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      Heterologous production of cyanobacterial compounds

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          Abstract

          Cyanobacteria produce a plethora of compounds with unique chemical structures and diverse biological activities. Importantly, the increasing availability of cyanobacterial genome sequences and the rapid development of bioinformatics tools have unraveled the tremendous potential of cyanobacteria in producing new natural products. However, the discovery of these compounds based on cyanobacterial genomes has progressed slowly as the majority of their corresponding biosynthetic gene clusters (BGCs) are silent. In addition, cyanobacterial strains are often slow-growing, difficult for genetic engineering, or cannot be cultivated yet, limiting the use of host genetic engineering approaches for discovery. On the other hand, genetically tractable hosts such as Escherichia coli, Actinobacteria, and yeast have been developed for the heterologous expression of cyanobacterial BGCs. More recently, there have been increased interests in developing model cyanobacterial strains as heterologous production platforms. Herein, we present recent advances in the heterologous production of cyanobacterial compounds in both cyanobacterial and noncyanobacterial hosts. Emerging strategies for BGC assembly, host engineering, and optimization of BGC expression are included for fostering the broader applications of synthetic biology tools in the discovery of new cyanobacterial natural products.

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          Most cited references168

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          One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

          We have developed a simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s). In this procedure, recombination requires the phage lambda Red recombinase, which is synthesized under the control of an inducible promoter on an easily curable, low copy number plasmid. To demonstrate the utility of this approach, we generated PCR products by using primers with 36- to 50-nt extensions that are homologous to regions adjacent to the gene to be inactivated and template plasmids carrying antibiotic resistance genes that are flanked by FRT (FLP recognition target) sites. By using the respective PCR products, we made 13 different disruptions of chromosomal genes. Mutants of the arcB, cyaA, lacZYA, ompR-envZ, phnR, pstB, pstCA, pstS, pstSCAB-phoU, recA, and torSTRCAD genes or operons were isolated as antibiotic-resistant colonies after the introduction into bacteria carrying a Red expression plasmid of synthetic (PCR-generated) DNA. The resistance genes were then eliminated by using a helper plasmid encoding the FLP recombinase which is also easily curable. This procedure should be widely useful, especially in genome analysis of E. coli and other bacteria because the procedure can be done in wild-type cells.
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            Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

            Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Here, we develop a method for controlling gene expression based on Cas9, an RNA-guided DNA endonuclease from a type II CRISPR system. We show that a catalytically dead Cas9 lacking endonuclease activity, when coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere with transcriptional elongation, RNA polymerase binding, or transcription factor binding. This system, which we call CRISPR interference (CRISPRi), can efficiently repress expression of targeted genes in Escherichia coli, with no detectable off-target effects. CRISPRi can be used to repress multiple target genes simultaneously, and its effects are reversible. We also show evidence that the system can be adapted for gene repression in mammalian cells. This RNA-guided DNA recognition platform provides a simple approach for selectively perturbing gene expression on a genome-wide scale. Copyright © 2013 Elsevier Inc. All rights reserved.
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              Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

              The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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                Author and article information

                Contributors
                Journal
                J Ind Microbiol Biotechnol
                J Ind Microbiol Biotechnol
                jimb
                Journal of Industrial Microbiology & Biotechnology
                Oxford University Press
                1367-5435
                1476-5535
                April 2021
                25 January 2021
                25 January 2021
                : 48
                : 3-4
                : kuab003
                Affiliations
                Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida , Gainesville, FL 31610, USA
                Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida , Gainesville, FL 31610, USA
                Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida , Gainesville, FL 31610, USA
                Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida , Gainesville, FL 31610, USA
                Author notes
                Correspondence should be addressed to: Hendrik Luesch at luesch@ 123456cop.ufl.edu
                Correspondence should be addressed to: Yousong Ding at yding@ 123456cop.ufl.edu
                Author information
                https://orcid.org/0000-0002-2492-8263
                https://orcid.org/0000-0002-4091-7492
                https://orcid.org/0000-0001-8610-0659
                Article
                kuab003
                10.1093/jimb/kuab003
                8210676
                33928376
                165eb7b9-2029-49dc-a3ac-795920fa6a2f
                © The Author(s) 2021. Published by Oxford University Press on behalf of Society of Industrial Microbiology and Biotechnology.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence ( https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                : 17 November 2020
                : 29 September 2020
                Page count
                Pages: 15
                Funding
                Funded by: National Institutes of Health, DOI 10.13039/100000002;
                Award ID: R01CA172310
                Award ID: R35GM128742
                Funded by: University of Florida, DOI 10.13039/100007698;
                Categories
                Natural Products
                Review
                AcademicSubjects/SCI01150
                AcademicSubjects/SCI00540

                Biotechnology
                cyanobacterial natural products,biosynthetic gene cluster,heterologous expression

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