4.6 Review

Synthetic Biology Advanced Natural Product Discovery

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Review Biotechnology & Applied Microbiology

Natural products in drug discovery: advances and opportunities

Atanas G. Atanasov et al.

Summary: Natural products and their analogues have historically played a significant role in pharmacotherapy, however, they also present challenges. Recent technological and scientific developments are addressing these challenges and revitalizing interest in natural products as drug leads, particularly for combating antimicrobial resistance.

NATURE REVIEWS DRUG DISCOVERY (2021)

Review Multidisciplinary Sciences

Mining and unearthing hidden biosynthetic potential

Kirstin Scherlach et al.

Summary: Genetically encoded small molecules play key roles in ecological interactions and drug discovery, but are often difficult to detect due to low production and high rediscovery rates. Genome mining for biosynthetic gene clusters can help address these limitations, leading to the discovery of previously overlooked natural products.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

GTR 2.0: gRNA-tRNA Array and Cas9-NG Based Genome Disruption and Single-Nucleotide Conversion in Saccharomyces cerevisiae

Guiping Gong et al.

Summary: This study developed an efficient tool for genome disruption and single-nucleotide conversion, utilizing a gRNAtRNA array and SpCas9-NG (GTR 2.0). The tool achieved near 100% efficiency for gene disruptions in yeast cells covering all 16 possible NGN PAMs and all 12 possible single-nucleotide conversions (N to N). Furthermore, the tool was able to achieve 66.67% mutation efficiency for multiplexed single-nucleotide conversions and 100% mutation efficiency for generating multiple conversions in different genes simultaneously. GTR 2.0 will significantly enhance the scope, efficiency, and capabilities of yeast genome editing, serving as a versatile and valuable addition to the toolbox of synthetic biology and metabolic engineering.

ACS SYNTHETIC BIOLOGY (2021)

Article Biochemical Research Methods

Protocol for the use of focused ion-beam milling to prepare crystalline lamellae for microcrystal electron diffraction (MicroED)

Michael W. Martynowycz et al.

Summary: This protocol provides a detailed guide on reproducibly preparing crystalline lamellae from protein crystals for MicroED experiments, covering both soluble and membrane proteins embedded in dense media. Following these steps allows users to prepare crystalline lamellae for protein structure determination. For more detailed information, refer to Martynowycz et al. (2019a, 2020a).

STAR PROTOCOLS (2021)

Article Biochemistry & Molecular Biology

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Charles J. Norsigian et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Multidisciplinary Sciences

Improved protein structure prediction using potentials from deep learning

Andrew W. Senior et al.

NATURE (2020)

Review Biotechnology & Applied Microbiology

Microbial Chassis Development for Natural Product Biosynthesis

Xianhao Xu et al.

TRENDS IN BIOTECHNOLOGY (2020)

Review Biotechnology & Applied Microbiology

Endogenous Type I CRISPR-Cas: From Foreign DNA Defense to Prokaryotic Engineering

Zheng Yanli et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

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Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019

David J. Newman et al.

JOURNAL OF NATURAL PRODUCTS (2020)

Review Chemistry, Multidisciplinary

Review on natural products databases: where to find data in 2020

Maria Sorokina et al.

JOURNAL OF CHEMINFORMATICS (2020)

Review Biochemical Research Methods

High-throughput screening for efficient microbial biotechnology

Aditya Sarnaik et al.

CURRENT OPINION IN BIOTECHNOLOGY (2020)

Review Biotechnology & Applied Microbiology

Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

Zhenquan Lin et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

Article Multidisciplinary Sciences

Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Deepanwita Banerjee et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae

Yueping Zhang et al.

NATURE COMMUNICATIONS (2019)

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Building a global alliance of biofoundries

Nathan Hillson et al.

NATURE COMMUNICATIONS (2019)

Review Microbiology

A Review of the Microbial Production of Bioactive Natural Products and Biologics

Janette Pham et al.

FRONTIERS IN MICROBIOLOGY (2019)

Article Chemistry, Analytical

CANPA: Computer-Assisted Natural Products Anticipation

Alexander E. Fox Ramos et al.

ANALYTICAL CHEMISTRY (2019)

Review Microbiology

Defining and combating antibiotic resistance from One Health and Global Health perspectives

Sara Hernando-Amado et al.

NATURE MICROBIOLOGY (2019)

Article Plant Sciences

Taxonomically Informed Scoring Enhances Confidence in Natural Products Annotation

Adriano Rutz et al.

FRONTIERS IN PLANT SCIENCE (2019)

Article Biochemistry & Molecular Biology

Start-Stop Assembly: a functionally scarless DNA assembly system optimized for metabolic engineering

George M. Taylor et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis

Yongzhen Xia et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Pharmacology & Pharmacy

Plazomicin: A Next-Generation Aminoglycoside

Kristy M. Shaeer et al.

PHARMACOTHERAPY (2019)

Article Biochemical Research Methods

Enhanced Heterologous Spinosad Production from a 79-kb Synthetic Multioperon Assembly

Chaoyi Song et al.

ACS SYNTHETIC BIOLOGY (2019)

Article Biochemical Research Methods

The BioCyc collection of microbial genomes and metabolic pathways

Peter D. Karp et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Review Biochemistry & Molecular Biology

Genetic platforms for heterologous expression of microbial natural products

Jia Jia Zhang et al.

NATURAL PRODUCT REPORTS (2019)

Review Spectroscopy

Identification of small molecules using accurate mass MS/MS search

Tobias Kind et al.

MASS SPECTROMETRY REVIEWS (2018)

Review Biotechnology & Applied Microbiology

Leveraging knowledge engineering and machine learning for microbial bio-manufacturing

Tolutola Oyetunde et al.

BIOTECHNOLOGY ADVANCES (2018)

Review Microbiology

Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms

Emilia Palazzotto et al.

CURRENT OPINION IN MICROBIOLOGY (2018)

Article Biotechnology & Applied Microbiology

Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision

Zehua Bao et al.

NATURE BIOTECHNOLOGY (2018)

Letter Biotechnology & Applied Microbiology

KBase: The United States Department of Energy Systems Biology Knowledgebase

Adam P. Arkin et al.

NATURE BIOTECHNOLOGY (2018)

Article Biochemistry & Molecular Biology

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

Jung-Hyun Kim et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics

David C. Earl et al.

NATURE COMMUNICATIONS (2018)

Article Biochemical Research Methods

Propagating annotations of molecular networks using in silico fragmentation

Ricardo R. da Silva et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

BRENDA in 2017: new perspectives and new tools in BRENDA

Sandra Placzek et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2017)

Review Pharmacology & Pharmacy

Using natural products for drug discovery: the impact of the genomics era

Mingzi M. Zhang et al.

EXPERT OPINION ON DRUG DISCOVERY (2017)

Article Chemistry, Multidisciplinary

Antimicrobials Inspired by Nonribosomal Peptide Synthetase Gene Clusters

Xavier Vila-Farres et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

Article Multidisciplinary Sciences

Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system

Jiazhang Lian et al.

NATURE COMMUNICATIONS (2017)

Review Microbiology

Omics-based natural product discovery and the lexicon of genome mining

Henrique Machado et al.

CURRENT OPINION IN MICROBIOLOGY (2017)

Review Biochemistry & Molecular Biology

Deep metabolome annotation in natural products research: towards a virtuous cycle in metabolite identification

Pierre-Marie Allard et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Ron Caspi et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

The Pfam protein families database: towards a more sustainable future

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Chemistry, Analytical

Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication

Pierre-Marie Allard et al.

ANALYTICAL CHEMISTRY (2016)

Review Biotechnology & Applied Microbiology

Natural product discovery: past, present, and future

Leonard Katz et al.

JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY (2016)

Article Biotechnology & Applied Microbiology

CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production

Seong Keun Kim et al.

METABOLIC ENGINEERING (2016)

Review Biochemistry & Molecular Biology

The evolution of genome mining in microbes - a review

Nadine Ziemert et al.

NATURAL PRODUCT REPORTS (2016)

Article Multidisciplinary Sciences

Human commensals producing a novel antibiotic impair pathogen colonization

Alexander Zipperer et al.

NATURE (2016)

Article Biotechnology & Applied Microbiology

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Mingxun Wang et al.

NATURE BIOTECHNOLOGY (2016)

Review Medicine, General & Internal

The Human Intestinal Microbiome in Health and Disease

Susan V. Lynch et al.

NEW ENGLAND JOURNAL OF MEDICINE (2016)

Article Biochemistry & Molecular Biology

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

Hiroyuki Kuwahara et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

CasHRA (Cas9-facilitated Homologous Recombination Assembly) method of constructing megabase-sized DNA

Jianting Zhou et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Biotechnology & Applied Microbiology

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

Tilmann Weber et al.

SYNTHETIC AND SYSTEMS BIOTECHNOLOGY (2016)

Review Biotechnology & Applied Microbiology

The application of microfluidic-based technologies in the cycle of metabolic engineering

Xiaoyan Ma et al.

SYNTHETIC AND SYSTEMS BIOTECHNOLOGY (2016)

Article Biochemical Research Methods

CRISPR/Cas9 nuclease cleavage combined with Gibson assembly for seamless cloning

Jia-Wang Wang et al.

BIOTECHNIQUES (2015)

Article Biotechnology & Applied Microbiology

Fungal artificial chromosomes for mining of the fungal secondary metabolome

Jin Woo Bok et al.

BMC GENOMICS (2015)

Review Biochemistry & Molecular Biology

Strategies for cloning and manipulating natural and synthetic chromosomes

Bogumil J. Karas et al.

CHROMOSOME RESEARCH (2015)

Review Biochemical Research Methods

Current approaches and challenges for the metabolite profiling of complex natural extracts

Jean-Luc Wolfender et al.

JOURNAL OF CHROMATOGRAPHY A (2015)

Review Biotechnology & Applied Microbiology

Genome scale engineering techniques for metabolic engineering

Rongming Liu et al.

METABOLIC ENGINEERING (2015)

Article Biochemistry & Molecular Biology

antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters

Tilmann Weber et al.

NUCLEIC ACIDS RESEARCH (2015)

Review Biochemistry & Molecular Biology

Development and Applications of CRISPR-Cas9 for Genome Engineering

Patrick D. Hsu et al.

Review Biochemistry & Molecular Biology

Impact of single-cell genomics and metagenomics on the emerging view of extremophile microbial dark matter

Brian P. Hedlund et al.

EXTREMOPHILES (2014)

Review Biotechnology & Applied Microbiology

DNA assembly techniques for next-generation combinatorial biosynthesis of natural products

Ryan E. Cobb et al.

JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY (2014)

Article Biochemistry & Molecular Biology

A roadmap for natural product discovery based on large-scale genomics and metabolomics

James R. Doroghazi et al.

NATURE CHEMICAL BIOLOGY (2014)

Article Biochemical Research Methods

Rapid and Reliable DNA Assembly via Ligase Cycling Reaction

Stefan de Kok et al.

ACS SYNTHETIC BIOLOGY (2014)

Article Biochemical Research Methods

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis

Marnix H. Medema et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Article Microbiology

Structure-Antifungal Activity Relationships of Polyene Antibiotics of the Amphotericin B Group

Anna N. Tevyashova et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2013)

Review Biotechnology & Applied Microbiology

Transcription activator-like effector nucleases (TALENs): A highly efficient and versatile tool for genome editing

Ning Sun et al.

BIOTECHNOLOGY AND BIOENGINEERING (2013)

Article Biochemical Research Methods

WholeCellViz: data visualization for whole-cell models

Ruby Lee et al.

BMC BIOINFORMATICS (2013)

Review Microbiology

Intrinsic antibiotic resistance: Mechanisms, origins, challenges and solutions

Georgina Cox et al.

INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY (2013)

Article Multidisciplinary Sciences

Implementation of stable and complex biological systems through recombinase-assisted genome engineering

Christine Nicole S. Santos et al.

NATURE COMMUNICATIONS (2013)

Article Biotechnology & Applied Microbiology

One-Step Sequence- and Ligation-Independent Cloning as a Rapid and Versatile Cloning Method for Functional Genomics Studies

Jae-Yeon Jeong et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2012)

Article Biochemistry & Molecular Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Jonathan R. Karr et al.

Review Plant Sciences

Natural Products As Sources for New Pesticides

Charles L. Cantrell et al.

JOURNAL OF NATURAL PRODUCTS (2012)

Article Mathematical & Computational Biology

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

Chen Li et al.

BMC SYSTEMS BIOLOGY (2010)

Article Multidisciplinary Sciences

Programming cells by multiplex genome engineering and accelerated evolution

Harris H. Wang et al.

NATURE (2009)

Article Biochemical Research Methods

Enzymatic assembly of DNA molecules up to several hundred kilobases

Daniel G. Gibson et al.

NATURE METHODS (2009)