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Article
In vivo hypermutation and continuous evolution
Directed evolution has revolutionized biomolecular engineering by applying cycles of mutation, amplification and selection to genes of interest (GOIs). However, classical directed evolution methods that rely o...
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Article
Revolutionizing agriculture with synthetic biology
Synthetic biology is here to stay and will transform agriculture if given the chance. The huge challenges facing food, fuel and chemical production make it vital to give synthetic biology that chance—notwithst...
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Plant metabolic engineering in the synthetic biology era: plant chassis selection
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Article
Open AccessSalvage of the 5-deoxyribose byproduct of radical SAM enzymes
5-Deoxyribose is formed from 5′-deoxyadenosine, a toxic byproduct of radical S-adenosylmethionine (SAM) enzymes. The degradative fate of 5-deoxyribose is unknown. Here, we define a salvage pathway for 5-deoxyribo...
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Open AccessAuthor Correction: Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
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Article
Open AccessCarboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis
Almost all cells require thiamin, vitamin B1 (B1), which is synthesized via the coupling of thiazole and pyrimidine precursors. Here we demonstrate that 5-(2-hydroxyethyl)-4-methyl-1,3-thiazole-2-carboxylic ac...
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Drought stress in Pinus taeda L. induces coordinated transcript accumulation of genes involved in the homogentisate pathway
Phenylalanine is a central amino acid in plants and is the precursor of many key secondary metabolites such as lignin, phenylpropanoids, and flavonoids. Phenylalanine hydroxylase (PheH, EC 1.14.16.1) is not de...
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Article
A family of metal-dependent phosphatases implicated in metabolite damage-control
Characterization of three DUF89 subfamilies representing all domains of life reveals that members function as metal-dependent phosphatases that help eliminate a wide range of damaged phosphometabolites. ...
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Article
Open AccessSystematic identification and analysis of frequent gene fusion events in metabolic pathways
Gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need upda...
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Article
Open AccessMINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics
In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography–mass spectrometry (LC–MS) has made it possible to gather data on tho...
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Open AccessGenomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family
It is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the re...
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Metabolite damage and its repair or pre-emption
Metabolites and cofactors can be converted to unwanted compounds by promiscuous enzymes and spontaneous chemical reactions. The growing list of enzymes that correct or prevent these reactions, akin to those th...
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Identification of mitochondrial thiamin diphosphate carriers from Arabidopsis and maize
It is currently held that thiamin is made in chloroplasts and converted in the cytosol to the active cofactor thiamin diphosphate (ThDP), and that mitochondria and plastids import ThDP. The organellar transpor...
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Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals
The transporter(s) that mediate uptake of nicotinate and its N-methyl derivative trigonelline are not known in plants, and certain mammalian nicotinate transporters also remain unidentified. Potential candidates ...
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Article
A 5-formyltetrahydrofolate cycloligase paralog from all domains of life: comparative genomic and experimental evidence for a cryptic role in thiamin metabolism
A paralog (here termed COG0212) of the ATP-dependent folate salvage enzyme 5-formyltetrahydrofolate cycloligase (5-FCL) occurs in all domains of life and, although typically annotated as 5-FCL in pro- and euka...
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Article
Open AccessSynergistic use of plant-prokaryote comparative genomics for functional annotations
Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown or vag...
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Article
Open AccessPhysiological responses to folate overproduction in Lactobacillus plantarum WCFS1
Using a functional genomics approach we addressed the impact of folate overproduction on metabolite formation and gene expression in Lactobacillus plantarum WCFS1. We focused specifically on the mechanism that re...
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Article
Open AccessComparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations
Folate synthesis and salvage pathways are relatively well known from classical biochemistry and genetics but they have not been subjected to comparative genomic analysis. The availability of genome sequences f...
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Article
A new route for synthesis of dimethylsulphoniopropionate in marine algae
The 3-dimethylsulphoniopropionate (DMSP) produced by marine algae is the main biogenic precursor of atmospheric dimethylsulphide (DMS)1,2,3. This biogenic DMS, formed by bacterial and algal degradation of DMSP4,5
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Article
Metabolic engineering of glycine betaine synthesis: plant betaine aldehyde dehydrogenases lacking typical transit peptides are targeted to tobacco chloroplasts where they confer betaine aldehyde resistance
Certain higher plants synthesize and accumulate glycine betaine, a compound with osmoprotectant properties. Biosynthesis of glycine betaine proceeds via the pathway choline → betaine aldehyde → glycine betaine...
