دورية أكاديمية
أعرض في EDS

Navigating and expanding the roadmap of natural product genome mining tools.

التفاصيل البيبلوغرافية
العنوان: Navigating and expanding the roadmap of natural product genome mining tools.
المؤلفون: Biermann F; Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany.; LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany., Wenski SL; Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany.; LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany., Helfrich EJN; Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany.; LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
المصدر: Beilstein journal of organic chemistry [Beilstein J Org Chem] 2022 Dec 06; Vol. 18, pp. 1656-1671. Date of Electronic Publication: 2022 Dec 06 (Print Publication: 2022).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Beilstein-Institut Country of Publication: Germany NLM ID: 101250746 Publication Model: eCollection Cited Medium: Print ISSN: 1860-5397 (Print) Linking ISSN: 18605397 NLM ISO Abbreviation: Beilstein J Org Chem Subsets: PubMed not MEDLINE
أسماء مطبوعة: Publication: [Frankfurt, Germany] : Beilstein-Institut
Original Publication: [Frankfurt, Germany] : [London] : Beilstein-Institut ; in cooperation with BioMed Central, [2005]-
مستخلص: Natural products are structurally highly diverse and exhibit a wide array of biological activities. As a result, they serve as an important source of new drug leads. Traditionally, natural products have been discovered by bioactivity-guided fractionation. The advent of genome sequencing technology has resulted in the introduction of an alternative approach towards novel natural product scaffolds: Genome mining. Genome mining is an in-silico natural product discovery strategy in which sequenced genomes are analyzed for the potential of the associated organism to produce natural products. Seemingly universal biosynthetic principles have been deciphered for most natural product classes that are used to detect natural product biosynthetic gene clusters using pathway-encoded conserved key enzymes, domains, or motifs as bait. Several generations of highly sophisticated tools have been developed for the biosynthetic rule-based identification of natural product gene clusters. Apart from these hard-coded algorithms, multiple tools that use machine learning-based approaches have been designed to complement the existing genome mining tool set and focus on natural product gene clusters that lack genes with conserved signature sequences. In this perspective, we take a closer look at state-of-the-art genome mining tools that are based on either hard-coded rules or machine learning algorithms, with an emphasis on the confidence of their predictions and potential to identify non-canonical natural product biosynthetic gene clusters. We highlight the genome mining pipelines' current strengths and limitations by contrasting their advantages and disadvantages. Moreover, we introduce two indirect biosynthetic gene cluster identification strategies that complement current workflows. The combination of all genome mining approaches will pave the way towards a more comprehensive understanding of the full biosynthetic repertoire encoded in microbial genome sequences.
(Copyright © 2022, Biermann et al.)
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فهرسة مساهمة: Keywords: NRPS; PKS; RiPP; genome mining; natural product biosynthesis; non-canonical pathways
تواريخ الأحداث: Date Created: 20221226 Latest Revision: 20230103
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC9749553
DOI: 10.3762/bjoc.18.178
PMID: 36570563
قاعدة البيانات: MEDLINE
الوصف
تدمد:1860-5397
DOI:10.3762/bjoc.18.178