Valerie de Crecy-Lagard

Publications

• Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes
• QueF-Like, a Non-Homologous Archaeosine Synthase from the Crenarchaeota
• The Levels of a Universally Conserved tRNA Modification Regulate Cell Growth
• Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea
• Deazaguanine derivatives, examples of crosstalk between RNA and DNA modification pathways
• Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics
• Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes
• Identification of the minimal bacterial 2′-deoxy-7-amido-7-deazaguanine synthesis machinery
• Uncovering the chemistry of C–C bond formation in C-nucleoside biosynthesis: crystal structure of a C-glycoside synthase/PRPP complex
• Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168
• The DUF328 family member YaaA is a DNA-binding protein with a novel fold
• A network approach to elucidate and prioritize microbial dark matter in microbial communities
• Can Protein Expression Be Regulated by Modulation of tRNA Modification Profiles?
• Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast
• Functional Annotations of Paralogs: A Blessing and a Curse
• Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase
• Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme
• PMP–diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis
• Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast
• Pantoea Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA
• Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase
• Dihydrouridine in the Transcriptome: New Life for This Ancient RNA Chemical Modification
• A roadmap for the functional annotation of protein families: a community perspective
• Evolutionary Diversity of Dus2 Enzymes Reveals Novel Structural and Functional Features among Members of the RNA Dihydrouridine Synthases Family
• Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5'-monophosphate as the biological substrate.
• Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
• 7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system
• 4′-Deoxypyridoxine disrupts vitamin B6 homeostasis in Escherichia coli K12 through combined inhibition of cumulative B6 uptake and PLP-dependent enzyme activity
• Beyond Blast: Enabling Microbiologists to Better Extract Literature, Taxonomic Distributions and Gene Neighborhood Information for Protein Families
• Four additional natural 7-deazaguanine derivatives in phages and how to make them
• Identification of the minimal bacterial 2′‐deoxy‐7‐amido‐7‐deazaguanine synthesis machinery
• Integrative Approach to Probe Alternative Redox Mechanisms in RNA Modifications
• Queuosine Salvage in Bartonella henselae Houston 1: A Unique Evolutionary Path
• Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families
• Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages
• Deciphering the Diversity of Bacterial Transporters that Salvage Queuosine Precursors
• Mapping the tRNA Modification Landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse
• Knowns and unknowns of vitamin b6 metabolism in escherichia coli
• Metabolite Damage and Damage Control in a Minimal Genome
• Quantitative mapping of the cellular small RNA landscape with AQRNA-seq
• An Enzyme Containing the Conserved Domain of Unknown Function DUF62 Acts as a Stereoselective (Rs,Sc)-S-Adenosylmethionine Hydrolase
• Dihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes
• The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12
• Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens
• Hypermodified dna in viruses of e coli and salmonella
• Bacterial RNA Degradosomes: Molecular Machines under Tight Control
• Characterization of the Escherichia coli pyridoxal 5′-phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability
• Metabolite Damage and Damage-Control in a Minimal Genome
• Archaeosine modification of archaeal tRNA: Role in structural stabilization
• Whole-Genome Sequence of Streptomyces kaniharaensis Shomura and Niida SF-557
• Essential metabolism for a minimal cell
• On the necessity to include multiple types of evidence when predicting molecular function of proteins
• 7-Deazaguanine modifications protect phage DNA from host restriction systems
• Clostridioides difficile Senses and Hijacks Host Heme for Incorporation into an Oxidative Stress Defense System
• Identifying Pathogenic Islands through Genome Comparison
• Alternate routes to mnm5s2U synthesis in Gram-positive bacteria
• Aminoglycoside tolerance in Vibrio cholerae engages translational reprogramming associated to queuosine tRNA modification
• Structure of the ForT/PRPP complex uncovers the mechanism of C-C bond formation in C-nucleotide antibiotic biosynthesis
• An unusual route for p-Aminobenzoate biosynthesis in Chlamydia trachomatis involves a probable self-sacrificing diiron oxygenase
• Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity
• Deoxyinosine and 7-deaza-2-deoxyguanosine as carriers of genetic information in the DNA of Campylobacter viruses
• Detection of preQ0deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs
• Specificity in the biosynthesis of the universal tRNA nucleoside N6-threonylcarbamoyl adenosine (t6A)—TsaD is the gatekeeper
• Modes of microbial culture
• Cross kingdom functional conservation of the core universally conserved threonylcarbamoyladenosine tRNA synthesis enzymes
• The t6A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans
• Systematic identification and analysis of frequent gene fusion events in metabolic pathways
• Novel genomic island modifies DNA with 7-deazaguanine derivatives
• Functional diversity of haloacid dehalogenase superfamily phosphatases from Saccharomyces cerevisiae: Biochemical, structural, and evolutionary insights
• Newly-discovered enzymes that function in metabolite damage-control
• Arabidopsis TH2 encodes the orphan enzyme thiamin monophosphate phosphatase
• MODOMICS: A database of RNA modification pathways. 2017 update
• Evidence that COG0325 proteins are involved in PLP homeostasis
• Experimental and metabolic modeling evidence for a folate-cleaving side-activity of ketopantoate hydroxymethyltransferase (PanB)
• Evidence that the metabolite repair enzyme NAD(P)HX epimerase has a moonlighting function
• Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes
• Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite
• Essentiality of threonylcarbamoyladenosine (t6A), a universal tRNA modification, in bacteria
• The emerging role of complex modifications of tRNALysUUU in signaling pathways
• A plastidial pantoate transporter with a potential role in pantothenate synthesis
• A family of metal-dependent phosphatases implicated in metabolite damage-control
• GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
• Global translational impacts of the loss of the tRNA modification t6A in yeast
• Bacterial and plant HAD enzymes catalyse a missing phosphatase step in thiamin diphosphate biosynthesis
• Quality annotations, A key frontier in the microbial sciences: With genomic sequencing expanding so rapidly, Gene annotation lags—posing challenges to catch up while correcting errors as needed
• A strictly monofunctional bacterial hydroxymethylpyrimidine phosphate kinase precludes damaging errors in thiamin biosynthesis
• Discovery of the β-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs
• Sequencing-based quantitative mapping of the cellular small RNA landscape
• Mannitol-1-phosphate dehydrogenases/phosphatases: A family of novel bifunctional enzymes for bacterial adaptation to osmotic stress
• Gene Graphics: A genomic neighborhood data visualization web application
• Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars
• The Response of Acinetobacter baumannii to Zinc Starvation
• Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t6A), a universal modification of tRNA
• Proteins of unknown biochemical function: A persistent problem and a roadmap to help overcome it
• Mutations in PROSC Disrupt Cellular Pyridoxal Phosphate Homeostasis and Cause Vitamin-B6-Dependent Epilepsy
• Nothing of chemistry disappears in biology': The Top 30 damage-prone endogenous metabolites
• Metabolite Damage and Metabolite Damage Control in Plants
• Discovery of a widespread prokaryotic 5-oxoprolinase that was hiding in plain sight
• Systematic genome assessment of B-vitamin biosynthesis suggests cooperation among gut microbes
• The escherichia coli COG1738 member YhhQ is involved in 7-cyanodeazaguanine (preQ0) transport
• A directed-overflow and damage-control N-glycosidase in riboflavin biosynthesis
• TRNA N6-adenosine threonylcarbamoyltransferase defect due to KAE1/TCS3 (OSGEP) mutation manifest by neurodegeneration and renal tubulopathy
• Survey and summary: Matching tRNA modifications in humans to their known and predicted enzymes
• tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs
• TRNA modification profiles and codon-decoding strategies in Methanocaldococcus jannaschii
• Comparative Genomics
• Modes of Culture/Microbial
• Towards a systems approach in the genetic analysis of archaea: Accelerating mutant construction and phenotypic analysis in Haloferax volcanii.
• Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii
• Genomics-driven reconstruction of Acinetobacter NAD metabolism: Insights for antibacterial target selection
• Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine
• Promiscuous and adaptable enzymes fill “Holes” in the tetrahydrofolate pathway in Chlamydia species
• Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes
• A genetic investigation of the KEOPS complex in Halophilic Archaea
• Experimental evolution of a facultative thermophile from a mesophilic ancestor
• Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes
• Genome Sequence of Candidatus riesia pediculischaeffi, endosymbiont of chimpanzee lice, and genomic comparison of recently acquired endosymbionts from human and chimpanzee lice
• Functional promiscuity of the COG0720 family
• Biosynthesis of threonylcarbamoyl adenosine (t 6A), a universal tRNA nucleoside
• Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway
• Plant B Vitamin Pathways and their Compartmentation: A Guide for the Perplexed
• Biosynthesis of wyosine derivatives in tRNA: An ancient and highly diverse pathway in archaea
• Diversity of archaeosine synthesis in crenarchaeota
• A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life
• Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t 6A modification of tRNAs
• SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes
• Erratum: Towards a systems approach in the genetic analysis of Archaea: Accelerating mutant construction and phenotypic analysis in Haloferax volcanii (Hindawi Publishing Corporation Archaea)
• Discovery and characterization of an amidinotransferase involved in the modification of archaeal tRNA
• Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage
• FolX and FolM are essential for tetrahydromonapterin synthesis in Escherichia coli and Pseudomonas aeruginosa
• Biosynthesis and function of posttranscriptional modifications of transfer RNAs
• Towards a systems approach in the genetic analysis of archaea: Accelerating mutant construction and phenotypic analysis in Haloferax volcanii
• Comparative genomics guided discovery of two missing archaeal enzyme families involved in the biosynthesis of the pterin moiety of tetrahydromethanopterin and tetrahydrofolate
• Moonlighting glutamate formiminotransferases can functionally replace 5-Formyltetrahydrofolate cycloligase
• Mining high-throughput experimental data to link gene and function
• A Gateway platform for functional genomics in Haloferax volcanii: Deletion of three tRNA modification genes
• Biosynthesis and function of tRNA modifications in Archaea
• Identification of the thiamin salvage enzyme thiazole kinase in Arabidopsis and maize
• A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification
• Synergistic use of plant-prokaryote comparative genomics for functional annotations
• Structural basis of biological nitrile reduction
• A 5-formyltetrahydrofolate cycloligase paralog from all domains of life: Comparative genomic and experimental evidence for a cryptic role in thiamin metabolism
• 'Unknown' proteins and 'orphans' enzymes: The mising half of the engineering part list - And how to find it
• The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10,catalyze the formation of 1-methylpseudouridine at position 54 of tRNA
• Identification and characterization of the missing pyrimidine reductase in the plant riboflavin biosynthesis pathway
• Role of a Zn-independent DksA in Zn homeostasis and stringent response
• Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family
• The COMBREX Project: Design, Methodology, and Initial Results
• Identification of mitochondrial coenzyme a transporters from maize and Arabidopsis
• Quinolinate salvage and insights for targeting NAD biosynthesis in group A streptococci
• Integrative data-mining tools to link gene and function
• High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
• YeiR: A metal-binding GTPase from Escherichia coli involved in metal homeostasis
• Predicting the pathway involved in post-translational modification of elongation factor P in a subset of bacterial species
• 6-Pyruvoyltetrahydropterin synthase paralogs replace the folate synthesis enzyme dihydroneopterin aldolase in diverse bacteria
• Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: A new role for GTP cyclohydrolase I
• RNA modification subsystems in the SEED database
• Comparative RNomics and Modomics in mollicutes: Prediction of gene function and evolutionary implications
• Multienzymatic non ribosomal peptide biosynthesis: Identification of the functional domains catalysing peptide elongation and epimerisation
• ClpX, an alternative subunit for the ATP-dependent Clp protease of Escherichia coli: Sequence and in vivo activities
• Fructose catabolism in Xanthomonas campestris pv. campestris: Sequence of the PTS operon, characterization of the fructose-specific enzymes
• Identification of two fructose transport and phosphorylation pathways in Xanthomonas campestris pv. campestris
• Virology: Major biocontrol of plant tumors targets tRNA synthetase
• Streptogramin B biosynthesis in Streptomyces pristinaespiralis and Streptomyces virginiae: Molecular characterization of the last structural peptide synthetase gene
• The various strategies of codon decoding in organisms of the three domains of life: evolutionary implications.
• Artificially ambiguous genetic code confers growth yield advantage
• Bridges cnd Chasms: Summary of the IMAGE 2 meeting in Montreal, Canada, 30 April to 3 May 2007
• Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: A queuosine-biosynthesis enzyme
• Mutational separation of two pathways for editing by a class I tRNA synthetase
• Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs
• Inhibition of mutation and combating the evolution of antibiotic resistance
• Enlarging the amino acid set of Escherichia coli by infiltration of the valine coding pathway
• Genetic code ambiguity confers a selective advantage on Acinetobacter baylyi
• Pristinamycin I biosynthesis in Streptomyces pristinaespiralis: Molecular characterization of the first two structural peptide synthetase genes
• Finding novel metabolic genes through plant-prokaryote phylogenomics
• Identification of Genes Encoding tRNA Modification Enzymes by Comparative Genomics
• Zinc-independent folate biosynthesis: Genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB
• A fast and accurate algorithm for comparative analysis of metabolic pathways
• Aminoacylation of the anticodon stem by a tRNA-synthetase paralog: Relic of an ancient code?
• The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA
• Fructose phosphotransferase system of Xanthomonas campestris pv. campestris: Characterization of the fruB gene
• Rapid evolution of diminished transformability in Acinetobacter baylyi
• Genetic code ambiguity: Cell viability related to severity of editing defects in mutant tRNA synthetases
• Consistent alignment of metabolic pathways without abstraction.
• Development of a novel continuous culture device for experimental evolution of bacterial populations
• Identification of the tRNA-dihydrouridine synthase family
• Alteration of the synthesis of the Clp ATP-dependent protease affects morphological and physiological differentiation in Streptomyces
• Comparative genomics of bacterial and plant folate synthesis and salvage: Predictions and validations
• An aminoacyl tRNA synthetase whose sequence fits into neither of the two known classes
• Incorporation of nonnatural amino acids into proteins
• The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
• A Xanthomonas campestris pv. campestris protein similar to catabolite activation factor is involved in regulation of phytopathogenicity
• RNomics and Modomics in the halophilic archaea Haloferax volcanii: Identification of RNA modification genes
• A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life
• Inhibited cell growth and protein functional changes from an editing-defective tRNA synthetase
• Molecular determinants of dihydrouridine synthase activity
• From cyclohydrolase to oxidoreductase: Discovery of nitrile reductase activity in a common fold
• Discovery of a new prokaryotic type I GTP cyclohydrolase family
• Acinetobacter sp. ADP1: An ideal model organism for genetic analysis and genome engineering
• Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms?
• Long term adaptation of a microbial population to a permanent metabolic constraint: Overcoming thymineless death by experimental evolution of Escherichia coli
• Phylogenomic and functional analysis of pterin-4a-carbinolamine dehydratase family (COG2154) proteins in plants and microorganisms
• Identification of Four Genes Necessary for Biosynthesis of the Modified Nucleoside Queuosine
• The ClpB ATPase of Streptomyces albus G belongs to the HspR heat shock regulon
• Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics
• Deciphering the Diversity in Bacterial Transporters That Salvage Queuosine Precursors
• Limitations of Current Machine-Learning Models in Predicting Enzymatic Functions for Uncharacterized Proteins
• Nutritional Control of Queuosine levels in Streptococcus mutans tRNAs
• Queuosine salvage in Bartonella henselae Houston 1: a unique evolutionary path
• Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies
• Mechanism of Catalysis and Substrate Binding of Epoxyqueuosine Reductase in the Biosynthetic Pathway to Queuosine-Modified tRNA
• Environmental Control of Queuosine Levels in Streptococcus mutanstRNAs
• Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity
• antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation