Nitrilases in Nitrile Biocatalysis
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WO 2007/084545 Al
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date (10) International Publication Number 26 July 2007 (26.07.2007) PCT WO 2007/084545 Al (51) International Patent Classification: (74) Agent: ZERULL, Susan, Moeller; The Dow Chemical C07C 227/32 (2006.01) C12P 41/00 (2006.01) Company, Intellectual Property Section, P.O. Box 1967, C07D 317/30 (2006.01) Midland, MI 48674-1967 (US). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/US2007/001207 kind of national protection available): AE, AG, AL, AM, AT,AU, AZ, BA, BB, BG, BR, BW, BY, BZ, CA, CH, CN, (22) International Filing Date: 17 January 2007 (17.01.2007) CO, CR, CU, CZ, DE, DK, DM, DZ, EC, EE, EG, ES, FI, (25) Filing Language: English GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, LR, LS, (26) Publication Language: English LT, LU, LV,LY,MA, MD, MG, MK, MN, MW, MX, MY, (30) Priority Data: MZ, NA, NG, NI, NO, NZ, OM, PG, PH, PL, PT, RO, RS, 11/333,937 18 January 2006 (18.01.2006) US RU, SC, SD, SE, SG, SK, SL, SM, SV, SY, TJ, TM, TN, (71) Applicant (for all designated States except US): DOW TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW GLOBAL TECHNOLOGIES INC. [US/US]; Washing (84) Designated States (unless otherwise indicated, for every ton Street, 1790 Building, Midland, MI 48674 (US). -
The Genomes of Polyextremophilic Cyanidiales Contain 1% 2 Horizontally Transferred Genes with Diverse Adaptive Functions 3 4 Alessandro W
bioRxiv preprint doi: https://doi.org/10.1101/526111; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 The genomes of polyextremophilic Cyanidiales contain 1% 2 horizontally transferred genes with diverse adaptive functions 3 4 Alessandro W. Rossoni1#, Dana C. Price2, Mark Seger3, Dagmar Lyska1, Peter Lammers3, 5 Debashish Bhattacharya4 & Andreas P.M. Weber1* 6 7 1Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich 8 Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany 9 2Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA 10 3Arizona Center for Algae Technology and Innovation, Arizona State University, Mesa, AZ 11 85212, USA 12 4Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 13 08901, USA 14 15 *Corresponding author: Prof. Dr. Andreas P.M. Weber, 16 e-mail: [email protected] 17 bioRxiv preprint doi: https://doi.org/10.1101/526111; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 18 Abstract 19 The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics 20 that impact our understanding regarding the origin of metabolic processes and the role of 21 organelles in cellular evolution. -
S8 Table. Mrna Levels of Secondary Metabolic Clustered Genes in A
S8 Table. mRNA levels of secondary metabolic clustered genes in A. flavus. Cluster Gene ID Log2 Fold Description Change 1 AFLA_125780 - ATP-binding cassette transporter, putative 1 AFLA_125770 -1.76 LysR family regulatory protein, putative 1 AFLA_125760 -1.24 squalene-hopene-cyclase, putative 2 AFLA_126710 - polyketide synthase, putative 2 AFLA_126720 - hypothetical protein 2 AFLA_126730 - conserved hypothetical protein 2 AFLA_126740 - lipase precursor, putative 3 AFLA_126970 - arginine permease, putative 3 AFLA_126980 - conserved hypothetical protein 3 AFLA_126990 - conserved hypothetical protein 3 AFLA_127000 - hypothetical protein 3 AFLA_127010 - conserved hypothetical protein 3 AFLA_127020 - monooxygenase, putative 3 AFLA_127030 - conserved hypothetical protein 3 AFLA_127040 - MFS monocarboxylate transporter, putative 3 AFLA_127050 - conserved hypothetical protein 3 AFLA_127060 - conserved hypothetical protein 3 AFLA_127070 - short-chain dehydrogenase, putative 3 AFLA_127080 - conserved hypothetical protein 3 AFLA_127100 - conserved hypothetical protein 3 AFLA_127110 - MFS transporter, putative 3 AFLA_127120 - hypothetical protein 3 AFLA_127130 - conserved hypothetical protein 3 AFLA_127140 - conserved hypothetical protein 3 AFLA_127150 - hypothetical protein 3 AFLA_127160 - NB-ARC and TPR domain protein 3 AFLA_127170 - penicillin-binding protein, putative 3 AFLA_127090 -2.42 polyketide synthase, putative 4 AFLA_128040 - efflux pump antibiotic resistance protein, putative 4 AFLA_128060 - polyketide synthase, putative 4 AFLA_128050 -
Comparative Genomics of Bradyrhizobium Japonicum CPAC
Siqueira et al. BMC Genomics 2014, 15:420 http://www.biomedcentral.com/1471-2164/15/420 RESEARCH ARTICLE Open Access Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean Arthur Fernandes Siqueira1,2†, Ernesto Ormeño-Orrillo3†,RangelCelsoSouza4,ElisetePainsRodrigues5, Luiz Gonzaga Paula Almeida4, Fernando Gomes Barcellos5, Jesiane Stefânia Silva Batista6, Andre Shigueyoshi Nakatani2, Esperanza Martínez-Romero3, Ana Tereza Ribeiro Vasconcelos4 and Mariangela Hungria1,2* Abstract Background: The soybean-Bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. Here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. B. japonicum CPAC 15 (=SEMIA 5079) is outstanding in its saprophytic capacity and competitiveness, whereas B. diazoefficiens CPAC 7 (=SEMIA 5080) is known for its high efficiency in fixing nitrogen. Both are well adapted to tropical soils. The genomes of CPAC 15 and CPAC 7 were compared to each other and also to those of B. japonicum USDA 6T and B. diazoefficiens USDA 110T. Results: Differences in genome size were found between species, with B. japonicum having larger genomes than B. diazoefficiens. Although most of the four genomes were syntenic, genome rearrangements within and between species were observed, including events in the symbiosis island. In addition to the symbiotic region, several genomic islands were identified. Altogether, these features must confer high genomic plasticity that might explain adaptation and differences in symbiotic performance. It was not possible to attribute known functions to half of the predicted genes. -
1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental
Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: [email protected]; [email protected] Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN. -
Nitrilase 1 Modulates Lung Tumor Progression in Vitro and in Vivo
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 16 Nitrilase 1 modulates lung tumor progression in vitro and in vivo Yong Antican Wang1, Yunguang Sun2,5, Justin M. Le Blanc1, Charalambos Solomides3, Tingting Zhan4, Bo Lu1 1Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, 19107, USA 2Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA 3Department of Pathology, Thomas Jefferson University, Philadelphia, PA, 19107, USA 4Department of Pharmacology, Thomas Jefferson University, Philadelphia, PA, 19107, USA 5Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA Correspondence to: Bo Lu, e-mail: [email protected]. Keywords: NIT1, lung cancer, KRAS, NSCLC, tumor suppressor Received: October 01, 2015 Accepted: January 23, 2016 Published: March 10, 2016 ABSTRACT Uncovering novel growth modulators for non-small cell lung cancer (NSCLC) may lead to new therapies for these patients. Previous studies suggest Nit1 suppresses chemically induced carcinogenesis of the foregut in a mouse model. In this study we aimed to determine the role of Nit1 in a transgenic mouse lung cancer model driven by a G12D Kras mutation. Nit1 knockout mice (Nit1−/−) were crossed with KrasG12D/+ mice to investigate whether a G12D Kras mutation and Nit1 inactivation interact to promote or inhibit the development of NSCLC. We found that lung tumorigenesis was suppressed in the Nit1-null background (Nit1−/−:KrasG12D/+). Micro-CT scans and gross tumor measurements demonstrated a 5-fold reduction in total tumor volumes compared to Nit1+/+KrasG12D/+ (p<0.01). Furthermore, we found that Nit1 is highly expressed in human lung cancer tissues and cell lines and use of siRNA against Nit1 decreased overall cell survival of lung cancer cells in culture. -
Purification and Characterization of a Novel Nitrilase of Rhodococcus
JOURNAL OF BACTERIOLOGY, Sept. 1990, p. 4807-4815 Vol. 172, No. 9 0021-9193/90/094807-09$02.00/0 Copyright X3 1990, American Society for Microbiology Purification and Characterization of a Novel Nitrilase of Rhodococcus rhodochrous K22 That Acts on Aliphatic Nitriles MICHIHIKO KOBAYASHI,* NORIYUKI YANAKA, TORU NAGASAWA, AND HIDEAKI YAMADA Department ofAgricultural Chemistry, Faculty ofAgriculture, Kyoto University, Sakyo-ku, Kyoto 606, Japan Received 18 April 1990/Accepted 8 June 1990 A novel nitrilase that preferentially catalyzes the hydrolysis of aliphatic nitriles to the corresponding carboxylic acids and ammonia was found in the cells of a facultative crotononitrile-utilizing actinomycete isolated from soil. The strain was taxonomically studied and identified as Rhodococcus rhodochrous. The nitrilase was purified, with 9.08% overall recovery, through five steps from a cell extract of the stain. After the last step, the purified enzyme appeared to be homogeneous, as judged by polyacrylamide gel electrophoresis, analytical centrifugation, and double immunodiffusion in agarose. The relative molecular weight values for the native enzyme, estimated from the ultracentrifugal equilibrium and by high-performance liquid chromatog- raphy, were approximately 604,000 + 30,000 and 650,000, respectively, and the enzyme consisted of 15 to 16 subunits identical in molecular weight (41,000). The enzyme acted on aliphatic olefinic nitriles such as crotononitrile and acrylonitrile as the most suitable substrates. The apparent Km values for crotononitrile and acrylonitrile were 18.9 and 1.14 mM, respectively. The nitrilase also catalyzed the direct hydrolysis of saturated aliphatic nitriles, such as valeronitrile, 4-chlorobutyronitrile, and glutaronitrile, to the correspond- ing acids without the formation of amide intermediates. -
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ISOLATION, IDENTIFICATION AND SUBSTRATE SPECIFICITY OF A NITRILASE PRODUCING BACTERIA, Acidovorax sp. SK1 Soumya Koippully, Subha Swaraj Pattnaik, Siddhardha Busi* Address(es): Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry-605 014, India. *Corresponding author: [email protected] doi: 10.15414/jmbfs.2018.8.2.788-793 ARTICLE INFO ABSTRACT Received 13. 5. 2018 The process of biocatalysis or biotransformation remains the core of industrial biotechnology owing to its importance in the synthesis of Revised 3. 9. 2018 high-value products in a cost effective manner. Nitrile biotransformation has also achieved considerable attention in last few decades Accepted 5. 9. 2018 due to its widespread biotechnological and industrial applications. In the present study, a versatile, potent nitrile-degrading bacterium, Published 1. 10. 2018 Acidovorax sp. SK1 was isolated from the cracker waste dumping site of Sivakasi, Tamilnadu and characterized for its biocatalytic potential, nitrilase production and enzyme activity. A pH sensitive indicator-based assay was performed to identify the nitrile degrading ability of the isolated samples. Semi quantitative High performance thin layer chromatographic (HPTLC) method was performed for Regular article quantitative measurement of mandelic acid produced from degradation of nitrile compound, mandelonitrile. The optimization of medium and nutritional parameters were studied for the improvement of nitrilase activity, which indicated that maximum nitrilase activity was observed at an optimum pH of 7.0, agitation at 100 rpm, glucose as best carbon source (10 g/L) and yeast extract (0.1 g/L) as principal nitrogen source. Biomass is also a critical parameter in the biocatalysis of mandelonitrile to mandelic acid and at a biomass of 100 mg/L, maximum nitrilase activity of 0.026 I.U was observed. -
Supplementary Material Supplementary Results And
R. D. Barabote SUPPLEMENTARY MATERIAL SUPPLEMENTARY RESULTS AND DISCUSSION tRNA and codon usage. Forty-five tRNAs representing 43 different anticodons are encoded in the genome (Supplementary Table S1). The tRNAMet is present in three copies in the genome. In contrast to the number of tRNAs, all 61 sense codons are encoded in the genome sequence. The codon usage correlates well with the tRNA complement and is consistent with the high G+C content of the genome as the GC-rich codons predominate in the organism (Supplementary Table S1). Codons ATA (Ile), CGC (Arg), and CGA (Arg) as well as all codons that have a T at the third position, with the exception of CGT (Arg), do not appear to have a cognate tRNA in A. cellulolyticus. As a likely evolutionary adaptation to the available tRNAs for any given amino acid, codons that do not have a cognate tRNA occur with the least frequency in the A. cellulolyticus genome when compared to synonymous codons differing just in the 3rd position. However, the exceptions to these are for glycine (GGT (18.8%) > GGA (14.4%)), leucine (CTT (10.6%) > CTA (1.4%)), arginine (CGC (33.3%) > CGT (11.1%)), and valine (GTT (10.4%) > GTA (3.8%)). The relative preference for CGC codon over CGT codon follows the high G+C content of the genome, while the remaining four biases mentioned above may simply reflect evolutionary conservation of codon usage, as a similar trend is seen in Frankia (Supplementary Table S2). The functional significance of this bias remains elusive. The A. cellulolyticus genome encodes a parsimonious complement of 46 tRNAs. -
Purification and Characterization of Nitrilase from Fusarium Solani
Process Biochemistry 45 (2010) 1115–1120 Contents lists available at ScienceDirect Process Biochemistry journal homepage: www.elsevier.com/locate/procbio Purification and characterization of nitrilase from Fusarium solani IMI196840 Vojtechˇ Vejvoda a, David Kubácˇ a,Alzbˇ etaˇ Davidová a, Ondrejˇ Kaplan a, Miroslav Sulcˇ a,b, Ondrejˇ Svedaˇ a, Radka Chaloupková c, Ludmila Martínková a,∗ a Institute of Microbiology, Centre of Biocatalysis and Biotransformation, Academy of Sciences of the Czech Republic, Vídenskᡠ1083, CZ-142 20 Prague, Czech Republic b Department of Biochemistry, Faculty of Science, Charles University Prague, Hlavova 8, CZ-128 40 Prague, Czech Republic c Loschmidt Laboratories, Department of Experimental Biology and Centre of Biocatalysis and Biotransformation, Faculty of Science, Masaryk University, Kamenice 5/A4, CZ-625 00 Brno, Czech Republic article info abstract Article history: Nitrilase activity in Fusarium solani IMI196840 (approx. 1500 U l−1 of culture broth) was induced by 2- Received 11 November 2009 cyanopyridine. The enzyme was purified by a factor of 20.3 at a yield of 26.9%. According to gel filtration, Received in revised form 26 March 2010 the holoenzyme was an approx. 550-kDa homooligomer consisting of subunits with a molecular weight Accepted 30 March 2010 of approximately 40 kDa, as determined by SDS-PAGE. Mass spectrometry analysis of the tryptic frag- ments suggested a high similarity of this enzyme to the hypothetical CN hydrolases from Aspergillus Keywords: oryzae, Gibberella zeae, Gibberella moniliformis and Nectria haematococca. Circular dichroism and fluo- Fusarium solani rescence spectra indicated that secondary structure content and overall tertiary structure, respectively, Nitrilase were almost identical in nitrilases from F. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Structures, Functions, and Mechanisms of Filament Forming Enzymes: a Renaissance of Enzyme Filamentation
Structures, Functions, and Mechanisms of Filament Forming Enzymes: A Renaissance of Enzyme Filamentation A Review By Chad K. Park & Nancy C. Horton Department of Molecular and Cellular Biology University of Arizona Tucson, AZ 85721 N. C. Horton ([email protected], ORCID: 0000-0003-2710-8284) C. K. Park ([email protected], ORCID: 0000-0003-1089-9091) Keywords: Enzyme, Regulation, DNA binding, Nuclease, Run-On Oligomerization, self-association 1 Abstract Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI system are also highlighted. 2 Contents INTRODUCTION…………………………………………………………..4 STRUCTURALLY CHARACTERIZED ENZYME FILAMENTS…….5 Acetyl CoA Carboxylase (ACC)……………………………………………………………………5 Phosphofructokinase (PFK)……………………………………………………………………….6