Imperial College London

DrJohnHeap

Faculty of Natural SciencesDepartment of Life Sciences

Lecturer in Synthetic Biology
 
 
 
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Contact

 

+44 (0)20 7594 5355j.heap

 
 
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Location

 

Bessemer BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

29 results found

Miari VF, Solanki P, Hieba Y, Stabler RA, Heap JTet al., 2017, In Vitro Susceptibility to Closthioamide among Clinical and Reference Strains of Neisseria gonorrhoeae, ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Vol: 61, ISSN: 0066-4804

JOURNAL ARTICLE

Ehsaan M, Kuit W, Zhang Y, Cartman ST, Heap JT, Winzer K, Minton NPet al., 2016, Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824, Biotechnology for Biofuels, Vol: 9, Pages: 4-4, ISSN: 1754-6834

BACKGROUND: Clostridium acetobutylicum represents a paradigm chassis for the industrial production of the biofuel biobutanol and a focus for metabolic engineering. We have previously developed procedures for the creation of in-frame, marker-less deletion mutants in the pathogen Clostridium difficile based on the use of pyrE and codA genes as counter selection markers. In the current study we sought to test their suitability for use in C. acetobutylicum. RESULTS: Both systems readily allowed the isolation of in-frame deletions of the C. acetobutylicum ATCC 824 spo0A and the cac824I genes, leading to a sporulation minus phenotype and improved transformation, respectively. The pyrE-based system was additionally used to inactivate a putative glycogen synthase (CA_C2239, glgA) and the pSOL1 amylase gene (CA_P0168, amyP), leading to lack of production of granulose and amylase, respectively. Their isolation provided the opportunity to make use of one of the key pyrE system advantages, the ability to rapidly complement mutations at appropriate gene dosages in the genome. In both cases, their phenotypes were restored in terms of production of granulose (glgA) and amylase (amyP). Genome re-sequencing of the ATCC 824 COSMIC consortium laboratory strain used revealed the presence of 177 SNVs and 49 Indels, including a 4916-bp deletion in the pSOL1 megaplasmid. A total of 175 SNVs and 48 Indels were subsequently shown to be present in an 824 strain re-acquired (Nov 2011) from the ATCC and are, therefore, most likely errors in the published genome sequence, NC_003030 (chromosome) and NC_001988 (pSOL1). CONCLUSIONS: The codA or pyrE counter selection markers appear equally effective in isolating deletion mutants, but there is considerable merit in using a pyrE mutant as the host as, through the use of ACE (Allele-Coupled Exchange) vectors, mutants created (by whatever means) can be rapidly complemented concomitant with restoration of the pyrE allele. This avoids the phenotypic eff

JOURNAL ARTICLE

Kelly CL, Liu Z, Yoshihara A, Jenkinson SF, Wormald MR, Otero J, Estévez A, Kato A, Marqvorsen MHS, Fleet GWJ, Estévez RJ, Izumori K, Heap JTet al., 2016, Synthetic Chemical Inducers and Genetic Decoupling Enable Orthogonal Control of the rhaBAD Promoter., ACS Synth Biol, Vol: 5, Pages: 1136-1145

External control of gene expression is crucial in synthetic biology and biotechnology research and applications, and is commonly achieved using inducible promoter systems. The E. coli rhamnose-inducible rhaBAD promoter has properties superior to more commonly used inducible expression systems, but is marred by transient expression caused by degradation of the native inducer, l-rhamnose. To address this problem, 35 analogues of l-rhamnose were screened for induction of the rhaBAD promoter, but no strong inducers were identified. In the native configuration, an inducer must bind and activate two transcriptional activators, RhaR and RhaS. Therefore, the expression system was reconfigured to decouple the rhaBAD promoter from the native rhaSR regulatory cascade so that candidate inducers need only activate the terminal transcription factor RhaS. Rescreening the 35 compounds using the modified rhaBAD expression system revealed several promising inducers. These were characterized further to determine the strength, kinetics, and concentration-dependence of induction; whether the inducer was used as a carbon source by E. coli; and the modality (distribution) of induction among populations of cells. l-Mannose was found to be the most useful orthogonal inducer, providing an even greater range of induction than the native inducer l-rhamnose, and crucially, allowing sustained induction instead of transient induction. These findings address the key limitation of the rhaBAD expression system and suggest it may now be the most suitable system for many applications.

JOURNAL ARTICLE

Liu Z, Yoshihara A, Kelly C, Heap JT, Marqvorsen MHS, Jenkinson SF, Wormald MR, Otero JM, Estevez A, Kato A, Fleet GWJ, Estevez RJ, Izumori Ket al., 2016, 6-Deoxyhexoses from l-Rhamnose in the Search for Inducers of the Rhamnose Operon: Synergy of Chemistry and Biotechnology, CHEMISTRY-A EUROPEAN JOURNAL, Vol: 22, Pages: 12557-12565, ISSN: 0947-6539

JOURNAL ARTICLE

Walker DJF, Heap JT, Winzer K, Minton NPet al., 2016, A genetic assay for gene essentiality in Clostridium, ANAEROBE, Vol: 42, Pages: 40-43, ISSN: 1075-9964

JOURNAL ARTICLE

Cartman ST, Heap JT, Kuehne S, Cooksley CM, Ehsaan M, Winzer K, Minton NPet al., 2014, Clostridial gene tools, Systems Biology of Clostridium, Pages: 21-55, ISBN: 9781783264414

BOOK CHAPTER

Heap JT, Theys J, Ehsaan M, Kubiak AM, Dubois L, Paesmans K, Van Mellaert L, Knox R, Kuehne SA, Lambin P, Minton NPet al., 2014, Spores of Clostridium engineered for clinical efficacy and safety cause regression and cure of tumors in vivo, ONCOTARGET, Vol: 5, Pages: 1761-1769, ISSN: 1949-2553

JOURNAL ARTICLE

Jabbari S, Steiner E, Heap JT, Winzer K, Minton NP, King JRet al., 2013, The putative influence of the agr operon upon survival mechanisms used by Clostridium acetobutylicum, MATHEMATICAL BIOSCIENCES, Vol: 243, Pages: 223-239, ISSN: 0025-5564

JOURNAL ARTICLE

Kovacs K, Willson BJ, Schwarz K, Heap JT, Jackson A, Bolam DN, Winzer K, Minton NPet al., 2013, Secretion and assembly of functional mini-cellulosomes from synthetic chromosomal operons in Clostridium acetobutylicum ATCC 824, BIOTECHNOLOGY FOR BIOFUELS, Vol: 6, ISSN: 1754-6834

JOURNAL ARTICLE

Zhang Z, Korkeala H, Dahlsten E, Sahala E, Heap JT, Minton NP, Lindstrom Met al., 2013, Two-Component Signal Transduction System CBO0787/CBO0786 Represses Transcription from Botulinum Neurotoxin Promoters in Clostridium botulinum ATCC 3502, PLOS PATHOGENS, Vol: 9, ISSN: 1553-7366

JOURNAL ARTICLE

Cartman ST, Kelly ML, Heeg D, Heap JT, Minton NPet al., 2012, Precise Manipulation of the Clostridium difficile Chromosome Reveals a Lack of Association between the tcdC Genotype and Toxin Production, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol: 78, Pages: 4683-4690, ISSN: 0099-2240

JOURNAL ARTICLE

Heap JT, Ehsaan M, Cooksley CM, Ng Y-K, Cartman ST, Winzer K, Minton NPet al., 2012, Integration of DNA into bacterial chromosomes from plasmids without a counter-selection marker, NUCLEIC ACIDS RESEARCH, Vol: 40, ISSN: 0305-1048

JOURNAL ARTICLE

Lindstrom M, Dahlsten E, Soderholm H, Selby K, Somervuo P, Heap JT, Minton NP, Korkeala Het al., 2012, Involvement of Two-Component System CBO0366/CBO0365 in the Cold Shock Response and Growth of Group I (Proteolytic) Clostridium botulinum ATCC 3502 at Low Temperatures, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol: 78, Pages: 5466-5470, ISSN: 0099-2240

JOURNAL ARTICLE

Saad NY, Schiel B, Braye M, Heap JT, Minton NP, Duerre P, Becker HDet al., 2012, Riboswitch (T-box)-mediated Control of tRNA-dependent Amidation in Clostridium acetobutylicum Rationalizes Gene and Pathway Redundancy for Asparagine and Asparaginyl-tRNA(Asn) Synthesis, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 287, Pages: 20382-20394, ISSN: 0021-9258

JOURNAL ARTICLE

Jabbari S, Heap JT, King JR, 2011, Mathematical Modelling of the Sporulation-Initiation Network in Bacillus Subtilis Revealing the Dual Role of the Putative Quorum-Sensing Signal Molecule PhrA, BULLETIN OF MATHEMATICAL BIOLOGY, Vol: 73, Pages: 181-211, ISSN: 0092-8240

JOURNAL ARTICLE

Selby K, Lindstrom M, Somervuo P, Heap JT, Minton NP, Korkeala Het al., 2011, Important Role of Class I Heat Shock Genes hrcA and dnaK in the Heat Shock Response and the Response to pH and NaCl Stress of Group I Clostridium botulinum Strain ATCC 3502, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol: 77, Pages: 2823-2830, ISSN: 0099-2240

JOURNAL ARTICLE

Soderholm H, Lindstrom M, Somervuo P, Heap J, Minton N, Linden J, Korkeala Het al., 2011, cspB encodes a major cold shock protein in Clostridium botulinum ATCC 3502, INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY, Vol: 146, Pages: 23-30, ISSN: 0168-1605

JOURNAL ARTICLE

Steiner E, Dago AE, Young DI, Heap JT, Minton NP, Hoch JA, Young Met al., 2011, Multiple orphan histidine kinases interact directly with Spo0A to control the initiation of endospore formation in Clostridium acetobutylicum, MOLECULAR MICROBIOLOGY, Vol: 80, Pages: 641-654, ISSN: 0950-382X

JOURNAL ARTICLE

Bradshaw M, Marshall KM, Heap JT, Tepp WH, Minton NP, Johnson EAet al., 2010, Construction of a Nontoxigenic Clostridium botulinum Strain for Food Challenge Studies, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol: 76, Pages: 387-393, ISSN: 0099-2240

JOURNAL ARTICLE

Burns DA, Heap JT, Minton NP, 2010, SleC Is Essential for Germination of Clostridium difficile Spores in Nutrient-Rich Medium Supplemented with the Bile Salt Taurocholate, JOURNAL OF BACTERIOLOGY, Vol: 192, Pages: 657-664, ISSN: 0021-9193

JOURNAL ARTICLE

Burns DA, Heap JT, Minton NP, 2010, Clostridium difficile spore germination: an update, RESEARCH IN MICROBIOLOGY, Vol: 161, Pages: 730-734, ISSN: 0923-2508

JOURNAL ARTICLE

Burns DA, Heap JT, Minton NP, 2010, The diverse sporulation characteristics of Clostridium difficile clinical isolates are not associated with type, ANAEROBE, Vol: 16, Pages: 618-622, ISSN: 1075-9964

JOURNAL ARTICLE

Cartman ST, Heap JT, Kuehne SA, Cockayne A, Minton NPet al., 2010, The emergence of 'hypervirulence' in Clostridium difficile, INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY, Vol: 300, Pages: 387-395, ISSN: 1438-4221

JOURNAL ARTICLE

Heap JT, Kuehne SA, Ehsaan M, Cartman ST, Cooksley CM, Scott JC, Minton NPet al., 2010, The ClosTron: Mutagenesis in Clostridium refined and streamlined, JOURNAL OF MICROBIOLOGICAL METHODS, Vol: 80, Pages: 49-55, ISSN: 0167-7012

JOURNAL ARTICLE

Kuehne SA, Cartman ST, Heap JT, Kelly ML, Cockayne A, Minton NPet al., 2010, The role of toxin A and toxin B in Clostridium difficile infection, NATURE, Vol: 467, Pages: 711-U97, ISSN: 0028-0836

JOURNAL ARTICLE

Heap JT, Pennington OJ, Cartman ST, Minton NPet al., 2009, A modular system for Clostridium shuttle plasmids, JOURNAL OF MICROBIOLOGICAL METHODS, Vol: 78, Pages: 79-85, ISSN: 0167-7012

JOURNAL ARTICLE

AbuKhader MM, Heap J, De Matteis CI, Doughty SW, Minton N, Paoli Met al., 2007, Crystallization and preliminary X-ray characterization of the Bacillus amyloliquefaciens YwrO enzyme, ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS, Vol: 63, Pages: 746-750, ISSN: 1744-3091

JOURNAL ARTICLE

Heap JT, Pennington OJ, Cartman ST, Carter GP, Minton NPet al., 2007, The ClosTron: A universal gene knock-out system for the genus Clostridium, JOURNAL OF MICROBIOLOGICAL METHODS, Vol: 70, Pages: 452-464, ISSN: 0167-7012

JOURNAL ARTICLE

AbuKhader M, Heap J, De Matteis C, Kellam B, Doughty SW, Minton N, Paoli Met al., 2005, Binding of the anticancer prodrug CB1954 to the activating enzyme NQO2 revealed by the crystal structure of their complex, JOURNAL OF MEDICINAL CHEMISTRY, Vol: 48, Pages: 7714-7719, ISSN: 0022-2623

JOURNAL ARTICLE

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