Publications

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

Oberg, Nils, Rémi Zallot, and John A. Gerlt. "EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools." Journal of Molecular Biology (2023): 168018.

Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases

Zhang, Zhen, Mochen Dong, Rémi Zallot, George Michael Blackburn, Nini Wang, Chengjian Wang, Long Chen et al. "Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases." ACS Catalysis 13 (2022): 824-836.

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

Li, Qiang, Rémi Zallot, Brian S. MacTavish, Alvaro Montoya, Daniel J. Payan, You Hu, John A. Gerlt, Alexander Angerhofer, Valérie de Crécy-Lagard, and Steven D. Bruner. 2021. ‘Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to TRNA Queuosine Is a Unique Metalloenzyme’. Biochemistry 60(42):3152–61. doi: 10.1021/acs.biochem.1c00164.

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

Zallot, Rémi, Nils Oberg, and John A. Gerlt. 2021. ‘Discovery of New Enzymatic Functions and Metabolic Pathways Using Genomic Enzymology Web Tools’. Current Opinion in Biotechnology 69:77–90. doi: 10.1016/j.copbio.2020.12.004.

The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways

Zallot, Rémi, Nils Oberg, and John A. Gerlt. 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):4169–82. doi: 10.1021/acs.biochem.9b00735.

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

Yuan, Yifeng, Rémi Zallot, Tyler L. Grove, Daniel J. Payan, Isabelle Martin-Verstraete, Sara Šepić, Seetharamsingh Balamkundu, Ramesh Neelakandan, Vinod K. Gadi, Chuan-Fa Liu, Manal A. Swairjo, Peter C. Dedon, Steven C. Almo, John A. Gerlt, and Valérie de Crécy-Lagard. 2019. ‘Discovery of Novel Bacterial Queuine Salvage Enzymes and Pathways in Human Pathogens’. Proceedings of the National Academy of Sciences 116(38):19126–35. doi: 10.1073/pnas.1909604116.

‘Democratized’ genomic enzymology web tools for functional assignment

Zallot, Rémi, Nils O. Oberg, and John A. Gerlt. 2018. ‘“Democratized” Genomic Enzymology Web Tools for Functional Assignment’. Current Opinion in Chemical Biology 47:77–85. doi: 10.1016/j.cbpa.2018.09.009.

Functional assignment of multiple catabolic pathways for d-apiose

Carter, Michael S., Xinshuai Zhang, Hua Huang, Jason T. Bouvier, Brian San Francisco, Matthew W. Vetting, Nawar Al-Obaidi, Jeffrey B. Bonanno, Agnidipta Ghosh, Rémi G. Zallot, Harvey M. Andersen, Steven C. Almo, and John A. Gerlt. 2018. ‘Functional Assignment of Multiple Catabolic Pathways for D-Apiose’. Nature Chemical Biology 14(7):696–705. doi: 10.1038/s41589-018-0067-7.

Gene Graphics: a genomic neighborhood data visualization web application

Harrison, Katherine J., Valérie de Crécy-Lagard, and Rémi Zallot. 2018. ‘Gene Graphics: A Genomic Neighborhood Data Visualization Web Application’ edited by J. Hancock. Bioinformatics 34(8):1406–8. doi: 10.1093/bioinformatics/btx793.

Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics

Zallot, Rémi, Robert Ross, Wei-Hung Chen, Steven D. Bruner, Patrick A. Limbach, and Valérie de Crécy-Lagard. 2017. ‘Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics’. ACS Chemical Biology 12(3):844–51. doi: 10.1021/acschembio.6b01100.

The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ0) Transport

Zallot, Rémi, Yifeng Yuan, and Valérie de Crécy-Lagard. 2017. ‘The Escherichia Coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (PreQ0) Transport’. Biomolecules 7(4):12. doi: 10.3390/biom7010012.

Plant, Animal, and Fungal Micronutrient Queuosine Is Salvaged by Members of the DUF2419 Protein Family

Zallot, Rémi, Céline Brochier-Armanet, Kirk W. Gaston, Farhad Forouhar, Patrick A. Limbach, John F. Hunt, and Valérie de Crécy-Lagard. 2014. ‘Plant, Animal, and Fungal Micronutrient Queuosine Is Salvaged by Members of the DUF2419 Protein Family’. ACS Chemical Biology 9(8):1812–25. doi: 10.1021/cb500278k.

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

Henry, Christopher S., Claudia Lerma-Ortiz, Svetlana Y. Gerdes, Jeffrey D. Mullen, Ric Colasanti, Aleksey Zhukov, Océane Frelin, Jennifer J. Thiaville, Rémi Zallot, Thomas D. Niehaus, Ghulam Hasnain, Neal Conrad, Andrew D. Hanson, and Valérie de Crécy-Lagard. 2016. ‘Systematic Identification and Analysis of Frequent Gene Fusion Events in Metabolic Pathways’. BMC Genomics 17(1):473. doi: 10.1186/s12864-016-2782-3.

Arabidopsis TH2 Encodes the Orphan Enzyme Thiamin Monophosphate Phosphatase

Mimura, Manaki, Rémi Zallot, Thomas D. Niehaus, Ghulam Hasnain, Satinder K. Gidda, Thuy N. D. Nguyen, Erin M. Anderson, Robert T. Mullen, Greg Brown, Alexander F. Yakunin, Valérie de Crécy-Lagard, Jesse F. Gregory, Donald R. McCarty, and Andrew D. Hanson. 2016. ‘Arabidopsis TH2 Encodes the Orphan Enzyme Thiamin Monophosphate Phosphatase’. The Plant Cell 28(10):2683–96. doi: 10.1105/tpc.16.00600.

Functional Annotations of Paralogs: A Blessing and a Curse

Zallot, Rémi, Katherine Harrison, Bryan Kolaczkowski, and Valérie de Crécy-Lagard. 2016. ‘Functional Annotations of Paralogs: A Blessing and a Curse’. Life 6(3):39. doi: 10.3390/life6030039.

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

Huang, Lili, Anna Khusnutdinova, Boguslaw Nocek, Greg Brown, Xiaohui Xu, Hong Cui, Pierre Petit, Robert Flick, Rémi Zallot, Kelly Balmant, Michael J. Ziemak, John Shanklin, Valérie de Crécy-Lagard, Oliver Fiehn, Jesse F. Gregory, Andrzej Joachimiak, Alexei Savchenko, Alexander F. Yakunin, and Andrew D. Hanson. 2016. ‘A Family of Metal-Dependent Phosphatases Implicated in Metabolite Damage-Control’. Nature Chemical Biology 12(8):621–27. doi: 10.1038/nchembio.2108.

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

Hasnain, Ghulam, Sanja Roje, Na Sa, Rémi Zallot, Michael J. Ziemak, Valérie de Crécy-Lagard, Jesse F. Gregory, and Andrew D. Hanson. 2016. ‘Bacterial and Plant HAD Enzymes Catalyse a Missing Phosphatase Step in Thiamin Diphosphate Biosynthesis’. Biochemical Journal 473(2):157–66. doi: 10.1042/BJ20150805.

Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae

Kuznetsova, Ekaterina, Boguslaw Nocek, Greg Brown, Kira S. Makarova, Robert Flick, Yuri I. Wolf, Anna Khusnutdinova, Elena Evdokimova, Ke Jin, Kemin Tan, Andrew D. Hanson, Ghulam Hasnain, Rémi Zallot, Valérie de Crécy-Lagard, Mohan Babu, Alexei Savchenko, Andrzej Joachimiak, Aled M. Edwards, Eugene V. Koonin, and Alexander F. Yakunin. 2015. ‘Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces Cerevisiae’. Journal of Biological Chemistry 290(30):18678–98. doi: 10.1074/jbc.M115.657916.

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

Zallot, Rémi, Mohammad Yazdani, Aymeric Goyer, Michael J. Ziemak, Jiahn-Chou Guan, Donald R. McCarty, Valérie de Crécy-Lagard, Svetlana Gerdes, Timothy J. Garrett, Jordi Benach, John F. Hunt, David K. Shintani, and Andrew D. Hanson. 2014. ‘Salvage of the Thiamin Pyrimidine Moiety by Plant TenA Proteins Lacking an Active-Site Cysteine’. Biochemical Journal 463(1):145–55. doi: 10.1042/BJ20140522.

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

Seaver, Samuel M. D., Svetlana Gerdes, Océane Frelin, Claudia Lerma-Ortiz, Louis M. T. Bradbury, Rémi Zallot, Ghulam Hasnain, Thomas D. Niehaus, Basma El Yacoubi, Shiran Pasternak, Robert Olson, Gordon Pusch, Ross Overbeek, Rick Stevens, Valérie de Crécy-Lagard, Doreen Ware, Andrew D. Hanson, and Christopher S. Henry. 2014. ‘High-Throughput Comparison, Functional Annotation, and Metabolic Modeling of Plant Genomes Using the PlantSEED Resource’. Proceedings of the National Academy of Sciences 111(26):9645–50. doi: 10.1073/pnas.1401329111.

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

Yazdani, Mohammad, Rémi Zallot, Meral Tunc-Ozdemir, Valérie de Crécy-Lagard, David K. Shintani, and Andrew D. Hanson. 2013. ‘Identification of the Thiamin Salvage Enzyme Thiazole Kinase in Arabidopsis and Maize’. Phytochemistry 94:68–73. doi: 10.1016/j.phytochem.2013.05.017.

Identification of Mitochondrial Coenzyme A Transporters from Maize and Arabidopsis

Zallot, Rémi, Gennaro Agrimi, Claudia Lerma-Ortiz, Howard J. Teresinski, Océane Frelin, Kenneth W. Ellens, Alessandra Castegna, Annamaria Russo, Valérie de Crécy-Lagard, Robert T. Mullen, Ferdinando Palmieri, and Andrew D. Hanson. 2013. ‘Identification of Mitochondrial Coenzyme A Transporters from Maize and Arabidopsis’. Plant Physiology 162(2):581–88. doi: 10.1104/pp.113.218081.

Acyl-Lipid Metabolism

Li-Beisson, Yonghua, Basil Shorrosh, Fred Beisson, Mats X. Andersson, Vincent Arondel, Philip D. Bates, Sébastien Baud, David Bird, Allan DeBono, Timothy P. Durrett, Rochus B. Franke, Ian A. Graham, Kenta Katayama, Amélie A. Kelly, Tony Larson, Jonathan E. Markham, Martine Miquel, Isabel Molina, Ikuo Nishida, Owen Rowland, Lacey Samuels, Katherine M. Schmid, Hajime Wada, Ruth Welti, Changcheng Xu, Rémi Zallot, and John Ohlrogge. 2013. ‘Acyl-Lipid Metabolism’. The Arabidopsis Book 11:e0161. doi: 10.1199/tab.0161.

Polyphosphoinositides Are Enriched in Plant Membrane Rafts and Form Microdomains in the Plasma Membrane

Furt, Fabienne, Sabine König, Jean-Jacques Bessoule, Françoise Sargueil, Rémi Zallot, Thomas Stanislas, Elodie Noirot, Jeanine Lherminier, Françoise Simon-Plas, Ingo Heilmann, and Sébastien Mongrand. 2010. ‘Polyphosphoinositides Are Enriched in Plant Membrane Rafts and Form Microdomains in the Plasma Membrane’. Plant Physiology 152(4):2173–87. doi: 10.1104/pp.109.149823.

Acyl-Lipid Metabolism

Li-Beisson, Yonghua, Basil Shorrosh, Fred Beisson, Mats X. Andersson, Vincent Arondel, Philip D. Bates, Sébastien Baud, David Bird, Allan DeBono, Timothy P. Durrett, Rochus B. Franke, Ian A. Graham, Kenta Katayama, Amélie A. Kelly, Tony Larson, Jonathan E. Markham, Martine Miquel, Isabel Molina, Ikuo Nishida, Owen Rowland, Lacey Samuels, Katherine M. Schmid, Hajime Wada, Ruth Welti, Changcheng Xu, Rémi Zallot, and John Ohlrogge. 2010. ‘Acyl-Lipid Metabolism’. The Arabidopsis Book 8:e0133. doi: 10.1199/tab.0133.