1
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Zheng Y, Zhang Y, Li X, Liu L. Proof of ssDNA degraded from dsDNA for ET recombination. Biochem Biophys Rep 2024; 39:101750. [PMID: 39035021 PMCID: PMC11257833 DOI: 10.1016/j.bbrep.2024.101750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/04/2024] [Indexed: 07/23/2024] Open
Abstract
The widely used ET recombination requires an ssDNA product degraded by Rac phage protein E588 from dsDNA for strand invasion. However, proof of the ssDNA product is still elusive. The study provided three levels of proof sequentially. The probable ssDNAs degraded by E588 from the fluorescent plus-, minus-, or double-stranded dsDNA pET28a-xylanase exhibited a half fluorescence intensity of the corresponding dsDNAs, equivalent to the E588 degradation nucleotides half that of the total nucleotides degraded from the corresponding dsDNA. The ssDNA product degraded by E588 from the fluorescent minus-stranded dsDNA was confirmed by gradient gel-electrophoresis and two nuclease degradation reactions. Degraded by E588 from the dsDNA pET28a-xylanase that had a phosphorothioated plus-stranded 5'-terminus, the plus-stranded ssDNA product was separated via gel electrophoresis and recovered via a DNAclean kit. The recovered ssDNA product was proven to have intact 5'- and 3'-ends by DNA sequencing analysis. This study provides a solid foundation for the mechanism of ssDNA invasion.
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Affiliation(s)
- Yuanxia Zheng
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yi Zhang
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuegang Li
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
| | - Liangwei Liu
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
- The Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, 450046, 218 Pingan Road, China
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2
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Liu J, He C, Tan W, Zheng JH. Path to bacteriotherapy: From bacterial engineering to therapeutic perspectives. Life Sci 2024; 352:122897. [PMID: 38971366 DOI: 10.1016/j.lfs.2024.122897] [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: 01/11/2024] [Revised: 06/30/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
The major reason for the failure of conventional therapies is the heterogeneity and complexity of tumor microenvironments (TMEs). Many malignant tumors reprogram their surface antigens to evade the immune surveillance, leading to reduced antigen-presenting cells and hindered T-cell activation. Bacteria-mediated cancer immunotherapy has been extensively investigated in recent years. Scientists have ingeniously modified bacteria using synthetic biology and nanotechnology to enhance their biosafety with high tumor specificity, resulting in robust anticancer immune responses. To enhance the antitumor efficacy, therapeutic proteins, cytokines, nanoparticles, and chemotherapeutic drugs have been efficiently delivered using engineered bacteria. This review provides a comprehensive understanding of oncolytic bacterial therapies, covering bacterial design and the intricate interactions within TMEs. Additionally, it offers an in-depth comparison of the current techniques used for bacterial modification, both internally and externally, to maximize their therapeutic effectiveness. Finally, we outlined the challenges and opportunities ahead in the clinical application of oncolytic bacterial therapies.
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Affiliation(s)
- Jinling Liu
- The Affiliated Xiangtan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, China; College of Biology, Hunan University, Changsha 410082, China
| | - Chongsheng He
- College of Biology, Hunan University, Changsha 410082, China
| | - Wenzhi Tan
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, Hunan 410114, China.
| | - Jin Hai Zheng
- The Affiliated Xiangtan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, China.
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3
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Lariviere PJ, Ashraf AHMZ, Navarro-Escalante L, Leonard SP, Miller LG, Moran NA, Barrick JE. One-step genome engineering in bee gut bacterial symbionts. mBio 2024:e0139224. [PMID: 39105596 DOI: 10.1128/mbio.01392-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/24/2024] [Indexed: 08/07/2024] Open
Abstract
Mechanistic understanding of interactions in many host-microbe systems, including the honey bee microbiome, is limited by a lack of easy-to-use genome engineering approaches. To this end, we demonstrate a one-step genome engineering approach for making gene deletions and insertions in the chromosomes of honey bee gut bacterial symbionts. Electroporation of linear or non-replicating plasmid DNA containing an antibiotic resistance cassette flanked by regions with homology to a symbiont genome reliably results in chromosomal integration. This lightweight approach does not require expressing any exogenous recombination machinery. The high concentrations of large DNAs with long homology regions needed to make the process efficient can be readily produced using modern DNA synthesis and assembly methods. We use this approach to knock out genes, including genes involved in biofilm formation, and insert fluorescent protein genes into the chromosome of the betaproteobacterial bee gut symbiont Snodgrassella alvi. We are also able to engineer the genomes of multiple strains of S. alvi and another species, Snodgrassella communis, which is found in the bumble bee gut microbiome. Finally, we use the same method to engineer the chromosome of another bee symbiont, Bartonella apis, which is an alphaproteobacterium. As expected, gene knockout in S. alvi using this approach is recA-dependent, suggesting that this straightforward procedure can be applied to other microbes that lack convenient genome engineering methods. IMPORTANCE Honey bees are ecologically and economically important crop pollinators with bacterial gut symbionts that influence their health. Microbiome-based strategies for studying or improving bee health have utilized wild-type or plasmid-engineered bacteria. We demonstrate that a straightforward, single-step method can be used to insert cassettes and replace genes in the chromosomes of multiple bee gut bacteria. This method can be used for investigating the mechanisms of host-microbe interactions in the bee gut community and stably engineering symbionts that benefit pollinator health.
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Affiliation(s)
- Patrick J Lariviere
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - A H M Zuberi Ashraf
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | | | - Sean P Leonard
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Laurel G Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Nancy A Moran
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
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4
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Bobonis J, Yang ALJ, Voogdt CGP, Typas A. TAC-TIC, a high-throughput genetics method to identify triggers or blockers of bacterial toxin-antitoxin systems. Nat Protoc 2024; 19:2231-2249. [PMID: 38724726 DOI: 10.1038/s41596-024-00988-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/14/2024] [Indexed: 08/09/2024]
Abstract
Toxin-antitoxin systems (TAs) are abundant in bacterial chromosomes and can arrest growth under stress, but usually remain inactive. TAs have been increasingly implicated in halting the growth of infected bacteria from bacteriophages or foreign genetic elements1,2 to protect the population (abortive infection, Abi). The vast diversity and abundance of TAs and other Abi systems3 suggest they play an important immunity role, yet what allows them to sense attack remains largely enigmatic. Here, we describe a method called toxin activation-inhibition conjugation (TAC-TIC), which we used to identify gene products that trigger or block the toxicity of phage-defending tripartite retron-TAs4. TAC-TIC employs high-density arrayed mobilizable gene-overexpression libraries, which are transferred into cells carrying the full TA system or only its toxic component, on inducible vectors. The double-plasmid transconjugants are then pinned on inducer-containing agar plates and their colony fitness is quantified to identify gene products that trigger a TA to inhibit growth (TAC), or that block it from acting (TIC). TAC-TIC is optimized for the Singer ROTOR pinning robot, but can also be used with other robots or manual pinners, and allows screening tens of thousands of genes against any TA or Abi (with toxicity) within a week. Finally, we present a dual conjugation donor/cloning strain (Escherichia coli DATC), which accelerates the construction of TAC-TIC gene-donor libraries from phages, enabling the use of TAC-TIC for identifying TA triggers and antidefense mechanisms in phage genomes.
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Affiliation(s)
- Jacob Bobonis
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alessio Ling Jie Yang
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Carlos Geert Pieter Voogdt
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
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5
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Luo J, Lu C, Yang X. Protocol for tissue-specific mutagenesis with fluorescent labeling in zebrafish. STAR Protoc 2024; 5:103207. [PMID: 39058589 DOI: 10.1016/j.xpro.2024.103207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/26/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Here, we present a protocol for tissue-specific mutagenesis in zebrafish. We describe the preparation of the Tol2 transposase donor vector containing a U6 promoter that drives the transcription of single-guide RNAs (sgRNAs) and Cas9 under the control of a tissue-specific promoter. We then detail the establishment, identification, and phenotypic analysis of the stable tissue-specific mutagenesis zebrafish line. This protocol is useful for generating stable tissue-specific knockout lines to analyze mosaic loss-of-function phenotypes. For complete details on the use and execution of this protocol, please refer to Luo et al.1.
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Affiliation(s)
- Juanjuan Luo
- Engineering Research Center of Key Technique for Biotherapy of Guangdong Province, Shantou University Medical College, Shantou, China.
| | - Chunjiao Lu
- Engineering Research Center of Key Technique for Biotherapy of Guangdong Province, Shantou University Medical College, Shantou, China
| | - Xiaojun Yang
- Engineering Research Center of Key Technique for Biotherapy of Guangdong Province, Shantou University Medical College, Shantou, China.
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6
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Cornejo-Corona I, Boland DJ, Devarenne TP. Method for isolation of high molecular weight genomic DNA from Botryococcus biomass. PLoS One 2024; 19:e0301680. [PMID: 39046949 PMCID: PMC11268603 DOI: 10.1371/journal.pone.0301680] [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: 09/19/2023] [Accepted: 03/19/2024] [Indexed: 07/27/2024] Open
Abstract
The development of high molecular weight (HMW) genomic DNA (gDNA) extraction protocols for non-model species is essential to fully exploit long-read sequencing technologies in order to generate genome assemblies that can help answer complex questions about these organisms. Obtaining enough high-quality HMW gDNA can be challenging for these species, especially for tissues rich in polysaccharides such as biomass from species within the Botryococcus genus. The existing protocols based on column-based DNA extraction and biochemical lysis kits can be inefficient and may not be useful due to variations in biomass polysaccharide content. We developed an optimized protocol for the efficient extraction of HMW gDNA from Botryococcus biomass for use in long-read sequencing technologies. The protocol utilized an initial wash step with sorbitol to remove polysaccharides and yielded HMW gDNA concentrations up to 220 ng/μL with high purity. We then demonstrated the suitability of the HMW gDNA isolated from this protocol for long-read sequencing on the Oxford Nanopore PromethION platform for three Botryococcus species. Our protocol can be used as a standard for efficient HMW gDNA extraction in microalgae rich in polysaccharides and may be adapted for other challenging species.
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Affiliation(s)
- Ivette Cornejo-Corona
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Devon J. Boland
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Timothy P. Devarenne
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
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7
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Liu M, Li Z, Huang J, Yan J, Zhao G, Zhang Y. OptoLacI: optogenetically engineered lactose operon repressor LacI responsive to light instead of IPTG. Nucleic Acids Res 2024; 52:8003-8016. [PMID: 38860425 PMCID: PMC11260447 DOI: 10.1093/nar/gkae479] [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: 03/09/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Optogenetics' advancement has made light induction attractive for controlling biological processes due to its advantages of fine-tunability, reversibility, and low toxicity. The lactose operon induction system, commonly used in Escherichia coli, relies on the binding of lactose or isopropyl β-d-1-thiogalactopyranoside (IPTG) to the lactose repressor protein LacI, playing a pivotal role in controlling the lactose operon. Here, we harnessed the light-responsive light-oxygen-voltage 2 (LOV2) domain from Avena sativa phototropin 1 as a tool for light control and engineered LacI into two light-responsive variants, OptoLacIL and OptoLacID. These variants exhibit direct responsiveness to light and darkness, respectively, eliminating the need for IPTG. Building upon OptoLacI, we constructed two light-controlled E. coli gene expression systems, OptoE.coliLight system and OptoE.coliDark system. These systems enable bifunctional gene expression regulation in E. coli through light manipulation and show superior controllability compared to IPTG-induced systems. We applied the OptoE.coliDark system to protein production and metabolic flux control. Protein production levels are comparable to those induced by IPTG. Notably, the titers of dark-induced production of 1,3-propanediol (1,3-PDO) and ergothioneine exceeded 110% and 60% of those induced by IPTG, respectively. The development of OptoLacI will contribute to the advancement of the field of optogenetic protein engineering, holding substantial potential applications across various fields.
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Affiliation(s)
- Meizi Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Zuhui Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- School of Biological Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jianfeng Huang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Junjun Yan
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yanfei Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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8
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Fernández-Yáñez V, Ibaceta V, Torres A, Vidal RM, Schneider I, Schilling V, Toro C, Arellano C, Scavone P, Muñoz I, Del Canto F. Presence and Role of the Type 3 Fimbria in the Adherence Capacity of Enterobacter hormaechei subsp. hoffmannii. Microorganisms 2024; 12:1441. [PMID: 39065209 PMCID: PMC11279048 DOI: 10.3390/microorganisms12071441] [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: 06/17/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Enterobacter hormaechei, one of the species within the Enterobacter cloacae complex, is a relevant agent of healthcare-associated infections. In addition, it has gained relevance because isolates have shown the capacity to resist several antibiotics, particularly carbapenems. However, knowledge regarding colonization and virulence mechanisms of E. hormaechei has not progressed to the same extent as other Enterobacteriaceae species as Escherichia coli or Klebsiella pneumoniae. Here, we describe the presence and role of the type 3 fimbria, a chaperone-usher assembled fimbria, which was first described in Klebsiella spp., and which has been detected in other representatives of the Enterobacteriaceae family. Eight Chilean E. cloacae isolates were examined, and among them, four E. hormaechei isolates were found to produce the type 3 fimbria. These isolates were identified as E. hormaechei subsp. hoffmannii, one of the five subspecies known. A mutant E. hormaechei subsp. hoffmannii strain lacking the mrkA gene, encoding the major structural subunit, displayed a significantly reduced adherence capacity to a plastic surface and to Caco-2 cells, compared to the wild-type strain. This phenotype of reduced adherence capacity was not observed in the mutant strains complemented with the mrkA gene under the control of an inducible promoter. Therefore, these data suggest a role of the type 3 fimbria in the adherence capacity of E. hormaechei subsp. hoffmannii. A screening in E. hormaechei genomes contained in the NCBI RefSeq Assembly database indicated that the overall presence of the type 3 fimbria is uncommon (5.94-7.37%), although genes encoding the structure were detected in representatives of the five E. hormaechei subspecies. Exploration of complete genomes indicates that, in most of the cases, the mrkABCDF locus, encoding the type 3 fimbria, is located in plasmids. Furthermore, sequence types currently found in healthcare-associated infections were found to harbor genes encoding the type 3 fimbria, mainly ST145, ST78, ST118, ST168, ST66, ST93, and ST171. Thus, although the type 3 fimbria is not widespread among the species, it might be a determinant of fitness for a subset of E. hormaechei representatives.
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Affiliation(s)
- Valentina Fernández-Yáñez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’Higgins 3363, Santiago 9170022, Chile;
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
| | - Valentina Ibaceta
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
| | - Alexia Torres
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
| | - Roberto M. Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
| | - Isidora Schneider
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380453, Chile
| | - Valeria Schilling
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380453, Chile
| | - Cecilia Toro
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
| | - Carolina Arellano
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
| | - Paola Scavone
- Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay
| | - Ignacio Muñoz
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
| | - Felipe Del Canto
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Independencia, Santiago 8380453, Chile
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Luan J, Song C, Liu Y, He R, Guo R, Cui Q, Jiang C, Li X, Hao K, Stewart AF, Fu J, Zhang Y, Wang H. Seamless site-directed mutagenesis in complex cloned DNA sequences using the RedEx method. Nat Protoc 2024:10.1038/s41596-024-01016-9. [PMID: 39009664 DOI: 10.1038/s41596-024-01016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/01/2024] [Indexed: 07/17/2024]
Abstract
Seamless site-directed mutagenesis is an important technique for studying protein functions, tuning enzyme catalytic activities and modifying genetic elements in multiple rounds because it can insert, delete or substitute nucleotides, DNA segments or even entire genes at the target site without introducing any unwanted change. To facilitate seamless site-directed mutagenesis in large plasmids and bacterial artificial chromosomes (BACs) with repetitive sequences, we recently developed the RedEx strategy. Compared with previous methods, our approach achieves the recovery of correct recombinants with high accuracy by circumventing unwanted recombination between repetitive sequences. RedEx readily yields more than 80% accuracy in seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters, which are among the most difficult targets due to the large number of repetitive DNA sequences in modules encoding almost identical enzymes. Here we present the RedEx method by describing in detail the seamless site-directed mutagenesis in a BAC vector. Overall, the process includes three parts: (1) insertion of the RedEx cassette containing the desired mutation together with selection-counterselection markers flanked by unique restriction sites and 20-bp overlapping sequences into the target site by recombineering, (2) removal of the selection-counterselection markers in the BAC by restriction digestion and (3) circularization of the linear BAC by exonuclease-mediated in vitro DNA annealing. This protocol can be performed within 3 weeks and will enable researchers with DNA cloning experience to master seamless site-directed mutagenesis to accelerate their research.
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Affiliation(s)
- Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Yan Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruoting He
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruofei Guo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Qingwen Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Kexin Hao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China.
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Meek S, Singh-Dolt K, Sutherland L, Sharp MGF, Del-Pozo J, Walker D, Burdon T. Redundancy of p75NTR neurotrophin receptor function in development, growth and fertility in the rat. Transgenic Res 2024:10.1007/s11248-024-00395-9. [PMID: 38981975 DOI: 10.1007/s11248-024-00395-9] [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: 04/04/2024] [Accepted: 07/01/2024] [Indexed: 07/11/2024]
Abstract
The p75NTR neurotrophin receptor has positive and negative roles regulating cell survival in the nervous system. Unambiguous interpretation of p75NTR function in vivo has been complicated, however, by residual expression of alternate forms of p75NTR protein in initial p75NTR knock-out mouse models. As rats are the preferred rodent for studying brain and behaviour, and to simplify interpretation of the knock-out phenotype, we report here the generation of a mutant rat devoid of the p75NTR protein. TALEN-mediated recombination in embryonic stem cells (ESCs) was used to flank exon 2 of p75NTR with Lox P sites and produce transgenic rats carrying either un-recombined floxed p75NTREx2-fl, or recombined, exon-2 deleted p75NTREx2-Δ alleles. Crossing p75NTREx2-fl rats with a Cre-deleter strain efficiently removed exon 2 in vivo. Excision of exon 2 causes a frameshift after p75NTR Gly23 and eliminated p75NTR protein expression. Rats lacking p75NTR were healthy, fertile, and histological analysis did not reveal significant changes in cellular density or overall structure in their brains. p75NTR function is therefore largely dispensable for normal development, growth and basal homeostasis in the rat. However, the availability of constitutive and conditional p75NTREx2-Δ rats provides new opportunities to investigate specific roles of p75NTR upon injury and during tissue repair.
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Affiliation(s)
- Stephen Meek
- The Roslin Institute, RDSVS, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Karamjit Singh-Dolt
- The Roslin Institute, RDSVS, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
- Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Linda Sutherland
- The Roslin Institute, RDSVS, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Matthew G F Sharp
- Bioresearch and Veterinary Services, University of Edinburgh, Chancellors Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - Jorge Del-Pozo
- The Royal Dick School of Veterinary Science, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - David Walker
- The Royal Dick School of Veterinary Science, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
- VPG Histology, 637 Gloucester Rd, Horfield, Bristol, BS7 0BJ, UK
| | - Tom Burdon
- The Roslin Institute, RDSVS, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
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11
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Xie Z, McAuliffe O, Jin YS, Miller MJ. Genomic Modifications of Lactic Acid Bacteria and Their Applications in Dairy Fermentation. J Dairy Sci 2024:S0022-0302(24)00981-0. [PMID: 38969005 DOI: 10.3168/jds.2024-24989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/11/2024] [Indexed: 07/07/2024]
Abstract
Lactic Acid Bacteria (LAB) have a long history of safe use in milk fermentation and are generally recognized as health-promoting microorganisms when present in fermented foods. LAB are also important components of the human intestinal microbiota and are widely used as probiotics. Considering their safe and health-beneficial properties, LAB are considered appropriate vehicles that can be genetically modified for food, industrial and pharmaceutical applications. Here, this review describes (1) the potential opportunities for application of genetically modified LAB strains in dairy fermentation and (2) the various genomic modification tools for LAB strains, such as random mutagenesis, adaptive laboratory evolution, conjugation, homologous recombination, recombineering, and CRISPR (clustered regularly interspaced short palindromic repeat)- Cas (CRISPR-associated protein) based genome engineering. Lastly, this review also discusses the potential future developments of these genomic modification technologies and their applications in dairy fermentations.
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Affiliation(s)
- Zifan Xie
- Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | - Yong-Su Jin
- Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Michael J Miller
- Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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12
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Qiao K, Zhao T, Wang L, Zhang W, Meng W, Liu F, Gao X, Zhu J. Screening and identification of functional bacterial attachment genes in aerobic granular sludge. J Environ Sci (China) 2024; 141:205-214. [PMID: 38408821 DOI: 10.1016/j.jes.2023.07.011] [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: 01/17/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 02/28/2024]
Abstract
The screening and identification of attachment genes is important to exploring the formation mechanism of biofilms at the gene level. It is helpful to the development of key culture technologies for aerobic granular sludge (AGS). In this study, genome-wide sequencing and gene editing were employed for the first time to investigate the effects and functions of attachment genes in AGS. With the help of whole-genome analysis, ten attachment genes were screened from thirteen genes, and the efficiency of gene screening was greatly improved. Then, two attachment genes were selected as examples to further confirm the gene functions by constructing gene-knockout recombinant mutants of Stenotrophomonas maltophilia; when the two attachment genes were knocked out, the attachment potential was reduced by 50.67% and 43.93%, respectively. The results provide a new theoretical principle and efficient method for the development of AGS from the perspective of attachment genes.
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Affiliation(s)
- Kai Qiao
- School of Environment, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Water Simulation, Beijing 100875, China
| | - Tingting Zhao
- School of Environment, Beijing Normal University, Beijing 100875, China; R & D Centre of Aerobic Granule Technology, Beijing 100875, China
| | - Lei Wang
- School of Environment, Beijing Normal University, Beijing 100875, China; R & D Centre of Aerobic Granule Technology, Beijing 100875, China
| | - Wei Zhang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Meng
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Fan Liu
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xu Gao
- School of Environment, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Water Simulation, Beijing 100875, China
| | - Jianrong Zhu
- School of Environment, Beijing Normal University, Beijing 100875, China; R & D Centre of Aerobic Granule Technology, Beijing 100875, China.
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13
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Wiegand T, Hoffmann FT, Walker MWG, Tang S, Richard E, Le HC, Meers C, Sternberg SH. TnpB homologues exapted from transposons are RNA-guided transcription factors. Nature 2024; 631:439-448. [PMID: 38926585 DOI: 10.1038/s41586-024-07598-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
Transposon-encoded tnpB and iscB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination1-4. These widespread gene families were repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas12 (refs. 5,6). We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas adaptive immunity. Here, using phylogenetics, structural predictions, comparative genomics and functional assays, we uncover multiple independent genesis events of programmable transcription factors, which we name TnpB-like nuclease-dead repressors (TldRs). These proteins use naturally occurring guide RNAs to specifically target conserved promoter regions of the genome, leading to potent gene repression in a mechanism akin to CRISPR interference technologies invented by humans7. Focusing on a TldR clade found broadly in Enterobacteriaceae, we discover that bacteriophages exploit the combined action of TldR and an adjacently encoded phage gene to alter the expression and composition of the host flagellar assembly, a transformation with the potential to impact motility8, phage susceptibility9, and host immunity10. Collectively, this work showcases the diverse molecular innovations that were enabled through repeated exaptation of transposon-encoded genes, and reveals the evolutionary trajectory of diverse RNA-guided transcription factors.
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Affiliation(s)
- Tanner Wiegand
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Florian T Hoffmann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Matt W G Walker
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Egill Richard
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Hoang C Le
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Chance Meers
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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14
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Aliakbari M, Karkhane AA. In vivo cloning of PCR product via site-specific recombination in Escherichia coli. Appl Microbiol Biotechnol 2024; 108:400. [PMID: 38951186 PMCID: PMC11217044 DOI: 10.1007/s00253-024-13239-7] [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: 03/25/2024] [Revised: 06/02/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
Over the past years, several methods have been developed for gene cloning. Choosing a cloning strategy depends on various factors, among which simplicity and affordability have always been considered. The aim of this study, on the one hand, is to simplify gene cloning by skipping in vitro assembly reactions and, on the other hand, to reduce costs by eliminating relatively expensive materials. We investigated a cloning system using Escherichia coli harboring two plasmids, pLP-AmpR and pScissors-CmR. The pLP-AmpR contains a landing pad (LP) consisting of two genes (λ int and λ gam) that allow the replacement of the transformed linear DNA using site-specific recombination. After the replacement process, the inducible expressing SpCas9 and specific sgRNA from the pScissors-CmR (CRISPR/Cas9) vector leads to the removal of non-recombinant pLP-AmpR plasmids. The function of LP was explored by directly transforming PCR products. The pScissors-CmR plasmid was evaluated for curing three vectors, including the origins of pBR322, p15A, and pSC101. Replacing LP with a PCR product and fast-eradicating pSC101 origin-containing vectors was successful. Recombinant colonies were confirmed following gene replacement and plasmid curing processes. The results made us optimistic that this strategy may potentially be a simple and inexpensive cloning method. KEY POINTS: •The in vivo cloning was performed by replacing the target gene with the landing pad. •Fast eradication of non-recombinant plasmids was possible by adapting key vectors. •This strategy is not dependent on in vitro assembly reactions and expensive materials.
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Affiliation(s)
- Moein Aliakbari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Asghar Karkhane
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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15
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Vignolini T, Capitanio M, Caldini C, Gardini L, Pavone FS. Highly inclined light sheet allows volumetric super-resolution imaging of efflux pumps distribution in bacterial biofilms. Sci Rep 2024; 14:12902. [PMID: 38839922 PMCID: PMC11153600 DOI: 10.1038/s41598-024-63729-x] [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: 12/21/2023] [Accepted: 05/31/2024] [Indexed: 06/07/2024] Open
Abstract
Bacterial biofilms are highly complex communities in which isogenic bacteria display different gene expression patterns and organize in a three-dimensional mesh gaining enhanced resistance to biocides. The molecular mechanisms behind such increased resistance remain mostly unknown, also because of the technical difficulties in biofilm investigation at the sub-cellular and molecular level. In this work we focus on the AcrAB-TolC protein complex, a multidrug efflux pump found in Enterobacteriaceae, whose overexpression is associated with most multiple drug resistance (MDR) phenotypes occurring in Gram-negative bacteria. We propose an optical method to quantify the expression level of the AcrAB-TolC pump within the biofilm volume at the sub-cellular level, with single-molecule sensitivity. Through a combination of super-resolution PALM with single objective light sheet and precision genome editing, we can directly quantify the spatial distribution of endogenous AcrAB-TolC pumps expressed in both planktonic bacteria and, importantly, within the bacterial biofilm volume. We observe a gradient of pump density within the biofilm volume and over the course of biofilm maturation. Notably, we propose an optical method that could be broadly employed to achieve volumetric super-resolution imaging of thick samples.
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Affiliation(s)
- T Vignolini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy.
- Parasite RNA Biology Group, Institut Pasteur, Université Paris Cité, 75015, Paris, France.
| | - M Capitanio
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
| | - C Caldini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
| | - L Gardini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
- National Institute of Optics, National Research Council, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
| | - F S Pavone
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
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16
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Islam T, Josephs EA. Genome editing outcomes reveal mycobacterial NucS participates in a short-patch repair of DNA mismatches. Nucleic Acids Res 2024:gkae402. [PMID: 38747340 DOI: 10.1093/nar/gkae402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/28/2024] Open
Abstract
In the canonical DNA mismatch repair (MMR) mechanism in bacteria, if a nucleotide is incorrectly mis-paired with the template strand during replication, the resulting repair of this mis-pair can result in the degradation and re-synthesis of hundreds or thousands of nucleotides on the newly-replicated strand (long-patch repair). While mycobacteria, which include important pathogens such as Mycobacterium tuberculosis, lack the otherwise highly-conserved enzymes required for the canonical MMR reaction, it was found that disruption of a mycobacterial mismatch-sensitive endonuclease NucS results in a hyper-mutative phenotype, leading to the idea that NucS might be involved in a cryptic, independently-evolved DNA MMR mechanism, perhaps mediated by homologous recombination (HR) with a sister chromatid. Using oligonucleotide recombination, which allows us to introduce mismatches specifically into the genomes of a model for M. tuberculosis, Mycobacterium smegmatis, we find that NucS participates in a direct repair of DNA mismatches where the patch of excised nucleotides is largely confined to within ∼5-6 bp of the mis-paired nucleotides, which is inconsistent with mechanistic models of canonical mycobacterial HR or other double-strand break (DSB) repair reactions. The results presented provide evidence of a novel NucS-associated mycobacterial MMR mechanism occurring in vivo to regulate genetic mutations in mycobacteria.
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Affiliation(s)
- Tanjina Islam
- Department of Nanoscience, University of North Carolina at Greensboro, Greensboro, NC 27401, USA
| | - Eric A Josephs
- Department of Nanoscience, University of North Carolina at Greensboro, Greensboro, NC 27401, USA
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27401, USA
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17
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Zhu X, Yang Y, Feng D, Wang O, Chen J, Wang J, Wang B, Liu Y, Edenfield BH, Haddock AN, Wang Y, Patel T, Bi Y, Ji B. Albumin promoter-driven FlpO expression induces efficient genetic recombination in mouse liver. Am J Physiol Gastrointest Liver Physiol 2024; 326:G495-G503. [PMID: 38469630 DOI: 10.1152/ajpgi.00263.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/13/2024]
Abstract
Tissue-specific gene manipulations are widely used in genetically engineered mouse models. A single recombinase system, such as the one using Alb-Cre, has been commonly used for liver-specific genetic manipulations. However, most diseases are complex, involving multiple genetic changes and various cell types. A dual recombinase system is required for conditionally modifying different genes sequentially in the same cell or inducing genetic changes in different cell types within the same organism. A FlpO cDNA was inserted between the last exon and 3'-UTR of the mouse albumin gene in a bacterial artificial chromosome (BAC-Alb-FlpO). The founders were crossed with various reporter mice to examine the efficiency of recombination. Liver cancer tumorigenesis was investigated by crossing the FlpO mice with FSF-KrasG12D mice and p53frt mice (KPF mice). BAC-Alb-FlpO mice exhibited highly efficient recombination capability in both hepatocytes and intrahepatic cholangiocytes. No recombination was observed in the duodenum and pancreatic cells. BAC-Alb-FlpO-mediated liver-specific expression of mutant KrasG12D and conditional deletion of p53 gene caused the development of liver cancer. Remarkably, liver cancer in these KPF mice manifested a distinctive mixed hepatocellular carcinoma and cholangiocarcinoma phenotype. A highly efficient and liver-specific BAC-Alb-FlpO mouse model was developed. In combination with other Cre lines, different genes can be manipulated sequentially in the same cell, or distinct genetic changes can be induced in different cell types of the same organism.NEW & NOTEWORTHY A liver-specific Alb-FlpO mouse line was generated. By coupling it with other existing CreERT or Cre lines, the dual recombinase approach can enable sequential gene modifications within the same cell or across various cell types in an organism for liver research through temporal and spatial gene manipulations.
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Affiliation(s)
- Xiaohui Zhu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Yan Yang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Dongfeng Feng
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Oliver Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Jiaxiang Chen
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Jiale Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Bin Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Yang Liu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Brandy H Edenfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Ashley N Haddock
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Ying Wang
- Departments of Cardiovascular Diseases and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Tushar Patel
- Department of Transplantation, Mayo Clinic, Jacksonville, Florida, United States
| | - Yan Bi
- Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, United States
| | - Baoan Ji
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
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18
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Poulos MG, Ramalingam P, Winiarski A, Gutkin MC, Katsnelson L, Carter C, Pibouin-Fragner L, Eichmann A, Thomas JL, Miquerol L, Butler JM. Complementary and Inducible creER T2 Mouse Models for Functional Evaluation of Endothelial Cell Subtypes in the Bone Marrow. Stem Cell Rev Rep 2024; 20:1135-1149. [PMID: 38438768 PMCID: PMC11087254 DOI: 10.1007/s12015-024-10703-9] [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] [Accepted: 02/21/2024] [Indexed: 03/06/2024]
Abstract
In the adult bone marrow (BM), endothelial cells (ECs) are an integral component of the hematopoietic stem cell (HSC)-supportive niche, which modulates HSC activity by producing secreted and membrane-bound paracrine signals. Within the BM, distinct vascular arteriole, transitional, and sinusoidal EC subtypes display unique paracrine expression profiles and create anatomically-discrete microenvironments. However, the relative contributions of vascular endothelial subtypes in supporting hematopoiesis is unclear. Moreover, constitutive expression and off-target activity of currently available endothelial-specific and endothelial-subtype-specific murine cre lines potentially confound data analysis and interpretation. To address this, we describe two tamoxifen-inducible cre-expressing lines, Vegfr3-creERT2 and Cx40-creERT2, that efficiently label sinusoidal/transitional and arteriole endothelium respectively in adult marrow, without off-target activity in hematopoietic or perivascular cells. Utilizing an established mouse model in which cre-dependent recombination constitutively-activates MAPK signaling within adult endothelium, we identify arteriole ECs as the driver of MAPK-mediated hematopoietic dysfunction. These results define complementary tamoxifen-inducible creERT2-expressing mouse lines that label functionally-discrete and non-overlapping sinusoidal/transitional and arteriole EC populations in the adult BM, providing a robust toolset to investigate the differential contributions of vascular subtypes in maintaining hematopoietic homeostasis.
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Affiliation(s)
- Michael G Poulos
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, 32610, USA
- Division of Hematology/Oncology, University of Florida, 1333 Center Drive, BH-022D, Gainesville, FL, 32610, USA
| | - Pradeep Ramalingam
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, 32610, USA
- Division of Hematology/Oncology, University of Florida, 1333 Center Drive, BH-022D, Gainesville, FL, 32610, USA
| | - Agatha Winiarski
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, 32610, USA
| | - Michael C Gutkin
- Ansary Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Lizabeth Katsnelson
- Ansary Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Cody Carter
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, 32610, USA
| | | | - Anne Eichmann
- Université de Paris Cité, Inserm, PARCC, 75015, Paris, France
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Jean-Leon Thomas
- Department of Neurology, Yale University School of Medicine, New Haven, CT, 06511, USA
- Paris Brain Institute, Université Pierre et Marie Curie Paris, 06 UMRS1127, Sorbonne Université, Paris Brain Institute, Paris, France
| | - Lucile Miquerol
- Aix-Marseille Université, CNRS UMR 7288, IBDM, 13288, Marseille, France
| | - Jason M Butler
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, 32610, USA.
- Ansary Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
- Division of Hematology/Oncology, University of Florida, 1333 Center Drive, BH-022D, Gainesville, FL, 32610, USA.
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19
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Zhang C, Wei G, Zhou N, Wang Y, Feng J, Wang X, Zhang A, Chen K. Systematic Engineering of Escherichia coli for Efficient Production of Pseudouridine from Glucose and Uracil. ACS Synth Biol 2024; 13:1303-1311. [PMID: 38529630 DOI: 10.1021/acssynbio.4c00028] [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: 03/27/2024]
Abstract
In this study, we proposed a biological approach to efficiently produce pseudouridine (Ψ) from glucose and uracil in vivo using engineered Escherichia coli. By screening host strains and core enzymes, E. coli MG1655 overexpressing Ψ monophosphate (ΨMP) glycosidase and ΨMP phosphatase was obtained, which displayed the highest Ψ concentration. Then, optimization of the RBS sequences, enhancement of ribose 5-phosphate supply in the cells, and overexpression of the membrane transport protein UraA were investigated. Finally, fed-batch fermentation of Ψ in a 5 L fermentor can reach 27.5 g/L with a yield of 89.2 mol % toward uracil and 25.6 mol % toward glucose within 48 h, both of which are the highest to date. In addition, the Ψ product with a high purity of 99.8% can be purified from the fermentation broth after crystallization. This work provides an efficient and environmentally friendly protocol for allowing for the possibility of Ψ bioproduction on an industrial scale.
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Affiliation(s)
- Chi Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Guoguang Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ning Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yingying Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jia Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Alei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
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20
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Tan W, Miao Q, Jia X, Liu Y, Li S, Yang D. Research Progress on the Assembly of Large DNA Fragments. Chembiochem 2024; 25:e202400054. [PMID: 38477700 DOI: 10.1002/cbic.202400054] [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: 01/21/2024] [Revised: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Synthetic biology, a newly and rapidly developing interdisciplinary field, has demonstrated increasing potential for extensive applications in the wide areas of biomedicine, biofuels, and novel materials. DNA assembly is a key enabling technology of synthetic biology and a central point for realizing fully synthetic artificial life. While the assembly of small DNA fragments has been successfully commercialized, the assembly of large DNA fragments remains a challenge due to their high molecular weight and susceptibility to breakage. This article provides an overview of the development and current state of DNA assembly technology, with a focus on recent advancements in the assembly of large DNA fragments in Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae. In particular, the methods and challenges associated with the assembly of large DNA fragment in different hosts are highlighted. The advancements in DNA assembly have the potential to facilitate the construction of customized genomes, giving us the ability to modify cellular functions and even create artificial life. It is also contributing to our ability to understand, predict, and manipulate living organisms.
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Affiliation(s)
- Wei Tan
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Qing Miao
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Xuemei Jia
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Ying Liu
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
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21
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Han SW, Won HS. Advancements in the Application of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs). Biomolecules 2024; 14:479. [PMID: 38672495 PMCID: PMC11048544 DOI: 10.3390/biom14040479] [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: 03/19/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a significant potential for novel therapeutic applications because of their bioactive properties, stability, and specificity. RiPPs are synthesized on ribosomes, followed by intricate post-translational modifications (PTMs), crucial for their diverse structures and functions. PTMs, such as cyclization, methylation, and proteolysis, play crucial roles in enhancing RiPP stability and bioactivity. Advances in synthetic biology and bioinformatics have significantly advanced the field, introducing new methods for RiPP production and engineering. These methods encompass strategies for heterologous expression, genetic refactoring, and exploiting the substrate tolerance of tailoring enzymes to create novel RiPP analogs with improved or entirely new functions. Furthermore, the introduction and implementation of cutting-edge screening methods, including mRNA display, surface display, and two-hybrid systems, have expedited the identification of RiPPs with significant pharmaceutical potential. This comprehensive review not only discusses the current advancements in RiPP research but also the promising opportunities that leveraging these bioactive peptides for therapeutic applications presents, illustrating the synergy between traditional biochemistry and contemporary synthetic biology and genetic engineering approaches.
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Affiliation(s)
- Sang-Woo Han
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical & Health Science, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea;
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical & Health Science, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea;
- BK21 Project Team, Department of Applied Life Science, Graduate School, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea
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22
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Gucwa K, Wons E, Wisniewska A, Jakalski M, Dubiak Z, Kozlowski LP, Mruk I. Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system's regulator and can be mitigated by excision of the cryptic prophage Rac. Nucleic Acids Res 2024; 52:2942-2960. [PMID: 38153127 PMCID: PMC11014345 DOI: 10.1093/nar/gkad1234] [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: 06/09/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Bacterial gene regulatory networks orchestrate responses to environmental challenges. Horizontal gene transfer can bring in genes with regulatory potential, such as new transcription factors (TFs), and this can disrupt existing networks. Serious regulatory perturbations may even result in cell death. Here, we show the impact on Escherichia coli of importing a promiscuous TF that has adventitious transcriptional effects within the cryptic Rac prophage. A cascade of regulatory network perturbations occurred on a global level. The TF, a C regulatory protein, normally controls a Type II restriction-modification system, but in E. coli K-12 interferes with expression of the RacR repressor gene, resulting in de-repression of the normally-silent Rac ydaT gene. YdaT is a prophage-encoded TF with pleiotropic effects on E. coli physiology. In turn, YdaT alters expression of a variety of bacterial regulons normally controlled by the RcsA TF, resulting in deficient lipopolysaccharide biosynthesis and cell division. At the same time, insufficient RacR repressor results in Rac DNA excision, halting Rac gene expression due to loss of the replication-defective Rac prophage. Overall, Rac induction appears to counteract the lethal toxicity of YdaT. We show here that E. coli rewires its regulatory network, so as to minimize the adverse regulatory effects of the imported C TF. This complex set of interactions may reflect the ability of bacteria to protect themselves by having robust mechanisms to maintain their regulatory networks, and/or suggest that regulatory C proteins from mobile operons are under selection to manipulate their host's regulatory networks for their own benefit.
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Affiliation(s)
- Katarzyna Gucwa
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Aleksandra Wisniewska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Marcin Jakalski
- 3P-Medicine Laboratory, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Zuzanna Dubiak
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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23
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Dessartine MM, Kosta A, Doan T, Cascales É, Côté JP. Type 1 fimbriae-mediated collective protection against type 6 secretion system attacks. mBio 2024; 15:e0255323. [PMID: 38497656 PMCID: PMC11005336 DOI: 10.1128/mbio.02553-23] [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: 09/27/2023] [Accepted: 01/25/2024] [Indexed: 03/19/2024] Open
Abstract
Bacterial competition may rely on secretion systems such as the type 6 secretion system (T6SS), which punctures and releases toxic molecules into neighboring cells. To subsist, bacterial targets must counteract the threats posed by T6SS-positive competitors. In this study, we used a comprehensive genome-wide high-throughput screening approach to investigate the dynamics of interbacterial competition. Our primary goal was to identify deletion mutants within the well-characterized E. coli K-12 single-gene deletion library, the Keio collection, that demonstrated resistance to T6SS-mediated killing by the enteropathogenic bacterium Cronobacter malonaticus. We identified 49 potential mutants conferring resistance to T6SS and focused our interest on a deletion mutant (∆fimE) exhibiting enhanced expression of type 1 fimbriae. We demonstrated that the presence of type 1 fimbriae leads to the formation of microcolonies and thus protects against T6SS-mediated assaults. Collectively, our study demonstrated that adhesive structures such as type 1 fimbriae confer collective protective behavior against T6SS attacks.IMPORTANCEType 6 secretion systems (T6SS) are molecular weapons employed by gram-negative bacteria to eliminate neighboring microbes. T6SS plays a pivotal role as a virulence factor, enabling pathogenic gram-negative bacteria to compete with the established communities to colonize hosts and induce infections. Gaining a deeper understanding of bacterial interactions will allow the development of strategies to control the action of systems such as the T6SS that can manipulate bacterial communities. In this context, we demonstrate that bacteria targeted by T6SS attacks from the enteric pathogen Cronobacter malonaticus, which poses a significant threat to infants, can develop a collective protective mechanism centered on the production of type I fimbriae. These adhesive structures promote the aggregation of bacterial preys and the formation of microcolonies, which protect the cells from T6SS attacks.
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Affiliation(s)
- Margot Marie Dessartine
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Artemis Kosta
- Plateforme de microscopie, Institut de Microbiologie de la Méditerranée (IMM, FR3479), Aix-Marseille Univ, CNRS, Marseille, France
| | - Thierry Doan
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, CNRS, Marseille, France
| | - Éric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, CNRS, Marseille, France
| | - Jean-Philippe Côté
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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24
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Cook GD, Stasulli NM. Employing synthetic biology to expand antibiotic discovery. SLAS Technol 2024; 29:100120. [PMID: 38340893 DOI: 10.1016/j.slast.2024.100120] [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: 06/16/2023] [Revised: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Antimicrobial-resistant (AMR) bacterial pathogens are a continually growing threat as our methods for combating these infections continue to be overcome by the evolution of resistance mechanisms. Recent therapeutic methods have not staved off the concern of AMR infections, so continued research focuses on new ways of identifying small molecules to treat AMR pathogens. While chemical modification of existing antibiotics is possible, there has been rapid development of resistance by pathogens that were initially susceptible to these compounds. Synthetic biology is becoming a key strategy in trying to predict and induce novel, natural antibiotics. Advances in cloning and mutagenesis techniques applied through a synthetic biology lens can help characterize the native regulation of antibiotic biosynthetic gene clusters (BGCs) to identify potential modifications leading to more potent antibiotic activity. Additionally, many cryptic antibiotic BGCs are derived from non-ribosomal peptide synthase (NRPS) and polyketide synthase (PKS) biosynthetic pathways; complex, clustered genetic sequences that give rise to amino acid-derived natural products. Synthetic biology can be applied to modify and metabolically engineer these enzyme-based systems to promote rapid and sustainable production of natural products and their variants. This review will focus on recent advances related to synthetic biology as applied to genetic pathway characterization and identification of antibiotics from naturally occurring BGCs. Specifically, we will summarize recent efforts to characterize BGCs via general genomic mutagenesis, endogenous gene expression, and heterologous gene expression.
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Affiliation(s)
- Greta D Cook
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA
| | - Nikolas M Stasulli
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA.
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25
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Banta AB, Myers KS, Ward RD, Cuellar RA, Place M, Freeh CC, Bacon EE, Peters JM. A Targeted Genome-scale Overexpression Platform for Proteobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582922. [PMID: 38496613 PMCID: PMC10942329 DOI: 10.1101/2024.03.01.582922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Targeted, genome-scale gene perturbation screens using Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) and activation (CRISPRa) have revolutionized eukaryotic genetics, advancing medical, industrial, and basic research. Although CRISPRi knockdowns have been broadly applied in bacteria, options for genome-scale overexpression face key limitations. Here, we develop a facile approach for genome-scale gene overexpression in bacteria we call, "CRISPRtOE" (CRISPR transposition and OverExpression). We create a platform for comprehensive gene targeting using CRISPR-associated transposition (CAST) and show that transposition occurs at a higher frequency in non-transcribed DNA. We then demonstrate that CRISPRtOE can upregulate gene expression in Proteobacteria with medical and industrial relevance by integrating synthetic promoters of varying strength upstream of target genes. Finally, we employ CRISPRtOE screening at the genome-scale in Escherichia coli, recovering known antibiotic targets and genes with unexplored roles in antibiotic function. We envision that CRISPRtOE will be a valuable overexpression tool for antibiotic mode of action, industrial strain optimization, and gene function discovery in bacteria.
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Affiliation(s)
- Amy B Banta
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Kevin S Myers
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan D Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Rodrigo A Cuellar
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Claire C Freeh
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Emily E Bacon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
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26
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Wolfe AR, Cui T, Baie S, Corrales-Guerrero S, Webb A, Castro-Aceituno V, Shyu DL, Karasinska JM, Topham JT, Renouf DJ, Schaeffer DF, Halloran M, Packard R, Robb R, Chen W, Denko N, Lisanti M, Thompson TC, Frank P, Williams TM. Nutrient scavenging-fueled growth in pancreatic cancer depends on caveolae-mediated endocytosis under nutrient-deprived conditions. SCIENCE ADVANCES 2024; 10:eadj3551. [PMID: 38427741 PMCID: PMC10906919 DOI: 10.1126/sciadv.adj3551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by its nutrient-scavenging ability, crucial for tumor progression. Here, we investigated the roles of caveolae-mediated endocytosis (CME) in PDAC progression. Analysis of patient data across diverse datasets revealed a strong association of high caveolin-1 (Cav-1) expression with higher histologic grade, the most aggressive PDAC molecular subtypes, and worse clinical outcomes. Cav-1 loss markedly promoted longer overall and tumor-free survival in a genetically engineered mouse model. Cav-1-deficient tumor cell lines exhibited significantly reduced proliferation, particularly under low nutrient conditions. Supplementing cells with albumin rescued the growth of Cav-1-proficient PDAC cells, but not in Cav-1-deficient PDAC cells under low glutamine conditions. In addition, Cav-1 depletion led to significant metabolic defects, including decreased glycolytic and mitochondrial metabolism, and downstream protein translation signaling pathways. These findings highlight the crucial role of Cav-1 and CME in fueling pancreatic tumorigenesis, sustaining tumor growth, and promoting survival through nutrient scavenging.
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Affiliation(s)
- Adam R. Wolfe
- Department of Radiation Oncology, The University of Arkansas for Medical Sciences, The Winthrop P. Rockefeller Cancer Institute, Little Rock, AR, USA
| | - Tiantian Cui
- Department of Radiation Oncology, City of Hope, Duarte, CA, USA
| | - Sooin Baie
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | | | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | | | - Duan-Liang Shyu
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | | | | | - Daniel J. Renouf
- Pancreas Centre BC, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - David F. Schaeffer
- Pancreas Centre BC, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Megan Halloran
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Rebecca Packard
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Ryan Robb
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wei Chen
- Department of Pathology, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Nicholas Denko
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Michael Lisanti
- Translational Medicine, University of Salford, Greater Manchester M5 4WT, UK
- Lunella Biotech, Inc., 145 Richmond Road, Ottawa, ON K1Z 1A1, Canada
| | - Timothy C. Thompson
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, USA
| | - Philippe Frank
- SGS France, Health & Nutrition, Saint-Benoît, France
- N2C, Nutrition Growth and Cancer, Faculté de Médecine, Université de Tours, Inserm, UMR, 1069 Tours, France
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27
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Baijal K, Abramchuk I, Herrera CM, Mah TF, Trent MS, Lavallée-Adam M, Downey M. Polyphosphate kinase regulates LPS structure and polymyxin resistance during starvation in E. coli. PLoS Biol 2024; 22:e3002558. [PMID: 38478588 PMCID: PMC10962826 DOI: 10.1371/journal.pbio.3002558] [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: 08/09/2023] [Revised: 03/25/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1,000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work, we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (Δppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and Δppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while Δppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of the required building blocks. From our data set, we were particularly interested in Arn and EptA proteins, which were down-regulated in Δppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins in K-12 strains and a uropathogenic isolate, and provide evidence that this mis-regulation in Δppk cells stems from a failure to induce the BasRS two-component system during starvation. We also show that Δppk mutants unable to up-regulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.
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Affiliation(s)
- Kanchi Baijal
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Iryna Abramchuk
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Carmen M. Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Thien-Fah Mah
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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28
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Izumiya Y, Algalil A, Espera JM, Miura H, Izumiya C, Inagaki T, Kumar A. Kaposi's sarcoma-associated herpesvirus terminal repeat regulates inducible lytic gene promoters. J Virol 2024; 98:e0138623. [PMID: 38240593 PMCID: PMC10878276 DOI: 10.1128/jvi.01386-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024] Open
Abstract
The Kaposi's sarcoma-associated herpesvirus (KSHV) genome consists of an approximately 140-kb unique coding region flanked by 30-40 copies of a 0.8-kb terminal repeat (TR) sequence. A gene enhancer recruits transcription-related enzymes by having arrays of transcription factor binding sites. Here, we show that KSHV TR possesses transcription regulatory function with latency-associated nuclear antigen (LANA). Cleavage under targets and release using nuclease demonstrated that TR fragments were occupied by LANA-interacting histone-modifying enzymes in naturally infected cells. The TR was enriched with histone H3K27 acetylation (H3K27Ac) and H3K4 tri-methylation (H3K4me3) modifications and also expressed nascent RNAs. The sites of H3K27Ac and H3K4me3 modifications were also conserved in the KSHV unique region among naturally infected primary effusion lymphoma cells. KSHV origin of lytic replication (Ori-Lyt) showed similar protein and histone modification occupancies with that of TR. In the Ori-Lyt region, the LANA and LANA-interacting proteins colocalized with an H3K27Ac-modified nucleosome along with paused RNA polymerase II. The KSHV transactivator KSHV replication and transcription activator (K-Rta) recruitment sites franked the LANA-bound nucleosome, and reactivation evicted the LANA-bound nucleosome. Including TR fragments in reporter plasmid enhanced inducible viral gene promoter activities independent of the orientations. In the presence of TR in reporter plasmids, K-Rta transactivation was drastically increased, while LANA acquired the promoter repression function. KSHV TR, therefore, functions as an enhancer for KSHV inducible genes. However, in contrast to cellular enhancers bound by multiple transcription factors, perhaps the KSHV enhancer is predominantly regulated by the LANA nuclear body.IMPORTANCEEnhancers are a crucial regulator of differential gene expression programs. Enhancers are the cis-regulatory sequences determining target genes' spatiotemporal and quantitative expression. Here, we show that Kaposi's sarcoma-associated herpesvirus (KSHV) terminal repeats fulfill the enhancer definition for KSHV inducible gene promoters. The KSHV enhancer is occupied by latency-associated nuclear antigen (LANA) and its interacting proteins, such as CHD4. Neighboring terminal repeat (TR) fragments to lytic gene promoters drastically enhanced KSHV replication and transcription activator and LANA transcription regulatory functions. This study, thus, proposes a new latency-lytic switch model in which TR accessibility to the KSHV gene promoters regulates viral inducible gene expression.
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Affiliation(s)
- Yoshihiro Izumiya
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Adhraa Algalil
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
- Midwestern University College of Dental Medicine, Glendale, Arizona, USA
| | - Jonna M. Espera
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Hiroki Miura
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Chie Izumiya
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Tomoki Inagaki
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Ashish Kumar
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
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29
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Deedwania A, Karmakar S, Kumar V, Shefrin S, Sundar D, Srivastava P. Construction and characterization of a temperature-sensitive pRC4 replicon for Rhodococcus and Gordonia. Gene 2024; 896:147990. [PMID: 37977321 DOI: 10.1016/j.gene.2023.147990] [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: 10/17/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Temperature-sensitive plasmids are useful for genome engineering and several synthetic biology applications. There are only limited reports on temperature-sensitive plasmids for Rhodococcus and none for Gordonia. Here, we report the construction of a temperature-sensitive pRC4 replicon that is functional in Rhodococcus and Gordonia. The amino acid residues were predicted for the temperature-sensitive phenotype in the pRC4 replicon using in silico methods and molecular simulation of the DNA-binding replication protein with the origin of replication. The amino acid residues were mutated, and the temperature-sensitive phenotype was validated in Gordonia sp. IITR100. Similar results were also observed in Rhodococcus erythropolis, suggesting that the temperature-sensitive phenotype was exhibited across genera.
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Affiliation(s)
- Agrima Deedwania
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Shreyoshi Karmakar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Vipul Kumar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Seyad Shefrin
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India.
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110 016, India.
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30
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Kaul M, Meher SK, Nallamotu KC, Reddy M. Glycan strand cleavage by a lytic transglycosylase, MltD contributes to the expansion of peptidoglycan in Escherichia coli. PLoS Genet 2024; 20:e1011161. [PMID: 38422114 DOI: 10.1371/journal.pgen.1011161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 03/12/2024] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Peptidoglycan (PG) is a protective sac-like exoskeleton present in most bacterial cell walls. It is a large, covalently crosslinked mesh-like polymer made up of many glycan strands cross-bridged to each other by short peptide chains. Because PG forms a continuous mesh around the bacterial cytoplasmic membrane, opening the mesh is critical to generate space for the incorporation of new material during its expansion. In Escherichia coli, the 'space-making activity' is known to be achieved by cleavage of crosslinks between the glycan strands by a set of redundant PG endopeptidases whose absence leads to rapid lysis and cell death. Here, we demonstrate a hitherto unknown role of glycan strand cleavage in cell wall expansion in E. coli. We find that overexpression of a membrane-bound lytic transglycosylase, MltD that cuts the glycan polymers of the PG sacculus rescues the cell lysis caused by the absence of essential crosslink-specific endopeptidases, MepS, MepM and MepH. We find that cellular MltD levels are stringently controlled by two independent regulatory pathways; at the step of post-translational stability by a periplasmic adaptor-protease complex, NlpI-Prc, and post-transcriptionally by RpoS, a stationary-phase specific sigma factor. Further detailed genetic and biochemical analysis implicated a role for MltD in cleaving the nascent uncrosslinked glycan strands generated during the expansion of PG. Overall, our results show that the combined activity of PG endopeptidases and lytic transglycosylases is necessary for successful expansion of the cell wall during growth of a bacterium.
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Affiliation(s)
- Moneca Kaul
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Suraj Kumar Meher
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Krishna Chaitanya Nallamotu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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31
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Seo H, Castro G, Trinh CT. Engineering a Synthetic Escherichia coli Coculture for Compartmentalized de novo Biosynthesis of Isobutyl Butyrate from Mixed Sugars. ACS Synth Biol 2024; 13:259-268. [PMID: 38091519 PMCID: PMC10804408 DOI: 10.1021/acssynbio.3c00493] [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: 08/11/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/23/2024]
Abstract
Short-chain esters are versatile chemicals that can be used as flavors, fragrances, solvents, and fuels. The de novo ester biosynthesis consists of diverging and converging pathway submodules, which is challenging to engineer to achieve optimal metabolic fluxes and selective product synthesis. Compartmentalizing the pathway submodules into specialist cells that facilitate pathway modularization and labor division is a promising solution. Here, we engineered a synthetic Escherichia coli coculture with the compartmentalized sugar utilization and ester biosynthesis pathways to produce isobutyl butyrate from a mixture of glucose and xylose. To compartmentalize the sugar-utilizing pathway submodules, we engineered a xylose-utilizing E. coli specialist that selectively consumes xylose over glucose and bypasses carbon catabolite repression (CCR) while leveraging the native CCR machinery to activate a glucose-utilizing E. coli specialist. We found that the compartmentalization of sugar catabolism enabled simultaneous co-utilization of glucose and xylose by a coculture of the two E. coli specialists, improving the stability of the coculture population. Next, we modularized the isobutyl butyrate pathway into the isobutanol, butyl-CoA, and ester condensation submodules, where we distributed the isobutanol submodule to the glucose-utilizing specialist and the other submodules to the xylose-utilizing specialist. Upon compartmentalization of the isobutyl butyrate pathway submodules into these sugar-utilizing specialist cells, a robust synthetic coculture was engineered to selectively produce isobutyl butyrate, reduce the biosynthesis of unwanted ester byproducts, and improve the production titer as compared to the monoculture.
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Affiliation(s)
- Hyeongmin Seo
- Department
of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Center
of Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Gillian Castro
- Department
of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Cong T. Trinh
- Department
of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Center
of Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
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32
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Noda S, Fujiwara R, Mori Y, Dainin M, Shirai T, Kondo A. Styrene Production in Genetically Engineered Escherichia coli in a Two-Phase Culture. BIOTECH 2024; 13:2. [PMID: 38247732 PMCID: PMC10801462 DOI: 10.3390/biotech13010002] [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: 11/13/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered Escherichia coli. First, we evaluated five types of phenylalanine ammonia lyases (PALs) from Arabidopsis thaliana (AtPAL) and Brachypodium distachyon (BdPAL) for their ability to produce trans-cinnamic acid (Cin), a styrene precursor. AtPAL2-expressing E. coli produced approximately 700 mg/L of Cin and we found that BdPALs could convert Cin into styrene. To assess styrene production, we constructed an E. coli strain that co-expressed AtPAL2 and ferulic acid decarboxylase from Saccharomyces cerevisiae. After a biphasic culture with oleyl alcohol, styrene production and yield from glucose were 3.1 g/L and 26.7% (mol/mol), respectively, which, to the best of our knowledge, are the highest values obtained in batch cultivation. Thus, this strain can be applied to the large-scale industrial production of styrene.
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Affiliation(s)
- Shuhei Noda
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi 332-0012, Saitama, Japan
| | - Ryosuke Fujiwara
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
| | - Yutaro Mori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
| | - Mayumi Dainin
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
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33
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Yan Z, Pan Y, Huang M, Liu JZ. De Novo Pterostilbene Production from Glucose Using Modular Coculture Engineering in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:516-528. [PMID: 38130104 DOI: 10.1021/acs.jafc.3c06629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Pterostilbene, a derivative of resveratrol, is of increasing interest due to its increased bioavailability and potential health benefits. Sustainable production of pterostilbene is important, especially given the challenges of traditional plant extraction and chemical synthesis methods. While engineered microbial cell factories provide a potential alternative for pterostilbene production, most approaches necessitate feeding intermediate compounds. To address these limitations, we adopted a modular coculture engineering strategy, dividing the pterostilbene biosynthetic pathway between two engineered E. coli strains. Using a combination of gene knockout, atmospheric and room-temperature plasma mutagenesis, and error-prone PCR-based whole genome shuffling to engineer strains for the coculture system, we achieved a pterostilbene production titer of 134.84 ± 9.28 mg/L from glucose using a 1:3 inoculation ratio and 0.1% dimethyl sulfoxide supplementation. This represents the highest reported de novo production titer. Our results underscore the potential of coculture systems and metabolic balance in microbial biosynthesis.
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Affiliation(s)
- Zhibo Yan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
| | - Yuyang Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
| | - Jian-Zhong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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34
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Kjellin J, Lee D, Steinsland H, Dwane R, Barth Vedoy O, Hanevik K, Koskiniemi S. Colicins and T6SS-based competition systems enhance enterotoxigenic E. coli (ETEC) competitiveness. Gut Microbes 2024; 16:2295891. [PMID: 38149626 PMCID: PMC10761095 DOI: 10.1080/19490976.2023.2295891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023] Open
Abstract
Diarrheal diseases are still a significant problem for humankind, causing approximately half a million deaths annually. To cause diarrhea, enteric bacterial pathogens must first colonize the gut, which is a niche occupied by the normal bacterial microbiota. Therefore, the ability of pathogenic bacteria to inhibit the growth of other bacteria can facilitate the colonization process. Although enterotoxigenic Escherichia coli (ETEC) is one of the major causative agents of diarrheal diseases, little is known about the competition systems found in and used by ETEC and how they contribute to the ability of ETEC to colonize a host. Here, we collected a set of 94 fully assembled ETEC genomes by performing whole-genome sequencing and mining the NCBI RefSeq database. Using this set, we performed a comprehensive search for delivered bacterial toxins and investigated how these toxins contribute to ETEC competitiveness in vitro. We found that type VI secretion systems (T6SS) were widespread among ETEC (n = 47). In addition, several closely related ETEC strains were found to encode Colicin Ia and T6SS (n = 8). These toxins provide ETEC competitive advantages during in vitro competition against other E. coli, suggesting that the role of T6SS as well as colicins in ETEC biology has until now been underappreciated.
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Affiliation(s)
- Jonas Kjellin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Danna Lee
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Hans Steinsland
- CISMAC, Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Rachel Dwane
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Oda Barth Vedoy
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- National centre for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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35
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Choi SY, Romero-Calle DX, Cho HG, Bae HW, Cho YH. Use of Cas9 Targeting and Red Recombination for Designer Phage Engineering. J Microbiol 2024; 62:1-10. [PMID: 38300409 DOI: 10.1007/s12275-024-00107-2] [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: 11/21/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 02/02/2024]
Abstract
Bacteriophages (phages) are natural antibiotics and biological nanoparticles, whose application is significantly boosted by recent advances of synthetic biology tools. Designer phages are synthetic phages created by genome engineering in a way to increase the benefits or decrease the drawbacks of natural phages. Here we report the development of a straightforward genome engineering method to efficiently obtain engineered phages in a model bacterial pathogen, Pseudomonas aeruginosa. This was achieved by eliminating the wild type phages based on the Streptococcus pyogenes Cas9 (SpCas9) and facilitating the recombinant generation based on the Red recombination system of the coliphage λ (λRed). The producer (PD) cells of P. aeruginosa strain PAO1 was created by miniTn7-based chromosomal integration of the genes for SpCas9 and λRed under an inducible promoter. To validate the efficiency of the recombinant generation, we created the fluorescent phages from a temperate phage MP29. A plasmid bearing the single guide RNA (sgRNA) gene for selectively targeting the wild type gp35 gene and the editing template for tagging the Gp35 with superfolder green fluorescent protein (sfGFP) was introduced into the PD cells by electroporation. We found that the targeting efficiency was affected by the position and number of sgRNA. The fluorescent phage particles were efficiently recovered from the culture of the PD cells expressing dual sgRNA molecules. This protocol can be used to create designer phages in P. aeruginosa for both application and research purposes.
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Affiliation(s)
- Shin-Yae Choi
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi, 13488, Republic of Korea
| | - Danitza Xiomara Romero-Calle
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi, 13488, Republic of Korea
| | - Han-Gyu Cho
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi, 13488, Republic of Korea
| | - Hee-Won Bae
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi, 13488, Republic of Korea
| | - You-Hee Cho
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi, 13488, Republic of Korea.
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36
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Cronan JE. Two neglected but valuable genetic tools for Escherichia coli and other bacteria: In vivo cosmid packaging and inducible plasmid replication. Mol Microbiol 2023; 120:783-790. [PMID: 37770255 DOI: 10.1111/mmi.15171] [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: 07/17/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/30/2023]
Abstract
In physiology and synthetic biology, it can be advantageous to introduce a gene into a naive bacterial host under conditions in which all cells receive the gene and remain fully functional. This cannot be done by the usual chemical transformation and electroporation methods due to low efficiency and cell death, respectively. However, in vivo packaging of plasmids (called cosmids) that contain the 223 bp cos site of phage λ results in phage particles that contain concatemers of the cosmid that can be transduced into all cells of a culture. An historical shortcoming of in vivo packaging of cosmids was inefficient packaging and contamination of the particles containing cosmid DNA with a great excess of infectious λ phage. Manipulation of the packaging phage and the host has eliminated these shortcomings resulting in particles that contain only cosmid DNA. Plasmids have the drawback that they can be difficult to remove from cells. Plasmids with conditional replication provide a means to "cure" plasmids from cells. The prevalent conditional replication plasmids are temperature-sensitive plasmids, which are cured at high growth temperature. However, inducible replication plasmids are in some cases more useful, especially since this approach has been applied to plasmids having diverse replication and compatibility properties.
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Affiliation(s)
- John E Cronan
- Departments of Microbiology and Biochemistry, University of Illinois, Urbana, Illinois, USA
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37
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Wiegand T, Hoffmann FT, Walker MWG, Tang S, Richard E, Le HC, Meers C, Sternberg SH. Emergence of RNA-guided transcription factors via domestication of transposon-encoded TnpB nucleases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569447. [PMID: 38076855 PMCID: PMC10705468 DOI: 10.1101/2023.11.30.569447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Transposon-encoded tnpB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination1-4. This widespread gene family was repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas125,6. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas. Here, using phylogenetics, structural predictions, comparative genomics, and functional assays, we uncover multiple instances of programmable transcription factors that we name TnpB-like nuclease-dead repressors (TldR). These proteins employ naturally occurring guide RNAs to specifically target conserved promoter regions of the genome, leading to potent gene repression in a mechanism akin to CRISPRi technologies invented by humans7. Focusing on a TldR clade found broadly in Enterobacteriaceae, we discover that bacteriophages exploit the combined action of TldR and an adjacently encoded phage gene to alter the expression and composition of the host flagellar assembly, a transformation with the potential to impact motility8, phage susceptibility9, and host immunity10. Collectively, this work showcases the diverse molecular innovations that were enabled through repeated exaptation of genes encoded by transposable elements, and reveals that RNA-guided transcription factors emerged long before the development of dCas9-based editors.
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Affiliation(s)
- Tanner Wiegand
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Florian T Hoffmann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Matt W G Walker
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Egill Richard
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Hoang C Le
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Chance Meers
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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38
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Islam T, Josephs EA. Genome Editing Outcomes Reveal Mycobacterial NucS Participates in a Short-Patch Repair of DNA Mismatches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563644. [PMID: 37961639 PMCID: PMC10634747 DOI: 10.1101/2023.10.23.563644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In the canonical DNA mismatch repair (MMR) mechanism in bacteria, if during replication a nucleotide is incorrectly mis-paired with the template strand, the resulting repair of this mis-pair can result in the degradation and re-synthesis of hundreds or thousands of nucleotides on the newly-replicated strand (long-patch repair). While mycobacteria, which include important pathogens such as Mycobacterium tuberculosis, lack the otherwise highly-conserved enzymes required for the canonical MMR reaction, it was found that disruption of a mycobacterial mismatch-sensitive endonuclease NucS results in a hyper-mutative phenotype, which has led to the idea that NucS might be involved in a cryptic, independently-evolved DNA MMR mechanism. It has been proposed that nuclease activity at a mismatch might result in correction by homologous recombination (HR) with a sister chromatid. Using oligonucleotide recombination, which allows us to introduce mismatches during replication specifically into the genomes of a model for M. tuberculosis, Mycobacterium smegmatis, we find that NucS participates in a direct repair of DNA mismatches where the patch of excised nucleotides is largely confined to within ~5 - 6 bp of the mis-paired nucleotides, which is inconsistent with mechanistic models of canonical mycobacterial HR or other double-strand break (DSB) repair reactions. The results presented provide evidence of a novel NucS-associated mycobacterial MMR mechanism occurring in vivo to regulate genetic mutations in mycobacteria.
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Affiliation(s)
- Tanjina Islam
- Department of Nanoscience, University of North Carolina at Greensboro, Greensboro, NC, 27401, USA
| | - Eric A. Josephs
- Department of Nanoscience, University of North Carolina at Greensboro, Greensboro, NC, 27401, USA
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27401, USA
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39
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Rudolph A, Nyerges A, Chiappino-Pepe A, Landon M, Baas-Thomas M, Church G. Strategies to identify and edit improvements in synthetic genome segments episomally. Nucleic Acids Res 2023; 51:10094-10106. [PMID: 37615546 PMCID: PMC10570025 DOI: 10.1093/nar/gkad692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/30/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Genome engineering projects often utilize bacterial artificial chromosomes (BACs) to carry multi-kilobase DNA segments at low copy number. However, all stages of whole-genome engineering have the potential to impose mutations on the synthetic genome that can reduce or eliminate the fitness of the final strain. Here, we describe improvements to a multiplex automated genome engineering (MAGE) protocol to improve recombineering frequency and multiplexability. This protocol was applied to recoding an Escherichia coli strain to replace seven codons with synonymous alternatives genome wide. Ten 44 402-47 179 bp de novo synthesized DNA segments contained in a BAC from the recoded strain were unable to complement deletion of the corresponding 33-61 wild-type genes using a single antibiotic resistance marker. Next-generation sequencing (NGS) was used to identify 1-7 non-recoding mutations in essential genes per segment, and MAGE in turn proved a useful strategy to repair these mutations on the recoded segment contained in the BAC when both the recoded and wild-type copies of the mutated genes had to exist by necessity during the repair process. Finally, two web-based tools were used to predict the impact of a subset of non-recoding missense mutations on strain fitness using protein structure and function calls.
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Affiliation(s)
- Alexandra Rudolph
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anush Chiappino-Pepe
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| | - Matthieu Landon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
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40
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Trasanidou D, Potocnik A, Barendse P, Mohanraju P, Bouzetos E, Karpouzis E, Desmet A, van Kranenburg R, van der Oost J, Staals RHJ, Mougiakos I. Characterization of the AcrIIC1 anti‒CRISPR protein for Cas9‒based genome engineering in E. coli. Commun Biol 2023; 6:1042. [PMID: 37833505 PMCID: PMC10576004 DOI: 10.1038/s42003-023-05418-5] [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: 05/25/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Anti-CRISPR proteins (Acrs) block the activity of CRISPR-associated (Cas) proteins, either by inhibiting DNA interference or by preventing crRNA loading and complex formation. Although the main use of Acrs in genome engineering applications is to lower the cleavage activity of Cas proteins, they can also be instrumental for various other CRISPR-based applications. Here, we explore the genome editing potential of the thermoactive type II-C Cas9 variants from Geobacillus thermodenitrificans T12 (ThermoCas9) and Geobacillus stearothermophilus (GeoCas9) in Escherichia coli. We then demonstrate that the AcrIIC1 protein from Neisseria meningitidis robustly inhibits their DNA cleavage activity, but not their DNA binding capacity. Finally, we exploit these AcrIIC1:Cas9 complexes for gene silencing and base-editing, developing Acr base-editing tools. With these tools we pave the way for future engineering applications in mesophilic and thermophilic bacteria combining the activities of Acr and CRISPR-Cas proteins.
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Affiliation(s)
- Despoina Trasanidou
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Ana Potocnik
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Patrick Barendse
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Evgenios Bouzetos
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Efthymios Karpouzis
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Amber Desmet
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Corbion, Gorinchem, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Ioannis Mougiakos
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
- SNIPR Biome, Copenhagen, Denmark.
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41
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Choudhury A, Gachet B, Dixit Z, Faure R, Gill RT, Tenaillon O. Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs. Nat Commun 2023; 14:6319. [PMID: 37813857 PMCID: PMC10562459 DOI: 10.1038/s41467-023-41882-7] [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: 02/23/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023] Open
Abstract
RNA polymerase (RNAP) is emblematic of complex biological systems that control multiple traits involving trade-offs such as growth versus maintenance. Laboratory evolution has revealed that mutations in RNAP subunits, including RpoB, are frequently selected. However, we lack a systems view of how mutations alter the RNAP molecular functions to promote adaptation. We, therefore, measured the fitness of thousands of mutations within a region of rpoB under multiple conditions and genetic backgrounds, to find that adaptive mutations cluster in two modules. Mutations in one module favor growth over maintenance through a partial loss of an interaction associated with faster elongation. Mutations in the other favor maintenance over growth through a destabilized RNAP-DNA complex. The two molecular handles capture the versatile RNAP-mediated adaptations. Combining both interaction losses simultaneously improved maintenance and growth, challenging the idea that growth-maintenance tradeoff resorts only from limited resources, and revealing how compensatory evolution operates within RNAP.
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Affiliation(s)
- Alaksh Choudhury
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France.
- Laboratoire Biophysique et Évolution (LBE), UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, CNRS, 75005, Paris, France.
| | - Benoit Gachet
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
| | - Zoya Dixit
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
- Université de Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, 75014, Paris, France
| | - Roland Faure
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
- Université de Rennes, INRIA RBA, CNRS UMR 6074, Rennes, France
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado-Boulder, Boulder, CO, 80309-0027, USA
- Novo Nordisk Foundation, Denmark Technical University, 2800 Kgs, Lyngby, Denmark
| | - Olivier Tenaillon
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France.
- Université de Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, 75014, Paris, France.
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Lariviere PJ, Ashraf AHMZ, Leonard SP, Miller LG, Moran NA, Barrick JE. Single-step genome engineering in the bee gut symbiont Snodgrassella alvi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558440. [PMID: 37786689 PMCID: PMC10541602 DOI: 10.1101/2023.09.19.558440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Honey bees are economically relevant pollinators experiencing population declines due to a number of threats. As in humans, the health of bees is influenced by their microbiome. The bacterium Snodgrassella alvi is a key member of the bee gut microbiome and has a role in excluding pathogens. Despite this importance, there are not currently any easy-to-use methods for modifying the S. alvi chromosome to study its genetics. To solve this problem, we developed a one-step procedure that uses electroporation and homologous recombination, which we term SnODIFY (Snodgrassella-specific One-step gene Deletion or Insertion to alter FunctionalitY). We used SnODIFY to create seven single-gene knockout mutants and recovered mutants for all constructs tested. Nearly all transformants had the designed genome modifications, indicating that SnODIFY is highly accurate. Mutant phenotypes were validated through knockout of Type 4 pilus genes, which led to reduced biofilm formation. We also used SnODIFY to insert heterologous sequences into the genome by integrating fluorescent protein-coding genes. Finally, we confirmed that genome modification is dependent on S. alvi's endogenous RecA protein. Because it does not require expression of exogenous recombination machinery, SnODIFY is a straightforward, accurate, and lightweight method for genome editing in S. alvi. This workflow can be used to study the functions of S. alvi genes and to engineer this symbiont for applications including protection of honey bee health.
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Affiliation(s)
- Patrick J. Lariviere
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - A. H. M. Zuberi Ashraf
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sean P. Leonard
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Laurel G. Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nancy A. Moran
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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Zheng W, Xia Y, Wang X, Gao S, Zhou D, Ravichandran V, Jiang C, Tu Q, Yin Y, Zhang Y, Fu J, Li R, Yin J. Precise genome engineering in Pseudomonas using phage-encoded homologous recombination and the Cascade-Cas3 system. Nat Protoc 2023; 18:2642-2670. [PMID: 37626246 DOI: 10.1038/s41596-023-00856-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/11/2023] [Indexed: 08/27/2023]
Abstract
A lack of generic and effective genetic manipulation methods for Pseudomonas has restricted fundamental research and utilization of this genus for biotechnology applications. Phage-encoded homologous recombination (PEHR) is an efficient tool for bacterial genome engineering. This PEHR system is based on a lambda Red-like operon (BAS) from Pseudomonas aeruginosa phage Ab31 and a Rac bacteriophage RecET-like operon (Rec-TEPsy) from P. syringae pv. syringae B728a and also contains exogenous elements, including the RecBCD inhibitor (Redγ or Pluγ) or single-stranded DNA-binding protein (SSB), that were added to enhance the PEHR recombineering efficiency. To solve the problem of false positives in Pseudomonas editing with the PEHR system, the processive enzyme Cas3 with a minimal Type I-C Cascade-based system was combined with PEHR. This protocol describes the utilization of a Pseudomonas-specific PEHR-Cas3 system that was designed to universally and proficiently modify the genomes of Pseudomonas species. The pipeline uses standardized cassettes combined with the concerted use of SacB counterselection and Cre site-specific recombinase for markerless or seamless genome modification, in association with vectors that possess the selectively replicating template R6K to minimize recombineering background. Compared with the traditional allelic exchange editing method, the PEHR-Cas3 system does not need to construct suicide plasmids carrying long homologous arms, thus simplifying the experimental procedure and shortening the traceless editing period. Compared with general editing systems based on phage recombinases, the PEHR-Cas3 system can effectively improve the screening efficiency of mutants using the cutting ability of Cas3 protein. The entire procedure requires ~12 days.
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Affiliation(s)
- Wentao Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yandong Xia
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
- College of Life Science and Technology, Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-wood Forest Cultivation and Conservation of Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Xue Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shiqing Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Diao Zhou
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | | | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qiang Tu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yulong Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Ruijuan Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Jia Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China.
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Hall AN, Hall BW, Kinney KJ, Olsen GG, Banta AB, Noguera DR, Donohue TJ, Peters JM. Tools for Genetic Engineering and Gene Expression Control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554875. [PMID: 37662258 PMCID: PMC10473679 DOI: 10.1101/2023.08.25.554875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts have the potential to form the backbone of the sustainable bioeconomy. Among the Alphaproteobacteria, Novosphingobium aromaticivorans, Rhodobacter sphaeroides, and Zymomonas mobilis, show particular promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit for Z. mobilis, N. aromaticivorans and R. sphaeroides still need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools for N. aromaticivorans and R. sphaeroides to address these issues. We demonstrate that Tn7 transposition is an effective approach for introducing engineered DNA into the chromosome of N. aromaticivorans and R. sphaeroides. We screen a synthetic promoter library to identify inducible promoters with strong, regulated activity in both organisms. Combining Tn7 integration with promoters from our library, we establish CRISPR interference systems for N. aromaticivorans and R. sphaeroides that can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these industrially important species and other Alphaproteobacteria.
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Affiliation(s)
- Ashley N. Hall
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin W. Hall
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kyle J. Kinney
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gabby G. Olsen
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amy B. Banta
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Timothy J. Donohue
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Peters
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Lv S, Wang Y, Jiang K, Guo X, Zhang J, Zhou F, Li Q, Jiang Y, Yang C, Teng T. Genetic Engineering and Biosynthesis Technology: Keys to Unlocking the Chains of Phage Therapy. Viruses 2023; 15:1736. [PMID: 37632078 PMCID: PMC10457950 DOI: 10.3390/v15081736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Phages possess the ability to selectively eliminate pathogenic bacteria by recognizing bacterial surface receptors. Since their discovery, phages have been recognized for their potent bactericidal properties, making them a promising alternative to antibiotics in the context of rising antibiotic resistance. However, the rapid emergence of phage-resistant strains (generally involving temperature phage) and the limited host range of most phage strains have hindered their antibacterial efficacy, impeding their full potential. In recent years, advancements in genetic engineering and biosynthesis technology have facilitated the precise engineering of phages, thereby unleashing their potential as a novel source of antibacterial agents. In this review, we present a comprehensive overview of the diverse strategies employed for phage genetic engineering, as well as discuss their benefits and drawbacks in terms of bactericidal effect.
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Affiliation(s)
- Sixuan Lv
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Yuhan Wang
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Kaixin Jiang
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Xinge Guo
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Jing Zhang
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Fang Zhou
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Qiming Li
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Yuan Jiang
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Changyong Yang
- School of Nursing and Health, Henan University, Kaifeng 475004, China
| | - Tieshan Teng
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
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Lin Y, Shi J, Feng W, Yue J, Luo Y, Chen S, Yang B, Jiang Y, Hu H, Zhou C, Shi F, Prominski A, Talapin DV, Xiong W, Gao X, Tian B. Periplasmic biomineralization for semi-artificial photosynthesis. SCIENCE ADVANCES 2023; 9:eadg5858. [PMID: 37478187 PMCID: PMC10361601 DOI: 10.1126/sciadv.adg5858] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
Semiconductor-based biointerfaces are typically established either on the surface of the plasma membrane or within the cytoplasm. In Gram-negative bacteria, the periplasmic space, characterized by its confinement and the presence of numerous enzymes and peptidoglycans, offers additional opportunities for biomineralization, allowing for nongenetic modulation interfaces. We demonstrate semiconductor nanocluster precipitation containing single- and multiple-metal elements within the periplasm, as observed through various electron- and x-ray-based imaging techniques. The periplasmic semiconductors are metastable and display defect-dominant fluorescent properties. Unexpectedly, the defect-rich (i.e., the low-grade) semiconductor nanoclusters produced in situ can still increase adenosine triphosphate levels and malate production when coupled with photosensitization. We expand the sustainability levels of the biohybrid system to include reducing heavy metals at the primary level, building living bioreactors at the secondary level, and creating semi-artificial photosynthesis at the tertiary level. The biomineralization-enabled periplasmic biohybrids have the potential to serve as defect-tolerant platforms for diverse sustainable applications.
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Affiliation(s)
- Yiliang Lin
- The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Jiuyun Shi
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Wei Feng
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, and Shenzhen Institute of Advanced Technology, Chinese Academy of Science, Shenzhen 518000, China
| | - Jiping Yue
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Yanqi Luo
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Bin Yang
- Bioscience Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Yuanwen Jiang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Huicheng Hu
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Chenkun Zhou
- The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Fengyuan Shi
- Electron Microscopy Core, University of Illinois Chicago, Chicago, IL 60607, USA
| | | | - Dmitri V. Talapin
- The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Wei Xiong
- Bioscience Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Xiang Gao
- The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, and Shenzhen Institute of Advanced Technology, Chinese Academy of Science, Shenzhen 518000, China
| | - Bozhi Tian
- The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
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Satoh Y, Fukui K, Koma D, Shen N, Lee TS. Engineered Escherichia coli platforms for tyrosine-derivative production from phenylalanine using phenylalanine hydroxylase and tetrahydrobiopterin-regeneration system. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:115. [PMID: 37464414 DOI: 10.1186/s13068-023-02365-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/02/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Aromatic compounds derived from tyrosine are important and diverse chemicals that have industrial and commercial applications. Although these aromatic compounds can be obtained by extraction from natural producers, their growth is slow, and their content is low. To overcome these problems, many of them have been chemically synthesized from petroleum-based feedstocks. However, because of the environmental burden and depleting availability of feedstock, microbial cell factories are attracting much attention as sustainable and environmentally friendly processes. RESULTS To facilitate development of microbial cell factories for producing tyrosine derivatives, we developed simple and convenient tyrosine-producing Escherichia coli platforms with a bacterial phenylalanine hydroxylase, which converted phenylalanine to tyrosine with tetrahydromonapterin as a cofactor, using a synthetic biology approach. By introducing a tetrahydrobiopterin-regeneration system, the tyrosine titer of the plasmid-based engineered strain was 4.63 g/L in a medium supplemented with 5.00 g/L phenylalanine with a test tube. The strains were successfully used to produce industrially attractive compounds, such as tyrosol with a yield of 1.58 g/L by installing a tyrosol-producing module consisting of genes encoding tyrosine decarboxylase and tyramine oxidase on a plasmid. Gene integration into E. coli chromosomes has an advantage over the use of plasmids because it increases genetic stability without antibiotic feeding to the culture media and enables more flexible pathway engineering by accepting more plasmids with artificial pathway genes. Therefore, we constructed a plasmid-free tyrosine-producing platform by integrating five modules, comprising genes encoding the phenylalanine hydroxylase and tetrahydrobiopterin-regeneration system, into the chromosome. The platform strain could produce 1.04 g/L of 3,4-dihydroxyphenylalanine, a drug medicine, by installing a gene encoding tyrosine hydroxylase and the tetrahydrobiopterin-regeneration system on a plasmid. Moreover, by installing the tyrosol-producing module, tyrosol was produced with a yield of 1.28 g/L. CONCLUSIONS We developed novel E. coli platforms for producing tyrosine from phenylalanine at multi-gram-per-liter levels in test-tube cultivation. The platforms allowed development and evaluation of microbial cell factories installing various designed tyrosine-derivative biosynthetic pathways at multi-grams-per-liter levels in test tubes.
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Affiliation(s)
- Yasuharu Satoh
- Faculty of Engineering, Hokkaido University, Sapporo, 060-8628, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan.
| | - Keita Fukui
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kanagawa, 210-8681, Japan
| | - Daisuke Koma
- Osaka Research Institute of Industrial Science and Technology, Osaka, 536-8553, Japan
| | - Ning Shen
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Taek Soon Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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Baijal K, Abramchuk I, Herrera CM, Stephen Trent M, Lavallée-Adam M, Downey M. Proteomics analysis reveals a role for E. coli polyphosphate kinase in membrane structure and polymyxin resistance during starvation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.546892. [PMID: 37461725 PMCID: PMC10350021 DOI: 10.1101/2023.07.06.546892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (∆ppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and ∆ppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while Δppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of required building blocks. From our dataset, we were particularly interested in Arn and EptA proteins, which were downregulated in ∆ppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins, and provide evidence that this mis-regulation in ∆ppk cells stems from a failure to induce the BasS/BasR two-component system during starvation. We also show that ∆ppk mutants unable to upregulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.
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Affiliation(s)
- Kanchi Baijal
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Iryna Abramchuk
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Carmen M. Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Su H, Lin J. Biosynthesis pathways of expanding carbon chains for producing advanced biofuels. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:109. [PMID: 37400889 DOI: 10.1186/s13068-023-02340-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/11/2023] [Indexed: 07/05/2023]
Abstract
Because the thermodynamic property is closer to gasoline, advanced biofuels (C ≥ 6) are appealing for replacing non-renewable fossil fuels using biosynthesis method that has presented a promising approach. Synthesizing advanced biofuels (C ≥ 6), in general, requires the expansion of carbon chains from three carbon atoms to more than six carbon atoms. Despite some specific biosynthesis pathways that have been developed in recent years, adequate summary is still lacking on how to obtain an effective metabolic pathway. Review of biosynthesis pathways for expanding carbon chains will be conducive to selecting, optimizing and discovering novel synthetic route to obtain new advanced biofuels. Herein, we first highlighted challenges on expanding carbon chains, followed by presentation of two biosynthesis strategies and review of three different types of biosynthesis pathways of carbon chain expansion for synthesizing advanced biofuels. Finally, we provided an outlook for the introduction of gene-editing technology in the development of new biosynthesis pathways of carbon chain expansion.
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Affiliation(s)
- Haifeng Su
- Key Laboratory of Degraded and Unused Land Consolidation Engineering, The Ministry of Natural and Resources, Xian, 710075, Shanxi, China
| | - JiaFu Lin
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
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Xiong X, Lu Z, Ma L, Zhai C. Applications of Programmable Endonucleases in Sequence- and Ligation-Independent Seamless DNA Assembly. Biomolecules 2023; 13:1022. [PMID: 37509059 PMCID: PMC10377497 DOI: 10.3390/biom13071022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Programmable endonucleases, such as Cas (Clustered Regularly-Interspaced Short Repeats-associated proteins) and prokaryotic Argonaute (pAgo), depend on base pairing of the target DNA with the guide RNA or DNA to cleave DNA strands. Therefore, they are capable of recognizing and cleaving DNA sequences at virtually any arbitrary site. The present review focuses on the commonly used in vivo and in vitro recombination-based gene cloning methods and the application of programmable endonucleases in these sequence- and ligation-independent DNA assembly methods. The advantages and shortcomings of the programmable endonucleases utilized as tools for gene cloning are also discussed in this review.
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Affiliation(s)
- Xingchen Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhiwen Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
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