ORCID Profile
0000-0001-6110-6982
Current Organisation
CSIRO
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Biochemistry and Cell Biology | Synthetic Biology | Microbial Genetics | Biocatalysis and Enzyme Technology | Nanobiotechnology |
ANZSRC Socio-Economic Objective (SEO)
Organic Industrial Chemicals (excl. Resins, Rubber and Plastics) | Expanding Knowledge in the Biological Sciences | Human Pharmaceutical Treatments (e.g. Antibiotics) | Expanding Knowledge in Technology
Related Links
Publications
Two operons that encode FNR‐like proteins in Lactococcus lactis
Publisher: Wiley
Date: 03-1999
DOI: 10.1046/J.1365-2958.1999.01298.X
Abstract: Global regulatory circuits of the type mediated by CRP and FNR in Escherichia coli were sought in Lactococcus lactis to provide a basis for redirecting carbon metabolism to specific fermentation products. Using a polymerase chain reaction (PCR) approach, two genes (flpA and flpB) encoding FNR-like proteins (FlpA and FlpB) with the potential for mediating a dithiol-disulphide-dependent regulatory switch, were identified. Transcript analysis indicated that they are distal genes of two paralogous operons, orfX-orfY-flp, in which the orfX and orfY genes were predicted to encode binding domain components of cation ATPases and storage proteins respectively. The corresponding promoters were each associated with a potential FNR site (TTGAT----ATCAA) at positions +4.5 (flpA operon) and -42.5 (flpB operon), suggesting that the respective operons might be negatively and positively autoregulated. The incomplete open reading frames (orfWA/B) located upstream of each operon were predicted to encode additional components of paralogous cation ATPases. No phenotypic effects were detected in flpA and flpB single mutants, but the double mutant had a lower intracellular zinc content, an increased sensitivity to hydrogen peroxide and an altered polypeptide profile (as determined by two-dimensional gel electrophoresis): formate production was not affected. It was concluded tentatively that FlpA and FlpB regulate overlapping modulons, including systems concerned with zinc uptake, in response to metal ion or oxidative stress.
Bacterial degradation of strobilurin fungicides: a role for a promiscuous methyl esterase activity of the subtilisin proteases?
Publisher: Informa UK Limited
Date: 04-07-2011
Cofactor F<sub>420</sub>-Dependent Enzymes: An Under-Explored Resource for Asymmetric Redox Biocatalysis
Publisher: MDPI AG
Date: 21-09-2019
DOI: 10.20944/PREPRINTS201909.0244.V1
Abstract: Asymmetric reduction of enoates, imines and ketones are among the most important reactions in biocatalysis. These reactions are routinely conducted using enzymes that use nicotinamide cofactors as reductants. The deazaflavin cofactor F420 also has electrochemical properties that make it suitable as an alternative to nicotinamide cofactors for use in asymmetric reduction reactions. However, cofactor F420-dependent enzymes remain under-explored as a resource for biocatalysis. In this review, we consider the cofactor F420-dependent enzyme families with greatest potential for the discovery of new biocatalysts: the flavin/deazaflavin-dependent oxidoreductases (FDORs) and the luciferase-like hydride transferases (LLHTs). We discuss characterized F420-dependent reductions that have potential for adaptation for biocatalysis, and we consider the enzymes best suited for use in the reduction of oxidized cofactor F420 to allow cofactor recycling in situ. We also discuss recent advances in the production of cofactor F420 and its functional analog FO-5& rsquo - phosphate, which remains an impediment to the adoption of this family of enzymes for industrial biocatalytic processes. Finally, we discuss the prospects for the use of this cofactor and dependent enzymes as a resource for industrial biocatalysis.
F420H2-dependent degradation of aflatoxin and other furanocoumarins is widespread throughout the Actinomycetales
Publisher: Public Library of Science (PLoS)
Date: 27-02-2012
Heterologous expression of the methyl carbamate-degrading hydrolase MCD
Publisher: Elsevier BV
Date: 10-2009
DOI: 10.1016/J.JBIOTEC.2009.09.009
Abstract: The methyl carbamate-degrading hydrolase (MCD) of Achromobacter WM111 has considerable potential as a pesticide bioremediation agent. However this potential has been unrealisable until now because of an inability to express MCD in heterologous hosts such as Escherichia coli. Herein, we describe the first successful attempt to express appreciable quantities of MCD in active form in E. coli, and the subsequent characterisation of the heterologously expressed material. We find that the properties of this material closely match the previously reported properties of MCD produced from Achromobacter WM111. This includes the presence of two distinct forms of the enzyme that we show are most likely due to the presence of two functional translational start sites. The purified enzyme catalyses the hydrolysis of a carbamate (carbaryl), a carboxyl ester (alpha-naphthyl acetate) and a phophotriester (dimethyl umbelliferyl phosphate) and it is relatively resistant to thermal and solvent-mediated denaturation. The robust nature and catalytic promiscuity of MCD suggest that it could be exploited for various biotechnological applications.
Functional versatility in the CRP-FNR superfamily of transcription factors: FNR and FLP
Publisher: Elsevier
Date: 2001
DOI: 10.1016/S0065-2911(01)44010-0
Abstract: The cAMP receptor protein (CRP sometimes known as CAP, the catabolite gene activator protein) and the fumarate and nitrate reduction regulator (FNR) of Escherichia coli are founder members of an expanding superfamily of structurally related transcription factors. The archetypal CRP structural fold provides a very versatile mechanism for transducing environmental and metabolic signals to the transcription machinery. It allows different functional specificities at the sensory, DNA-recognition and RNA-polymerase-interaction levels to be 'mixed and matched' in order to create a erse range of transcription factors tailored to respond to particular physiological conditions. This versatility is clearly illustrated by comparing the properties of the CRP, FNR and FLP (FNR-like protein) regulators. At the sensory level, the basic structural fold has been adapted in FNR and FLP by the acquisition in the N-terminal region of different combinations of cysteine or other residues which bestow oxygen/redox sensing mechanisms that are poised according to the oxidative stress thresholds affecting the metabolism of specific bacteria. At the DNA-recognition level, discrimination between distinct but related DNA targets is mediated by amino acid sequence modifications in the conserved core contact between the DNA-recognition helix and target DNA. And, at the level of RNA-polymerase-interaction, different combinations of three discrete regions contacting the polymerase (the activating regions) are used for polymerase recruitment and promoting transcription.
Physiology, Biochemistry, and Applications of F-420- and F-o-Dependent Redox Reactions
Publisher: American Society for Microbiology
Date: 06-2016
Abstract: 5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (F o ) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F 420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for ex le mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F 420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F 420 in methanogenic archaea in processes such as substrate oxidation, C 1 pathways, respiration, and oxygen detoxification. We also describe how two F 420 -dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis , and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of F o and F 420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.
Engineered enzymes that retain and regenerate their cofactors enable continuous-flow biocatalysis
Publisher: Springer Science and Business Media LLC
Date: 30-09-2019
Sugar analog synthesis by in vitro biocatalytic cascade
Publisher: Public Library of Science (PLoS)
Date: 07-11-2017
Asymmetric ene-reduction of α,β-unsaturated compounds by F420-dependent oxidoreductases A (FDOR-A) enzymes fromMycobacterium smegmatis
Publisher: Cold Spring Harbor Laboratory
Date: 05-11-2022
DOI: 10.1101/2022.11.05.515281
Abstract: The stereoselective reduction of alkenes conjugated to electron-withdrawing groups by ene-reductases has been extensively applied to the commercial preparation of fine chemicals. Although several different enzyme families are known to possess ene-reductase activity, the Old Yellow Enzyme (OYE) family has been the most thoroughly investigated. Recently, it was shown that a subset of ene-reductases belonging to the flavin/deazaflavin oxidoreductase (FDOR) superfamily exhibit enantioselectivity that is generally complementary to that seen in the OYE family. These enzymes belong to one of several FDOR subgroups that use the unusual deazaflavin cofactor F 420 . Here, we explore several enzymes of the FDOR-A subgroup, characterizing their substrate range and enantioselectivity, including the complete conversion of both isomers of citral to (R )-citronellel with 99% ee . Protein crystallography combined with computational docking has allowed the observed stereoselectivity to be mechanistically rationalized for two enzymes. These findings add further support for the FDOR and OYE families of ene-reductases being generally stereocomplementary to each other and highlight their potential value in asymmetric ene-reduction.
Organophosphate and Pyrethroid Hydrolase Activities of Mutant Esterases from the Cotton Bollworm Helicoverpa armigera
Publisher: Public Library of Science (PLoS)
Date: 29-10-2013
Identification and characterization of two families of F420H2-dependent reductases from Mycobacteria that catalyse aflatoxin degradation
Publisher: Wiley
Date: 16-09-2010
Crystallization and preliminary X-ray diffraction analysis of the amidase domain of allophanate hydrolase from Pseudomonas sp strain ADP
Publisher: International Union of Crystallography (IUCr)
Date: 19-02-2014
Synthetic biology approaches to hydrocarbon biosensors: a review
Publisher: Frontiers Media SA
Date: 10-01-2202
DOI: 10.3389/FBIOE.2021.804234
Abstract: Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature’s own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases have been identified, yet the regulation of only a few of these have been investigated in detail. A wealth of genetic and functional ersity of regulatory enzymes and promoter elements still remains unexplored and unexploited, both in published genome sequences and in yet-to-be-cultured bacteria. In this review we examine in detail the current state of research on monooxygenase gene regulation, and on the development of transcription-factor-based microbial biosensors for detection of alkanes and alkenes. A new framework for the systematic characterisation of the underlying genetic components and for further development of biosensors is presented, and we identify focus areas that should be targeted to enable progression of more biosensor candidates to commercialisation and deployment in industry and in the environment.
The evolving story of AtzT, a periplasmic binding protein
Publisher: International Union of Crystallography (IUCr)
Date: 31-10-2019
DOI: 10.1107/S2059798319013883
Abstract: Atrazine is an s -triazine-based herbicide that is used in many countries around the world in many millions of tons per year. A small number of organisms, such as Pseudomonas sp. strain ADP, have evolved to use this modified s -triazine as a food source, and the various genes required to metabolize atrazine can be found on a single plasmid. The atomic structures of seven of the eight proteins involved in the breakdown of atrazine by Pseudomonas sp. strain ADP have been determined by X-ray crystallography, but the structures of the proteins required by the cell to import atrazine for use as an energy source are still lacking. The structure of AtzT, a periplasmic binding protein that may be involved in the transport of a derivative of atrazine, 2-hydroxyatrazine, into the cell for mineralization, has now been determined. The structure was determined by SAD phasing using an ethylmercury phosphate derivative that diffracted X-rays to beyond 1.9 Å resolution. `Native' (guanine-bound) and 2-hydroxyatrazine-bound structures were also determined to high resolution (1.67 and 1.65 Å, respectively), showing that 2-hydroxyatrazine binds in a similar way to the purportedly native ligand. Structural similarities led to the belief that it may be possible to evolve AtzT from a purine-binding protein to a protein that can bind and detect atrazine in the environment.
Identification of novel transaminases from a 12‐aminododecanoic acid‐metabolizing P seudomonas strain
Publisher: Wiley
Date: 24-04-2015
Cofactor promiscuity among F420-dependent reductases enables them to catalyse both oxidation and reduction of the same substrate
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2CY20129A
Asymmetric ene-reduction by F420-dependent oxidoreductases B (FDOR-B) enzymes from Mycobacterium smegmatis
Publisher: Wiley
Date: 08-03-2023
Abstract: Asymmetric reduction by ene‐reductases has received considerable attention in recent decades. While several enzyme families possess ene‐reductase activity, the Old Yellow Enzyme (OYE) family has received the most scientific and industrial attention. However, there is a limited substrate range and few stereocomplementary pairs of current ene‐reductases, necessitating the development of a complementary class. Flavin/deazaflavin oxidoreductases (FDORs) that use the uncommon cofactor F 420 have recently gained attention as ene‐reductases for use in biocatalysis due to their stereocomplementarity with OYEs. Although the enzymes of the FDOR‐As sub‐group have been characterized in this context and reported to catalyse ene‐reductions enantioselectively, enzymes from the similarly large, but more erse, FDOR‐B sub‐group have not been investigated in this context. In this study, we investigated the activity of eight FDOR‐B enzymes distributed across this sub‐group, evaluating their specific activity, kinetic properties, and stereoselectivity against α,β‐unsaturated compounds. The stereochemical outcomes of the FDOR‐Bs are compared with enzymes of the FDOR‐A sub‐group and OYE family. Computational modelling and induced‐fit docking are used to rationalize the observed catalytic behaviour and proposed a catalytic mechanism.
Enzyme enabled remediation of pesticide residues
Publisher: Elsevier BV
Date: 11-2010
Computer-Guided Surface Engineering for Enzyme Improvement
Publisher: Springer Science and Business Media LLC
Date: 10-08-2018
DOI: 10.1038/S41598-018-30434-5
Abstract: Protein engineering strategies are often guided by our understanding of how the structure of a protein determines its function. However, our understanding is generally restricted to small regions of a protein, namely the active site and its immediate vicinity, while the remainder of the protein is something of an enigma. Studying highly homologous transaminases with strictly conserved active sites, but different substrate preferences and activities, we predict and experimentally validate that the surface of the protein far from the active site carries out a decisive role in substrate selectivity and catalytic efficiency. Using a unique molecular dynamics approach and novel trajectory analysis, we demonstrate the phenomenon of surface-directed ligand diffusion in this well-known protein family for the first time. Further, we identify the residues involved in directing substrate, design surface channel variants endowed for improved kinetic properties and establish a broadly applicable new approach for protein engineering.
Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP
Publisher: Microbiology Society
Date: 02-2008
DOI: 10.1099/MIC.0.2007/012146-0
Abstract: In Escherichia coli K-12 the expression of many genes is controlled by the oxygen-responsive transcription factor FNR and the nitrate- and nitrite-responsive two-component systems NarXL and NarPQ. Here, the ydhY gene is shown to be the first gene of a six-gene operon (ydhYVWXUT) that encodes proteins predicted to be components of an oxidoreductase. Mapping the ydhY-T transcript start and site-directed mutagenesis confirmed that the ydhY-T genes are transcribed from an FNR-dependent class II promoter and showed that the FNR site is centred at -42.5. In the presence of nitrate or nitrite, NarXL and NarPQ repressed ydhY-T expression. Analysis of the DNA sequence of the ydhY promoter region (PydhY) revealed the presence of four heptameric sequences similar to NarL/P binding sites centred at -42, -16, +6 and +15. The latter heptamers are arranged as a 7-2-7 inverted repeat, which is required for recognition by NarP. Accordingly, NarP protected the 7-2-7 region in DNase I footprints, and mutation of either heptamer +6 or heptamer +15 impaired nitrite-mediated repression, whereas mutation of heptamer -42 and heptamer -16 did not affect the response to nitrite. The NarL protein also protected the 7-2-7 region, but in contrast to NarP, the NarL footprint extended further upstream to encompass the -16 heptamer. The extended NarL footprint was consistent with the presence of multiple NarL-PydhY complexes in gel retardation assays. Mutation of heptamer -42, which is located within the FNR binding site, or heptamer +6 (but not heptamers -16 or +15) impaired nitrate-mediated repression. Thus, although the region of the ydhY-T promoter containing the -16 and +15 heptamers was recognized by NarL in vitro, mutation of these heptamers did not affect NarL-mediated repression in vivo.
Ongoing functional evolution of the bacterial atrazine chlorohydrolase AtzA
Publisher: Springer Science and Business Media LLC
Date: 13-04-2013
DOI: 10.1007/S10532-013-9637-2
Abstract: Triazine herbicides such as atrazine and simazine which were heavily used in the latter half of the twentieth century constituted a rich new source of nitrogen for soil microbes. An atzA dechlorinase active against both atrazine and simazine was isolated from various soil bacteria from erse locations in the mid 1990s. We have surveyed the atzA genes from eight triazine-degrading Aminobacter aminovorans strains isolated from French agricultural soils recurrently exposed to triazines in 2000. Six amino acid differences from the original isolate were each found in more than one of the A. aminovorans strains. Three of these in particular (V92L, A170T and A296T) were recovered from a majority of the isolates and from locations separated by up to 900 km, so may reflect ongoing selection for the new function. Two of the latter (A170T and A296T) were indeed found to confer higher specificity for simazine, albeit not atrazine, and greater affinity for a metal ion required for activity, than did the original variant. In contrast, we found that ongoing maintenance of the original atzA-containing isolate in laboratory culture for 12 years in a medium containing high concentrations of atrazine has led to the fixation of another amino acid substitution that substantially reduces activity for the triazines. The high concentrations of atrazine in the medium may have relaxed the selection for a highly efficient triazine dechlorinase activity, and that there is some, as yet uncharacterised, counter selection against the activity of this enzyme under these conditions.
A novel decarboxylating amidohydrolase involved in avoiding metabolic dead ends during cyanuric acid catabolism in Pseudomonas sp. strain ADP
Publisher: Public Library of Science (PLoS)
Date: 06-11-2018
Over the rainbow: structural characterisation of the chromoproteins gfasPurple, amilCP, spisPink and eforRed
Publisher: International Union of Crystallography (IUCr)
Date: 08-04-2022
DOI: 10.1107/S2059798322002625
Abstract: Anthozoan chromoproteins are highly pigmented, ersely coloured and readily produced in recombinant expression systems. While they are a versatile and powerful building block in synthetic biology for applications such as biosensor development, they are not widely used in comparison to the related fluorescent proteins, partly due to a lack of structural characterization to aid protein engineering. Here, high-resolution X-ray crystal structures of four open-source chromoproteins, gfasPurple, amilCP, spisPink and eforRed, are presented. These proteins are dimers in solution, and mutation at the conserved dimer interface leads to loss of visible colour development in gfasPurple. The chromophores are trans and noncoplanar in gfasPurple, amilCP and spisPink, while that in eforRed is cis and noncoplanar, and also emits fluorescence. Like other characterized chromoproteins, gfasPurple, amilCP and eforRed contain an sp 2 -hybridized N -acylimine in the peptide bond preceding the chromophore, while spisPink is unusual and demonstrates a true sp 3 -hybridized trans -peptide bond at this position. It was found that point mutations at the chromophore-binding site in gfasPurple that substitute similar amino acids to those in amilCP and spisPink generate similar colours. These features and observations have implications for the utility of these chromoproteins in protein engineering and synthetic biology applications.
Carbamate Pesticides and Their Biological Degradation: Prospects for Enzymatic Bioremediation
Publisher: American Chemical Society
Date: 21-09-2007
Gene identification and proteomic analysis of the esterases of the cotton bollworm, Helicoverpa armigera
Publisher: Elsevier BV
Date: 2010
DOI: 10.1016/J.IBMB.2009.12.002
Abstract: Some of the resistance of Helicoverpa armigera to conventional insecticides such as organophosphates and synthetic pyrethroids appears to be due to metabolic detoxification by carboxylesterases. To investigate the H. armigera carboxyl/cholinesterases, we created a data set of 39 putative paralogous H. armigera carboxyl/cholinesterase sequences from cDNA libraries and other sources. Phylogenetic analysis revealed a close relationship between these sequences and 70 carboxyl/cholinesterases from the recently sequenced genome of the silkworm, Bombyx mori, including several conserved clades of non-catalytic proteins. A juvenile hormone esterase candidate from H. armigera was identified, and B. mori orthologues were proposed for 31% of the sequences examined, however low similarity was found between lepidopteran sequences and esterases previously associated with insecticide resistance from other insect orders. A proteomic analysis of larval esterases then enabled us to match seven of the H. armigera carboxyl/cholinesterase sequences to specific esterase isozymes. All identified sequences were predicted to encode catalytically active carboxylesterases, including six proteins with N-terminal signal peptides and N-glycans, with two also containing C-terminal signals for glycosylphosphatidylinositol anchor attachment. Five of these sequences were matched to zones of activity on native PAGE at relative mobility values previously associated with insecticide resistance in this species.
How many genetic options for evolving insecticide resistance in heliothine and spodopteran pests?
Publisher: Wiley
Date: 20-06-2013
DOI: 10.1002/PS.3542
Reverse engineering
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C7GC02343J
Abstract: The use of ancestral sequence reconstruction to design novel biocatalysts with improved catalytic properties for the production of polyamide precursors.
Miscoordination of the Iron-Sulfur Clusters of the Anaerobic Transcription Factor, FNR, Allows Simple Repression but Not Activation
Publisher: Elsevier BV
Date: 2002
Hacking nature: genetic tools for reprograming enzymes
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/MA17032
Abstract: Enzymes have many modern industrial applications, from biomass decomposition in the production of biofuels to highly stereospecific biotransformations in pharmaceutical manufacture. The capacity to find or engineer enzymes with activities pertinent to specific applications has been essential for the growth of a multibillion dollar enzyme industry. Over the course of the past 50–60 years our capacity to address this issue has become increasingly sophisticated, supported by innumerable advances, from early discoveries such as the co-linearity of DNA and protein sequence1 to modern computational technologies for enzyme design. The design of enzyme function is an exciting nexus of fundamental biochemical understanding and applied engineering. Herein, we will cover some of the methods used in discovery and design, including some ‘next generation’ tools.
A β-alanine catabolism pathway containing a highly promiscuous ω-transaminase in the 12-aminododecanate-degrading Pseudomonas sp. strain AAC
Publisher: American Society for Microbiology
Date: 07-2016
DOI: 10.1128/AEM.00665-16
Abstract: We previously isolated the transaminase KES23458 from Pseudomonas sp. strain AAC as a promising biocatalyst for the production of 12-aminododecanoic acid, a constituent building block of nylon-12. Here, we report the subsequent characterization of this transaminase. It exhibits activity with a broad substrate range which includes α-, β-, and ω-amino acids, as well as α,ω-diamines and a number of other industrially relevant compounds. It is therefore a prospective candidate for the biosynthesis of a range of polyamide monomers. The crystal structure of KES23458 revealed that the protein forms a dimer containing a large active site pocket and unusual phosphorylated histidine residues. To infer the physiological role of the transaminase, we expressed, purified, and characterized a dehydrogenase from the same operon, KES23460. Unlike the transaminase, the dehydrogenase was shown to be quite selective, catalyzing the oxidation of malonic acid semialdehyde, formed from β-alanine transamination via KES23458. In keeping with previous reports, the dehydrogenase was shown to catalyze both a coenzyme A (CoA)-dependent reaction to form acetyl-CoA and a significantly slower CoA-independent reaction to form acetate. These findings support the original functional assignment of KES23458 as a β-alanine transaminase. However, a seemingly well-adapted active site and promiscuity toward unnatural compounds, such as 12-aminododecanoic acid, suggest that this enzyme could perform multiple functions for Pseudomonas sp. strain AAC. IMPORTANCE We describe the characterization of an industrially relevant transaminase able to metabolize 12-aminododecanoic acid, a constituent building block of the widely used polymer nylon-12, and we report the biochemical and structural characterization of the transaminase protein. A physiological role for this highly promiscuous enzyme is proposed based on the characterization of a related gene from the host organism. Molecular dynamics simulations were carried out to compare the conformational changes in the transaminase protein to better understand the determinants of specificity in the protein. This study makes a substantial contribution that is of interest to the broad biotechnology and enzymology communities, providing insights into the catalytic activity of an industrially relevant biocatalyst as well as the biological function of this operon.
DNA target sequence and FNR-dependent gene expression
Publisher: No publisher found
Date: 2003
DOI: 10.1016/S0014-5793(03)00312-0
Abstract: FNR proteins are global transcription regulators that respond to fluctuations in environmental oxygen. They recognise a DNA target consisting of an inverted repeat, TTGATN(1)N(2)N(3)N(4)ATCAA (where N(1-4) represents a non-conserved tetrad, NCT). Analysis of 68 known and predicted FNR sites from the Escherichia coli K12 genome revealed a bias toward A or T at positions N(2) and N(3) of the NCT. The effect of the NCT sequence on FNR-dependent transcription in vivo was assessed using a series of class II and class I model promoters with different NCT sequences. Changing the NCT sequence did not affect basal activity but altered anaerobic induction by as much as an order of magnitude. Thus, the NCT sequence is a fundamental component in setting the dynamic range of the FNR switch.
Cofactor and Process Engineering for Nicotinamide Recycling and Retention in Intensified Biocatalysis
Publisher: MDPI AG
Date: 17-11-2022
Abstract: There is currently considerable interest in the intensification of biocatalytic processes to reduce the cost of goods for biocatalytically produced chemicals, including pharmaceuticals and advanced pharmaceutical intermediates. Continuous-flow biocatalysis shows considerable promise as a method for process intensification however, the reliance of some reactions on the use of diffusible cofactors (such as the nicotinamide cofactors) has proven to be a technical barrier for key enzyme classes. This minireview covers attempts to overcome this limitation, including the cofactor recapture and recycling retention of chemically modified cofactors. For the latter, we also consider the state of science for cofactor modification, a field reinvigorated by the current interest in continuous-flow biocatalysis.
The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/CH16426
Abstract: An increasing number of bacterial metalloenzymes have been shown to catalyse the breakdown of xenobiotics in the environment, while others exhibit a variety of promiscuous xenobiotic-degrading activities. Several different evolutionary processes have allowed these enzymes to gain or enhance xenobiotic-degrading activity. In this review, we have surveyed the range of xenobiotic-degrading metalloenzymes, and discuss the molecular and catalytic basis for the development of new activities. We also highlight how our increased understanding of the natural evolution of xenobiotic-degrading metalloenzymes can be been applied to laboratory enzyme design.
X-Ray structure and mutagenesis studies of the n-isopropylammelide isopropylaminohydrolase, AtzC
Publisher: Public Library of Science (PLoS)
Date: 21-09-2015
X-Ray structure of the amidase domain of AtzF, the allophanate hydrolase from the cyanuric acid-mineralizing multienzyme complex
Publisher: American Society for Microbiology
Date: 15-01-2015
DOI: 10.1128/AEM.02783-14
Abstract: The activity of the allophanate hydrolase from Pseudomonas sp. strain ADP, AtzF, provides the final hydrolytic step for the mineralization of s -triazines, such as atrazine and cyanuric acid. Indeed, the action of AtzF provides metabolic access to two of the three nitrogens in each triazine ring. The X-ray structure of the N-terminal amidase domain of AtzF reveals that it is highly homologous to allophanate hydrolases involved in a different catabolic process in other organisms (i.e., the mineralization of urea). The smaller C-terminal domain does not appear to have a physiologically relevant catalytic function, as reported for the allophanate hydrolase of Kluyveromyces lactis , when purified enzyme was tested in vitro . However, the C-terminal domain does have a function in coordinating the quaternary structure of AtzF. Interestingly, we also show that AtzF forms a large, ca. 660-kDa, multienzyme complex with AtzD and AtzE that is capable of mineralizing cyanuric acid. The function of this complex may be to channel substrates from one active site to the next, effectively protecting unstable metabolites, such as allophanate, from solvent-mediated decarboxylation to a dead-end metabolic product.
Engineering Enzyme Properties for Improved Biocatalytic Processes in Batch and Continuous Flow
Publisher: American Chemical Society (ACS)
Date: 15-02-2022
Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841
Publisher: Public Library of Science (PLoS)
Date: 09-02-2018
Isomer-specific comparisons of the hydrolysis of synthetic pyrethroids and their fluorogenic analogues by esterases from the cotton bollworm Helicoverpa armigera
Publisher: Elsevier BV
Date: 06-2015
DOI: 10.1016/J.PESTBP.2014.12.010
Abstract: The low aqueous solubility and chiral complexity of synthetic pyrethroids, together with large differences between isomers in their insecticidal potency, have hindered the development of meaningful assays of their metabolism and metabolic resistance to them. To overcome these problems, Shan and Hammock (2001) [7] therefore developed fluorogenic and more water-soluble analogues of all the in idual isomers of the commonly used Type 2 pyrethroids, cypermethrin and fenvalerate. The analogues have now been used in several studies of esterase-based metabolism and metabolic resistance. Here we test the validity of these analogues by quantitatively comparing their hydrolysis by a battery of 22 heterologously expressed insect esterases with the hydrolysis of the corresponding pyrethroid isomers by these esterases in an HPLC assay recently developed by Teese et al. (2013) [14]. We find a strong, albeit not complete, correlation (r = 0.7) between rates for the two sets of substrates. The three most potent isomers tested were all relatively slowly degraded in both sets of data but three esterases previously associated with pyrethroid resistance in Helicoverpa armigera did not show higher activities for these isomers than did allelic enzymes derived from susceptible H. armigera. Given their amenability to continuous assays at low substrate concentrations in microplate format, and ready detection of product, we endorse the ongoing utility of the analogues in many metabolic studies of pyrethroids.
Determination of the structure of the catabolic N-succinylornithine transaminase (AstC) from Escherichia coli
Publisher: Public Library of Science (PLoS)
Date: 06-03-2013
X-ray crystal structure of a malonate-semialdehyde dehydrogenase from Pseudomonas sp strain AAC
Publisher: International Union of Crystallography (IUCr)
Date: 2017
DOI: 10.1107/S2053230X16020008
Abstract: The NAD-dependent malonate-semialdehyde dehydrogenase KES23460 from Pseudomonas sp. strain AAC makes up half of a bicistronic operon responsible for β-alanine catabolism to produce acetyl-CoA. The KES23460 protein has been heterologously expressed, purified and used to generate crystals suitable for X-ray diffraction studies. The crystals belonged to space group P 2 1 2 1 2 1 and diffracted X-rays to beyond 3 Å resolution using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4zz7 as the search model.
Crystal structure of a putrescine aminotransferase from Pseudomonas sp strain AAC
Publisher: International Union of Crystallography (IUCr)
Date: 2017
DOI: 10.1107/S2053230X16019658
Abstract: The putrescine aminotransferase KES24511 from Pseudomonas sp. strain AAC was previously identified as an industrially relevant enzyme based on the discovery that it is able to promiscuously catalyse the transamination of 12-aminododecanoic acid. Here, the cloning, heterologous expression, purification and successful crystallization of the KES24511 protein are reported, which ultimately generated crystals adopting space group I 2. The crystals diffracted X-rays to 2.07 Å resolution and data were collected using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4a6t as the search model.
NO sensing by FNR: regulation of the Escherichia coli NO-detoxifying flavohaemoglobin, Hmp
Publisher: Wiley
Date: 07-2002
DOI: 10.1093/EMBOJ/CDF339
Intramolecular epistasis and the evolution of a new enzymatic function
Publisher: Public Library of Science (PLoS)
Date: 29-06-2012
One-Pot Multienzymatic Transformation of NH3, CO2, and Ornithine into the Organic Nitrogen Plant Fertilizer Citrulline Using a Single Recombinant Lysate of E. coli
Publisher: American Chemical Society (ACS)
Date: 19-04-2019
The structure of the hexameric atrazine chlorohydrolase AtzA
Publisher: International Union of Crystallography (IUCr)
Date: 26-02-2015
DOI: 10.1107/S1399004715000619
Abstract: Atrazine chlorohydrolase (AtzA) was discovered and purified in the early 1990s from soil that had been exposed to the widely used herbicide atrazine. It was subsequently found that this enzyme catalyzes the first and necessary step in the breakdown of atrazine by the soil organism Pseudomonas sp. strain ADP. Although it has taken 20 years, a crystal structure of the full hexameric form of AtzA has now been obtained. AtzA is less well adapted to its physiological role ( i.e. atrazine dechlorination) than the alternative metal-dependent atrazine chlorohydrolase (TrzN), with a substrate-binding pocket that is under considerable strain and for which the substrate is a poor fit.
Engineering eukaryote-like regulatory circuits to expand artificial control mechanisms for metabolic engineering in Saccharomyces cerevisiae
Publisher: Springer Science and Business Media LLC
Date: 16-02-2022
DOI: 10.1038/S42003-022-03070-Z
Abstract: Temporal control of heterologous pathway expression is critical to achieve optimal efficiency in microbial metabolic engineering. The broadly-used GAL promoter system for engineered yeast ( Saccharomyces cerevisiae ) suffers from several drawbacks specifically, unintended induction during laboratory development, and unintended repression in industrial production applications, which decreases overall production capacity. Eukaryotic synthetic circuits have not been well examined to address these problems. Here, we explore a modularised engineering method to deploy new genetic circuits applicable for expanding the control of GAL promoter-driven heterologous pathways in S. cerevisiae . Trans - and cis - modules, including eukaryotic trans -activating-and-repressing mechanisms, were characterised to provide new and better tools for circuit design. A eukaryote-like tetracycline-mediated circuit that delivers stringent repression was engineered to minimise metabolic burden during strain development and maintenance. This was combined with a novel 37 °C induction circuit to relief glucose-mediated repression on the GAL promoter during the bioprocess. This delivered a 44% increase in production of the terpenoid nerolidol, to 2.54 g L −1 in flask cultivation. These negative ositive transcriptional regulatory circuits expand global strategies of metabolic control to facilitate laboratory maintenance and for industry applications.
A free-enzyme catalyst for the bioremediation of environmental atrazine contamination
Publisher: Elsevier BV
Date: 10-2010
DOI: 10.1016/J.JENVMAN.2010.05.007
Abstract: Herbicide contamination from agriculture is a major issue worldwide, and has been identified as a threat to freshwater and marine environments in the Great Barrier Reef World Heritage Area in Australia. The triazine herbicides are of particular concern because of potential adverse effects, both on photosynthetic organisms and upon vertebrate development. To date a number of bioremediation strategies have been proposed for triazine herbicides, but are unlikely to be implemented due to their reliance upon the release of genetically modified organisms. We propose an alternative strategy using a free-enzyme bioremediant, which is unconstrained by the issues surrounding the use of live organisms. Here we report an initial field trial with an enzyme-based product, demonstrating that the technology is technically capable of remediating water bodies contaminated with the most common triazine herbicide, atrazine.
Mycobacterial F420H2-dependent reductases promiscuously reduce diverse compounds through a common mechanism
Publisher: Frontiers Media SA
Date: 31-05-2017
Efficacy of an organophosphorus hydrolase enzyme (OpdA) in human serum and minipig models of organophosphorus insecticide poisoning
Publisher: Informa UK Limited
Date: 27-08-2019
A global response to sulfur starvation in Pseudomonas putida and its relationship to the expression of low-sulfur-content proteins
Publisher: Oxford University Press (OUP)
Date: 02-2007
DOI: 10.1111/J.1574-6968.2006.00575.X
Abstract: Sulfur is essential for life on Earth, but its availability is limited in many environments. Here the sulfur-starvation response of the model soil bacterium Pseudomonas putida KT2440 is shown to be associated with an approximately fivefold reduction in the total soluble thiol content of the cell. A bioinformatic survey of the P. putida KT2440 genome identified 646 genes encoding proteins with a significantly lower than average sulfur content (low sulfur-content proteins, LSPs), the expression of which may have a role in the global reduction of cellular thiol content during sulfur starvation. Analysis of the genetic organization of the LSP-encoding genes showed that 31% were potentially transcriptionally associated with at least one other gene encoding a protein defined as an LSP. In particular, 55 LSP genes were located in three large clusters, termed low-sulfur islands (LSIs) here. The predicted identities of the proteins encoded by the LSIs strongly suggest that the LSIs have a role in acquiring sulfur from organic sulfur sources during sulfur starvation. This hypothesis was supported by transcription fusion studies on a limited number of LSP promoters under low-sulfur conditions. In a wider survey of bacterial species, LSIs were found to be more prevalent in free-living, Gram-negative bacteria than in Gram-positive or obligately intracellular bacteria.
Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application
Publisher: Elsevier
Date: 2020
The evolution of new enzyme function
Publisher: Wiley
Date: 17-02-2011
DOI: 10.1111/J.1752-4571.2010.00175.X
Abstract: Here, we compare the evolutionary routes by which bacteria and insects have evolved enzymatic processes for the degradation of four classes of synthetic chemical insecticide. For insects, the selective advantage of such degradative activities is survival on exposure to the insecticide, whereas for the bacteria the advantage is simply a matter of access to additional sources of nutrients. Nevertheless, bacteria have evolved highly efficient enzymes from a wide variety of enzyme families, whereas insects have relied upon generalist esterase‐, cytochrome P450‐ and glutathione‐ S ‐transferase‐dependent detoxification systems. Moreover, the mutant insect enzymes are less efficient kinetically and less erged in sequence from their putative ancestors than their bacterial counterparts. This presumably reflects several advantages that bacteria have over insects in the acquisition of new enzymatic functions, such as a broad biochemical repertoire from which new functions can be evolved, large population sizes, high effective mutation rates, very short generation times and access to genetic ersity through horizontal gene transfer. Both the insect and bacterial systems support recent theory proposing that new biochemical functions often evolve from ‘promiscuous’ activities in existing enzymes, with subsequent mutations then enhancing those activities. Study of the insect enzymes will help in resistance management, while the bacterial enzymes are potential bioremediants of insecticide residues in a range of contaminated environments.
Catalytic improvement and evolution of atrazine chlorohydrolase
Publisher: American Society for Microbiology
Date: 04-2009
DOI: 10.1128/AEM.02634-08
Abstract: The atrazine chlorohydrolase AtzA has evolved within the past 50 years to catalyze the hydrolytic dechlorination of the herbicide atrazine. It is of wide research interest for two reasons: first, catalytic improvement of the enzyme would facilitate its application in bioremediation, and second, because of its recent evolution, it presents a rare opportunity to examine the early stages in the acquisition of new catalytic activities. Using a structural model of the AtzA-atrazine complex, a region of the substrate-binding pocket was targeted for combinatorial randomization. Identification of improved variants through this process informed the construction of a variant AtzA enzyme with 20-fold improvement in its k cat / K m value compared with that of the wild-type enzyme. The reduction in K m observed in the AtzA variants has allowed the full kinetic profile for the AtzA-catalyzed dechlorination of atrazine to be determined for the first time, revealing the hitherto-unreported substrate cooperativity in AtzA. Since substrate cooperativity is common among deaminases, which are the closest structural homologs of AtzA, it is possible that this phenomenon is a remnant of the catalytic activity of the evolutionary progenitor of AtzA. A catalytic mechanism that suggests a plausible mechanistic route for the evolution of dechlorinase activity in AtzA from an ancestral deaminase is proposed.
Cyanuric acid hydrolase: evolutionary innovation by structural concatenation
Publisher: Wiley
Date: 20-05-2013
DOI: 10.1111/MMI.12249
300-Fold Increase in Production of the Zn 2+ -Dependent Dechlorinase TrzN in Soluble Form via Apoenzyme Stabilization
Publisher: American Society for Microbiology
Date: 07-2014
DOI: 10.1128/AEM.00916-14
Abstract: Microbial metalloenzymes constitute a large library of biocatalysts, a number of which have already been shown to catalyze the breakdown of toxic chemicals or industrially relevant chemical transformations. However, while there is considerable interest in harnessing these catalysts for biotechnology, for many of the enzymes, their large-scale production in active, soluble form in recombinant systems is a significant barrier to their use. In this work, we demonstrate that as few as three mutations can result in a 300-fold increase in the expression of soluble TrzN, an enzyme from Arthrobacter aurescens with environmental applications that catalyzes the hydrolysis of triazine herbicides, in Escherichia coli . Using a combination of X-ray crystallography, kinetic analysis, and computational simulation, we show that the majority of the improvement in expression is due to stabilization of the apoenzyme rather than the metal ion-bound holoenzyme. This provides a structural and mechanistic explanation for the observation that many compensatory mutations can increase levels of soluble-protein production without increasing the stability of the final, active form of the enzyme. This study provides a molecular understanding of the importance of the stability of metal ion free states to the accumulation of soluble protein and shows that differences between apoenzyme and holoenzyme structures can result in mutations affecting the stability of either state differently.
Proteomic and molecular analyses of esterases associated with monocrotophos resistance in Helicoverpa armigera
Publisher: Elsevier BV
Date: 11-2012
OpdA, a bacterial organophosphorus hydrolase, prevents lethality in rats after poisoning with highly toxic organophosphorus pesticides
Publisher: Elsevier BV
Date: 05-2008
Non-covalent binding tags for batch and flow biocatalysis
Publisher: Elsevier BV
Date: 09-2023
Characterization of the Lactococcus lactis transcription factor FlpA and demonstration of an in vitro switch
Publisher: Wiley
Date: 03-2000
DOI: 10.1046/J.1365-2958.2000.01799.X
Abstract: The commercially important bacterium Lactococcus lactis contains two FNR-like proteins (FlpA and FlpB) which have a high degree of identity to each other and to the FLP of Lactobacillus casei. FlpA was isolated from a GST-FlpA fusion protein produced in Escherichia coli. Like FLP, isolated FlpA is a homodimeric protein containing both Zn and Cu. However, the properties of FlpA were more like those of the E. coli oxygen-responsive transcription factor FNR than the FLP of L. casei. As prepared FlpA recognized an FNR site (TTGAT-N4-ATCAA) but not an FLP site (CCTGA-N4-TCAGG) in band-shift assays. In contrast to FLP, DNA binding by FlpA did not require the formation of an intramolecular disulphide bond. However, despite containing only two cysteine residues per monomer, FlpA was able to acquire an FNR-like, oxygen-labile [4Fe 4S] cluster. But, whereas the incorporation of a [4Fe 4S] cluster into FNR enhances interaction with target DNA, it abolished DNA binding by FlpA. An FlpA variant (FlpA') with an N-terminal region designed to be more FLP-like failed to incorporate an iron-sulphur cluster but could now form an intramolecular disulphide. This simple ex le of protein engineering, converting an oxygen-labile [4Fe 4S] containing FNR-like protein into a dithiol-disulphide FLP-like redox sensor demonstrates the versatility of the basic CRP structure. Attempts to demonstrate an FlpA-based aerobic-anaerobic switch in the heterologous host E. coli were unsuccessful. However, studies with a series of FNR-dependent lac reporter fusions in strains of E. coli expressing flpA or flpB revealed that both homologues were able to activate expression of FNR-dependent promoters in vivo but only when positioned 61 base pairs upstream of the transcription start.
Pharmacokinetics of OpdA, an organophosphorus hydrolase, in the African green monkey
Publisher: Elsevier BV
Date: 10-2010
Constrained evolution of a bispecific enzyme: lessons for biocatalyst design
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C6OB02355J
Abstract: Analysis of the natural evolution of bispecificity in triazine hydrolase highlights the importance of epistasis in protein engineering and evolution.
The enzymatic basis for pesticide bioremediation
Publisher: Springer Science and Business Media LLC
Date: 03-2008
An in vivo gene amplification system for high level expression in Saccharomyces cerevisiae
Publisher: Springer Science and Business Media LLC
Date: 24-05-2022
DOI: 10.1038/S41467-022-30529-8
Abstract: Bottlenecks in metabolic pathways due to insufficient gene expression levels remain a significant problem for industrial bioproduction using microbial cell factories. Increasing gene dosage can overcome these bottlenecks, but current approaches suffer from numerous drawbacks. Here, we describe HapAmp, a method that uses haploinsufficiency as evolutionary force to drive in vivo gene lification. HapAmp enables efficient, titratable, and stable integration of heterologous gene copies, delivering up to 47 copies onto the yeast genome. The method is exemplified in metabolic engineering to significantly improve production of the sesquiterpene nerolidol, the monoterpene limonene, and the tetraterpene lycopene. Limonene titre is improved by 20-fold in a single engineering step, delivering ∼1 g L −1 in the flask cultivation. We also show a significant increase in heterologous protein production in yeast. HapAmp is an efficient approach to unlock metabolic bottlenecks rapidly for development of microbial cell factories.
High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes
Publisher: American Society for Microbiology
Date: 05-2017
DOI: 10.1128/AEM.03365-16
Abstract: The Toblerone fold was discovered recently when the first structure of the cyclic amide hydrolase, AtzD (a cyanuric acid hydrolase), was elucidated. We surveyed the cyclic amide hydrolase family, finding a strong correlation between phylogenetic distribution and specificity for either cyanuric acid or barbituric acid. One of six classes (IV) could not be tested due to a lack of expression of the proteins from it, and another class (V) had neither cyanuric acid nor barbituric acid hydrolase activity. High-resolution X-ray structures were obtained for a class VI barbituric acid hydrolase (1.7 Å) from a Rhodococcus species and a class V cyclic amide hydrolase (2.4 Å) from a Frankia species for which we were unable to identify a substrate. Both structures were homologous with the tetrameric Toblerone fold enzyme AtzD, demonstrating a high degree of structural conservation within the cyclic amide hydrolase family. The barbituric acid hydrolase structure did not contain zinc, in contrast with early reports of zinc-dependent activity for this enzyme. Instead, each barbituric acid hydrolase monomer contained either Na + or Mg 2+ , analogous to the structural metal found in cyanuric acid hydrolase. The Frankia cyclic amide hydrolase contained no metal but instead formed unusual, reversible, intermolecular vicinal disulfide bonds that contributed to the thermal stability of the protein. The active sites were largely conserved between the three enzymes, differing at six positions, which likely determine substrate specificity. IMPORTANCE The Toblerone fold enzymes catalyze an unusual ring-opening hydrolysis with cyclic amide substrates. A survey of these enzymes shows that there is a good correlation between physiological function and phylogenetic distribution within this family of enzymes and provide insights into the evolutionary relationships between the cyanuric acid and barbituric acid hydrolases. This family of enzymes is structurally and mechanistically distinct from other enzyme families however, to date the structure of just two, physiologically identical, enzymes from this family has been described. We present two new structures: a barbituric acid hydrolase and an enzyme of unknown function. These structures confirm that members of the CyAH family have the unusual Toblerone fold, albeit with some significant differences.
An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme
Publisher: Elsevier BV
Date: 05-2018
Front Cover: Asymmetric Ene‐Reduction by F420‐Dependent Oxidoreductases B (FDOR‐B) from Mycobacterium smegmatis (ChemBioChem 8/2023)
Publisher: Wiley
Date: 22-03-2023
Esterase-based metabolic resistance to insecticides in heliothine and spodopteran pests
Publisher: Pesticide Science Society of Japan
Date: 2010
A member of the cAMP receptor protein family of transcription regulators in Mycobacterium tuberculosis is required for virulence in mice and controls transcription of the rpfA gene codin
Publisher: Wiley
Date: 30-03-2005
Zinc uptake, oxidative stress and the FNR-like proteins of Lactococcus lactis
Publisher: Oxford University Press (OUP)
Date: 11-2000
DOI: 10.1111/J.1574-6968.2000.TB09363.X
Abstract: Lactococcus lactis ssp. cremoris MG1363 contains two FNR homologues, FlpA and FlpB, encoded by the distal genes of two paralogous operons (orfX(A/B)-orfY(A/B)-flpA/B). An flpA flpB double mutant strain is hypersensitive to hydrogen peroxide and has a depleted intracellular Zn(II) pool. The phenotypes of the flp mutant strains suggest that FlpA and FlpB control the expression of high and low affinity ATP-dependent Zn(II) uptake systems, respectively. Plate tests revealed that expression from a orfX(B)::lac reporter was activated by Cd(II), consistent with other Zn(II)-regulated systems. The link between a failure to acquire Zn(II) and hypersensitivity to oxidative stress suggests that Zn(II) may be required to protect vulnerable protein thiols from oxidation.
Active site mutations of F420-dependent alkene reductases reverse stereoselectivity
Publisher: Cold Spring Harbor Laboratory
Date: 21-02-2023
DOI: 10.1101/2023.02.21.529347
Abstract: Ene-reductases from the Flavin/Deazaflavin Oxidoreductase (FDOR) family have potential value in biocatalysis as they typically exhibit complementary stereoselectivity to the widely utilized Old Yellow Enzyme (OYE) family, yet they are comparatively poorly understood at a mechanistic level. Here, we use a rational design approach to generate a library of 46 active site mutants of two FDORs from Mycobacterium smegmatis and examine the effects on conversion and stereoselectivity against a panel of substrates. Analysis of the effects of these mutations on stereoselectivity across all substrates revealed that the catalytic mechanism is highly sensitive to the polarity of the immediate active site. A conserved active site tyrosine in these enzymes, which does not serve as the proton donor, strongly affects stereochemical outcomes with Cα- (but not Cβ-) substituted substrates. Notably, a Tyr-Met mutation at this position reversed the diastereomeric excess ( de ) with ( R )-carvone from 85.3% to −17.3% (cis/trans). Additionally, this mutation significantly increases activity with (1 S )- verbenone. Finally, we show that the altered stereoselectivity is not due to a “flipped” substrate binding mode in these mutants, but rather that the hydrogenation mode is altered to favor syn relative to anti addition. These results show that the FDORs are highly engineerable and that, despite their superficial similarity, the OYE and FDOR families differ in crucial mechanistic aspects.
Detoxification of G- and V-series nerve agents by the phosphotriesterase OpdA
Publisher: Informa UK Limited
Date: 15-02-2012
A revised biosynthetic pathway for the cofactor F420 in bacteria
Publisher: Cold Spring Harbor Laboratory
Date: 15-11-2018
DOI: 10.1101/470336
Abstract: Cofactor F 420 plays critical roles in primary and secondary metabolism in a range of bacteria and archaea as a low-potential hydride transfer agent. It mediates a variety of important redox transformations involved in bacterial persistence, antibiotic biosynthesis, pro-drug activation and methanogenesis. However, the biosynthetic pathway for F 420 has not been fully eluci-dated: neither the enzyme that generates the putative intermediate 2-phospho- L -lactate, nor the function of the FMN-binding C-terminal domain of the γ-glutamyl ligase (FbiB) in bacteria are known. Here we show that the guanylyltransferases FbiD and CofC accept phosphoenolpyruvate, rather than 2-phospho- L -lactate, as their substrate, leading to the formation of the previously uncharacterized intermediate, dehydro-F 420 -0. The C-terminal domain of FbiB then utilizes FMNH2 to reduce dehydro-F 420 -0, which produces mature F 420 species when combined with the γ-glutamyl ligase activity of the N-terminal domain. This new insight has allowed the heterologous expression F 420 from a recombinant F 420 biosynthetic pathway in Escherichia coli .
Characterization of the phenylurea hydrolases A and B: founding members of a novel amidohydrolase subgroup
Publisher: Portland Press Ltd.
Date: 11-02-2009
DOI: 10.1042/BJ20081488
Abstract: Mycobacterium brisbanense strain JK1, a bacterium capable of degrading the herbicide diuron, was isolated from herbicide-exposed soil. A gene/enzyme system with diuron hydrolase activity was isolated from this strain and named PUH (phenylurea hydrolase) B (puhB/PuhB) because of its close similarity to the previously characterized PUH A (puhA/PuhA). Both PUHs were heterologously expressed, purified and characterized. The PUHs were found to oligomerize as hexamers in solution, with each monomer containing a mononuclear Zn2+ active site. Sequence analysis showed that these enzymes belong to the metal-dependent amidohydrolase superfamily, although they contain a hitherto unreported Asn-X-His metal-binding motif and appear to form a novel sub-group within this superfamily. The effects of temperature and solvent on the enzymes were characterized. Determination of the kinetic parameters of the PUHs was used alongside Brønsted plots to develop a plausible catalytic mechanism, which is similar to that used by urease. In addition to the primary PUH activity, both enzymes are catalytically promiscuous, efficiently hydrolysing esters, carbamates and phosphotriesters. In fact, an analogue of diuron, in which the C–N bond was replaced by a C–O bond, was found to be turned over as efficiently as diuron, suggesting that the substrate specificity is predominantly determined by steric factors. The discovery of PuhA and PuhB on separate continents, and the absence of any other close homologues in the available sequence databases, poses a challenging question regarding the evolutionary origins of these enzymes.
Characterisation of Hybrid Polymersome Vesicles Containing the Efflux Pumps NaAtm1 or P-Glycoprotein
Publisher: MDPI AG
Date: 03-05-2020
Abstract: Investigative systems for purified membrane transporters are almost exclusively reliant on the use of phospholipid vesicles or liposomes. Liposomes provide an environment to support protein function however, they also have numerous drawbacks and should not be considered as a “one-size fits all” system. The use of artificial vesicles comprising block co-polymers (polymersomes) offers considerable advantages in terms of structural stability provision of sufficient lateral pressure and low passive permeability, which is a particular issue for transport assays using hydrophobic compounds. The present investigation demonstrates strategies to reconstitute ATP binding cassette (ABC) transporters into hybrid vesicles combining phospholipids and the block co-polymer poly (butadiene)-poly (ethylene oxide). Two efflux pumps were chosen namely the Novosphingobium aromaticivorans Atm1 protein and human P-glycoprotein (Pgp). Polymersomes were generated with one of two lipid partners, either purified palmitoyl-oleoyl-phosphatidylcholine, or a mixture of crude E. coli lipid extract and cholesterol. Hybrid polymersomes were characterised for size, structural homogeneity, stability to detergents, and permeability. Two transporters, NaAtm1 and P-gp, were successfully reconstituted into pre-formed and surfactant-destabilised hybrid polymersomes using a detergent adsorption strategy. Reconstitution of both proteins was confirmed by density gradient centrifugation and the hybrid polymersomes supported substrate dependent ATPase activity of both transporters. The hybrid polymersomes also displayed low passive permeability to a fluorescent probe (calcein acetomethoxyl-ester (C-AM)) and offer the potential for quantitative measurements of transport activity for hydrophobic compounds.
Adaptive laboratory evolution of native methanol assimilation in Saccharomyces cerevisiae
Publisher: Springer Science and Business Media LLC
Date: 04-11-2020
DOI: 10.1038/S41467-020-19390-9
Abstract: Utilising one-carbon substrates such as carbon dioxide, methane, and methanol is vital to address the current climate crisis. Methylotrophic metabolism enables growth and energy generation from methanol, providing an alternative to sugar fermentation. Saccharomyces cerevisiae is an important industrial microorganism for which growth on one-carbon substrates would be relevant. However, its ability to metabolize methanol has been poorly characterised. Here, using adaptive laboratory evolution and 13 C-tracer analysis, we discover that S. cerevisiae has a native capacity for methylotrophy. A systems biology approach reveals that global rearrangements in central carbon metabolism fluxes, gene expression changes, and a truncation of the uncharacterized transcriptional regulator Ygr067cp supports improved methylotrophy in laboratory evolved S. cerevisiae . This research paves the way for further biotechnological development and fundamental understanding of methylotrophy in the preeminent eukaryotic model organism and industrial workhorse, S. cerevisiae .
Geoffroy Saint-Hilaire on his Principle of Connexion
Publisher: Figshare
Date: 2016
F-420-dependent enzymes - potential for applications in biotechnology
Publisher: Elsevier BV
Date: 02-2013
Asymmetric Ene-Reduction of α,β-Unsaturated Compounds by F420-Dependent Oxidoreductases A Enzymes from Mycobacterium smegmatis
Publisher: American Chemical Society (ACS)
Date: 05-12-2023
Engineered Enzymes that Retain and Regenerate their Cofactors Enable Continuous-Flow Biocatalysis
Publisher: Cold Spring Harbor Laboratory
Date: 05-03-2019
DOI: 10.1101/568972
Active Site Desolvation and Thermostability Trade-Offs in the Evolution of Catalytically Diverse Triazine Hydrolases
Publisher: American Chemical Society (ACS)
Date: 02-11-2016
DOI: 10.1021/ACS.BIOCHEM.6B00731
Abstract: The desolvation of ionizable residues in the active sites of enzymes and the subsequent effects on catalysis and thermostability have been studied in model systems, yet little about how enzymes can naturally evolve to include active sites with highly reactive and desolvated charges is known. Variants of triazine hydrolase (TrzN) with significant differences in their active sites have been isolated from different bacterial strains: TrzN from Nocardioides sp. strain MTD22 contains a catalytic glutamate residue (Glu241) that is surrounded by hydrophobic and aromatic second-shell residues (Pro214 and Tyr215), whereas TrzN from Nocardioides sp. strain AN3 has a noncatalytic glutamine residue (Gln241) at an equivalent position, surrounded by hydrophilic residues (Thr214 and His215). To understand how and why these variants have evolved, a series of TrzN mutants were generated and characterized. These results show that desolvation by second-shell residues increases the pK
Hyperthermophilic Carbamate Kinase Stability and Anabolic In Vitro Activity at Alkaline pH
Publisher: American Society for Microbiology
Date: 02-2018
DOI: 10.1128/AEM.02250-17
Abstract: Carbamate kinases catalyze the conversion of carbamate to carbamoyl phosphate, which is readily transformed into other compounds. Carbamate forms spontaneously from ammonia and carbon dioxide in aqueous solutions, so the kinases have potential for sequestrative utilization of the latter compounds. Here, we compare seven carbamate kinases from mesophilic, thermophilic, and hyperthermophilic sources. In addition to the known enzymes from Enterococcus faecalis and Pyrococcus furiosus , the previously unreported enzymes from the hyperthermophiles Thermococcus sibiricus and Thermococcus barophilus , the thermophiles Fervidobacterium nodosum and Thermosipho melanesiensis , and the mesophile Clostridium tetani were all expressed recombinantly, each in high yield. Only the clostridial enzyme did not show catalysis. In direct assays of carbamate kinase activity, the three hyperthermophilic enzymes display higher specific activities at elevated temperatures, greater stability, and remarkable substrate turnover at alkaline pH (9.9 to 11.4). Thermococcus barophilus and Thermococcus sibiricus carbamate kinases were found to be the most active when the enzymes were tested at 80°C, and maintained activity over broad temperature and pH ranges. These robust thermococcal enzymes therefore represent ideal candidates for biotechnological applications involving aqueous ammonia solutions, since nonbuffered 0.0001 to 1.0 M solutions have pH values of approximately 9.8 to 11.8. As proof of concept, here we also show that carbamoyl phosphate produced by the Thermococcus barophilus kinase is efficiently converted in situ to carbamoyl aspartate by aspartate transcarbamoylase from the same source organism. Using acetyl phosphate to simultaneously recycle the kinase cofactor ATP, at pH 9.9 carbamoyl aspartate is produced in high yield and directly from solutions of ammonia, carbon dioxide, and aspartate. IMPORTANCE Much of the nitrogen in animal wastes and used in fertilizers is commonly lost as ammonia in water runoff, from which it must be removed to prevent downstream pollution and evolution of nitrogenous greenhouse gases. Since carbamate kinases transform ammonia and carbon dioxide to carbamoyl phosphate via carbamate, and carbamoyl phosphate may be converted into other valuable compounds, the kinases provide a route for useful sequestration of ammonia, as well as of carbon dioxide, another greenhouse gas. At the same time, recycling the ammonia in chemical synthesis reduces the need for its energy-intensive production. However, robust catalysts are required for such biotransformations. Here we show that carbamate kinases from hyperthermophilic archaea display remarkable stability and high catalytic activity across broad ranges of pH and temperature, making them promising candidates for biotechnological applications. We also show that carbamoyl phosphate produced by the kinases may be efficiently used to produce carbamoyl aspartate.
Evolution of atrazine-degrading capabilities in the environment
Publisher: Springer Science and Business Media LLC
Date: 18-10-2012
DOI: 10.1007/S00253-012-4495-0
Abstract: Since their first introduction in the mid 1950s, man-made s-triazine herbicides such as atrazine have extensively been used in agriculture to control broadleaf weed growth in different crops, and thus contributed to improving crop yield and quality. Atrazine is the most widely used s-triazine herbicide for the control of weeds in crops such as corn and sorghum. Although atrazine was initially found to be slowly and partially biodegradable, predominantly by nonspecific P450 monoxygenases which do not sustain microbial growth, microorganisms gradually evolved as a result of repeated exposure, started using it as a growth substrate and eventually succeeded in mineralizing it. Within three decades, an entirely new hydrolase-dependent pathway for atrazine mineralization emerged and rapidly spread worldwide among genetically different bacteria. This review focuses on the enzymes involved in atrazine mineralization and their evolutionary histories, the genetic composition of microbial populations involved in atrazine degradation and the biotechnologies that have been developed, based on these systems, for the bioremediation of atrazine contamination in the environment.
An improved and general streamlined phylogenetic protocol applied to the fatty acid desaturase family
Publisher: Elsevier BV
Date: 10-2017
DOI: 10.1016/J.YMPEV.2017.07.012
Abstract: Numerous tools to generate phylogenetic estimates are available, but there is no single protocol that will produce an accurate phylogenetic tree for any dataset. Here, we investigated some of those tools, paying particular attention to different alignment algorithms, in order to produce a phylogeny for the integral membrane fatty acid desaturase (FAD) family. Herein, we report a novel streamlined protocol which utilises peptide pattern recognition (PPR). This protocol can theoretically be applied universally to generate accurate multiple sequence alignments and improve downstream phylogenetic analyses. Applied to the desaturases, the protocol generated the first detailed phylogenetic estimates for the family since 2003, which suggested they may have evolved from three functionally distinct desaturases and further, that desaturases evolved first in cyanobacteria. In addition to the phylogenetic outputs, we mapped PPR sequence motifs onto an X-ray protein structure to provide insights into biochemical function and demonstrate the complementarity of PPR and phylogenetics.
Cofactor F420-Dependent Enzymes: An Under-Explored Resource for Asymmetric Redox Biocatalysis
Publisher: MDPI AG
Date: 20-10-2019
DOI: 10.3390/CATAL9100868
Abstract: The asymmetric reduction of enoates, imines and ketones are among the most important reactions in biocatalysis. These reactions are routinely conducted using enzymes that use nicotinamide cofactors as reductants. The deazaflavin cofactor F420 also has electrochemical properties that make it suitable as an alternative to nicotinamide cofactors for use in asymmetric reduction reactions. However, cofactor F420-dependent enzymes remain under-explored as a resource for biocatalysis. This review considers the cofactor F420-dependent enzyme families with the greatest potential for the discovery of new biocatalysts: the flavin/deazaflavin-dependent oxidoreductases (FDORs) and the luciferase-like hydride transferases (LLHTs). The characterized F420-dependent reductions that have the potential for adaptation for biocatalysis are discussed, and the enzymes best suited for use in the reduction of oxidized cofactor F420 to allow cofactor recycling in situ are considered. Further discussed are the recent advances in the production of cofactor F420 and its functional analog FO-5′-phosphate, which remains an impediment to the adoption of this family of enzymes for industrial biocatalytic processes. Finally, the prospects for the use of this cofactor and dependent enzymes as a resource for industrial biocatalysis are discussed.
A 5000-Fold Increase in the Specificity of a Bacterial Phosphotriesterase for Malathion through Combinatorial Active Site Mutagenesis
Publisher: Public Library of Science (PLoS)
Date: 10-04-2014
An Enzyme to Protect Waterways from the Herbicide, Atrazine
Publisher: Research Information Ltd.
Date: 08-2009
DOI: 10.1564/20AUG09
Heterologous Expression and Biochemical Characterisation of Fourteen Esterases from Helicoverpa armigera
Publisher: Public Library of Science (PLoS)
Date: 17-06-2013
Improved production of the non-native cofactor F420 in Escherichia coli
Publisher: Springer Science and Business Media LLC
Date: 05-11-2021
DOI: 10.1038/S41598-021-01224-3
Abstract: The deazaflavin cofactor F 420 is a low-potential, two-electron redox cofactor produced by some Archaea and Eubacteria that is involved in methanogenesis and methanotrophy, antibiotic biosynthesis, and xenobiotic metabolism. However, it is not produced by bacterial strains commonly used for industrial biocatalysis or recombinant protein production, such as Escherichia coli , limiting our ability to exploit it as an enzymatic cofactor and produce it in high yield. Here we have utilized a genome-scale metabolic model of E. coli and constraint-based metabolic modelling of cofactor F 420 biosynthesis to optimize F 420 production in E. coli. This analysis identified phospho-enol pyruvate (PEP) as a limiting precursor for F 420 biosynthesis, explaining carbon source-dependent differences in productivity. PEP availability was improved by using gluconeogenic carbon sources and overexpression of PEP synthase. By improving PEP availability, we were able to achieve a ~ 40-fold increase in the space–time yield of F 420 compared with the widely used recombinant Mycobacterium smegmatis expression system. This study establishes E. coli as an industrial F 420 -production system and will allow the recombinant in vivo use of F 420 -dependent enzymes for biocatalysis and protein engineering applications.
A revised biosynthetic pathway for the cofactor F420 in prokaryotes
Publisher: Springer Science and Business Media LLC
Date: 05-04-2019
DOI: 10.1038/S41467-019-09534-X
Abstract: Cofactor F 420 plays critical roles in primary and secondary metabolism in a range of bacteria and archaea as a low-potential hydride transfer agent. It mediates a variety of important redox transformations involved in bacterial persistence, antibiotic biosynthesis, pro-drug activation and methanogenesis. However, the biosynthetic pathway for F 420 has not been fully elucidated: neither the enzyme that generates the putative intermediate 2-phospho- l -lactate, nor the function of the FMN-binding C-terminal domain of the γ-glutamyl ligase (FbiB) in bacteria are known. Here we present the structure of the guanylyltransferase FbiD and show that, along with its archaeal homolog CofC, it accepts phosphoenolpyruvate, rather than 2-phospho- l -lactate, as the substrate, leading to the formation of the previously uncharacterized intermediate dehydro-F 420 -0. The C-terminal domain of FbiB then utilizes FMNH 2 to reduce dehydro-F 420 -0, which produces mature F 420 species when combined with the γ-glutamyl ligase activity of the N-terminal domain. These new insights have allowed the heterologous production of F 420 from a recombinant F 420 biosynthetic pathway in Escherichia coli .
Escherichia coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions
Publisher: Elsevier BV
Date: 09-2006
Free-Enzyme Bioremediation of Pesticides: A case study for the enzymatic remediation of organophosphorous insecticide residues
Publisher: American Chemical Society
Date: 2011
Structure-based rational design of a phosphotriesterase
Publisher: American Society for Microbiology
Date: 08-2009
DOI: 10.1128/AEM.00629-09
Abstract: In silico substrate docking of both stereoisomers of the pesticide chlorfenvinphos (CVP) in the phosphotriesterase from Agrobacterium radiobacter identified two residues (F131 and W132) that prevent productive substrate binding and cause stereospecificity. A variant (W131H/F132A) was designed that exhibited ca. 480-fold and 8-fold increases in the rate of Z -CVP and E -CVP hydrolysis, respectively, eliminating stereospecificity.
Related Organisations
University Of Wales Aberystwyth
Location: United Kingdom of Great Britain and Northern Ireland
University Of Sheffield
Location: United Kingdom of Great Britain and Northern Ireland
Related Funding Activities
Discovery Projects - Grant ID: DP200102837
Start Date: 07-2020
End Date: 12-2024
Amount: $451,284.00
Funder: Australian Research Council
View Funded ActivityARC Centres Of Excellence - Grant ID: CE200100029
Start Date: 11-2020
End Date: 11-2027
Amount: $35,000,000.00
Funder: Australian Research Council
View Funded Activity