Dr Rémi Zallot

FHEA

Marie Skłodowska-Curie Individual Fellowship (awarded through competition and funded centrally by the EU)

r.g.zallot@swansea.ac.uk

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.

*- Co-first author