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Annotation of the modular polyketide synthase and nonribosomal peptide synthetase gene clusters in the genome of Streptomyces tsukubaensis NRRL18488


Blažić, Marko; Starčević, Antonio; Lisfi, Mohamed; Baranašić, Damir; Goranovič, Dušan; Fujs, Štefan; Kuščer, Enej; Kosec, Gregor; Petković, Hrvoje; Cullum, John et al.
Annotation of the modular polyketide synthase and nonribosomal peptide synthetase gene clusters in the genome of Streptomyces tsukubaensis NRRL18488 // Applied and environmental microbiology, 78 (2012), 23; 8183-8190 doi:10.1128/AEM.01891-12 (međunarodna recenzija, članak, znanstveni)


Naslov
Annotation of the modular polyketide synthase and nonribosomal peptide synthetase gene clusters in the genome of Streptomyces tsukubaensis NRRL18488

Autori
Blažić, Marko ; Starčević, Antonio ; Lisfi, Mohamed ; Baranašić, Damir ; Goranovič, Dušan ; Fujs, Štefan ; Kuščer, Enej ; Kosec, Gregor ; Petković, Hrvoje ; Cullum, John ; Hranueli, Daslav ; Žučko, Jurica

Izvornik
Applied and environmental microbiology (0099-2240) 78 (2012), 23; 8183-8190

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
Streptomyces tsukubaensis NRRL18488; genom; poliketid sintaze; sintetaze nonribosomalno sintetiziranih peptide; program ClustScan

Sažetak
The high G+C content and large genome size make the sequencing and assembly of Streptomyces genomes more difficult than for other bacteria. Many pharmaceutically important natural products are synthesized by modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The analysis of such gene clusters is difficult if the genome sequence is not of the highest quality, because clusters can be distributed over several contigs, and sequencing errors can introduce apparent frameshifts into the large PKS and NRPS proteins. An additional problem is that the modular nature of the clusters results in the presence of imperfect repeats, which may cause assembly errors. The genome sequence of Streptomyces tsukubaensis NRRL18488 was scanned for potential PKS and NRPS modular clusters. A phylogenetic approach was used to identify multiple contigs belonging to the same cluster. Four PKS clusters and six NRPS clusters were identified. Contigs containing cluster sequences were analyzed in detail by using the ClustScan program, which suggested the order and orientation of the contigs. The sequencing of the appropriate PCR products confirmed the ordering and allowed the correction of apparent frameshifts resulting from sequencing errors. The product chemistry of such correctly assembled clusters could also be predicted. The analysis of one PKS cluster showed that it should produce a bafilomycin-like compound, and reverse transcription (RT)-PCR was used to show that the cluster was transcribed.

Izvorni jezik
Engleski

Znanstvena područja
Biotehnologija



POVEZANOST RADA


Projekt / tema
058-0000000-3475 - Generiranje potencijalnih lijekova u uvjetima in silico (Daslav Hranueli, )

Ustanove
Prehrambeno-biotehnološki fakultet, Zagreb

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


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