Dr. Patrik R. Jones

Akhtar MK, Jones PR, 2014, Cofactor engineering for enhancing the flux of metabolic pathways., Front Bioeng Biotechnol, Vol: 2, Pages: 30-30, ISSN: 2296-4185

The manufacture of a diverse array of chemicals is now possible with biologically engineered strains, an approach that is greatly facilitated by the emergence of synthetic biology. This is principally achieved through pathway engineering in which enzyme activities are coordinated within a genetically amenable host to generate the product of interest. A great deal of attention is typically given to the quantitative levels of the enzymes with little regard to their overall qualitative states. This highly constrained approach fails to consider other factors that may be necessary for enzyme functionality. In particular, enzymes with physically bound cofactors, otherwise known as holoenzymes, require careful evaluation. Herein, we discuss the importance of cofactors for biocatalytic processes and show with empirical examples why the synthesis and integration of cofactors for the formation of holoenzymes warrant a great deal of attention within the context of pathway engineering.

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Jones PR, Pásztor AP, Kallio P, Akhtar MK, Malatinszky Det al., 2014, A synthetic O2-tolerant butanol pathway exploiting native fatty acid biosynthesis in Escherichia coli, Biotechnology and Bioengineering, Vol: 112, Pages: 120-128, ISSN: 1097-0290

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Jones PR, 2014, Genetic instability in cyanobacteria – an elephant in the room?, Frontiers in Bioengineering and Biotechnology, Vol: 2, Pages: 1-5

Many research groups are interested in engineering the metabolism of cyanobacteria with the objective to convert solar energy, CO2, and water (perhaps also N2) into commercially valuable products. Toward this objective, many challenges stand in the way before sustainable production can be realized. One of these challenges, potentially, is genetic instability. Although only a handful of reports of this phenomenon are available in the scientific literature, it does appear to be a real issue that so far has not been studied much in cyanobacteria. With this brief perspective, I wish to raise the awareness of this potential issue and hope to inspire future studies on the topic as I believe it will make an important contribution to enabling sustainable large-scale biotechnology in the future using aquatic photobiological microorganisms.

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Kallio P, Pásztor A, Akhtar MK, Jones PRet al., 2014, Renewable jet fuel, Current Opinion in Biotechnology, Vol: 26, Pages: 50-55, ISSN: 0958-1669

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Akhtar MK, Turner NJ, Jones PR, 2013, Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: 87-92, ISSN: 0027-8424

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• Citations: 258

Kaewphan S, Kreula S, Van Landeghem S, Van de Peer Y, Jones PR, Ginter Fet al., 2013, Integrating Large-Scale Text Mining and Co-Expression Networks: Targeting NADP (H) Metabolism in E. coli with Event Extraction, BioTxtM 2012 Third workshop on Building and Evaluating Resources for Biomedical Text Mining, Pages: 8-15

We present an application of EVEX, a literature-scale event extraction resource, in the concrete biological use case of NADP(H)metabolism regulation inEscherichia coli. We make extensive use of the EVEX event generalization based on gene family definitionsin Ensembl Genomes, to extract cross-species candidate regulators. We manually evaluate the resulting network so as to only preservecorrect events and facilitate its integration with microarray-based co-expression data. When analysing the combined network obtainedfrom text mining and co-expression, we identify 41 candidate genes involved in triangular patterns involving both subnetworks. Severalof these candidates are of particular interest, and we discuss their biological relevance further. This study is the first to present areal-world evaluation of the EVEX resource in particular and literature-scale application of the systems emerging from the BioNLPShared Task series in general. We summarize the lessons learned from this use case in order to focus future development of EVEX andsimilar literature-scale resources.

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Kamarainen J, Knoop H, Stanford NJ, Guerrero F, Akhtar MK, Aro E-M, Steuer R, Jones PRet al., 2012, Physiological tolerance and stoichiometric potential of cyanobacteria for hydrocarbon fuel production, JOURNAL OF BIOTECHNOLOGY, Vol: 162, Pages: 67-74, ISSN: 0168-1656

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• Citations: 43

Guerrero F, Carbonell V, Cossu M, Correddu D, Jones PRet al., 2012, Ethylene Synthesis and Regulated Expression of Recombinant Protein in <i>Synechocystis</i> sp PCC 6803, PLOS ONE, Vol: 7, ISSN: 1932-6203

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• Citations: 122

Eser BE, Das D, Han J, Jones PR, Marsh ENGet al., 2011, Oxygen-Independent Alkane Formation by Non-Heme Iron-Dependent Cyanobacterial Aldehyde Decarbonylase: Investigation of Kinetics and Requirement for an External Electron Donor, BIOCHEMISTRY, Vol: 50, Pages: 10743-10750, ISSN: 0006-2960

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• Citations: 57

Akhtar MK, Jones PR, 2009, Construction of a synthetic YdbK-dependent pyruvate:H₂ pathway in <i>Escherichia coli</i> BL21(DE3), METABOLIC ENGINEERING, Vol: 11, Pages: 139-147, ISSN: 1096-7176

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• Citations: 53

Jones PR, 2008, Improving fermentative biomass-derived H₂-production by engineering microbial metabolism, 2nd Asian Bio-Hydrogen Symposium, Publisher: PERGAMON-ELSEVIER SCIENCE LTD, Pages: 5122-5130, ISSN: 0360-3199

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• Citations: 40

Jones PR, Gawel R, Francis IL, Waters EJet al., 2008, The influence of interactions between major white wine components on the aroma, flavour and texture of model white wine, FOOD QUALITY AND PREFERENCE, Vol: 19, Pages: 596-607, ISSN: 0950-3293

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• Citations: 140

Veit A, Akhtar MK, Mizutani T, Jones PRet al., 2008, Constructing and testing the thermodynamic limits of synthetic NAD(P)H:H₂ pathways, MICROBIAL BIOTECHNOLOGY, Vol: 1, Pages: 382-394, ISSN: 1751-7915

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• Citations: 57

Akhtar MK, Jones PR, 2008, Deletion of <i>iscR</i> stimulates recombinant clostridial Fe-Fe hydrogenase activity and H₂-accumulation in <i>Escherichia coli</i> BL21(DE3), APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, Vol: 78, Pages: 853-862, ISSN: 0175-7598

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• Citations: 92

Akhtar MK, Jones PR, 2008, Engineering of a synthetic <i>hydF</i>-<i>hydE</i>-<i>hydG</i>-<i>hydA</i> operon for biohydrogen production, ANALYTICAL BIOCHEMISTRY, Vol: 373, Pages: 170-172, ISSN: 0003-2697

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• Citations: 30

Nielsen KA, Tattersall DB, Jones PR, Moller BLet al., 2008, Metabolon formation in dhurrin biosynthesis, PHYTOCHEMISTRY, Vol: 69, Pages: 88-98, ISSN: 0031-9422

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• Citations: 105

Park M-O, Mizutani T, Jones PR, 2007, Glyceraldehyde-3-phosphate ferredoxin oxidoreductase from <i>Methanococcus maripaludis</i>, JOURNAL OF BACTERIOLOGY, Vol: 189, Pages: 7281-7289, ISSN: 0021-9193

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• Citations: 13

Pocock KF, Alexander GM, Hayasaka Y, Jones PR, Waters EJet al., 2007, Sulfate - a candidate for the missing essential factor that is required for the formation of protein haze in white wine, JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, Vol: 55, Pages: 1799-1807, ISSN: 0021-8561

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• Citations: 68

WATERS EJ, ALEXANDER G, MUHLACK R, POCOCK KF, COLBY C, O'NEILL BK, HØJ PB, JONES Pet al., 2005, Preventing protein haze in bottled white wine, Australian Journal of Grape and Wine Research, Vol: 11, Pages: 215-225, ISSN: 1322-7130

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Jones P, Messner B, Nakajima J-I, Schäffner AR, Saito Ket al., 2003, UGT73C6 and UGT78D1, Glycosyltransferases Involved in Flavonol Glycoside Biosynthesis in Arabidopsis thaliana, Journal of Biological Chemistry, Vol: 278, Pages: 43910-43918, ISSN: 0021-9258

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Hansen KS, Kristensen C, Tattersall DB, Jones PR, Olsen CE, Bak S, Moller BLet al., 2003, The in vitro substrate regiospecificity of recombinant UGT85B1, the cyanohydrin glucosyltransferase from <i>Sorghum bicolor</i>, PHYTOCHEMISTRY, Vol: 64, Pages: 143-151, ISSN: 0031-9422

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• Citations: 80

Jones PR, Manabe T, Awazuhara M, Saito Ket al., 2003, A new member of plant CS-lyases -: A cystine lyase from <i>Arabidopsis thaliana</i>, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 278, Pages: 10291-10296, ISSN: 0021-9258

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• Citations: 31

Tattersall DB, Bak S, Jones PR, Olsen CE, Nielsen JK, Hansen ML, Hoj PB, Moller BLet al., 2001, Resistance to an herbivore through engineered cyanogenic glucoside synthesis, SCIENCE, Vol: 293, Pages: 1826-1828, ISSN: 0036-8075

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• Citations: 200

Jones P, Vogt T, 2001, Glycosyltransferases in secondary plant metabolism: tranquilizers and stimulant controllers, PLANTA, Vol: 213, Pages: 164-174, ISSN: 0032-0935

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• Citations: 312

Vogt T, Jones P, 2000, Glycosyltransferases in plant natural product synthesis: characterization of a supergene family, TRENDS IN PLANT SCIENCE, Vol: 5, Pages: 380-386, ISSN: 1360-1385

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• Citations: 484

Jones PR, Moller BL, Hoj PB, 1999, The UDP-glucose:<i>p</i>-hydroxymandelonitrile-<i>O</i>-glucosyltransferase that catalyzes the last step in synthesis of the cyanogenic glucoside dhurrin in <i>Sorghum bicolor</i> -: Isolation, cloning, heterologous expression, and substrate specificity, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 274, Pages: 35483-35491, ISSN: 0021-9258

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• Citations: 142