1
|
Pozhydaieva N, Höfer K. Utilizing Golden Gate Assembly to Streamline CRISPR-Cas/NgTET-Based Phage Mutagenesis. Methods Mol Biol 2025; 2850:329-343. [PMID: 39363080 DOI: 10.1007/978-1-0716-4220-7_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
Phage engineering is an emerging technology due to the promising potential application of phages in medical and biotechnological settings. Targeted phage mutagenesis tools are required to customize the phages for a specific application and generate, in addition to that, so-called designer phages. CRISPR-Cas technique is used in various organisms to perform targeted mutagenesis. Yet, its efficacy is notably limited for phage mutagenesis due to the highly abundant phage DNA modifications. Addressing this challenge, we have developed a novel approach that involves the temporal removal of phage DNA cytosine modifications, allowing for effective CRISPR-Cas targeting and subsequent introduction of mutations into the phage genome. The removal of cytosine modification relies on the catalytic activity of a eukaryotic ten-eleven translocation methylcytosine (TET) dioxygenase. TET enzymes iteratively de-modify methylated or hydroxymethylated cytosines on phage DNA. The temporal removal of cytosine modification ultimately enables efficient DNA cleavage by Cas enzymes and facilitates mutagenesis. To streamline the application of the coupled TET-CRISPR-Cas system, we use Golden Gate cloning for fast and efficient assembly of a vector that comprises a TET oxidase and a donor DNA required for scarless site-specific phage mutagenesis. Our approach significantly advances the engineering of modified phage genomes, enabling the efficient generation of customized phages for specific applications.
Collapse
Affiliation(s)
| | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
| |
Collapse
|
2
|
Yang S, Zhang Y, Li C, Tan X. Repurposing endogenous Type I-D CRISPR-Cas system for genome editing in Synechococcus sp. PCC7002. Microbiol Res 2024; 288:127884. [PMID: 39226667 DOI: 10.1016/j.micres.2024.127884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/29/2024] [Accepted: 08/25/2024] [Indexed: 09/05/2024]
Abstract
Synechococcus sp. PCC7002 has been considered as a photosynthetic chassis for the conversion of CO2 into biochemicals through genetic modification. However, conventional genetic manipulation techniques prove inadequate for comprehensive genetic modifications in this strain. Here, we present the development of a genome editing tool tailored for S. PCC7002, leveraging its endogenous type I-D CRISPR-Cas system. Utilizing this novel tool, we successfully deleted the glgA1 gene and iteratively edited the genome to obtain a double mutant of glgA1 and glgA2 genes. Additionally, large DNA fragments encompassing the entire type I-A (∼14 kb) or III-B CRISPR-Cas (∼21 kb) systems were completely knocked-out in S. PCC7002 using our tool. Furthermore, the endogenous pAQ5 plasmid, approximately 38 kb in length, was successfully cured from S. PCC7002. Our work demonstrates the feasibility of harnessing the endogenous CRISPR-Cas system for genome editing in S. PCC7002, thereby enriching the genetic toolkit for this species and providing a foundation for future enhancements in its biosynthetic efficiency.
Collapse
Affiliation(s)
- Shuxiao Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yongjiu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chunyan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaoming Tan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan 430062, China.
| |
Collapse
|
3
|
Tsuji A, Inabe K, Hidese R, Kato Y, Domingues L, Kondo A, Hasunuma T. Pioneering precision in markerless strain development for Synechococcus sp. PCC 7002. Microb Cell Fact 2024; 23:268. [PMID: 39379966 PMCID: PMC11462663 DOI: 10.1186/s12934-024-02543-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Accepted: 09/27/2024] [Indexed: 10/10/2024] Open
Abstract
Marine cyanobacteria such as Picosynechococcus sp. (formerly called Synechococcus sp.) PCC 7002 are promising chassis for photosynthetic production of commodity chemicals with low environmental burdens. Genetic engineering of cyanobacteria conventionally employs antibiotic resistance markers. However, limited availability of antibiotic-resistant markers is a problem for highly multigenic strain engineering. Although several markerless genetic manipulation methods have been developed for PCC 7002, they often lack versatility due to the requirement of gene disruption in the host strain. To achieve markerless transformation in Synechococcus sp. with no requirements for the host strain, this study developed a method in which temporarily introduces a mutated phenylalanyl-tRNA synthetase gene (pheS) into the genome for counter selection. Amino acid substitutions in the PheS that cause high susceptibility of PCC 7002 to the phenylalanine analog p-chlorophenylalanine were examined, and the combination of T261A and A303G was determined as the most suitable mutation. The mutated PheS-based selection was utilized for the markerless knockout of the nblA gene in PCC 7002. In addition, the genetic construct containing the lldD and lldP genes from Escherichia coli was introduced into the ldhA gene site using the counter selection strategy, resulting in a markerless recombinant strain. The repeatability of this method was demonstrated by the double markerless knockin recombinant strain, suggesting it will be a powerful tool for multigenic strain engineering of cyanobacteria.
Collapse
Affiliation(s)
- Ayaka Tsuji
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Kosuke Inabe
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Ryota Hidese
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Yuichi Kato
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, Braga, 4710-057, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
| |
Collapse
|
4
|
Li XD, Liu LM, Xi YC, Sun QW, Luo Z, Huang HL, Wang XW, Jiang HB, Chen W. Development of a base editor for convenient and multiplex genome editing in cyanobacteria. Commun Biol 2024; 7:994. [PMID: 39143188 PMCID: PMC11324792 DOI: 10.1038/s42003-024-06696-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
Cyanobacteria are important primary producers, contributing to 25% of the global carbon fixation through photosynthesis. They serve as model organisms to study the photosynthesis, and are important cell factories for synthetic biology. To enable efficient genetic dissection and metabolic engineering in cyanobacteria, effective and accurate genetic manipulation tools are required. However, genetic manipulation in cyanobacteria by the conventional homologous recombination-based method and the recently developed CRISPR-Cas gene editing system require complicated cloning steps, especially during multi-site editing and single base mutation. This restricts the extensive research on cyanobacteria and reduces its application potential. In this study, a highly efficient and convenient cytosine base editing system was developed which allows rapid and precise C → T point mutation and gene inactivation in the genomes of Synechocystis and Anabaena. This base editing system also enables efficient multiplex editing and can be easily cured after editing by sucrose counter-selection. This work will expand the knowledge base regarding the engineering of cyanobacteria. The findings of this study will encourage the biotechnological applications of cyanobacteria.
Collapse
Affiliation(s)
- Xing-Da Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ling-Mei Liu
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yi-Cao Xi
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Qiao-Wei Sun
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Zhen Luo
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Long Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Xin-Wei Wang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Bo Jiang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, 519080, China.
| | - Weizhong Chen
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| |
Collapse
|
5
|
Gao H, Wang Y, Huang Z, Yu F, Hu X, Ning D, Xu X. Development of Leptolyngbya sp. BL0902 into a model organism for synthetic biological research in filamentous cyanobacteria. Front Microbiol 2024; 15:1409771. [PMID: 39104590 PMCID: PMC11298460 DOI: 10.3389/fmicb.2024.1409771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024] Open
Abstract
Cyanobacteria have great potential in CO2-based bio-manufacturing and synthetic biological studies. The filamentous cyanobacterium, Leptolyngbya sp. strain BL0902, is comparable to Arthrospira (Spirulina) platensis in commercial-scale cultivation while proving to be more genetically tractable. Here, we report the analyses of the whole genome sequence, gene inactivation/overexpression in the chromosome and deletion of non-essential chromosomal regions in this strain. The genetic manipulations were performed via homologous double recombination using either an antibiotic resistance marker or the CRISPR/Cpf1 editing system for positive selection. A desD-overexpressing strain produced γ-linolenic acid in an open raceway photobioreactor with the productivity of 0.36 g·m-2·d-1. Deletion mutants of predicted patX and hetR, two genes with opposite effects on cell differentiation in heterocyst-forming species, were used to demonstrate an analysis of the relationship between regulatory genes in the non-heterocystous species. Furthermore, a 50.8-kb chromosomal region was successfully deleted in BL0902 with the Cpf1 system. These results supported that BL0902 can be developed into a stable photosynthetic cell factory for synthesizing high value-added products, or used as a model strain for investigating the functions of genes that are unique to filamentous cyanobacteria, and could be systematically modified into a genome-streamlined chassis for synthetic biological purposes.
Collapse
Affiliation(s)
- Hong Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yali Wang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Ziling Huang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Feiqi Yu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xi Hu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Degang Ning
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xudong Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- School of Life Sciences, Central China Normal University, Wuhan, China
| |
Collapse
|
6
|
Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.
Collapse
Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| |
Collapse
|
7
|
Grosjean N, Yee EF, Kumaran D, Chopra K, Abernathy M, Biswas S, Byrnes J, Kreitler DF, Cheng JF, Ghosh A, Almo SC, Iwai M, Niyogi KK, Pakrasi HB, Sarangi R, van Dam H, Yang L, Blaby IK, Blaby-Haas CE. A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nat Commun 2024; 15:3167. [PMID: 38609367 PMCID: PMC11014987 DOI: 10.1038/s41467-024-47486-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.
Collapse
Affiliation(s)
- Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Estella F Yee
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, USA
| | - Macon Abernathy
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sandeep Biswas
- Department of Biology, Washington University, St. Louis, MO, USA
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masakazu Iwai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | | | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hubertus van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Ian K Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
8
|
Rachedi R, Risoul V, Foglino M, Aoudache Y, Lang K, Champ S, Kaplan E, Orelle C, Douzi B, Jault JM, Latifi A. Unravelling HetC as a peptidase-based ABC exporter driving functional cell differentiation in the cyanobacterium Nostoc PCC 7120. Microbiol Spectr 2024; 12:e0405823. [PMID: 38358282 PMCID: PMC10986499 DOI: 10.1128/spectrum.04058-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
The export of peptides or proteins is essential for a variety of important functions in bacteria. Among the diverse protein-translocation systems, peptidase-containing ABC transporters (PCAT) are involved in the maturation and export of quorum-sensing or antimicrobial peptides in Gram-positive bacteria and of toxins in Gram-negative organisms. In the multicellular and diazotrophic cyanobacterium Nostoc PCC 7120, the protein HetC is essential for the differentiation of functional heterocysts, which are micro-oxic and non-dividing cells specialized in atmospheric nitrogen fixation. HetC shows similarities to PCAT systems, but whether it actually acts as a peptidase-based exporter remains to be established. In this study, we show that the N-terminal part of HetC, encompassing the peptidase domain, displays a cysteine-type protease activity. The conserved catalytic residues conserved in this family of proteases are essential for the proteolytic activity of HetC and the differentiation of heterocysts. Furthermore, we show that the catalytic residue of the ATPase domain of HetC is also essential for cell differentiation. Interestingly, HetC has a cyclic nucleotide-binding domain at its N-terminus which can bind ppGpp in vitro and which is required for its function in vivo. Our results indicate that HetC is a peculiar PCAT that might be regulated by ppGpp to potentially facilitate the export of a signaling peptide essential for cell differentiation, thereby broadening the scope of PCAT role in Gram-negative bacteria.IMPORTANCEBacteria have a great capacity to adapt to various environmental and physiological conditions; it is widely accepted that their ability to produce extracellular molecules contributes greatly to their fitness. Exported molecules are used for a variety of purposes ranging from communication to adjust cellular physiology, to the production of toxins that bacteria secrete to fight for their ecological niche. They use export machineries for this purpose, the most common of which energize transport by hydrolysis of adenosine triphosphate. Here, we demonstrate that such a mechanism is involved in cell differentiation in the filamentous cyanobacterium Nostoc PCC 7120. The HetC protein belongs to the ATP-binding cassette transporter superfamily and presumably ensures the maturation of a yet unknown substrate during export. These results open interesting perspectives on cellular signaling pathways involving the export of regulatory peptides, which will broaden our knowledge of how these bacteria use two cell types to conciliate photosynthesis and nitrogen fixation.
Collapse
Affiliation(s)
- Raphaël Rachedi
- Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne LCB, IMM, Marseille, France
| | - Véronique Risoul
- Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne LCB, IMM, Marseille, France
| | - Maryline Foglino
- Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne LCB, IMM, Marseille, France
| | | | - Kevin Lang
- Microbiologie Moléculaire et Biochimie Structurale, UMR5086 Université de Lyon/CNRS, IBCP, Lyon, France
| | - Stéphanie Champ
- Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne LCB, IMM, Marseille, France
| | - Elise Kaplan
- Microbiologie Moléculaire et Biochimie Structurale, UMR5086 Université de Lyon/CNRS, IBCP, Lyon, France
| | - Cédric Orelle
- Microbiologie Moléculaire et Biochimie Structurale, UMR5086 Université de Lyon/CNRS, IBCP, Lyon, France
| | | | - Jean-Michel Jault
- Microbiologie Moléculaire et Biochimie Structurale, UMR5086 Université de Lyon/CNRS, IBCP, Lyon, France
| | - Amel Latifi
- Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne LCB, IMM, Marseille, France
| |
Collapse
|
9
|
Baunach M, Guljamow A, Miguel-Gordo M, Dittmann E. Harnessing the potential: advances in cyanobacterial natural product research and biotechnology. Nat Prod Rep 2024; 41:347-369. [PMID: 38088806 DOI: 10.1039/d3np00045a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Covering: 2000 to 2023Cyanobacteria produce a variety of bioactive natural products that can pose a threat to humans and animals as environmental toxins, but also have potential for or inspire pharmaceutical use. As oxygenic phototrophs, cyanobacteria furthermore hold great promise for sustainable biotechnology. Yet, the necessary tools for exploiting their biotechnological potential have so far been established only for a few model strains of cyanobacteria, while large untapped biosynthetic resources are hidden in slow-growing cyanobacterial genera that are difficult to access by genetic techniques. In recent years, several approaches have been developed to circumvent the bottlenecks in cyanobacterial natural product research. Here, we summarize current progress that has been made in unlocking or characterizing cryptic metabolic pathways using integrated omics techniques, orphan gene cluster activation, use of genetic approaches in original producers, heterologous expression and chemo-enzymatic techniques. We are mainly highlighting genomic mining concepts and strategies towards high-titer production of cyanobacterial natural products from the last 10 years and discuss the need for further research developments in this field.
Collapse
Affiliation(s)
- Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
- University of Bonn, Institute of Pharmaceutical Biology, Nußallee 6, 53115 Bonn, Germany
| | - Arthur Guljamow
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - María Miguel-Gordo
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| |
Collapse
|
10
|
Arévalo S, Pérez Rico D, Abarca D, Dijkhuizen LW, Sarasa-Buisan C, Lindblad P, Flores E, Nierzwicki-Bauer S, Schluepmann H. Genome Engineering by RNA-Guided Transposition for Anabaena sp. PCC 7120. ACS Synth Biol 2024; 13:901-912. [PMID: 38445989 PMCID: PMC10949235 DOI: 10.1021/acssynbio.3c00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/30/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In genome engineering, the integration of incoming DNA has been dependent on enzymes produced by dividing cells, which has been a bottleneck toward increasing DNA insertion frequencies and accuracy. Recently, RNA-guided transposition with CRISPR-associated transposase (CAST) was reported as highly effective and specific in Escherichia coli. Here, we developed Golden Gate vectors to test CAST in filamentous cyanobacteria and to show that it is effective in Anabaena sp. strain PCC 7120. The comparatively large plasmids containing CAST and the engineered transposon were successfully transferred into Anabaena via conjugation using either suicide or replicative plasmids. Single guide (sg) RNA encoding the leading but not the reverse complement strand of the target were effective with the protospacer-associated motif (PAM) sequence included in the sgRNA. In four out of six cases analyzed over two distinct target loci, the insertion site was exactly 63 bases after the PAM. CAST on a replicating plasmid was toxic, which could be used to cure the plasmid. In all six cases analyzed, only the transposon cargo defined by the sequence ranging from left and right elements was inserted at the target loci; therefore, RNA-guided transposition resulted from cut and paste. No endogenous transposons were remobilized by exposure to CAST enzymes. This work is foundational for genome editing by RNA-guided transposition in filamentous cyanobacteria, whether in culture or in complex communities.
Collapse
Affiliation(s)
- Sergio Arévalo
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Daniel Pérez Rico
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dolores Abarca
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Laura W. Dijkhuizen
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cristina Sarasa-Buisan
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Peter Lindblad
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
| | - Enrique Flores
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Sandra Nierzwicki-Bauer
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Henriette Schluepmann
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
11
|
Sengupta A, Bandyopadhyay A, Sarkar D, Hendry JI, Schubert MG, Liu D, Church GM, Maranas CD, Pakrasi HB. Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973. mBio 2024; 15:e0353023. [PMID: 38358263 PMCID: PMC10936165 DOI: 10.1128/mbio.03530-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Cyanobacteria are photosynthetic organisms that have garnered significant recognition as potential hosts for sustainable bioproduction. However, their complex regulatory networks pose significant challenges to major metabolic engineering efforts, thereby limiting their feasibility as production hosts. Genome streamlining has been demonstrated to be a successful approach for improving productivity and fitness in heterotrophs but is yet to be explored to its full potential in phototrophs. Here, we present the systematic reduction of the genome of the cyanobacterium exhibiting the fastest exponential growth, Synechococcus elongatus UTEX 2973. This work, the first of its kind in a photoautotroph, involved an iterative process using state-of-the-art genome-editing technology guided by experimental analysis and computational tools. CRISPR-Cas3 enabled large, progressive deletions of predicted dispensable regions and aided in the identification of essential genes. The large deletions were combined to obtain a strain with 55-kb genome reduction. The strains with streamlined genome showed improvement in growth (up to 23%) and productivity (by 22.7%) as compared to the wild type (WT). This streamlining strategy not only has the potential to develop cyanobacterial strains with improved growth and productivity traits but can also facilitate a better understanding of their genome-to-phenome relationships.IMPORTANCEGenome streamlining is an evolutionary strategy used by natural living systems to dispense unnecessary genes from their genome as a mechanism to adapt and evolve. While this strategy has been successfully borrowed to develop synthetic heterotrophic microbial systems with desired phenotype, it has not been extensively explored in photoautotrophs. Genome streamlining strategy incorporates both computational predictions to identify the dispensable regions and experimental validation using genome-editing tool, and in this study, we have employed a modified strategy with the goal to minimize the genome size to an extent that allows optimal cellular fitness under specified conditions. Our strategy has explored a novel genome-editing tool in photoautotrophs, which, unlike other existing tools, enables large, spontaneous optimal deletions from the genome. Our findings demonstrate the effectiveness of this modified strategy in obtaining strains with streamlined genome, exhibiting improved fitness and productivity.
Collapse
Affiliation(s)
- Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Debolina Sarkar
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - John I. Hendry
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - Max G. Schubert
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Deng Liu
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | | |
Collapse
|
12
|
Liu SJ, Lin GM, Yuan YQ, Chen W, Zhang JY, Zhang CC. A conserved protein inhibitor brings under check the activity of RNase E in cyanobacteria. Nucleic Acids Res 2024; 52:404-419. [PMID: 38000383 PMCID: PMC10783494 DOI: 10.1093/nar/gkad1094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 09/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The bacterial ribonuclease RNase E plays a key role in RNA metabolism. Yet, with a large substrate spectrum and poor substrate specificity, its activity must be well controlled under different conditions. Only a few regulators of RNase E are known, limiting our understanding on posttranscriptional regulatory mechanisms in bacteria. Here we show that, RebA, a protein universally present in cyanobacteria, interacts with RNase E in the cyanobacterium Anabaena PCC 7120. Distinct from those known regulators of RNase E, RebA interacts with the catalytic region of RNase E, and suppresses the cleavage activities of RNase E for all tested substrates. Consistent with the inhibitory function of RebA on RNase E, depletion of RNase E and overproduction of RebA caused formation of elongated cells, whereas the absence of RebA and overproduction of RNase E resulted in a shorter-cell phenotype. We further showed that the morphological changes caused by altered levels of RNase E or RebA are dependent on their physical interaction. The action of RebA represents a new mechanism, potentially conserved in cyanobacteria, for RNase E regulation. Our findings provide insights into the regulation and the function of RNase E, and demonstrate the importance of balanced RNA metabolism in bacteria.
Collapse
Affiliation(s)
- Su-Juan Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gui-Ming Lin
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China
| | - Yu-Qi Yuan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ju-Yuan Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China
| | - Cheng-Cai Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China
- Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| |
Collapse
|
13
|
Li J, Wu S, Zhang K, Sun X, Lin W, Wang C, Lin S. Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects. Microorganisms 2024; 12:118. [PMID: 38257946 PMCID: PMC10820777 DOI: 10.3390/microorganisms12010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.
Collapse
Affiliation(s)
- Jiashun Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Shuaishuai Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Kaidian Zhang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou 570203, China
| | - Xueqiong Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Wenwen Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| |
Collapse
|
14
|
Wu S, Zheng H, Wang Y, Wang L, Chen W. Cyanobacterial bioreporter of nitrate bioavailability in aquatic ecosystems. WATER RESEARCH 2023; 247:120749. [PMID: 37918203 DOI: 10.1016/j.watres.2023.120749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
The water eutrophication, resulting from the discharge of industrial and agricultural wastewater, leads to ecological degradation. However, to date, how to assess and manage the risks of water pollution, especially nitrogen pollution, remains a particularly noteworthy issue. Nitrate, the most important nitrogen compound, has become a bottleneck restricting total nitrogen management. The development of bioreporters monitoring nitrate pollution contributes to the estimation of water quality, especially the availability of nutrients. In this study, we obtained 9 bioreporters from 40 cyanobacterial derivatives which were constructed based on different hosts, copy numbers, and sensing elements and evaluated the performance of bioreporters. The results showed that single-celled Synechocystis was more sensitive to nitrate than filamentous Anabaena, that the reporter gene luxABCDE responded faster than sfgfp in most bioreporters, and that relatively medium-copy plasmid improved the performance of sensing elements. Nine bioreporters performed well in bioavailable nitrate detection, of which AD-AS-X and AR-NI-X, activated by nitrate repletion, had the shortest response time (2 h) and the widest response range (20-800 μM), respectively. Moreover, SR-GLN-SG, activated by nitrate deficiency, exhibited the best linear response (R2 = 0.998). After parameter optimization, exponential growth phase bioreporters, culture temperature of 30 °C, sample volume of 200 μL were determined as optimal monitoring conditions. We found that common water contaminants (copper, cadmium, and phosphorus) had no impact on the performance of bioreporters, indicating the stability of bioreporters. Six out of 9 bioreporters, especially the SR-NB-X, were highly effective in detecting the bioavailable nitrate in wastewater sample. This study provides valuable references for developing more cyanobacterial bioreporters and their practical application in nitrate detection.
Collapse
Affiliation(s)
- Shanyu Wu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hongyan Zheng
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuwei Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Li Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenli Chen
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| |
Collapse
|
15
|
Xing WY, Liu J, Zhang CC. HetF defines a transition point from commitment to morphogenesis during heterocyst differentiation in the cyanobacterium Anabaena sp. PCC 7120. Mol Microbiol 2023; 120:740-753. [PMID: 37804047 DOI: 10.1111/mmi.15177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023]
Abstract
The filamentous cyanobacterium Anabaena sp. PCC 7120 is able to form heterocysts for nitrogen fixation. Heterocyst differentiation is initiated by combined-nitrogen deprivation, followed by the commitment step during which the developmental process becomes irreversible. Mature heterocysts are terminally differentiated cells unable to divide, and cell division is required for heterocyst differentiation. Previously, we have shown that the HetF protease regulates cell division and heterocyst differentiation by cleaving PatU3, which is an inhibitor for both events. When hetF is required during the developmental program remains unknown. Here, by controlling the timing of hetF expression during heterocyst differentiation, we provide evidence that hetF is required just before the beginning of heterocyst morphogenesis. Consistent with this finding, transcriptome data show that most of the genes known to be involved in the early step (such as hetR and ntcA) or the commitment step (such as hetP and hetZ) of heterocyst development could be expressed in the ΔhetF mutant. In contrast, most of the genes involved in heterocyst morphogenesis and nitrogen fixation remain repressed in the mutant. These results indicated that in the absence of hetF, heterocyst differentiation is able to be initiated and proceeds to the stage just before heterocyst envelope formation.
Collapse
Affiliation(s)
- Wei-Yue Xing
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Jing Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Cheng-Cai Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| |
Collapse
|
16
|
Wang ZQ, Yang Y, Zhang JY, Zeng X, Zhang CC. Global translational control by the transcriptional repressor TrcR in the filamentous cyanobacterium Anabaena sp. PCC 7120. Commun Biol 2023; 6:643. [PMID: 37322092 PMCID: PMC10272220 DOI: 10.1038/s42003-023-05012-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Transcriptional and translational regulations are important mechanisms for cell adaptation to environmental conditions. In addition to house-keeping tRNAs, the genome of the filamentous cyanobacterium Anabaena sp. strain PCC 7120 (Anabaena) has a long tRNA operon (trn operon) consisting of 26 genes present on a megaplasmid. The trn operon is repressed under standard culture conditions, but is activated under translational stress in the presence of antibiotics targeting translation. Using the toxic amino acid analog β-N-methylamino-L-alanine (BMAA) as a tool, we isolated and characterized several BMAA-resistance mutants from Anabaena, and identified one gene of unknown function, all0854, named as trcR, encoding a transcription factor belonging to the ribbon-helix-helix (RHH) family. We provide evidence that TrcR represses the expression of the trn operon and is thus the missing link between the trn operon and translational stress response. TrcR represses the expression of several other genes involved in translational control, and is required for maintaining translational fidelity. TrcR, as well as its binding sites, are highly conserved in cyanobacteria, and its functions represent an important mechanism for the coupling of the transcriptional and translational regulations in cyanobacteria.
Collapse
Affiliation(s)
- Zi-Qian Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
- Institute AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei, People's Republic of China.
| |
Collapse
|
17
|
Hou F, Ke Z, Xu Y, Wang Y, Zhu G, Gao H, Ji S, Xu X. Systematic Large Fragment Deletions in the Genome of Synechococcus elongatus and the Consequent Changes in Transcriptomic Profiles. Genes (Basel) 2023; 14:genes14051091. [PMID: 37239451 DOI: 10.3390/genes14051091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/12/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Genome streamlining, as a natural process in the evolution of microbes, has become a common approach for generating ideal chassis cells for synthetic biology studies and industrial applications. However, systematic genome reduction remains a bottleneck in the generation of such chassis cells with cyanobacteria, due to very time-consuming genetic manipulations. Synechococcus elongatus PCC 7942, a unicellular cyanobacterium, is a candidate for systematic genome reduction, as its essential and nonessential genes have been experimentally identified. Here, we report that at least 20 of the 23 over 10 kb nonessential gene regions could be deleted and that stepwise deletions of these regions could be achieved. A septuple-deletion mutant (genome reduced by 3.8%) was generated, and the effects of genome reduction on the growth and genome-wide transcription were investigated. In the ancestral triple to sextuple mutants (b, c, d, e1), an increasingly large number of genes (up to 998) were upregulated relative to the wild type, while slightly fewer genes (831) were upregulated in the septuple mutant (f). In a different sextuple mutant (e2) derived from the quintuple mutant d, much fewer genes (232) were upregulated. Under the standard conditions in this study, the mutant e2 showed a higher growth rate than the wild type, e1 and f. Our results indicate that it is feasible to extensively reduce the genomes of cyanobacteria for generation of chassis cells and for experimental evolutionary studies.
Collapse
Affiliation(s)
- Feifei Hou
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116000, China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhufang Ke
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yi Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yali Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Geqian Zhu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Hong Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shuiling Ji
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xudong Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| |
Collapse
|
18
|
Cheng J, Zhang K, Hou Y. The current situations and limitations of genetic engineering in cyanobacteria: a mini review. Mol Biol Rep 2023; 50:5481-5487. [PMID: 37119415 DOI: 10.1007/s11033-023-08456-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/12/2023] [Indexed: 05/01/2023]
Abstract
Cyanobacteria are an ancient group of photoautotrophic prokaryotes, and play an essential role in the global carbon cycle. They are also model organisms for studying photosynthesis and circadian regulation, and metabolic engineering and synthetic biology strategies grants light-driven biotechnological applications to cyanobacteria, especially for engineering cyanobacteria cells to achieve an efficient light-driven system for synthesizing any product of interest from renewable feedstocks. However, lower yield limits the potential of industrial application of cyanobacterial synthetic biology, and some key limitations must be overcome to realize the full biotechnological potential of these versatile microorganisms. Although genetic engineering toolkits for cyanobacteria have made some progress, the tools available still lag behind conventional heterotrophic microorganism. Consequently, this study describes the current situations and limitations of genetic engineering in cyanobacteria, and further improvements are proposed to improve the output of targeted products. We believe that cyanobacteria-mediated light-driven platforms towards efficient synthesis of green chemicals could unlock a bright future by developing the tools for strain manipulation and novel chassis organisms with excellent performance for biotechnological applications, which could also accelerate the advancement of bio-manufacturing industries.
Collapse
Affiliation(s)
- Jie Cheng
- School of Life Sciences, Liaocheng University, Liaocheng, 252000, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Kaidian Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, 570100, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
| | - Yuyong Hou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| |
Collapse
|
19
|
Zeng X, Huang M, Sun QX, Peng YJ, Xu X, Tang YB, Zhang JY, Yang Y, Zhang CC. A c-di-GMP binding effector controls cell size in a cyanobacterium. Proc Natl Acad Sci U S A 2023; 120:e2221874120. [PMID: 36947515 PMCID: PMC10068817 DOI: 10.1073/pnas.2221874120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial signaling molecule. It is also a critical player in the regulation of cell size and cell behaviors such as cell aggregation and phototaxis in cyanobacteria, which constitute an important group of prokaryotes for their roles in the ecology and evolution of the Earth. However, c-di-GMP receptors have never been revealed in cyanobacteria. Here, we report the identification of a c-di-GMP receptor, CdgR, from the filamentous cyanobacterium Anabaena PCC 7120. Crystal structural analysis and genetic studies demonstrate that CdgR binds c-di-GMP at the dimer interface and this binding is required for the control of cell size in a c-di-GMP-dependent manner. Different functions of CdgR, in ligand binding and signal transmission, could be separated genetically, allowing us to dissect its molecular signaling functions. The presence of the apo-form of CdgR triggers cell size reduction, consistent with the similar effects observed with a decrease of c-di-GMP levels in cells. Furthermore, we found that CdgR exerts its function by interacting with a global transcription factor DevH, and this interaction was inhibited by c-di-GMP. The lethal effect triggered by conditional depletion of DevH or by the production of several point-mutant proteins of CdgR in cells indicates that this signaling pathway plays critical functions in Anabaena. Our studies revealed a mechanism of c-di-GMP signaling in the control of cell size, an important and complex trait for bacteria. CdgR is highly conserved in cyanobacteria, which will greatly expand our understanding of the roles of c-di-GMP signaling in these organisms.
Collapse
Affiliation(s)
- Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Min Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Qing-Xue Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Ye-Jun Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Xiaomei Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Yun-Bin Tang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Institut AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei430070, People’s Republic of China
- Innovation Academy for Seed Design Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| |
Collapse
|
20
|
Patel VK, Das A, Kumari R, Kajla S. Recent progress and challenges in CRISPR-Cas9 engineered algae and cyanobacteria. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
21
|
Control of Cell Size by c-di-GMP Requires a Two-Component Signaling System in the Cyanobacterium Anabaena sp. Strain PCC 7120. Microbiol Spectr 2023; 11:e0422822. [PMID: 36625639 PMCID: PMC9927289 DOI: 10.1128/spectrum.04228-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Each bacterial species possesses a specific cell size and morphology, which constitute important and recognizable physical traits. How bacteria maintain their particular cell size and morphology remains an essential question in microbiology. Cyanobacteria are oxygen-evolving photosynthetic prokaryotes. Although monophyletic, these organisms are highly diverse in their cell morphology and cell size. How these physical traits of cyanobacteria are controlled is poorly understood. Here, we report the identification of a two-component signaling system, composed of a histidine kinase CdgK and a response regulator CdgS, involved in cell size regulation in the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Inactivation of cdgK or cdgS led to reduction of cell length and width with little effect on cell growth capacity. CdgS has a GGDEF domain responsible for the synthesis of the second messenger c-di-GMP. Based on genetic and biochemical studies, we proposed a signaling pathway initiated by CdgK, leading to the phosphorylation of CdgS, and thereby an enhanced enzymatic activity for c-di-GMP synthesis of the latter. The GGDEF domain of CdgS was essential in cell size control, and the reduction of cell size observed in various mutants could be rescued by the expression of a c-di-GMP synthetase from E. coli. These results provided evidence that a minimal threshold of c-di-GMP level was required for maintaining cell size in Anabaena. IMPORTANCE Cyanobacteria are considered the first organisms to produce oxygen on Earth, and their activities shaped the evolution of our ecosystems. Cell size is an important trait fixed early in evolution, with the diversification of micro- and macrocyanobacterial species during the Great Oxidation Event. However, the genetic basis underlying cell size control in cyanobacteria was not understood. Our studies demonstrated that the CdgK-CdgS signaling pathway participates in the control of cell size, and their absence did not affect cell growth. CdgK has multiple domains susceptible to signal input, which are necessary for cell size regulation. This observation suggests that cell size in Anabaena could respond to environmental signals. These studies paved the way for genetic dissection of cell size regulation in cyanobacteria.
Collapse
|
22
|
Kumar A, Baldia A, Rajput D, Kateriya S, Babu V, Dubey KK. Multiomics and optobiotechnological approaches for the development of microalgal strain for production of aviation biofuel and biorefinery. BIORESOURCE TECHNOLOGY 2023; 369:128457. [PMID: 36503094 DOI: 10.1016/j.biortech.2022.128457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Demand and consumption of fossil fuels is increasing daily, and oil reserves are depleting. Technological developments are required towards developing sustainable renewable energy sources and microalgae are emerging as a potential candidate for various application-driven research. Molecular understanding attained through omics and system biology approach empowering researchers to modify various metabolic pathways of microalgal system for efficient extraction of biofuel and important biomolecules. This review furnish insight into different "advanced approaches" like optogenetics, systems biology and multi-omics for enhanced production of FAS (Fatty Acid Synthesis) and lipids in microalgae and their associated challenges. These new approaches would be helpful in the path of developing microalgae inspired technological platforms for optobiorefinery, which could be explored as source material to produce biofuels and other valuable bio-compounds on a large scale.
Collapse
Affiliation(s)
- Akshay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Anshu Baldia
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Deepanshi Rajput
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vikash Babu
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Kashyap Kumar Dubey
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
| |
Collapse
|
23
|
Wang SY, Li X, Wang SG, Xia PF. Base editing for reprogramming cyanobacterium Synechococcus elongatus. Metab Eng 2023; 75:91-99. [PMID: 36403709 DOI: 10.1016/j.ymben.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022]
Abstract
Cyanobacteria can directly convert carbon dioxide (CO2) at the atmospheric level to biofuels, value-added chemicals and food products, making them ideal candidates to alleviate global climate change. Despite decades-long pioneering successes, the development of genome-editing tools, especially the CRISPR-Cas-based approaches, seems to lag behind other microbial chassis, slowing down the innovations of cyanobacteria. Here, we adapted and tailored base editing for cyanobacteria based on the CRISPR-Cas system and deamination. We achieved precise and efficient genome editing at a single-nucleotide resolution and demonstrated multiplex base editing in the model cyanobacterium Synechococcus elongatus. By using the base-editing tool, we successfully manipulated the glycogen metabolic pathway via the introduction of premature STOP codons in the relevant genes, building engineered strains with elevated potentials to produce chemicals and food from CO2. We present here the first report of base editing in the phylum of cyanobacteria, and a paradigm for applying CRISPR-Cas systems in bacteria. We believe that our work will accelerate the metabolic engineering and synthetic biology of cyanobacteria and drive more innovations to alleviate global climate change.
Collapse
Affiliation(s)
- Shu-Yan Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Xin Li
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China; Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao, 266237, China
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
24
|
Tan C, Xu P, Tao F. Carbon-negative synthetic biology: challenges and emerging trends of cyanobacterial technology. Trends Biotechnol 2022; 40:1488-1502. [PMID: 36253158 DOI: 10.1016/j.tibtech.2022.09.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/05/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022]
Abstract
Global warming and climate instability have spurred interest in using renewable carbon resources for the sustainable production of chemicals. Cyanobacteria are ideal cellular factories for carbon-negative production of chemicals owing to their great potentials for directly utilizing light and CO2 as sole energy and carbon sources, respectively. However, several challenges in adapting cyanobacterial technology to industry, such as low productivity, poor tolerance, and product harvesting difficulty, remain. Synthetic biology may finally address these challenges. Here, we summarize recent advances in the production of value-added chemicals using cyanobacterial cell factories, particularly in carbon-negative synthetic biology and emerging trends in cyanobacterial applications. We also propose several perspectives on the future development of cyanobacterial technology for commercialization.
Collapse
Affiliation(s)
- Chunlin Tan
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- The State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
25
|
Coevolution of tandemly repeated hlips and RpaB-like transcriptional factor confers desiccation tolerance to subaerial Nostoc species. Proc Natl Acad Sci U S A 2022; 119:e2211244119. [PMID: 36215485 PMCID: PMC9586280 DOI: 10.1073/pnas.2211244119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Desert-inhabiting cyanobacteria can tolerate extreme desiccation and quickly revive after rehydration. The regulatory mechanisms that enable their vegetative cells to resurrect upon rehydration are poorly understood. In this study, we identified a single gene family of high light-inducible proteins (Hlips) with dramatic expansion in the Nostoc flagelliforme genome and found an intriguingly special convergence formed through four tandem gene duplication. The emerged four independent hlip genes form a gene cluster (hlips-cluster) and respond to dehydration positively. The gene mutants in N. flagelliforme were successfully generated by using gene-editing technology. Phenotypic analysis showed that the desiccation tolerance of hlips-cluster-deleted mutant decreased significantly due to impaired photosystem II repair, whereas heterologous expression of hlips-cluster from N. flagelliforme enhanced desiccation tolerance in Nostoc sp. PCC 7120. Furthermore, a transcription factor Hrf1 (hlips-cluster repressor factor 1) was identified and shown to coordinately regulate the expression of hlips-cluster and desiccation-induced psbAs. Hrf1 acts as a negative regulator for the adaptation of N. flagelliforme to the harsh desert environment. Phylogenetic analysis revealed that most species in the Nostoc genus possess both tandemly repeated Hlips and Hrf1. Our results suggest convergent evolution of desiccation tolerance through the coevolution of tandem Hlips duplication and Hrf1 in subaerial Nostoc species, providing insights into the mechanism of desiccation tolerance in photosynthetic organisms.
Collapse
|
26
|
Light-Driven Synthetic Biology: Progress in Research and Industrialization of Cyanobacterial Cell Factory. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101537. [PMID: 36294972 PMCID: PMC9605453 DOI: 10.3390/life12101537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Light-driven synthetic biology refers to an autotrophic microorganisms-based research platform that remodels microbial metabolism through synthetic biology and directly converts light energy into bio-based chemicals. This technology can help achieve the goal of carbon neutrality while promoting green production. Cyanobacteria are photosynthetic microorganisms that use light and CO2 for growth and production. They thus possess unique advantages as "autotrophic cell factories". Various fuels and chemicals have been synthesized by cyanobacteria, indicating their important roles in research and industrial application. This review summarized the progresses and remaining challenges in light-driven cyanobacterial cell factory. The choice of chassis cells, strategies used in metabolic engineering, and the methods for high-value CO2 utilization will be discussed.
Collapse
|
27
|
Cengic I, Cañadas IC, Minton NP, Hudson EP. Inducible CRISPR/Cas9 Allows for Multiplexed and Rapidly Segregated Single-Target Genome Editing in Synechocystis Sp. PCC 6803. ACS Synth Biol 2022; 11:3100-3113. [PMID: 35969224 PMCID: PMC9486961 DOI: 10.1021/acssynbio.2c00375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Establishing various synthetic biology tools is crucial for the development of cyanobacteria for biotechnology use, especially tools that allow for precise and markerless genome editing in a time-efficient manner. Here, we describe a riboswitch-inducible CRISPR/Cas9 system, contained on a single replicative vector, for the model cyanobacterium Synechocystis sp. PCC 6803. A theophylline-responsive riboswitch allowed tight control of Cas9 expression, which enabled reliable transformation of the CRISPR/Cas9 vector intoSynechocystis. Induction of the CRISPR/Cas9 mediated various types of genomic edits, specifically deletions and insertions of varying size. The editing efficiency varied depending on the target and intended edit; smaller edits performed better, reaching, e.g., 100% for insertion of a FLAG-tag onto rbcL. Importantly, the single-vector CRISPR/Cas9 system mediated multiplexed editing of up to three targets in parallel inSynechocystis. All single-target and several double-target mutants were also fully segregated after the first round of induction. Lastly, a vector curing system based on the nickel-inducible expression of the toxic mazF (from Escherichia coli) was added to the CRISPR/Cas9 vector. This inducible system allowed for curing of the vector in 25-75% of screened colonies, enabling edited mutants to become markerless.
Collapse
Affiliation(s)
- Ivana Cengic
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, Stockholm 17121, Sweden
| | - Inés C. Cañadas
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Nigel P. Minton
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Elton P. Hudson
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, Stockholm 17121, Sweden,
| |
Collapse
|
28
|
A proteolytic pathway coordinates cell division and heterocyst differentiation in the cyanobacterium Anabaena sp. PCC 7120. Proc Natl Acad Sci U S A 2022; 119:e2207963119. [PMID: 36037363 PMCID: PMC9457339 DOI: 10.1073/pnas.2207963119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The filamentous, multicellular cyanobacterium Anabaena sp. PCC 7120 (Anabaena) is a prokaryotic model for the study of cell differentiation and cell-cell interactions. Upon combined-nitrogen deprivation, Anabaena forms a particular cell type, heterocyst, for aerobic nitrogen fixation. Heterocysts are semiregularly spaced among vegetative cells. Heterocyst differentiation is coupled to cell division, but the underlying mechanism remains unclear. This mechanism could be mediated by the putative protease HetF, which is a divisome component and is necessary for heterocyst differentiation. In this study, by suppressor screening, we identified PatU3, as a negative regulator acting downstream of HetF for cell division and heterocyst development. The inactivation of patU3 restored the capacity of cell division and heterocyst differentiation in the ΔhetF mutant, and overexpression of patU3 inhibited both processes in the wild-type background. We demonstrated that PatU3 was a specific substrate of the protease activity of HetF. Consequently, PatU3 accumulated in the hetF-deficient mutant, which was responsible for the resultant mutant phenotype. The cleavage site of PatU3 by HetF was mapped after the Arg117 residue, whose mutation made PatU3 resistant to HetF processing, and mimicked the effect of hetF deletion. Our results provided evidence that HetF regulated cell division and heterocyst differentiation by controlling the inhibitory effects of PatU3. This proteolytic pathway constituted a mechanism for the coordination between cell division and differentiation in a prokaryotic model used for studies on developmental biology and multicellularity.
Collapse
|
29
|
Baldanta S, Guevara G, Navarro-Llorens JM. SEVA-Cpf1, a CRISPR-Cas12a vector for genome editing in cyanobacteria. Microb Cell Fact 2022; 21:103. [PMID: 35643551 PMCID: PMC9148489 DOI: 10.1186/s12934-022-01830-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/13/2022] [Indexed: 12/01/2022] Open
Abstract
Background Cyanobacteria are photosynthetic autotrophs that have tremendous potential for fundamental research and industrial applications due to their high metabolic plasticity and ability to grow using CO2 and sunlight. CRISPR technology using Cas9 and Cpf1 has been applied to different cyanobacteria for genome manipulations and metabolic engineering. Despite significant advances with genome editing in several cyanobacteria strains, the lack of proper genetic toolboxes is still a limiting factor compared to other model laboratory species. Among the limitations, it is essential to have versatile plasmids that could ease the benchwork when using CRISPR technology. Results In the present study, several CRISPR-Cpf1 vectors were developed for genetic manipulations in cyanobacteria using SEVA plasmids. SEVA collection is based on modular vectors that enable the exchangeability of diverse elements (e.g. origins of replication and antibiotic selection markers) and the combination with many cargo sequences for varied end-applications. Firstly, using SEVA vectors containing the broad host range RSF1010 origin we demonstrated that these vectors are replicative not only in model cyanobacteria but also in a new cyanobacterium specie, Chroococcidiopsis sp., which is different from those previously published. Then, we constructed SEVA vectors by harbouring CRISPR elements and showed that they can be easily assimilated not only by conjugation, but also by natural transformation. Finally, we used our SEVA-Cpf1 tools to delete the nblA gene in Synechocystis sp. PCC 6803, demonstrating that our plasmids can be applied for CRISPR-based genome editing technology. Conclusions The results of this study provide new CRISPR-based vectors based on the SEVA (Standard European Vector Architecture) collection that can improve editing processes using the Cpf1 nuclease in cyanobacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01830-4.
Collapse
|
30
|
Selão TT. Exploring cyanobacterial diversity for sustainable biotechnology. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3057-3071. [PMID: 35467729 DOI: 10.1093/jxb/erac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are an evolutionarily ancient and diverse group of microorganisms. Their genetic diversity has
allowed them to occupy and play vital roles in a wide range of ecological niches, from desert soil crusts to tropical oceans. Owing to bioprospecting efforts and the development of new platform technologies enabling their study and manipulation, our knowledge of cyanobacterial metabolism is rapidly expanding. This review explores our current understanding of the genetic and metabolic features of cyanobacteria, from the more established cyanobacterial model strains to the newly isolated/described species, particularly the fast-growing, highly productive, and genetically amenable strains, as promising chassis for renewable biotechnology. It also discusses emerging technologies for their study and manipulation, enabling researchers to harness the astounding diversity of the cyanobacterial genomic and metabolic treasure trove towards the establishment of a sustainable bioeconomy.
Collapse
Affiliation(s)
- Tiago Toscano Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| |
Collapse
|
31
|
Verma S, Thapa S, Siddiqui N, Chakdar H. Cyanobacterial secondary metabolites towards improved commercial significance through multiomics approaches. World J Microbiol Biotechnol 2022; 38:100. [PMID: 35486205 DOI: 10.1007/s11274-022-03285-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are ubiquitous photosynthetic prokaryotes responsible for the oxygenation of the earth's reducing atmosphere. Apart from oxygen they are producers of a myriad of bioactive metabolites with diverse complex chemical structures and robust biological activities. These secondary metabolites are known to have a variety of medicinal and therapeutic applications ranging from anti-microbial, anti-viral, anti-inflammatory, anti-cancer, and immunomodulating properties. The present review discusses various aspects of secondary metabolites viz. biosynthesis, types and applications, which highlights the repertoire of bioactive constituents they harbor. Majority of these products have been produced from only a handful of genera. Moreover, with the onset of various OMICS approaches, cyanobacteria have become an attractive chassis for improved secondary metabolites production. Also the intervention of synthetic biology tools such as gene editing technologies and a variety of metabolomics and fluxomics approaches, used for engineering cyanobacteria, have significantly enhanced the production of secondary metabolites.
Collapse
Affiliation(s)
- Shaloo Verma
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India.,Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Shobit Thapa
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India
| | - Nahid Siddiqui
- Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India.
| |
Collapse
|
32
|
Parveen H, Yazdani SS. Insights into cyanobacterial alkane biosynthesis. J Ind Microbiol Biotechnol 2022; 49:kuab075. [PMID: 34718648 PMCID: PMC9118987 DOI: 10.1093/jimb/kuab075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/09/2021] [Indexed: 11/12/2022]
Abstract
Alkanes are high-energy molecules that are compatible with enduring liquid fuel infrastructures, which make them highly suitable for being next-generation biofuels. Though biological production of alkanes has been reported in various microorganisms, the reports citing photosynthetic cyanobacteria as natural producers have been the most consistent for the long-chain alkanes and alkenes (C15-C19). However, the production of alkane in cyanobacteria is low, leading to its extraction being uneconomical for commercial purposes. In order to make alkane production economically feasible from cyanobacteria, the titre and yield need to be increased by several orders of magnitude. In the recent past, efforts have been made to enhance alkane production, although with a little gain in yield, leaving space for much improvement. Genetic manipulation in cyanobacteria is considered challenging, but recent advancements in genetic engineering tools may assist in manipulating the genome in order to enhance alkane production. Further, advancement in a basic understanding of metabolic pathways and gene functioning will guide future research for harvesting the potential of these tiny photosynthetically efficient factories. In this review, our focus would be to highlight the current knowledge available on cyanobacterial alkane production, and the potential aspects of developing cyanobacterium as an economical source of biofuel. Further insights into different metabolic pathways and hosts explored so far, and possible challenges in scaling up the production of alkanes will also be discussed.
Collapse
Affiliation(s)
- Humaira Parveen
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| |
Collapse
|
33
|
Treece TR, Gonzales JN, Pressley JR, Atsumi S. Synthetic Biology Approaches for Improving Chemical Production in Cyanobacteria. Front Bioeng Biotechnol 2022; 10:869195. [PMID: 35372310 PMCID: PMC8965691 DOI: 10.3389/fbioe.2022.869195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/25/2022] [Indexed: 11/15/2022] Open
Abstract
Biological chemical production has gained traction in recent years as a promising renewable alternative to traditional petrochemical based synthesis. Of particular interest in the field of metabolic engineering are photosynthetic microorganisms capable of sequestering atmospheric carbon dioxide. CO2 levels have continued to rise at alarming rates leading to an increasingly uncertain climate. CO2 can be sequestered by engineered photosynthetic microorganisms and used for chemical production, representing a renewable production method for valuable chemical commodities such as biofuels, plastics, and food additives. The main challenges in using photosynthetic microorganisms for chemical production stem from the seemingly inherent limitations of carbon fixation and photosynthesis resulting in slower growth and lower average product titers compared to heterotrophic organisms. Recently, there has been an increase in research around improving photosynthetic microorganisms as renewable chemical production hosts. This review will discuss the various efforts to overcome the intrinsic inefficiencies of carbon fixation and photosynthesis, including rewiring carbon fixation and photosynthesis, investigating alternative carbon fixation pathways, installing sugar catabolism to supplement carbon fixation, investigating newly discovered fast growing photosynthetic species, and using new synthetic biology tools such as CRISPR to radically alter metabolism.
Collapse
Affiliation(s)
- Tanner R. Treece
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Jake N. Gonzales
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, United States
| | - Joseph R. Pressley
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, United States
- *Correspondence: Shota Atsumi,
| |
Collapse
|
34
|
CRISPR-based metabolic engineering in non-model microorganisms. Curr Opin Biotechnol 2022; 75:102698. [PMID: 35217297 DOI: 10.1016/j.copbio.2022.102698] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/20/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022]
Abstract
Non-model microorganisms possess unique and versatile metabolic characteristics, offering great opportunities as cell factories for biosynthesis of target products. However, lack of efficient genetic tools for pathway engineering represents a big challenge to unlock the full production potential of these microbes. Over the past years, CRISPR systems have been extensively developed and applied to domesticate non-model microorganisms. In this paper, we summarize the current significant advances in designing and constructing CRISPR-mediated genetic modification systems in non-model microorganisms, such as bacteria, fungi and cyanobacteria. We particularly put emphasis on reviewing some successful implementations in metabolic pathway engineering via CRISPR-based genome editing tools. Moreover, the current barriers and future perspectives on improving the editing efficiency of CRISPR systems in non-model microorganisms are also discussed.
Collapse
|
35
|
Chakdar H, Thapa S, Srivastava A, Shukla P. Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127609. [PMID: 34772552 DOI: 10.1016/j.jhazmat.2021.127609] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/16/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Heavy metals (HMs) pose a global ecological threat due to their toxic effects on aquatic and terrestrial life. Effective remediation of HMs from the environment can help to restore soil's fertility and ecological vigor, one of the key Sustainable Development Goals (SDG) set by the United Nations. The cyanobacteria have emerged as a potential option for bioremediation of HMs due to their unique adaptations and robust metabolic machineries. Generally, cyanobacteria deploy multifarious mechanisms such as biosorption, bioaccumulation, activation of metal transporters, biotransformation and induction of detoxifying enzymes to sequester and minimize the toxic effects of heavy metals. Therefore, understanding the physiological responses and regulation of adaptation mechanisms at molecular level is necessary to unravel the candidate genes and proteins which can be manipulated to improve the bioremediation efficiency of cyanobacteria. Chaperons, cellular metabolites (extracellular polymers, biosurfactants), transcriptional regulators, metal transporters, phytochelatins and metallothioneins are some of the potential targets for strain engineering. In the present review, we have discussed the potential of cyanobacteria for HM bioremediation and provided a deeper insight into their genomic and proteomic regulation of various tolerance mechanisms. These approaches might pave new possibilities of implementing genetic engineering strategies for improving bioremediation efficiency with a future perspective.
Collapse
Affiliation(s)
- Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Shobit Thapa
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Amit Srivastava
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, ID 47907-2048, United States
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
| |
Collapse
|
36
|
Menestreau M, Rachedi R, Risoul V, Foglino M, Latifi A. The CcdB toxin is an efficient selective marker for CRISPR-plasmids developed for genome editing in cyanobacteria. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000512. [PMID: 35622522 PMCID: PMC9015812 DOI: 10.17912/micropub.biology.000512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/01/1970] [Accepted: 01/10/2022] [Indexed: 11/19/2022]
Abstract
Cyanobacteria, the only prokaryotes able of oxygenic photosynthesis are important primary producers that play a key role in the fields of agriculture, aquatic ecology and environmental protection. Their versatile metabolism makes them interesting candidates for various biotechnological applications. Recently, a great progress has been made in the field of their genetic manipulations by the development of CRISPR-based approaches. However, most of the available plasmids are rather difficult to manipulate, which renders their use challenging. In this study, we used the CcdB toxin as a selection marker to improve Cpf1-based plasmids designed for genome-editing in cyanobacteria. Our results demonstrate that this selection increased the rate of success of plasmid construction, and thus of genome editing.
Collapse
Affiliation(s)
- Martin Menestreau
- Aix Marseille Univ, CNRS, IMM, LCB, Laboratoire de Chimie Bactérienne, Marseille, France
| | - Raphaël Rachedi
- Aix Marseille Univ, CNRS, IMM, LCB, Laboratoire de Chimie Bactérienne, Marseille, France
| | - Véronique Risoul
- Aix Marseille Univ, CNRS, IMM, LCB, Laboratoire de Chimie Bactérienne, Marseille, France
| | - Maryline Foglino
- Aix Marseille Univ, CNRS, IMM, LCB, Laboratoire de Chimie Bactérienne, Marseille, France
| | - Amel Latifi
- Aix Marseille Univ, CNRS, IMM, LCB, Laboratoire de Chimie Bactérienne, Marseille, France
,
Correspondence to: Amel Latifi (
)
| |
Collapse
|
37
|
Sengupta A, Liu D, Pakrasi HB. CRISPR-Cas mediated genome engineering of cyanobacteria. Methods Enzymol 2022; 676:403-432. [DOI: 10.1016/bs.mie.2022.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
38
|
Zhang JY, Niu TC, Lin GM, Zhang CC. A CRISPR-Based Method for Constructing Conditional Mutations of Essential Genes in Cyanobacteria. Methods Mol Biol 2022; 2377:143-157. [PMID: 34709615 DOI: 10.1007/978-1-0716-1720-5_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cyanobacteria, a group of diverse bacteria capable of oxygenic photosynthesis, are excellent models for investigating many important cellular processes, such as photosynthesis, nitrogen fixation, and prokaryotic cell differentiation. They also have great potential to become the next-generation cell factories for sustainable biosynthesis of valuable products. However, genetic manipulation in cyanobacteria is not as convenient as in other model bacteria. Particularly, handling essential genes in cyanobacteria has been difficult due to the lack of appropriate tools, limiting our understanding of many important cellular functions encoded by them. We recently develop a CRISPR-based method for constructing the conditional mutants of cyanobacterial essential genes by engineering the ribosome binding site to a theophylline-responsive riboswitch. Here, we provide the details of this method. The principle of this method could be used to construct conditional mutants in a wide range of bacterial species.
Collapse
Affiliation(s)
- Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China.
| | - Tian-Cai Niu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Gui-Ming Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| |
Collapse
|
39
|
Wen Z, Qian F, Zhang J, Jiang Y, Yang S. Genome Editing of Corynebacterium glutamicum Using CRISPR-Cpf1 System. Methods Mol Biol 2022; 2479:189-206. [PMID: 35583740 DOI: 10.1007/978-1-0716-2233-9_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Corynebacterium glutamicum, as an important microbial chassis, has great potential in industrial application. However, complicated genetic modification is severely slowed by lack of efficient genome editing tools. The Streptococcus pyogenes (Sp) CRISPR-Cas9 system has been verified as a very powerful tool for mediating genome alteration in many microorganisms but cannot work well in C. glutamicum. We recently developed two Francisella novicida (Fn) CRISPR-Cpf1 assisted systems for genome editing via homologous recombination in C. glutamicum. Here, we describe the protocols and demonstrated that N iterative rounds of genome editing can be achieved in 3 N + 4 or 3 N + 2 days, respectively.
Collapse
Affiliation(s)
- Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Fenghui Qian
- Shanghai Research and Development Center of Industrial Biotechnology, Shanghai, China
| | - Jiao Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Jiang
- Shanghai Taoyusheng Biotechnology Co., Ltd., Shanghai, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Zhejiang, China.
| |
Collapse
|
40
|
The Molecular Toolset and Techniques Required to Build Cyanobacterial Cell Factories. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022. [DOI: 10.1007/10_2022_210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
41
|
Huang M, Zhang JY, Zeng X, Zhang CC. c-di-GMP Homeostasis Is Critical for Heterocyst Development in Anabaena sp. PCC 7120. Front Microbiol 2021; 12:793336. [PMID: 34925302 PMCID: PMC8682488 DOI: 10.3389/fmicb.2021.793336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/09/2021] [Indexed: 12/04/2022] Open
Abstract
c-di-GMP is a ubiquitous bacterial signal regulating various physiological process. Anabaena PCC 7120 (Anabaena) is a filamentous cyanobacterium able to form regularly-spaced heterocysts for nitrogen fixation, in response to combined-nitrogen deprivation in 24h. Anabaena possesses 16 genes encoding proteins for c-di-GMP metabolism, and their functions are poorly characterized, except all2874 (cdgS) whose deletion causes a decrease in heterocyst frequency 48h after nitrogen starvation. We demonstrated here that c-di-GMP levels increased significantly in Anabaena after combined-nitrogen starvation. By inactivating each of the 16 genes, we found that the deletion of all1175 (cdgSH) led to an increase of heterocyst frequency 24h after nitrogen stepdown. A double mutant ΔcdgSHΔcdgS had an additive effect over the single mutants in regulating heterocyst frequency, indicating that the two genes acted at different time points for heterocyst spacing. Biochemical and genetic data further showed that the functions of CdgSH and CdgS in the setup or maintenance of heterocyst frequency depended on their opposing effects on the intracellular levels of c-di-GMP. Finally, we demonstrated that heterocyst differentiation was completely inhibited when c-di-GMP levels became too high or too low. Together, these results indicate that the homeostasis of c-di-GMP level is important for heterocyst differentiation in Anabaena.
Collapse
Affiliation(s)
- Min Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.,Institut AMU-WUT, Aix-Marseille University and Wuhan University of Technology, Wuhan, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
42
|
Cui N, Yang F, Zhang JT, Sun H, Chen Y, Yu RC, Chen ZP, Jiang YL, Han SJ, Xu X, Li Q, Zhou CZ. Capsid Structure of Anabaena Cyanophage A-1(L). J Virol 2021; 95:e0135621. [PMID: 34549983 PMCID: PMC8610606 DOI: 10.1128/jvi.01356-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/19/2021] [Indexed: 01/09/2023] Open
Abstract
A-1(L) is a freshwater cyanophage with a contractile tail that specifically infects Anabaena sp. PCC 7120, one of the model strains for molecular studies of cyanobacteria. Although isolated for half a century, its structure remains unknown, which limits our understanding on the interplay between A-1(L) and its host. Here we report the 3.35 Å cryo-EM structure of A-1(L) capsid, representing the first near-atomic resolution structure of a phage capsid with a T number of 9. The major capsid gp4 proteins assemble into 91 capsomers, including 80 hexons: 20 at the center of the facet and 60 at the facet edge, in addition to 11 identical pentons. These capsomers further assemble into the icosahedral capsid, via gradually increasing curvatures. Different from the previously reported capsids of known-structure, A-1(L) adopts a noncovalent chainmail structure of capsid stabilized by two kinds of mortise-and-tenon inter-capsomer interactions: a three-layered interface at the pseudo 3-fold axis combined with the complementarity in shape and electrostatic potential around the 2-fold axis. This unique capsomer construction enables A-1(L) to possess a rigid capsid, which is solely composed of the major capsid proteins with an HK97 fold. IMPORTANCE Cyanobacteria are the most abundant photosynthetic bacteria, contributing significantly to the biomass production, O2 generation, and CO2 consumption on our planet. Their community structure and homeostasis in natural aquatic ecosystems are largely regulated by the corresponding cyanophages. In this study, we solved the structure of cyanophage A-1(L) capsid at near-atomic resolution and revealed a unique capsid construction. This capsid structure provides the molecular details for better understanding the assembly of A-1(L), and a structural platform for future investigation and application of A-1(L) in combination with its host Anabaena sp. PCC 7120. As the first isolated freshwater cyanophage that infects the genetically tractable model cyanobacterium, A-1(L) should become an ideal template for the genetic engineering and synthetic biology studies.
Collapse
Affiliation(s)
- Ning Cui
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Feng Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Jun-Tao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Hui Sun
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yu Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Rong-Cheng Yu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhi-Peng Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Shu-Jing Han
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xudong Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiong Li
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| |
Collapse
|
43
|
Liu J, Xing WY, Zhang JY, Zeng X, Yang Y, Zhang CC. Functions of the Essential Gene mraY in Cellular Morphogenesis and Development of the Filamentous Cyanobacterium Anabaena PCC 7120. Front Microbiol 2021; 12:765878. [PMID: 34745074 PMCID: PMC8566892 DOI: 10.3389/fmicb.2021.765878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/01/2021] [Indexed: 11/30/2022] Open
Abstract
Bacterial cell shape is determined by the peptidoglycan (PG) layer. The cyanobacterium Anabaena sp. PCC 7120 (Anabaena) is a filamentous strain with ovoid-shaped cells connected together with incomplete cell constriction. When deprived of combined nitrogen in the growth medium, about 5–10% of the cells differentiate into heterocysts, cells devoted to nitrogen fixation. It has been shown that PG synthesis is modulated during heterocyst development and some penicillin-binding proteins (PBPs) participating in PG synthesis are required for heterocyst morphogenesis or functioning. Anabaena has multiple PBPs with functional redundancy. In this study, in order to examine the function of PG synthesis and its relationship with heterocyst development, we created a conditional mutant of mraY, a gene necessary for the synthesis of the PG precursor, lipid I. We show that mraY is required for cell and filament integrity. Furthermore, when mraY expression was being limited, persistent septal PG synthetic activity was observed, resulting in increase in cell width. Under non-permissive conditions, filaments and cells were rapidly lysed, and no sign of heterocyst development within the time window allowed was detected after nitrogen starvation. When mraY expression was being limited, a high percentage of heterocyst doublets were found. These doublets are formed likely as a consequence of delayed cell division and persistent septal PG synthesis. MraY interacts with components of both the elongasome and the divisome, in particular those directly involved in PG synthesis, including HetF, which is required for both cell division and heterocyst formation.
Collapse
Affiliation(s)
- Jing Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Yue Xing
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Institut WUT-AMU, Aix-Marseille University and Wuhan University of Technology, Wuhan, China
| |
Collapse
|
44
|
Dhakal D, Chen M, Luesch H, Ding Y. Heterologous production of cyanobacterial compounds. J Ind Microbiol Biotechnol 2021; 48:6119914. [PMID: 33928376 PMCID: PMC8210676 DOI: 10.1093/jimb/kuab003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
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.
Collapse
Affiliation(s)
- Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| |
Collapse
|
45
|
Abstract
Bacterial cell division, with a few exceptions, is driven by FtsZ through a treadmilling mechanism to remodel and constrict the rigid peptidoglycan (PG) layer. Yet different organisms may differ in the composition of the cell division complex (divisome). In the filamentous cyanobacterium Anabaena sp. strain PCC 7120, hetF is required for the initiation of the differentiation of heterocysts, cells specialized in N2 fixation under combined-nitrogen deprivation. In this study, we demonstrate that hetF is expressed in vegetative cells and necessary for cell division under certain conditions. Under nonpermissive conditions, cells of a ΔhetF mutant stop dividing, consistent with increased levels of HetF under similar conditions in the wild type. Furthermore, HetF is a membrane protein located at midcell and cell-cell junctions. In the absence of HetF, FtsZ rings are still present in the elongated cells; however, PG remodeling is abolished. This phenotype is similar to that observed with the inhibition of the septal PG synthase FtsI. We further reveal that HetF is recruited to or stabilized at the divisome by interacting with FtsI and that this interaction is necessary for HetF function in cell division. Our results indicate that HetF is a member of the divisome depending mainly on light intensity and reveal distinct features of the cell division machinery in cyanobacteria that are of high ecological and environmental importance.
Collapse
|
46
|
Xu HF, Raanan H, Dai GZ, Oren N, Berkowicz S, Murik O, Kaplan A, Qiu BS. Reading and surviving the harsh conditions in desert biological soil crust: The cyanobacterial viewpoint. FEMS Microbiol Rev 2021; 45:6308820. [PMID: 34165541 DOI: 10.1093/femsre/fuab036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/22/2021] [Indexed: 12/18/2022] Open
Abstract
Biological soil crusts (BSCs) are found in drylands, cover ∼12% of the Earth's surface in arid and semi-arid lands and their destruction is considered an important promoter of desertification. These crusts are formed by the adhesion of soil particles to polysaccharides excreted mostly by filamentous cyanobacteria, which are the pioneers and main primary producers in BSCs. Desert BSCs survive in one of the harshest environments on Earth, and are exposed to daily fluctuations of extreme conditions. The cyanobacteria inhabiting these habitats must precisely read the changing conditions and predict, for example, the forthcoming desiccation. Moreover, they evolved a comprehensive regulation of multiple adaptation strategies to enhance their stress tolerance. Here we focus on what distinguishes cyanobacteria able to revive after dehydration from those that cannot. While important progress has been made in our understanding of physiological, biochemical and omics aspects, clarification of the sensing, signal transduction and responses enabling desiccation tolerance are just emerging. We plot the trajectory of current research and open questions ranging from general strategies and regulatory adaptations in the hydration/desiccation cycle, to recent advances in our understanding of photosynthetic adaptation. The acquired knowledge provides new insights to mitigate desertification and improve plant productivity under drought conditions.
Collapse
Affiliation(s)
- Hai-Feng Xu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079 China
| | - Hagai Raanan
- Department of Plant Pathology and Weed Research, Gilat Research Center, Agricultural Research Organization, Mobile Post Negev 2, 8531100 Israel
| | - Guo-Zheng Dai
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079 China
| | - Nadav Oren
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel
| | - Simon Berkowicz
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel.,Interuniversity Institute for Marine Sciences in Eilat, P.O.B 469, Eilat, 8810302 Israel
| | - Omer Murik
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079 China
| |
Collapse
|
47
|
New insights into the function of the proteins IsiC and IsiD from Synechocystis sp. PCC 6803 under iron limitation. Appl Microbiol Biotechnol 2021; 105:4693-4707. [PMID: 34019114 DOI: 10.1007/s00253-021-11347-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 10/25/2022]
Abstract
Iron is a common cofactor in biological processes such as respiration, photosynthesis, and nitrogen fixation. The genes isiC and isiD encode unknown proteins, and the growth of ΔisiC and ΔisiD mutants is inhibited under iron-deficient conditions. To study the regulatory mechanisms of IsiC and IsiD during iron starvation, we carried out transcriptome and metabolome sequencing. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the photosynthesis, nitrogen metabolism, and ABC transporter pathways play a vital role in regulating iron deficiency. Upon iron repletion, IsiC and IsiD also have a regulatory effect on these pathways. Additionally, KEGG analysis of the differential metabolites of wild type (WT) and mutants showed that they were all enriched in starch and sucrose metabolism after iron limitation. Weighted gene co-expression network analysis (WGCNA) constructed a co-expression network of differentially expressed genes with phenotypes and metabolites, and finally identified five modules. The turquoise module was positively correlated with iron deficiency. In contrast, the WT and blue module exhibited a negative correlation, and the mutants ΔisiC and ΔisiD were positively correlated with the gray and brown modules, respectively. WGCNA also analyzed the relationship between metabolites and phenotypes, and the green module was related to iron starvation. The co-expression network determined the hub genes and metabolites of each module. This study lays a foundation for a better understanding of cyanobacteria in response to iron deficiency. KEY POINTS: • Nitrogen metabolism and ABC transporters are involved in iron regulation. • Starch and sucrose metabolism is related to the regulation of iron deficiency. • WGCNA analyzes the correlation between genes and metabolites.
Collapse
|
48
|
Recent advances in tuning the expression and regulation of genes for constructing microbial cell factories. Biotechnol Adv 2021; 50:107767. [PMID: 33974979 DOI: 10.1016/j.biotechadv.2021.107767] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022]
Abstract
To overcome environmental problems caused by the use of fossil resources, microbial cell factories have become a promising technique for the sustainable and eco-friendly development of valuable products from renewable resources. Constructing microbial cell factories with high titers, yields, and productivity requires a balance between growth and production; to this end, tuning gene expression and regulation is necessary to optimise and precisely control complicated metabolic fluxes. In this article, we review the current trends and advances in tuning gene expression and regulation and consider their engineering at each of the three stages of gene regulation: genomic, mRNA, and protein. In particular, the technological approaches utilised in a diverse range of genetic-engineering-based tools for the construction of microbial cell factories are reviewed and representative applications of these strategies are presented. Finally, the prospects for strategies and systems for tuning gene expression and regulation are discussed.
Collapse
|
49
|
Lin Z, Li H, He L, Jing Y, Pistolozzi M, Wang T, Ye Y. Efficient genome editing for Pseudomonas aeruginosa using CRISPR-Cas12a. Gene 2021; 790:145693. [PMID: 33961975 DOI: 10.1016/j.gene.2021.145693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/29/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
The CRISPR-Cas12a system has been demonstrated as an attractive tool for bacterial genome engineering. In particular, FnCas12a recognizes protospacer-adjacent motif (PAM) sites with medium or low GC content, which complements the Cas9-based systems. Here we explored Francisella novicida Cas12a (FnCas12a) for genome editing in Pseudomonas aeruginosa. By using a two-plasmid system expressing the constitutive FnCas12a nuclease, the inducible λRed recombinase, a CRISPR RNA (crRNA), we achieved gene deletion, insertion and replacement with high efficiency (in most cases > 75%), including the deletion of large DNA fragments up to 15 kb and the serial deletion of duplicate gene clusters. This work should provide a useful and complementary addition to the genome engineering toolbox for the study of P. aeruginosa biology and physiology.
Collapse
Affiliation(s)
- Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
| | - Huanhuan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Lan He
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yanyun Jing
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Marco Pistolozzi
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Tingting Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
| | - Yanrui Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
| |
Collapse
|
50
|
Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications. Genes (Basel) 2021; 12:genes12040500. [PMID: 33805386 PMCID: PMC8066212 DOI: 10.3390/genes12040500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.
Collapse
|