Publications

Journal Articles

1. A cloaked glutamate decarboxylase sustains the GABA shunt in Mycobacterium tuberculosis H. Minh Thai, Debbie M. Hunt, Yugen Miyahara, Manisha Priya, Htin L. Aung, Rémi Zallot, Luiz Pedro S. de Carvalho. Proceedings of the National Academy of Sciences, 123(34), e2619778123, 2026. · doi:10.1073/pnas.2619778123
2. Cryptic enzymatic assembly of peptides armed with β-lactone warheads Guangcai Xu, Daniele Torri, Sebastian Cuesta-Hoyos, Deepanjan Panda, Luke Yates, Rémi Zallot, Kehan Bian, Dongxu Jia, Andreea Iorgu, Colin Levy. Nature chemical biology, 2024. · doi:10.1038/s41589-024-01657-7
3. Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages Valérie Crécy-Lagard, Geoffrey Hutinet, José Cediel-Becerra, Yifeng Yuan, Rémi Zallot, Marc Chevrette, RM Ratnayake, Marshall Jaroch, Samia Quaiyum, Steven Bruner. Microbiology and Molecular Biology Reviews, 2024. · doi:10.1128/mmbr.00199-23
4. Bioinformatics-facilitated identification of novel bacterial sulfoglycosidases that hydrolyze 6-Sulfo-N-acetylglucosamine Mochen Dong, Zhuoyun Chen, Yuan He, Rémi Zallot, Yi Jin. ACS Bio & Med Chem Au, 2024. · doi:10.1021/acsbiomedchemau.4c00088
5. EFI-EST, EFI-GNT, and EFI-CGFP: enzyme function initiative (EFI) web resource for genomic enzymology tools Nils Oberg, Rémi Zallot, John Gerlt. Journal of molecular biology, 2023. · doi:10.1016/j.jmb.2023.168018
6. Mechanistic and structural insights into the specificity and biological functions of bacterial sulfoglycosidases Zhen Zhang, Mochen Dong, Rémi Zallot, George Blackburn, Nini Wang, Chengjian Wang, Long Chen, Patrick Baumann, Zuyan Wu, Zhongfu Wang. ACS Catalysis, 2022. · doi:10.1021/acscatal.2c05405
7. Epoxyqueuosine reductase QueH in the biosynthetic pathway to tRNA queuosine is a unique metalloenzyme Qiang Li, Rémi Zallot, Brian MacTavish, Alvaro Montoya, Daniel Payan, You Hu, John Gerlt, Alexander Angerhofer, Valérie Crécy-Lagard, Steven Bruner. Biochemistry, 2021. · doi:10.1021/acs.biochem.1c00164
8. Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools Remi Zallot, Nils Oberg, John Gerlt. Current opinion in biotechnology, 2021. · doi:10.1016/j.copbio.2020.12.004
9. The EFI web resource for genomic enzymology tools: leveraging protein, genome, and metagenome databases to discover novel enzymes and metabolic pathways Rémi Zallot, Nils Oberg, John Gerlt. Biochemistry, 2019. · doi:10.1021/acs.biochem.9b00735
10. Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens Yifeng Yuan, Rémi Zallot, Tyler Grove, Daniel Payan, Isabelle Martin-Verstraete, Sara Šepić, Seetharamsingh Balamkundu, Ramesh Neelakandan, Vinod Gadi, Chuan-Fa Liu. Proceedings of the National Academy of Sciences, 2019. · doi:10.1073/pnas.1909604116
11. Gene Graphics: a genomic neighborhood data visualization web application Katherine Harrison, Valérie Crécy-Lagard, Rémi Zallot. Bioinformatics, 2018. · doi:10.1093/bioinformatics/btx793
12. Functional assignment of multiple catabolic pathways for D-apiose Michael Carter, Xinshuai Zhang, Hua Huang, Jason Bouvier, Brian Francisco, Matthew Vetting, Nawar Al-Obaidi, Jeffrey Bonanno, Agnidipta Ghosh, Rémi Zallot. Nature chemical biology, 2018. · doi:10.1038/s41589-018-0067-7
13. ‘Democratized’ genomic enzymology web tools for functional assignment Rémi Zallot, Nils Oberg, John Gerlt. Current opinion in chemical biology, 2018. · doi:10.1016/j.cbpa.2018.09.009
14. The Escherichia coli COG1738 member YhhQ is involved in 7-cyanodeazaguanine (preQ0) transport Rémi Zallot, Yifeng Yuan, Valérie Crécy-Lagard. Biomolecules, 2017. · doi:10.3390/biom7010012
15. Identification of a novel epoxyqueuosine reductase family by comparative genomics Rémi Zallot, Robert Ross, Wei-Hung Chen, Steven Bruner, Patrick Limbach, Valérie Crécy-Lagard. ACS chemical biology, 2017. · doi:10.1021/acschembio.6b01100
16. Systematic identification and analysis of frequent gene fusion events in metabolic pathways Christopher Henry, Claudia Lerma-Ortiz, Svetlana Gerdes, Jeffrey Mullen, Ric Colasanti, Aleksey Zhukov, Océane Frelin, Jennifer Thiaville, Rémi Zallot, Thomas Niehaus. BMC genomics, 2016. · doi:10.1186/s12864-016-2782-3
17. Functional annotations of paralogs: a blessing and a curse Rémi Zallot, Katherine Harrison, Bryan Kolaczkowski, Valérie Crécy-Lagard. Life, 2016. · doi:10.3390/life6030039
18. Bacterial and plant HAD enzymes catalyse a missing phosphatase step in thiamin diphosphate biosynthesis Ghulam Hasnain, Sanja Roje, Na Sa, Rémi Zallot, Michael Ziemak, Valérie Crécy-Lagard, Jesse Gregory, Andrew Hanson. Biochemical Journal, 2016. · doi:10.1042/bj20150805
19. Arabidopsis TH2 encodes the orphan enzyme thiamin monophosphate phosphatase Manaki Mimura, Rémi Zallot, Thomas Niehaus, Ghulam Hasnain, Satinder Gidda, Thuy Nguyen, Erin Anderson, Robert Mullen, Greg Brown, Alexander Yakunin. The Plant Cell, 2016. · doi:10.1105/tpc.16.00600
20. A family of metal-dependent phosphatases implicated in metabolite damage-control Lili Huang, Anna Khusnutdinova, Boguslaw Nocek, Greg Brown, Xiaohui Xu, Hong Cui, Pierre Petit, Robert Flick, Remi Zallot, Kelly Balmant. Nature Chemical Biology, 2016. · doi:10.1038/nchembio.2108
21. Functional diversity of haloacid dehalogenase superfamily phosphatases from Saccharomyces cerevisiae: biochemical, structural, and evolutionary insights Ekaterina Kuznetsova, Boguslaw Nocek, Greg Brown, Kira Makarova, Robert Flick, Yuri Wolf, Anna Khusnutdinova, Elena Evdokimova, Ke Jin, Kemin Tan. Journal of Biological Chemistry, 2015. · doi:10.1074/jbc.m115.657916
22. Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine Rémi Zallot, Mohammad Yazdani, Aymeric Goyer, Michael Ziemak, Jiahn-Chou Guan, Donald McCarty, Valérie Crécy-Lagard, Svetlana Gerdes, Timothy Garrett, Jordi Benach. Biochemical Journal, 2014. · doi:10.1042/bj20140522
23. Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family Rémi Zallot, Céline Brochier-Armanet, Kirk Gaston, Farhad Forouhar, Patrick Limbach, John Hunt, Valérie Crécy-Lagard. ACS chemical biology, 2014. · doi:10.1021/cb500278k
24. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource Samuel Seaver, Svetlana Gerdes, Océane Frelin, Claudia Lerma-Ortiz, Louis Bradbury, Rémi Zallot, Ghulam Hasnain, Thomas Niehaus, Basma El, Shiran Pasternak. Proceedings of the National Academy of Sciences, 2014. · doi:10.1073/pnas.1401329111
25. Identification of the thiamin salvage enzyme thiazole kinase in Arabidopsis and maize Mohammad Yazdani, Rémi Zallot, Meral Tunc-Ozdemir, Valérie Crécy-Lagard, David Shintani, Andrew Hanson. Phytochemistry, 2013. · doi:10.1016/j.phytochem.2013.05.017
26. Identification of mitochondrial coenzyme a transporters from maize and Arabidopsis Rémi Zallot, Gennaro Agrimi, Claudia Lerma-Ortiz, Howard Teresinski, Océane Frelin, Kenneth Ellens, Alessandra Castegna, Annamaria Russo, Valérie Crécy-Lagard, Robert Mullen. Plant physiology, 2013. · doi:10.1104/pp.113.218081
27. Acyl-lipid metabolism Yonghua Li-Beisson, Basil Shorrosh, Fred Beisson, Mats Andersson, Vincent Arondel, Philip Bates, Sébastien Baud, David Bird, Allan DeBono, Timothy Durrett. The Arabidopsis book/American Society of Plant Biologists, 2013. · doi:10.1199/tab.0161
28. Identification et caractérisation d'une lipase exprimée pendant l'hydrolyse des réserves chez Arabidopsis thaliana Rémi Zallot. , 2011. · doi:10.70675/9dd49aa6zb8d6z4630z8574zc0b1ebd25e43
29. Acyl-lipid metabolism Y. Li-Beisson, B. Shorrosh, F. Beisson, M. Andersson, V. Arondel, P. Bates, S. Baud, D. Bird, A. DeBono, T. Durrett. The Arabidopsis book/American Society of Plant Biologists, 2010. · doi:10.1199/tab.0133
30. Polyphosphoinositides are enriched in plant membrane rafts and form microdomains in the plasma membrane Fabienne Furt, Sabine König, Jean-Jacques Bessoule, Françoise Sargueil, Rémi Zallot, Thomas Stanislas, Elodie Noirot, Jeanine Lherminier, Françoise Simon-Plas, Ingo Heilmann. Plant physiology, 2010. · doi:10.1104/pp.109.149823