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Genome mining in Streptomyces

Grant number: 14/12727-5
Support Opportunities:Regular Research Grants
Duration: July 01, 2015 - June 30, 2017
Field of knowledge:Physical Sciences and Mathematics - Chemistry - Organic Chemistry
Principal Investigator:Luciana Gonzaga de Oliveira
Grantee:Luciana Gonzaga de Oliveira
Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil

Abstract

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 representes a promising avenue to isolate new molecules, elucidate biosynthetic pathways and enzymes function and to elucidate biosynthesis intermediates. The endophytic strains Streptomyces wadayamensis and Streptomyces sp. Isolated from Citrus ssp were recently sequenced in our research group using Illumina MiSeq Technology. These strains were 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. Exploring the information generated by sequencing we intend to explore diferente methodologies to access known and unknown metabolites: guided incorporation of labeled precursors via genomisotopic approach; gene deletion and metabolite profile evaluation; heterologous expression. Additionally we intend to study and characterize specific enzymes annotated from the genome analysis including terpene cyclases, hydrolases cyclases, monooxygenases and epoxide hydrolases. (AU)

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Scientific publications (12)
(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, . (19/10564-5, 17/24017-0, 14/50249-8, 16/25735-1, 14/12727-5, 15/01013-4)
SACHITO, DOUGLAS C.; DE OLIVEIRA, LUCIANA G.. Unveiling the Bacterial Sesquiterpenome of Streptomyces sp. CBMAI 2042 Discloses Cyclases with Versatile Performances. Journal of the Brazilian Chemical Society, v. 33, n. 8, p. 9-pg., . (19/04855-7, 19/10564-5, 14/12727-5, 14/50249-8)
FIORAMONTE, MARIANA; RAMOS DE JESUS, HUGO CESAR; RAMOS FERRARI, ALLAN JHONATHAN; LIMA, DIOGO BORGES; DREKENER, ROBERTA LOPES; DUARTE CORREIA, CARLOS ROQUE; OLIVEIRA, LUCIANA GONZAGA; DA COSTA NEVES-FERREIRA, ANA GISELE; CARVALHO, PAULO COSTA; GOZZO, FABIO CESAR. XPlex: An Effective, Multiplex Cross-Linking Chemistry for Acidic Residues. Analytical Chemistry, v. 90, n. 10, p. 6043-6050, . (14/50249-8, 16/13195-2, 14/17264-3, 12/10862-7, 14/12727-5)
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, v. N/A, n. 157, p. 12-pg., . (19/10564-5, 15/01013-4, 14/50249-8, 19/08853-9, 13/12598-8, 14/12727-5)
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, . (15/01013-4, 14/12727-5, 14/50249-8, 13/12598-8)
DOUGLAS C. SACHITO; LUCIANA G. DE OLIVEIRA. Unveiling the Bacterial Sesquiterpenome of Streptomyces sp. CBMAI 2042 Discloses Cyclases with Versatile Performances. Journal of the Brazilian Chemical Society, v. 33, n. 7, p. 734-742, . (14/12727-5, 14/50249-8, 19/10564-5)
TORMET-GONZALEZ, GABRIELA D.; WILSON, CAROLINA; DE OLIVEIRA, GABRIEL STEPHANI; DOS SANTOS, JADEMILSON CELESTINO; DE OLIVEIRA, LUCIANA G.; DIAS, MARCIO VINICIUS BERTACINE. An epoxide hydrolase from endophytic Streptomycess hows unique structural features and wide biocatalytic activity. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 76, p. 8-pg., . (19/10564-5, 18/00351-1, 15/09188-8, 11/06209-3, 14/50249-8, 10/15971-3, 13/26242-0, 14/12727-5)
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; et al. Genome Mining of Endophytic Streptomyces wadayamensis Reveals High Antibiotic Production Capability. Journal of the Brazilian Chemical Society, v. 27, n. 8, p. 1465-1475, . (15/01013-4, 14/12727-5, 10/51677-2, 13/12598-8)
BRUNO S. PAULO; RENATA SIGRIST; LUCIANA G. DE OLIVEIRA. AVANÇOS RECENTES EM BIOSSÍNTESE COMBINATÓRIA DE POLICETÍDEOS: PERSPECTIVAS E DESAFIOS. Química Nova, v. 42, n. 1, p. 71-83, . (14/50249-8, 15/01013-4, 14/12727-5, 13/12598-8)
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, . (14/50249-8, 15/01013-4, 10/51677-2, 14/12727-5, 13/12598-8)
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, . (19/10564-5, 14/50249-8, 19/08853-9, 15/01013-4, 13/12598-8, 14/12727-5)
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, . (15/01013-4, 13/12598-8, 14/50249-8, 14/12727-5)

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Filed patent(s) as a result of this research project

VETOR, MICRO-ORGANISMO RECOMBINANTE, MÉTODO DE OBTENÇÃO DE ENZIMA EPÓXIDO-HIDROLASE RECOMBINANTE, ENZIMA EPÔXIDO-HIDROLASE RECOMBINANTE E USO DA MESMA BR1020160263417 - Universidade Estadual de Campinas (UNICAMP) . Gabriela Desiree Tormet Gonzalez ; Luciana Gonzaga De Oliveira - November 2016, 10

MÉTODO DE OBTENÇÃO DE MICRO-ORGANISMO RECOMBINANTE, MICRO-ORGANISMO RECOMBINANTE, MÉTODO DE OBTENÇÃO DA VALINOMICINA, VALINOMICINA ASSIM OBTIDA E USO DA VALLNOMLCLNA BR1020170180239 - Universidade Estadual de Campinas (UNICAMP) . Luciana Gonzaga de Oliveira ; Renata Sigrist - August 2017, 23

VETOR, MICRO-ORGANISMO RECOMBINANTE, MÉTODO DE OBTENÇÃO DE ENZIMA EPÓXIDO-HIDROLASE RECOMBINANTE, ENZIMA EPÓXIDO-HIDROLASE RECOMBINANTE E USO DA MESMA PCT/BR2017/000056 - Universidade Estadual de Campinas (UNICAMP) . Luciana Gonzaga de Oliveira ; GABRIELA DESIREE TORMET GONZALEZ - May 2017, 30