Wayne M. Patrick
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View article: The more we learn, the more diverse it gets: structures, functions and evolution in the Phosphofructokinase Superfamily
The more we learn, the more diverse it gets: structures, functions and evolution in the Phosphofructokinase Superfamily Open
The enzyme 6-phosphofructokinase (PFK) phosphorylates d-fructose 6-phosphate, producing d-fructose 1,6-bisphosphate. The canonical version—discovered almost 90 years ago—is ATP-dependent, allosterically regulated and catalyses the first co…
View article: Multifunctional alkaline phosphatases drive the phosphorus cycle in the ocean
Multifunctional alkaline phosphatases drive the phosphorus cycle in the ocean Open
Background Phosphorus plays a crucial role in limiting marine ecosystems productivity. To overcome this limitation, organisms use alkaline phosphatases (APases) to obtain phosphate from organic compounds. Although traditionally viewed as i…
View article: Abstract 1398 A very cool and novel phosphofructokinase sheds light on the evolution of substrate specificity and on the metabolic networks in our closest prokaryotic relatives
Abstract 1398 A very cool and novel phosphofructokinase sheds light on the evolution of substrate specificity and on the metabolic networks in our closest prokaryotic relatives Open
Phosphofructokinase (PFK) is a key enzyme in the central metabolic pathway of glycolysis. PFKs are categorized according to whether they use ATP, ADP, or pyrophosphate as their phosphate donor for the sugar kinase reaction. Typically, euka…
View article: Characterisation and engineering of a thermophilic RNA ligase from <i>Palaeococcus pacificus</i>
Characterisation and engineering of a thermophilic RNA ligase from <i>Palaeococcus pacificus</i> Open
RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to t…
View article: An enzyme‐centric approach for constructing an amperometric <scp>l</scp>‐malate biosensor with a long and programmable linear range
An enzyme‐centric approach for constructing an amperometric <span>l</span>‐malate biosensor with a long and programmable linear range Open
l ‐Malate is a key flavor enhancer and acidulant in the food and beverage industry, particularly winemaking. Enzyme‐based amperometric biosensors offer convenience for monitoring its concentration. However, only a small number of off‐the‐s…
View article: Ceftazidime resistance in Pseudomonas aeruginosa is multigenic and complex
Ceftazidime resistance in Pseudomonas aeruginosa is multigenic and complex Open
Pseudomonas aeruginosa causes a wide range of severe infections. Ceftazidime, a cephalosporin, is a key antibiotic for treating infections but a significant proportion of isolates are ceftazidime-resistant. The aim of this research was to …
View article: Uniform binding and negative catalysis at the origin of enzymes
Uniform binding and negative catalysis at the origin of enzymes Open
Enzymes are well known for their catalytic abilities, some even reaching “catalytic perfection” in the sense that the reaction they catalyze has reached the physical bound of the diffusion rate. However, our growing understanding of enzyme…
View article: Dan Tawfik’s Lessons for Protein Engineers about Enzymes Adapting to New Substrates
Dan Tawfik’s Lessons for Protein Engineers about Enzymes Adapting to New Substrates Open
Natural evolution has been creating new complex systems for billions of years. The process is spontaneous and requires neither intelligence nor moral purpose but is nevertheless difficult to understand. The late Dan Tawfik spent years stud…
View article: Draft Genome Sequence of a Novel <i>Rhizobium</i> Species Isolated from the Marine Macroalga <i>Codium fragile</i> (Oyster Thief)
Draft Genome Sequence of a Novel <i>Rhizobium</i> Species Isolated from the Marine Macroalga <i>Codium fragile</i> (Oyster Thief) Open
In the process of studying the relationship between marine macroalgae and their bacterial symbionts, we isolated a new species of Rhizobium , which we designated Rhizobium sp. nov. C1 (for “ Codium 1”). Here, we report the complete genome …
View article: Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (βα) <sub>8</sub> Barrel Enzymes of Histidine and Tryptophan Biosynthesis
Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (βα) <sub>8</sub> Barrel Enzymes of Histidine and Tryptophan Biosynthesis Open
Enzymes are conformationally dynamic, and their dynamical properties play an important role in regulating their specificity and evolvability. In this context, substantial attention has been paid to the role of ligand-gated conformational c…
View article: Complex Loop Dynamics Underpin Activity, Specificity and Evolvability in the (βα)8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis
Complex Loop Dynamics Underpin Activity, Specificity and Evolvability in the (βα)8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis Open
Enzymes are conformationally dynamic, and their dynamical properties play an important role in regulating their specificity and evolvability. In this context, substantial attention has been paid to the role of ligand-gated conformational c…
View article: Complete Genome Sequence of a Novel Pseudomonas fluorescens Strain Isolated from the Flower of Kūmarahou (Pomaderris kumeraho)
Complete Genome Sequence of a Novel Pseudomonas fluorescens Strain Isolated from the Flower of Kūmarahou (Pomaderris kumeraho) Open
Kūmarahou ( Pomaderris kumeraho ) is a shrub endemic to New Zealand used in rongoā (traditional medicine). While studying the antimicrobial properties of kūmarahou, we isolated a new strain of Pseudomonas fluorescens , which we designated …
View article: Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean
Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean Open
Alkaline phosphatase (APase) is one of the marine enzymes used by oceanic microbes to obtain inorganic phosphorus (Pi) from dissolved organic phosphorus to overcome P-limitation. Marine APase is generally recognized to perform P-monoestera…
View article: Assessing the effectiveness of oxathiapiprolin towards<i>Phytophthora agathidicida</i>, the causal agent of kauri dieback disease
Assessing the effectiveness of oxathiapiprolin towards<i>Phytophthora agathidicida</i>, the causal agent of kauri dieback disease Open
Phytophthora species cause disease and devastation of plants in ecological and horticultural settings worldwide. A recently identified species, P. agathidicida , infects and ultimately kills the treasured kauri trees that are endemic to Ne…
View article: Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active site residues
Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active site residues Open
© 2020, eLife Sciences Publications Ltd. All rights reserved. Selection for a promiscuous enzyme activity provides substantial opportunity for competition between endogenous and newly-encountered substrates to influence the evolutionary tr…
View article: Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active site residues
Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active site residues Open
© 2020, eLife Sciences Publications Ltd. All rights reserved. Selection for a promiscuous enzyme activity provides substantial opportunity for competition between endogenous and newly-encountered substrates to influence the evolutionary tr…
View article: Quantifying the taxonomic bias in enzymology
Quantifying the taxonomic bias in enzymology Open
The ongoing biotechnological revolution is rooted in our knowledge of enzymes. However, metagenomics is showing how little we know about Earth's enzyme repertoire. Deep sequencing has revolutionized our view of the tree of life. The genome…
View article: Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues
Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues Open
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View article: Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues
Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues Open
No description supplied
View article: Assessing the effectiveness of oxathiapiprolin toward <i>Phytophthora agathidicida</i> , the causal agent of kauri dieback disease
Assessing the effectiveness of oxathiapiprolin toward <i>Phytophthora agathidicida</i> , the causal agent of kauri dieback disease Open
Phytophthora species cause disease and devastation of plants in ecological and horticultural settings worldwide. A recently identified species, Phytophthoraagathidicida, infects and ultimately kills the treasured kauri trees (Agathis austr…
View article: Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues
Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues Open
Selection for a promiscuous enzyme activity provides substantial opportunity for competition between endogenous and newly-encountered substrates to influence the evolutionary trajectory, an aspect that is often overlooked in laboratory dir…
View article: Author response: Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues
Author response: Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Selection for a promiscuous e…
View article: A giant leap in sequence space reveals the intracellular complexities of evolving a new function
A giant leap in sequence space reveals the intracellular complexities of evolving a new function Open
Selection for a promiscuous enzyme activity provides substantial opportunity for competition between endogenous and new substrates to influence the evolutionary trajectory, an aspect that has generally been overlooked in laboratory directe…
Assessment of Phenotype Microarray plates for rapid and high-throughput analysis of collateral sensitivity networks Open
The crisis of antimicrobial resistance is driving research into the phenomenon of collateral sensitivity. Sometimes, when a bacterium evolves resistance to one antimicrobial, it becomes sensitive to others. In this study, we have investiga…
View article: A Large-Scale Whole-Genome Comparison Shows that Experimental Evolution in Response to Antibiotics Predicts Changes in Naturally Evolved Clinical Pseudomonas aeruginosa
A Large-Scale Whole-Genome Comparison Shows that Experimental Evolution in Response to Antibiotics Predicts Changes in Naturally Evolved Clinical Pseudomonas aeruginosa Open
Pseudomonas aeruginosa is an opportunistic pathogen that causes a wide range of acute and chronic infections. An increasing number of isolates have mutations that make them antibiotic resistant, making treatment difficult. To identify resi…