biosynthetic pathways

Summary

Summary: Sets of enzymatic reactions occurring in organisms and that form biochemicals by making new covalent bonds.

Top Publications

  1. Kim H, Liu Y, McCarty R, Liu H. Reaction Catalyzed by GenK, a Cobalamin-Dependent Radical S-Adenosyl-l-methionine Methyltransferase in the Biosynthetic Pathway of Gentamicin, Proceeds with Retention of Configuration. J Am Chem Soc. 2017;139:16084-16087 pubmed publisher
  2. Thapa H, Tang S, Sacchettini J, Devarenne T. Tetraterpene Synthase Substrate and Product Specificity in the Green Microalga Botryococcus braunii Race L. ACS Chem Biol. 2017;12:2408-2416 pubmed publisher
    ..These studies also offer insights into tetraterpene hydrocarbon metabolism in B. braunii and provide a foundation for engineering LOS for robust production of specific hydrocarbons of a desired chain length. ..
  3. Abdelrahman M, El Sayed M, Sato S, Hirakawa H, Ito S, Tanaka K, et al. RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum-A. cepa monosomic addition lines. PLoS ONE. 2017;12:e0181784 pubmed publisher
    ..An understanding of the saponin compounds and biosynthesis-related genes would facilitate the development of plants with unique saponin content and, subsequently, improved disease resistance. ..
  4. Jiménez Alemán G, Seçinti S, Boland W. A succinct access to ?-hydroxylated jasmonates via olefin metathesis. Z Naturforsch C. 2017;72:285-292 pubmed publisher
    ..The approach utilizes olefin cross-metathesis as the key step employing inexpensive, commercially available substrates and catalysts. ..
  5. Zhang D, Jiang L, Li N, Yu X, Zhao P, Li T, et al. Overexpression of the Squalene Epoxidase Gene Alone and in Combination with the 3-Hydroxy-3-methylglutaryl Coenzyme A Gene Increases Ganoderic Acid Production in Ganoderma lingzhi. J Agric Food Chem. 2017;65:4683-4690 pubmed publisher
    ..These values were 5.9, 4.5, 2.4, and 5.8 times higher than those produced by the WT strain. This is the first example of the successful manipulation of multiple biosynthetic genes to improve GA content in G. lingzhi. ..
  6. Hou Y, Hossain G, Li J, Shin H, Du G, Chen J, et al. Metabolic engineering of cofactor flavin adenine dinucleotide (FAD) synthesis and regeneration in Escherichia coli for production of ?-keto acids. Biotechnol Bioeng. 2017;114:1928-1936 pubmed publisher
    ..Notably, the strategy reported herein may be generally applicable to other flavin-dependent biocatalysis reactions and metabolic pathway optimizations. Biotechnol. Bioeng. 2017;114: 1928-1936. © 2017 Wiley Periodicals, Inc. ..
  7. Batista A, Santos Pinto J, Batista J, Souza Moreira T, Santoni M, Zanelli C, et al. The Combined Use of Proteomics and Transcriptomics Reveals a Complex Secondary Metabolite Network in Peperomia obtusifolia. J Nat Prod. 2017;80:1275-1286 pubmed publisher
    ..obtusifolia. However, the polyketide synthases possibly involved in the production of orsellinic acid could not be identified, suggesting that orsellinic acid may be produced by endophytes intimately associated with the plant...
  8. Zhang L, Xu B, Wu T, Yang Y, Fan L, Wen M, et al. Transcriptomic profiling of two Pak Choi varieties with contrasting anthocyanin contents provides an insight into structural and regulatory genes in anthocyanin biosynthetic pathway. BMC Genomics. 2017;18:288 pubmed publisher
  9. Wang X, Huang N, Yang M, Wei D, Tai H, Han X, et al. FTO is required for myogenesis by positively regulating mTOR-PGC-1α pathway-mediated mitochondria biogenesis. Cell Death Dis. 2017;8:e2702 pubmed publisher
    ..Summarily, our findings provide the first evidence for the contribution of FTO for skeletal muscle differentiation and a new insight to study the physiologic significance of RNA methylation. ..
  10. Schaller G, Binder B. Inhibitors of Ethylene Biosynthesis and Signaling. Methods Mol Biol. 2017;1573:223-235 pubmed publisher
    ..Inhibitor use as well as off-target effects are described with a focus on ethylene responses in dark-grown Arabidopsis seedlings. Methods for the use of these inhibitors can be applied to other plant growth assays. ..

Detail Information

Publications62

  1. Kim H, Liu Y, McCarty R, Liu H. Reaction Catalyzed by GenK, a Cobalamin-Dependent Radical S-Adenosyl-l-methionine Methyltransferase in the Biosynthetic Pathway of Gentamicin, Proceeds with Retention of Configuration. J Am Chem Soc. 2017;139:16084-16087 pubmed publisher
  2. Thapa H, Tang S, Sacchettini J, Devarenne T. Tetraterpene Synthase Substrate and Product Specificity in the Green Microalga Botryococcus braunii Race L. ACS Chem Biol. 2017;12:2408-2416 pubmed publisher
    ..These studies also offer insights into tetraterpene hydrocarbon metabolism in B. braunii and provide a foundation for engineering LOS for robust production of specific hydrocarbons of a desired chain length. ..
  3. Abdelrahman M, El Sayed M, Sato S, Hirakawa H, Ito S, Tanaka K, et al. RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum-A. cepa monosomic addition lines. PLoS ONE. 2017;12:e0181784 pubmed publisher
    ..An understanding of the saponin compounds and biosynthesis-related genes would facilitate the development of plants with unique saponin content and, subsequently, improved disease resistance. ..
  4. Jiménez Alemán G, Seçinti S, Boland W. A succinct access to ?-hydroxylated jasmonates via olefin metathesis. Z Naturforsch C. 2017;72:285-292 pubmed publisher
    ..The approach utilizes olefin cross-metathesis as the key step employing inexpensive, commercially available substrates and catalysts. ..
  5. Zhang D, Jiang L, Li N, Yu X, Zhao P, Li T, et al. Overexpression of the Squalene Epoxidase Gene Alone and in Combination with the 3-Hydroxy-3-methylglutaryl Coenzyme A Gene Increases Ganoderic Acid Production in Ganoderma lingzhi. J Agric Food Chem. 2017;65:4683-4690 pubmed publisher
    ..These values were 5.9, 4.5, 2.4, and 5.8 times higher than those produced by the WT strain. This is the first example of the successful manipulation of multiple biosynthetic genes to improve GA content in G. lingzhi. ..
  6. Hou Y, Hossain G, Li J, Shin H, Du G, Chen J, et al. Metabolic engineering of cofactor flavin adenine dinucleotide (FAD) synthesis and regeneration in Escherichia coli for production of ?-keto acids. Biotechnol Bioeng. 2017;114:1928-1936 pubmed publisher
    ..Notably, the strategy reported herein may be generally applicable to other flavin-dependent biocatalysis reactions and metabolic pathway optimizations. Biotechnol. Bioeng. 2017;114: 1928-1936. © 2017 Wiley Periodicals, Inc. ..
  7. Batista A, Santos Pinto J, Batista J, Souza Moreira T, Santoni M, Zanelli C, et al. The Combined Use of Proteomics and Transcriptomics Reveals a Complex Secondary Metabolite Network in Peperomia obtusifolia. J Nat Prod. 2017;80:1275-1286 pubmed publisher
    ..obtusifolia. However, the polyketide synthases possibly involved in the production of orsellinic acid could not be identified, suggesting that orsellinic acid may be produced by endophytes intimately associated with the plant...
  8. Zhang L, Xu B, Wu T, Yang Y, Fan L, Wen M, et al. Transcriptomic profiling of two Pak Choi varieties with contrasting anthocyanin contents provides an insight into structural and regulatory genes in anthocyanin biosynthetic pathway. BMC Genomics. 2017;18:288 pubmed publisher
  9. Wang X, Huang N, Yang M, Wei D, Tai H, Han X, et al. FTO is required for myogenesis by positively regulating mTOR-PGC-1α pathway-mediated mitochondria biogenesis. Cell Death Dis. 2017;8:e2702 pubmed publisher
    ..Summarily, our findings provide the first evidence for the contribution of FTO for skeletal muscle differentiation and a new insight to study the physiologic significance of RNA methylation. ..
  10. Schaller G, Binder B. Inhibitors of Ethylene Biosynthesis and Signaling. Methods Mol Biol. 2017;1573:223-235 pubmed publisher
    ..Inhibitor use as well as off-target effects are described with a focus on ethylene responses in dark-grown Arabidopsis seedlings. Methods for the use of these inhibitors can be applied to other plant growth assays. ..
  11. Bachmann B. Biosynthesis: is it time to go retro?. Nat Chem Biol. 2010;6:390-3 pubmed publisher
  12. Yun C, Motoyama T, Osada H. Regulatory Mechanism of Mycotoxin Tenuazonic Acid Production in Pyricularia oryzae. ACS Chem Biol. 2017;12:2270-2274 pubmed publisher
    ..We also demonstrate that two TeA-inducing signals, 1% DMSO addition and OSM1 deletion, were transmitted through PoLAE1. Our results indicate that TeA production is regulated by two specific regulators, TAS2 and PoLAE1, in P. oryzae. ..
  13. Yokoyama C, Takei M, Kouzuma Y, Nagata S, Suzuki Y. Novel tryptophan metabolic pathways in auxin biosynthesis in silkworm. J Insect Physiol. 2017;101:91-96 pubmed publisher
    ..The failure to detect IAAld, even in the presence of an inhibitor of the conversion IAAld?IAA, is explained by a switch in the conversion from IAAld?IAA to IAAld?IEtOH. ..
  14. Abramson H. The lipogenesis pathway as a cancer target. J Med Chem. 2011;54:5615-38 pubmed publisher
  15. Chen Z, Shen X, Wang J, Wang J, Yuan Q, Yan Y. Rational engineering of p-hydroxybenzoate hydroxylase to enable efficient gallic acid synthesis via a novel artificial biosynthetic pathway. Biotechnol Bioeng. 2017;114:2571-2580 pubmed publisher
    ..Biotechnol. Bioeng. 2017;114: 2571-2580. © 2017 Wiley Periodicals, Inc. ..
  16. Goncerzewicz A, Kamińska Wojteczek K, Młynarczyk I, Misiewicz A. Expression of GPD1 and SIP18 genes during rehydration in active dry industrial Saccharomyces cerevisiae cider-making yeast strains (ADY). Acta Biochim Pol. 2017;64:287-294 pubmed publisher
    ..This is the first attempt to confront rehydration time and molecular mechanisms acting upon rehydration with the course of the fermentation process. ..
  17. Adekenov S. Sesquiterpene lactones with unusual structure. Their biogenesis and biological activity. Fitoterapia. 2017;121:16-30 pubmed publisher
    ..An attempt was made to biologically justify a wide structural formation variety of new sesquiterpene lactones with the unique structure. ..
  18. Pulido P, Perelló C, Rodríguez Concepción M. New insights into plant isoprenoid metabolism. Mol Plant. 2012;5:964-7 pubmed publisher
  19. Dalmais M, Antelme S, Ho Yue Kuang S, Wang Y, Darracq O, d Yvoire M, et al. A TILLING Platform for Functional Genomics in Brachypodium distachyon. PLoS ONE. 2013;8:e65503 pubmed publisher
    ..The mutant population and the TILLING platform should greatly facilitate functional genomics approaches in this model organism. ..
  20. Cabezas Wallscheid N, Buettner F, Sommerkamp P, Klimmeck D, Ladel L, Thalheimer F, et al. Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy. Cell. 2017;169:807-823.e19 pubmed publisher
    ..Our results highlight the impact of dietary vitamin A on the regulation of cell-cycle-mediated stem cell plasticity. VIDEO ABSTRACT. ..
  21. Moon Y, Kim L, Chun H, Lee S. 4-Hydroxy-7-methyl-3-phenylcoumarin Suppresses Aflatoxin Biosynthesis via Downregulation of aflK Expressing Versicolorin B Synthase in Aspergillus flavus. Molecules. 2017;22: pubmed publisher
  22. Wheeler G, Ishikawa T, Pornsaksit V, Smirnoff N. Evolution of alternative biosynthetic pathways for vitamin C following plastid acquisition in photosynthetic eukaryotes. elife. 2015;4: pubmed publisher
    ..GULO has therefore been lost repeatedly throughout eukaryote evolution. The formation of the alternative biosynthetic pathways in photosynthetic eukaryotes uncoupled ascorbate synthesis from hydrogen peroxide production and likely ..
  23. Winstel V, Sanchez Carballo P, Holst O, Xia G, Peschel A. Biosynthesis of the unique wall teichoic acid of Staphylococcus aureus lineage ST395. MBio. 2014;5:e00869 pubmed publisher
    ..The elucidation of ST395 WTA biosynthesis will help to understand how Gram-positive bacteria produce highly variable WTA types and elucidate functional consequences of WTA variation. ..
  24. Eustáquio A, Nam S, Penn K, Lechner A, Wilson M, Fenical W, et al. The discovery of salinosporamide K from the marine bacterium "Salinispora pacifica" by genome mining gives insight into pathway evolution. Chembiochem. 2011;12:61-4 pubmed publisher
  25. Kim K, Chiba Y, Kobayashi A, Arai H, Ishii M. Phosphoserine Phosphatase Is Required for Serine and One-Carbon Unit Synthesis in Hydrogenobacter thermophilus. J Bacteriol. 2017;199: pubmed publisher
    ..thermophilus. ..
  26. Du Z, Zhang Y, Qian Z, Xiao H, Zhong J. Combination of traditional mutation and metabolic engineering to enhance ansamitocin P-3 production in Actinosynnema pretiosum. Biotechnol Bioeng. 2017;114:2794-2806 pubmed publisher
    ..This work demonstrated that combination of random mutation and metabolic engineering could promote AP-3 biosynthesis and might be helpful for increasing the production of other industrially important secondary metabolites. ..
  27. Wang W, Fu X, Dai X, Hua F, Chu G, Chu M, et al. Novel acetylcholinesterase inhibitors from Zijuan tea and biosynthetic pathway of caffeoylated catechin in tea plant. Food Chem. 2017;237:1172-1178 pubmed publisher
    ..Our results show that they bind acetylcholinesterase (AChE) tightly and have strong AChE inhibitory activity with IC50 value at 2.49, 11.41, 62.26?M, respectively. ..
  28. Gao W, Wu Z, Sun J, Ni X, Xia H. Modulation of kanamycin B and kanamycin A biosynthesis in Streptomyces kanamyceticus via metabolic engineering. PLoS ONE. 2017;12:e0181971 pubmed publisher
    ..kanamyceticus. Moreover, based on the clarified biosynthetic pathway, we obtained a kanamycin B-high-yield strain and an optimized kanamycin A-producing strain with minimal byproduct. ..
  29. Müller A, Klöckner A, Schneider T. Targeting a cell wall biosynthesis hot spot. Nat Prod Rep. 2017;34:909-932 pubmed publisher
  30. Palmu K, Rosenqvist P, Thapa K, Ilina Y, Siitonen V, Baral B, et al. Discovery of the Showdomycin Gene Cluster from Streptomyces showdoensis ATCC 15227 Yields Insight into the Biosynthetic Logic of C-Nucleoside Antibiotics. ACS Chem Biol. 2017;12:1472-1477 pubmed publisher
    ..The study provides the first steps toward generation of novel C-nucleosides by pathway engineering. ..
  31. Xu F, Napan K, Zhang S, Gladwin T, Takemoto J, Zhan J. New insights into pradimicin biosynthesis revealed by two O-methyltransferases. Bioorg Med Chem Lett. 2017;27:3499-3502 pubmed publisher
    ..Characterization of PdmT suggests a novel pathway that leads to the "flip" of 7-OH to C-14 in pradimicin biosynthesis. ..
  32. Prince D, Rallapalli G, Xu D, Schoonbeek H, Çevik V, Asai S, et al. Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana. BMC Biol. 2017;15:20 pubmed publisher
    ..infestans. Understanding the basis of non-host resistance to pathogens such as P. infestans could assist in development of strategies to elevate food security. ..
  33. Blouin Y, Cazajous G, Dehan C, Soler C, Vong R, Hassan M, et al. Progenitor “Mycobacterium canettii” clone responsible for lymph node tuberculosis epidemic, Djibouti. Emerg Infect Dis. 2014;20:21-8 pubmed publisher
    ..canettii. Evolution of this clone, which has been recovered regularly since 1983, may mimic the birth of M. tuberculosis. Thus, recognizing this organism and identifying its reservoir are clinically important. ..
  34. Su H, Lin J, Wang Y, Chen Q, Wang G, Tan F. Engineering Brevibacterium flavum for the production of renewable bioenergy: C4-C5 advanced alcohols. Biotechnol Bioeng. 2017;114:1946-1958 pubmed publisher
    ..Biotechnol. Bioeng. 2017;114: 1946-1958. © 2017 Wiley Periodicals, Inc. ..
  35. Onodera Y, Nam J, Bissell M. Increased sugar uptake promotes oncogenesis via EPAC/RAP1 and O-GlcNAc pathways. J Clin Invest. 2014;124:367-84 pubmed publisher
    ..Our findings show that increased glucose uptake activates known oncogenic pathways to induce malignant phenotype, and provide possible targets for diagnosis and therapeutics. ..
  36. Elamin A, Steinicke S, Oehlmann W, Braun Y, Wanas H, Shuralev E, et al. Novel drug targets in cell wall biosynthesis exploited by gene disruption in Pseudomonas aeruginosa. PLoS ONE. 2017;12:e0186801 pubmed publisher
    ..aeruginosa. In conclusion, these findings establish a link between cell wall targets and virulence of P. aeruginosa and thus may lead to development of novel drugs for the treatment of P. aeruginosa infection...
  37. Atanasova Penichon V, Bernillon S, Marchegay G, Lornac A, Pinson Gadais L, Ponts N, et al. Bioguided isolation, characterization, and biotransformation by Fusarium verticillioides of maize kernel compounds that inhibit fumonisin production. Mol Plant Microbe Interact. 2014;27:1148-58 pubmed publisher
    ..verticillioides broths. Our data indicate that F. verticillioides was able to biotransform these phenolic compounds and that the resulting products can contribute to their inhibitory activity. ..
  38. Roberts W, Roalson E. Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae). BMC Genomics. 2017;18:240 pubmed publisher
  39. Mira M, Wally O, Elhiti M, El Shanshory A, Reddy D, Hill R, et al. Jasmonic acid is a downstream component in the modulation of somatic embryogenesis by Arabidopsis Class 2 phytoglobin. J Exp Bot. 2016;67:2231-46 pubmed
    ..Suppression of PGB2 increases JA through NO. Elevated levels of JA repress MYC2 and induce JAZ1, favoring the accumulation of IAA in the explants and the subsequent production of somatic embryos. ..
  40. Wang C, Zada B, Wei G, Kim S. Metabolic engineering and synthetic biology approaches driving isoprenoid production in Escherichia coli. Bioresour Technol. 2017;241:430-438 pubmed publisher
    ..developments in metabolic engineering and synthetic biology have facilitated the engineering of isoprenoid biosynthetic pathways in Escherichia coli to induce high levels of production of many different isoprenoids...
  41. Fresquet Corrales S, Roque E, Sarrión Perdigones A, Rochina M, López Gresa M, Díaz Mula H, et al. Metabolic engineering to simultaneously activate anthocyanin and proanthocyanidin biosynthetic pathways in Nicotiana spp. PLoS ONE. 2017;12:e0184839 pubmed publisher
    ..To engineer the anthocyanin and proanthocyanidin biosynthetic pathways to de novo produce PAs in two Nicotiana species, we incorporated four transgenes to the plant chassis...
  42. Tang X, Li J, Moore B. Minimization of the Thiolactomycin Biosynthetic Pathway Reveals that the Cytochrome P450 Enzyme TlmF Is Required for Five-Membered Thiolactone Ring Formation. Chembiochem. 2017;18:1072-1076 pubmed publisher
    ..Our findings pave the way for future biochemical investigation of the biosynthesis of this structurally unique group of thiotetronic acid natural products. ..
  43. Hui X, Hua S, Wu Q, Li H, Gao W. Antimicrobial mechanism of epigallocatechin gallate and gallocatechin gallate: They target 1-deoxy-d-xylulose 5-phosphate reductoisomerase, the key enzyme of the MEP terpenoid biosynthetic pathway. Arch Biochem Biophys. 2017;622:1-8 pubmed publisher
    ..Meanwhile, the possible interactions between DXR and the catechine, esyth onlols were simulated via docking experiments. ..
  44. Chen H, Liu J. Secondary Metabolites from Higher Fungi. Prog Chem Org Nat Prod. 2017;106:1-201 pubmed publisher
    ..into four categories, namely, those from the shikimate-chorismate, acetate-malonate, and mevalonate biosynthetic pathways, and pigments containing nitrogen, with 145 references covering the years 2010-2016...
  45. Igielski R, Kepczynska E. Gene expression and metabolite profiling of gibberellin biosynthesis during induction of somatic embryogenesis in Medicago truncatula Gaertn. PLoS ONE. 2017;12:e0182055 pubmed publisher
  46. Čavužić M, Liu Y. Biosynthesis of Sulfur-Containing tRNA Modifications: A Comparison of Bacterial, Archaeal, and Eukaryotic Pathways. Biomolecules. 2017;7: pubmed publisher
    ..Their biosynthetic pathways have two major types depending on the requirement of iron-sulfur (Fe-S) clusters...