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Mining a t1PKS-transAT PKS-NRPS in Streptomyces sp. genome

Grant number: 15/01013-4
Support type:Scholarships in Brazil - Doctorate (Direct)
Effective date (Start): August 01, 2015
Effective date (End): July 31, 2019
Field of knowledge:Physical Sciences and Mathematics - Chemistry - Organic Chemistry
Principal researcher:Luciana Gonzaga de Oliveira
Grantee:Renata Sigrist
Home Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Associated scholarship(s):16/25735-1 - Mining Streptomyces sp. B1 metabolites: isolation and characterization, BE.EP.DD


Recent analysis of the genomic information from several Streptomyces strains has revealed an enormous abundance of gene clusters codifying enzymes from secondary metabolismo. The whole set of information infers that the capability to produce metabolites by Streptomyces and other actinobacteria is underestimated. As alternatives to tradicional screening methodologies, genomic tools represents a promising avenue to isolate new molecules, elucidate biosynthetic pathways and enzymes function and to elucidate biosynthesis intermediates. The endophytic strain Streptomyces sp isolated from Citrus ssp. was recently sequenced in our research group using Illumina MiSeq Technology. This strain was choosen after previous studies using metabolic probes to reveal biosynthetic gene clusters and biochemical assays. After sequencing, trimmering and assembly, the genes were annotated and in silico analysis allowed the assignment of the secondary metabolism gene clusters. This analysis also identified a cluster of genes involved in the biosynthesis of a supposed unknown metabolite by action of type 1 PKS, trans-AT PKS and NRPS enzymes. By the same analysis was also identified genes responsible for indigoidine and valinomycin biosynthesis, known compounds which genes clusters have already been described in the literature. In the present study we intend to use different methodologies to decipher the metabolite produced by the action of t1PKS-transAT PKS-NRPS and characterize indigoidine and valinomycin biosynthetic gene clusters, annotated from Streptomyces sp.: 1) PAC (P1-derived Artificial chromosome) library from Streptomyces sp.; 2) in vivo and in vitro recombineering/reconstruction, using cluster fragments and a plasmid containing homology regions; 3) clusters transfer to heterologous host (S. coelicolor and S. lividans) and heterologous production will be evaluated. (AU)

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Scientific publications (8)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
SIGRIST, RENATA; LUHAVAYA, HANNA; MCKINNIE, SHAUN M. K.; DA SILVA, AMANDA FERREIRA; JURBERG, IGOR D.; MOORE, BRADLEY S.; DE OLIVEIRA, LUCIANA GONZAGA. Nonlinear Biosynthetic Assembly of Alpiniamide by a Hybrid cis/trans-AT PKS-NRPS. ACS Chemical Biology, v. 15, n. 4, p. 1067-1077, APR 17 2020. Web of Science Citations: 0.
SIGRIST, RENATA; PAULO, BRUNO S.; ANGOLINI, CELIO F. F.; DE OLIVEIRA, LUCIANA G. Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products. JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, n. 157 MAR 2020. Web of Science Citations: 0.
PAULO, BRUNO S.; SIGRIST, RENATA; ANGOLINI, CELIO F. F.; DE OLIVEIRA, LUCIANA G. New Cyclodepsipeptide Derivatives Revealed by Genome Mining and Molecular Networking. CHEMISTRYSELECT, v. 4, n. 27, p. 7785-7790, JUL 23 2019. Web of Science Citations: 1.
BRUNO S. PAULO; RENATA SIGRIST; CÉLIO F. F. ANGOLINI; MARCOS N. EBERLIN; LUCIANA G. DE OLIVEIRA. Gene Deletion Leads to Improved Valinomycin Production by Streptomyces sp. CBMAI 2042. Journal of the Brazilian Chemical Society, v. 30, n. 3, p. 673-679, Mar. 2019.
PAULO, BRUNO S.; SIGRIST, RENATA; ANGOLINI, CELIO F. F.; EBERLIN, MARCOS N.; DE OLIVEIRA, LUCIANA G. Gene Deletion Leads to Improved Valinomycin Production by Streptomyces sp. CBMAI 2042. Journal of the Brazilian Chemical Society, v. 30, n. 3, SI, p. 673-679, MAR 2019. Web of Science Citations: 2.
DE OLIVEIRA, LUCIANA GONZAGA; SIGRIST, RENATA; PAULO, BRUNO SACHETTO; SAMBORSKYY, MARKYIAN. Whole-Genome Sequence of the Endophytic Streptomyces sp. Strain CBMAI 2042, Isolated from Citrus sinensis. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, v. 8, n. 2 JAN 2019. Web of Science Citations: 1.
CÉLIO F. F. ANGOLINI; ANA B. GONÇALVES; RENATA SIGRIST; BRUNO S. PAULO; MARKIYAN SAMBORSKYY; PEDRO L. R. CRUZ; ADRIANA F. VIVIAN; EDUARDO M. SCHMIDT; MARCOS N. EBERLIN; WELINGTON L. ARAÚJO; LUCIANA G. DE OLIVEIRA. Genome Mining of Endophytic Streptomyces wadayamensis Reveals High Antibiotic Production Capability. Journal of the Brazilian Chemical Society, v. 27, n. 8, p. 1465-1475, Ago. 2016.
Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
SIGRIST, Renata. "Genome mining" and cloning strategies for characterization of PKS and NRPS biosynthetic pathways from "Streptomyces" sp. CBMAI 2042. 2019. Doctoral Thesis - Universidade Estadual de Campinas, Instituto de Química.

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