocek B, Brown G, Makarova KS, Flick R, Wolf YI, Khusnutdinova A, Evdokimova E, Jin K, Tan K, Hanson AD, Hasnain G, Zallot R, de Crécy-Lagard V, Babu M, Savchenko A, Joachimiak A, Edwards AM, Koonin EV, Yakunin AF. 

J Biol Chem. 2015 290(30), 18678–18698

8      Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine.

Zallot R, Yazdani M, Goyer A, Ziemak MJ, Guan JC, McCarty DR, de Crécy-Lagard V, Gerdes S, Garrett TJ, Benach J, Hunt JF, Shintani DK, Hanson AD. First author.

Biochem J. 2014 463(1), 145–155

7      High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.

Seaver SM, Gerdes S, Frelin O, Lerma-Ortiz C, Bradbury LM, Zallot R, Hasnain  G, Niehaus TD, El Yacoubi B, Pasternak S, Olson R, Pusch G, Overbeek R, Stevens R, de Crécy-Lagard V, Ware D, Hanson AD, Henry CS.

Proc Natl Acad Sci U S A. 2014 111(26), 9645–9650

6      Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. 

Zallot R, Brochier-Armanet C, Gaston KW, Forouhar F, Limbach PA, Hunt JF, de  Crécy-Lagard V.

ACS Chem Biol. 2014 9(8), 1812–1825. First author.

5    Identification of the thiamin salvage enzyme thiazole kinase in Arabidopsis and maize. 

Yazdani M, Zallot R, Tunc-Ozdemir M, de Crécy-Lagard V, Shintani DK, Hanson AD. Co-first author.

Phytochemistry. 2013 94, 68–73

4      Identification of mitochondrial coenzyme a transporters from maize and Arabidopsis.

Zallot R, Agrimi G, Lerma-Ortiz C, Teresinski HJ, Frelin O, Ellens KW, Castegna A, Russo A, de Crécy-Lagard V, Mullen RT, Palmieri F, Hanson AD. Co-first author.

Plant Physiol. 2013 162(2), 581–588

3      Acyl-lipid metabolism.

Li-Beisson Y, Shorrosh B, Beisson F, Andersson MX, Arondel V, Bates PD, Baud S, Bird D, Debono A, Durrett TP, Franke RB, Graham IA, Katayama K, Kelly AA, Larson T, Markham JE, Miquel M, Molina I, Nishida I, Rowland O, Samuels L, Schmid

KM, Wada H, Welti R, Xu C, Zallot R, Ohlrogge J. 

Arabidopsis Book. 2013 11, e0161

2     Polyphosphoinositides are enriched in plant membrane rafts and form microdomains in the plasma membrane.

Furt F, König S, Bessoule JJ, Sargueil F, Zallot R, Stanislas T, Noirot E, Lherminier J, Simon-Plas F, Heilmann I, Mongrand S. 

Plant Physiol. 2010 152(4), 2173–2187

1     Acyl-lipid metabolism.

Li-Beisson Y, Shorrosh B, Beisson F, Andersson MX, Arondel V, Bates PD, Baud  S, Bird D, Debono A, Durrett TP, Franke RB, Graham IA, Katayama K, Kelly AA, Larson T, Markham JE, Miquel M, Molina I, Nishida I, Rowland O, Samuels L, Schmid KM, Wada H, Welti R, Xu C, Zallot R, Ohlrogge J. 

Arabidopsis Book. 2010 8, e0133

  • Journal articles

    Xu, G., Torri, D., Cuesta-Hoyos, S., Panda, D., Yates, L.R.L., Zallot, R., Bian, K., Jia, D., Iorgu, A.I., Levy, C., Shepherd, S.A., Micklefield, J. (2024) 'Cryptic enzymatic assembly of peptides armed with β-lactone warheads.' Nature Chemical Biology, 20(10) pp. 1371-1379.

    de Crécy-Lagard, V., Hutinet, G., Cediel-Becerra, J.D.D., Yuan, Y., Zallot, R., Chevrette, M.G., Ratnayake, R.M.M.N., Jaroch, M., Quaiyum, S., Bruner, S. (2024) 'Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages.' Microbiology and Molecular Biology Reviews,

    Oberg, N., Zallot, R., Gerlt, J.A. (2023) 'EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools.' Journal of Molecular Biology, 435(14)

    Zhang, Z., Dong, M., Zallot, R., Blackburn, G.M., Wang, N., Wang, C., Chen, L., Baumann, P., Wu, Z., Wang, Z., Fan, H., Roth, C., Jin, Y., He, Y. (2023) 'Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases.' ACS Catalysis, 13(1) pp. 824-836.

    Li, Q., Zallot, R., Mactavish, B.S., Montoya, A., Payan, D.J., Hu, Y., Gerlt, J.A., Angerhofer, A., De Crécy-Lagard, V., Bruner, S.D. (2021) 'Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme.' Biochemistry, 60(42) pp. 3152-3161.

    Zallot, R., Oberg, N., Gerlt, J.A. (2021) 'Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools.' Current Opinion in Biotechnology, 69pp. 77-90.

    Zallot, R., Oberg, N., Gerlt, J.A. (2019) 'The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways.' Biochemistry, 58(41) pp. 4169-4182.

    Yuan, Y., Zallot, R., Grove, T.L., Payan, D.J., Martin-Verstraete, I., Šepić, S., Balamkundu, S., Neelakandan, R., Gadi, V.K., Liu, C.F., Swairjo, M.A., Dedon, P.C., Almo, S.C., Gerlt, J.A., de Crécy-Lagard, V. (2019) 'Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens.' Proceedings of the National Academy of Sciences of the United States of America, 116(38) pp. 19126-19135.

    Zallot, R., Oberg, N.O., Gerlt, J.A. (2018) '‘Democratized’ genomic enzymology web tools for functional assignment.' Current Opinion in Chemical Biology, 47pp. 77-85.

    Carter, M.S., Zhang, X., Huang, H., Bouvier, J.T., Francisco, B.S., Vetting, M.W., Al-Obaidi, N., Bonanno, J.B., Ghosh, A., Zallot, R.G., Andersen, H.M., Almo, S.C., Gerlt, J.A. (2018) 'Functional assignment of multiple catabolic pathways for d-apiose article.' Nature Chemical Biology, 14(7) pp. 696-705.

    Harrison, K.J., Crécy-Lagard, V.D., Zallot, R. (2018) 'Gene Graphics: A genomic neighborhood data visualization web application.' Bioinformatics, 34(8) pp. 1406-1408.

    Zallot, R., Ross, R., Chen, W.H., Bruner, S.D., Limbach, P.A., De Crécy-Lagard, V. (2017) 'Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics.' ACS Chemical Biology, 12(3) pp. 844-851.

    Zallot, R., Yuan, Y., De Crécy-Lagard, V. (2017) 'The escherichia coli COG1738 member YhhQ is involved in 7-cyanodeazaguanine (preQ0) transport.' Biomolecules, 7(1)

    Mimura, M., Zallot, R., Niehaus, T.D., Hasnain, G., Gidda, S.K., Nguyen, T.N.D., Anderson, E.M., Mullen, R.T., Brown, G., Yakunin, A.F., de Crécy-Lagard, V., Gregory, J.F., McCarty, D.R., Hanson, A.D. (2016) 'Arabidopsis TH2 encodes the orphan enzyme thiamin monophosphate phosphatase.' Plant Cell, 28(10) pp. 2683-2696.

    Zallot, R., Harrison, K.J., Kolaczkowski, B., De Crécy-Lagard, V. (2016) 'Functional annotations of paralogs: A blessing and a curse.' Life, 6(3)

    Huang, L., Khusnutdinova, A., Nocek, B., Brown, G., Xu, X., Cui, H., Petit, P., Flick, R., Zallot, R., Balmant, K., Ziemak, M.J., Shanklin, J., De Crécy-Lagard, V., Fiehn, O., Gregory, J.F., Joachimiak, A., Savchenko, A., Yakunin, A.F., Hanson, A.D. (2016) 'A family of metal-dependent phosphatases implicated in metabolite damage-control.' Nature Chemical Biology, 12(8) pp. 621-627.

    Henry, C.S., Lerma-Ortiz, C., Gerdes, S.Y., Mullen, J.D., Colasanti, R., Zhukov, A., Frelin, O., Thiaville, J.J., Zallot, R., Niehaus, T.D., Hasnain, G., Conrad, N., Hanson, A.D., de Crécy-Lagard, V. (2016) 'Systematic identification and analysis of frequent gene fusion events in metabolic pathways.' BMC Genomics, 17(1)

    Hasnain, G., Roje, S., Sa, N., Zallot, R., Ziemak, M.J., De Crécy-Lagard, V., Gregory, J.F., Hanson, A.D. (2016) 'Bacterial and plant HAD enzymes catalyse a missing phosphatase step in thiamin diphosphate biosynthesis.' Biochemical Journal, 473(2) pp. 157-166.

    Kuznetsova, E., Nocek, B., Brown, G., Makarova, K.S., Flick, R., Wolf, Y.I., Khusnutdinova, A., Evdokimova, E., Jin, K., Tan, K., Hanson, A.D., Hasnain, G., Zallot, R., De Crécy-Lagard, V., Babu, M., Savchenko, A., Joachimiak, A., Edwards, A.M., Koonin, E.V., Yakunin, A.F. (2015) 'Functional diversity of haloacid dehalogenase superfamily phosphatases from Saccharomyces cerevisiae: Biochemical, structural, and evolutionary insights.' Journal of Biological Chemistry, 290(30) pp. 18678-18698.

    Zallot, R., Yazdani, M., Goyer, A., Ziemak, M.J., Guan, J.C., McCarty, D.R., De Crécy-Lagard, V., Gerdes, S., Garrett, T.J., Benach, J., Hunt, J.F., Shintani, D.K., Hanson, A.D. (2014) 'Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine.' Biochemical Journal, 463(1) pp. 145-155.

    Zallot, R., Brochier-Armanet, C., Gaston, K.W., Forouhar, F., Limbach, P.A., Hunt, J.F., De Crécy-Lagard, V. (2014) 'Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family.' ACS Chemical Biology, 9(8) pp. 1812-1825.

    Seaver, S.M.D., Gerdes, S., Frelin, O., Lerma-Ortiz, C., Bradbury, L.M.T., Zallot, R., Hasnain, G., Niehaus, T.D., El Yacoubi, B., Pasternak, S., Olson, R., Pusch, G., Overbeek, R., Stevens, R., De Crécy-Lagard, V., Ware, D., Hanson, A.D., Henry, C.S. (2014) 'High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.' Proceedings of the National Academy of Sciences of the United States of America, 111(26) pp. 9645-9650.

    Yazdani, M., Zallot, R., Tunc-Ozdemir, M., De Crécy-Lagard, V., Shintani, D.K., Hanson, A.D. (2013) 'Identification of the thiamin salvage enzyme thiazole kinase in Arabidopsis and maize.' Phytochemistry, 94pp. 68-73.

    Li-Beisson, Y., Shorrosh, B., Beisson, F., Andersson, M.X., Arondel, V., Bates, P.D., Baud, S., Bird, D., Debono, A., Durrett, T.P., Franke, R.B., Graham, I.A., Katayama, K., Kelly, A.A., Larson, T., Markham, J.E., Miquel, M., Molina, I., Nishida, I., Rowland, O., Samuels, L., Schmid, K.M., Wada, H., Welti, R., Xu, C., Zallot, R., Ohlrogge, J. (2013) 'Acyl-lipid metabolism..' The arabidopsis book, 11

    Zallot, R., Agrimi, G., Lerma-Ortiz, C., Teresinski, H.J., Frelin, O., Ellens, K.W., Castegna, A., Russo, A., de Crécy-Lagard, V., Mullen, R.T., Palmieri, F., Hanson, A.D. (2013) 'Identification of mitochondrial coenzyme a transporters from maize and Arabidopsis.' Plant Physiology, 162(2) pp. 581-588.

    Furt, F., König, S., Bessoule, J.J., Sargueil, F., Zallot, R., Stanislas, T., Noirot, E., Lherminier, J., Simon-Plas, F., Heilmann, I., Mongrand, S. (2010) 'Polyphosphoinositides are enriched in plant membrane rafts and form microdomains in the plasma membrane.' Plant Physiology, 152(4) pp. 2173-2187.

    Li-Beisson, Y., Shorrosh, B., Beisson, F., Andersson, M.X., Arondel, V., Bates, P.D., Baud, S., Bird, D., Debono, A., Durrett, T.P., Franke, R.B., Graham, I.A., Katayama, K., Kelly, A.A., Larson, T., Markham, J.E., Miquel, M., Molina, I., Nishida, I., Rowland, O., Samuels, L., Schmid, K.M., Wada, H., Welti, R., Xu, C., Zallot, R., Ohlrogge, J. (2010) 'Acyl-lipid metabolism..' The arabidopsis book, 8