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Gene Graphics

Published: January 2018

A web application for visualizing genomic neighborhoods, published in Bioinformatics (2018).

EFI web tools (EFI-EST, EFI-GNT, EFI-CGFP)

Published: January 2019

Genomic enzymology web tools for the Enzyme Function Initiative, developed and maintained with Nils Oberg and John Gerlt.

publications

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

Published in Plant physiology, 2010

DOI: 10.1104/pp.109.149823

Recommended citation: Fabienne Furt, Sabine König, Jean-Jacques Bessoule, Françoise Sargueil, Rémi Zallot, Thomas Stanislas, Elodie Noirot, Jeanine Lherminier, Françoise Simon-Plas, Ingo Heilmann. "Polyphosphoinositides are enriched in plant membrane rafts and form microdomains in the plasma membrane." Plant physiology, 2010.

The arabidopsis book

Published in American Society of Plant Biologists, 2010

DOI: 10.1199/tab.0133

Recommended citation: 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.

Identification et caractérisation d'une lipase exprimée pendant l'hydrolyse des réserves chez Arabidopsis thaliana

Published in , 2011

DOI: 10.70675/9dd49aa6zb8d6z4630z8574zc0b1ebd25e43

Recommended citation: Rémi Zallot. "Identification et caractérisation d'une lipase exprimée pendant l'hydrolyse des réserves chez Arabidopsis thaliana." , 2011.

Acyl-lipid metabolism

Published in The Arabidopsis book/American Society of Plant Biologists, 2013

DOI: 10.1199/tab.0161

Recommended citation: Yonghua Li-Beisson, Basil Shorrosh, Fred Beisson, Mats Andersson, Vincent Arondel, Philip Bates, Sébastien Baud, David Bird, Allan DeBono, Timothy Durrett. "Acyl-lipid metabolism." The Arabidopsis book/American Society of Plant Biologists, 2013.

Identification of mitochondrial coenzyme a transporters from maize and Arabidopsis

Published in Plant physiology, 2013

DOI: 10.1104/pp.113.218081

Recommended citation: Rémi Zallot, Gennaro Agrimi, Claudia Lerma-Ortiz, Howard Teresinski, Océane Frelin, Kenneth Ellens, Alessandra Castegna, Annamaria Russo, Valérie Crécy-Lagard, Robert Mullen. "Identification of mitochondrial coenzyme a transporters from maize and Arabidopsis." Plant physiology, 2013.

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

Published in Phytochemistry, 2013

DOI: 10.1016/j.phytochem.2013.05.017

Recommended citation: Mohammad Yazdani, Rémi Zallot, Meral Tunc-Ozdemir, Valérie Crécy-Lagard, David Shintani, Andrew Hanson. "Identification of the thiamin salvage enzyme thiazole kinase in Arabidopsis and maize." Phytochemistry, 2013.

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

Published in Proceedings of the National Academy of Sciences, 2014

DOI: 10.1073/pnas.1401329111

Recommended citation: Samuel Seaver, Svetlana Gerdes, Océane Frelin, Claudia Lerma-Ortiz, Louis Bradbury, Rémi Zallot, Ghulam Hasnain, Thomas Niehaus, Basma El, Shiran Pasternak. "High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource." Proceedings of the National Academy of Sciences, 2014.

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

Published in ACS chemical biology, 2014

DOI: 10.1021/cb500278k

Recommended citation: Rémi Zallot, Céline Brochier-Armanet, Kirk Gaston, Farhad Forouhar, Patrick Limbach, John Hunt, Valérie Crécy-Lagard. "Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family." ACS chemical biology, 2014.

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

Published in Biochemical Journal, 2014

DOI: 10.1042/bj20140522

Recommended citation: Rémi Zallot, Mohammad Yazdani, Aymeric Goyer, Michael Ziemak, Jiahn-Chou Guan, Donald McCarty, Valérie Crécy-Lagard, Svetlana Gerdes, Timothy Garrett, Jordi Benach. "Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine." Biochemical Journal, 2014.

Functional diversity of haloacid dehalogenase superfamily phosphatases from Saccharomyces cerevisiae: biochemical, structural, and evolutionary insights

Published in Journal of Biological Chemistry, 2015

DOI: 10.1074/jbc.m115.657916

Recommended citation: Ekaterina Kuznetsova, Boguslaw Nocek, Greg Brown, Kira Makarova, Robert Flick, Yuri Wolf, Anna Khusnutdinova, Elena Evdokimova, Ke Jin, Kemin Tan. "Functional diversity of haloacid dehalogenase superfamily phosphatases from Saccharomyces cerevisiae: biochemical, structural, and evolutionary insights." Journal of Biological Chemistry, 2015.

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

Published in Nature Chemical Biology, 2016

DOI: 10.1038/nchembio.2108

Recommended citation: Lili Huang, Anna Khusnutdinova, Boguslaw Nocek, Greg Brown, Xiaohui Xu, Hong Cui, Pierre Petit, Robert Flick, Remi Zallot, Kelly Balmant. "A family of metal-dependent phosphatases implicated in metabolite damage-control." Nature Chemical Biology, 2016.

Arabidopsis TH2 encodes the orphan enzyme thiamin monophosphate phosphatase

Published in The Plant Cell, 2016

DOI: 10.1105/tpc.16.00600

Recommended citation: Manaki Mimura, Rémi Zallot, Thomas Niehaus, Ghulam Hasnain, Satinder Gidda, Thuy Nguyen, Erin Anderson, Robert Mullen, Greg Brown, Alexander Yakunin. "Arabidopsis TH2 encodes the orphan enzyme thiamin monophosphate phosphatase." The Plant Cell, 2016.

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

Published in Biochemical Journal, 2016

DOI: 10.1042/bj20150805

Recommended citation: Ghulam Hasnain, Sanja Roje, Na Sa, Rémi Zallot, Michael Ziemak, Valérie Crécy-Lagard, Jesse Gregory, Andrew Hanson. "Bacterial and plant HAD enzymes catalyse a missing phosphatase step in thiamin diphosphate biosynthesis." Biochemical Journal, 2016.

Functional annotations of paralogs: a blessing and a curse

Published in Life, 2016

DOI: 10.3390/life6030039

Recommended citation: Rémi Zallot, Katherine Harrison, Bryan Kolaczkowski, Valérie Crécy-Lagard. "Functional annotations of paralogs: a blessing and a curse." Life, 2016.

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

Published in BMC genomics, 2016

DOI: 10.1186/s12864-016-2782-3

Recommended citation: Christopher Henry, Claudia Lerma-Ortiz, Svetlana Gerdes, Jeffrey Mullen, Ric Colasanti, Aleksey Zhukov, Océane Frelin, Jennifer Thiaville, Rémi Zallot, Thomas Niehaus. "Systematic identification and analysis of frequent gene fusion events in metabolic pathways." BMC genomics, 2016.

Identification of a novel epoxyqueuosine reductase family by comparative genomics

Published in ACS chemical biology, 2017

DOI: 10.1021/acschembio.6b01100

Recommended citation: Rémi Zallot, Robert Ross, Wei-Hung Chen, Steven Bruner, Patrick Limbach, Valérie Crécy-Lagard. "Identification of a novel epoxyqueuosine reductase family by comparative genomics." ACS chemical biology, 2017.

The Escherichia coli COG1738 member YhhQ is involved in 7-cyanodeazaguanine (preQ0) transport

Published in Biomolecules, 2017

DOI: 10.3390/biom7010012

Recommended citation: Rémi Zallot, Yifeng Yuan, Valérie Crécy-Lagard. "The Escherichia coli COG1738 member YhhQ is involved in 7-cyanodeazaguanine (preQ0) transport." Biomolecules, 2017.

‘Democratized’genomic enzymology web tools for functional assignment

Published in Current opinion in chemical biology, 2018

DOI: 10.1016/j.cbpa.2018.09.009

Recommended citation: Rémi Zallot, Nils Oberg, John Gerlt. "‘Democratized’genomic enzymology web tools for functional assignment." Current opinion in chemical biology, 2018.

Functional assignment of multiple catabolic pathways for D-apiose

Published in Nature chemical biology, 2018

DOI: 10.1038/s41589-018-0067-7

Recommended citation: Michael Carter, Xinshuai Zhang, Hua Huang, Jason Bouvier, Brian Francisco, Matthew Vetting, Nawar Al-Obaidi, Jeffrey Bonanno, Agnidipta Ghosh, Rémi Zallot. "Functional assignment of multiple catabolic pathways for D-apiose." Nature chemical biology, 2018.

Gene Graphics: a genomic neighborhood data visualization web application

Published in Bioinformatics, 2018

DOI: 10.1093/bioinformatics/btx793

Recommended citation: Katherine Harrison, Valérie Crécy-Lagard, Rémi Zallot. "Gene Graphics: a genomic neighborhood data visualization web application." Bioinformatics, 2018.

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

Published in Proceedings of the National Academy of Sciences, 2019

DOI: 10.1073/pnas.1909604116

Recommended citation: Yifeng Yuan, Rémi Zallot, Tyler Grove, Daniel Payan, Isabelle Martin-Verstraete, Sara Šepić, Seetharamsingh Balamkundu, Ramesh Neelakandan, Vinod Gadi, Chuan-Fa Liu. "Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens." Proceedings of the National Academy of Sciences, 2019.

The EFI web resource for genomic enzymology tools: leveraging protein, genome, and metagenome databases to discover novel enzymes and metabolic pathways

Published in Biochemistry, 2019

DOI: 10.1021/acs.biochem.9b00735

Recommended citation: Rémi Zallot, Nils Oberg, John Gerlt. "The EFI web resource for genomic enzymology tools: leveraging protein, genome, and metagenome databases to discover novel enzymes and metabolic pathways." Biochemistry, 2019.

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

Published in Current opinion in biotechnology, 2021

DOI: 10.1016/j.copbio.2020.12.004

Recommended citation: Remi Zallot, Nils Oberg, John Gerlt. "Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools." Current opinion in biotechnology, 2021.

Epoxyqueuosine reductase QueH in the biosynthetic pathway to tRNA queuosine is a unique metalloenzyme

Published in Biochemistry, 2021

DOI: 10.1021/acs.biochem.1c00164

Recommended citation: Qiang Li, Rémi Zallot, Brian MacTavish, Alvaro Montoya, Daniel Payan, You Hu, John Gerlt, Alexander Angerhofer, Valérie Crécy-Lagard, Steven Bruner. "Epoxyqueuosine reductase QueH in the biosynthetic pathway to tRNA queuosine is a unique metalloenzyme." Biochemistry, 2021.

Mechanistic and structural insights into the specificity and biological functions of bacterial sulfoglycosidases

Published in ACS Catalysis, 2022

DOI: 10.1021/acscatal.2c05405

Recommended citation: Zhen Zhang, Mochen Dong, Rémi Zallot, George Blackburn, Nini Wang, Chengjian Wang, Long Chen, Patrick Baumann, Zuyan Wu, Zhongfu Wang. "Mechanistic and structural insights into the specificity and biological functions of bacterial sulfoglycosidases." ACS Catalysis, 2022.

EFI-EST, EFI-GNT, and EFI-CGFP: enzyme function initiative (EFI) web resource for genomic enzymology tools

Published in Journal of molecular biology, 2023

DOI: 10.1016/j.jmb.2023.168018

Recommended citation: Nils Oberg, Rémi Zallot, John Gerlt. "EFI-EST, EFI-GNT, and EFI-CGFP: enzyme function initiative (EFI) web resource for genomic enzymology tools." Journal of molecular biology, 2023.

Bioinformatics-facilitated identification of novel bacterial sulfoglycosidases that hydrolyze 6-Sulfo-N-acetylglucosamine

Published in ACS Bio & Med Chem Au, 2024

DOI: 10.1021/acsbiomedchemau.4c00088

Recommended citation: Mochen Dong, Zhuoyun Chen, Yuan He, Rémi Zallot, Yi Jin. "Bioinformatics-facilitated identification of novel bacterial sulfoglycosidases that hydrolyze 6-Sulfo-N-acetylglucosamine." ACS Bio & Med Chem Au, 2024.

Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages

Published in Microbiology and Molecular Biology Reviews, 2024

DOI: 10.1128/mmbr.00199-23

Recommended citation: Valérie Crécy-Lagard, Geoffrey Hutinet, José Cediel-Becerra, Yifeng Yuan, Rémi Zallot, Marc Chevrette, RM Ratnayake, Marshall Jaroch, Samia Quaiyum, Steven Bruner. "Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages." Microbiology and Molecular Biology Reviews, 2024.

Cryptic enzymatic assembly of peptides armed with β-lactone warheads

Published in Nature chemical biology, 2024

DOI: 10.1038/s41589-024-01657-7

Recommended citation: Guangcai Xu, Daniele Torri, Sebastian Cuesta-Hoyos, Deepanjan Panda, Luke Yates, Rémi Zallot, Kehan Bian, Dongxu Jia, Andreea Iorgu, Colin Levy. "Cryptic enzymatic assembly of peptides armed with β-lactone warheads." Nature chemical biology, 2024.