Dr Rémi Zallot
FHEA
Marie Skłodowska-Curie Individual Fellowship (awarded through competition and funded centrally by the EU)
Qualifications
BSc Biology - Biochemistry (Université Bordeaux Ségalen, 2006)
MSc Plant Biology and Biotechnology (Université Bordeaux I, 2008)
PhD Plant Biology (Université Bordeaux Ségalen, 2011)
Areas of Expertise
Bioinformatics
Comparative genomics, genomic enzymology, genomic annotation
Biochemistry
Enzyme purification and assays, FPLC, HPLC, HPLC-MS, GC, TLC
Microbiology
Anaerobic prokaryotes, prokaryotes, eukaryotes
Genetics
KO, KD, CRISPR-Cas9, over-expression, functional complementation
Molecular Biology
RNAi, PCR, gene cloning and expression in bacterial and plant systems, nothern blots
Teaching
PM-256 Communicating Medical Sciences
PM-361 Bioinformatics: From Sequence to Function
PM-344 Capstone Project
Publications
2019
Zallot R, Oberg NO, Gerlt JA. The Enzyme Function Initiative (EFI) suite of genomic enzymology web tools: Leveraging protein, genome, and metagenome databases to discover novel enzymes and metabolic pathways. Biochemistry. 2019, https://doi.org/10.1021/acs.biochem.9b00735.
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, de Crécy-Lagard V. Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens. PNAS. 2019, 116(38), 19126-19135.
2018
Zallot R, Oberg NO, Gerlt JA. ‘Democratized’ genomic enzymology web tools for functional assignment. Curr Opin Chem Bio. 2018, 47, 77-85.
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. Functional assignment of multiple catabolic pathways for D-apiose. Nat Chem Biol. 2018, 14, 696-705.
Harrison KJ, de Crécy-Lagard V, Zallot R. Gene Graphics: a genomic neighborhood data visualization web application. Bioinformatics. 2018, 34(8), 1406-1408.
2017
Zallot R, Yuan Y, de Crécy-Lagard V. The Escherichia coli COG1738 member YhhQ is involved in 7-Cyanodeazaguanine (preQ₀) transport. Biomolecules. 2017, 7(1), 12.
Zallot R, Ross R, Chen WH, Bruner SD, Limbach PA, de Crécy-Lagard V. Identification of a novel epoxyqueuosine reductase family by comparative genomics. ACS Chem Biol. 2017, 12(3), 844-851.
2016
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. Arabidopsis TH2 encodes the orphan enzyme thiamin monophosphate phosphatase. Plant Cell. 2016, 28(10), 2683-2696.
Zallot R, Harrison KJ, Kolaczkowski B, de Crécy-Lagard V. Annotations of Paralogs: A Blessing and a Curse. Life (Basel). 2016, 6(3), 39.
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. Systematic identification and analysis of frequent gene fusion events in metabolic pathways. BMC Genomics. 2016, 17, 473.
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. A family of metal-dependent phosphatases implicated in metabolite damage-control. Nat Chem Biol. 2016, 12(8):621-7.
Hasnain G, Roje S, Sa N, Zallot R , Ziemak MJ, de Crécy-Lagard V, Gregory JF 3rd, Hanson AD. Bacterial and plant HAD enzymes catalyse a missing phosphatase step in thiamin diphosphate biosynthesis. Biochem J. 2016, 473(2):157-66.
2015
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. Functional diversity of haloacid dehalogenase superfamily phosphatases from Saccharomyces cerevisiae : BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS. J Biol Chem. 2015, 290(30):18678-98.
2014
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. Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine. Biochem J. 2014, 463(1):145-55.
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. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proc Natl Acad Sci U S A. 2014, 111(26):9645-50.
Zallot R , Brochier-Armanet C, Gaston KW, Forouhar F, Limbach PA, Hunt JF, de Crécy-Lagard V. Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. ACS Chem Biol. 2014, 9(8):1812-25.
2013
Yazdani M*, Zallot R* , Tunc-Ozdemir M, de Crécy-Lagard V, Shintani DK, Hanson AD. Identification of the thiamin salvage enzyme thiazole kinase in Arabidopsis and maize. Phytochemistry. 2013, 94:68-73.
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. Identification of mitochondrial coenzyme a transporters from maize and Arabidopsis. Plant Physiol. 2013, 162(2):581-8.
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. Acyl-lipid metabolism. Arabidopsis Book. 2013, 11:e0161.
2010
Furt F, König S, Bessoule JJ, Sargueil F, Zallot R , Stanislas T, Noirot E, Lherminier J, Simon-Plas F, Heilmann I, Mongrand S. Polyphosphoinositides are enriched in plant membrane rafts and form microdomains in the plasma membrane. Plant Physiol. 2010, 152(4):2173-87.
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. Acyl-lipid metabolism. Arabidopsis Book. 2013, 8:e0133.
*- Co-first author