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Wang Y, Liu F, Lu X, Zong H, Zhuge B. Regulatory mechanisms and cell membrane properties of Candida glycerinogenes differ under 2-phenylethanol addition or fermentation conditions. Biotechnol J 2024; 19:e2300181. [PMID: 37840403 DOI: 10.1002/biot.202300181] [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: 04/25/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
The biosynthesis of 2-phenylethanol (2-PE) at high yields and titers is often limited by its toxicity. In this study, we describe the molecular mechanisms of 2-PE tolerance in the multi-stress tolerant industrial yeast, Candida glycerinogenes. They were different under 2-PE addition or fermentation conditions. After extracellular addition of 2-PE, C. glycerinogenes cells became rounder and bigger, which reduced specific surface area. However, during 2-PE fermentation C. glycerinogenes cells were smaller, which increased specific surface area. Other differences in the tolerance mechanisms were studied by analyzing the composition and molecular parameters of the cell membrane. Extracellular 2-PE stress resulted in down-regulation of transcriptional expression of unsaturated fatty acid synthesis genes. This raised the proportion of saturated fatty acids in the cell membrane, which increased rigidity of the cell membrane and reduced 2-PE entry to the cell. However, intracellular 2-PE stress resulted in up-regulation of transcriptional expression of unsaturated fatty acid synthesis genes, and increased the proportion of unsaturated fatty acids in the cell membrane; this in turn enhanced flexibility of the cell membrane which accelerated efflux of 2-PE. These contrasting mechanisms are mediated by transcriptional factors Hog1 and Swi5. Under 2-PE addition, C. glycerinogenes activated Hog1 and repressed Swi5 to upregulate erg5 and erg4 expression, which increased cell membrane rigidity and resisted 2-PE import. During 2-PE fermentation, C. glycerinogenes activated Hog1 and repressed Swi5 to upregulate 2-PE transporter proteins cdr1 and Acyl-CoA desaturase 1 ole1 to increase 2-PE export, thus reducing 2-PE intracellular toxicity. The results provide new insights into 2-PE tolerance mechanisms at the cell membrane level and suggest a novel strategy to improve 2-PE production by engineering anti-stress genes.
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Affiliation(s)
- Yuqin Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Fang Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xinyao Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hong Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
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2
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Zhao X, Xu C, Qu J, Jin Y, Bai F, Cheng Z, Wu W, Pan X. PitA Controls the H2- and H3-T6SSs through PhoB in Pseudomonas aeruginosa. Appl Environ Microbiol 2023; 89:e0209422. [PMID: 37184394 PMCID: PMC10304775 DOI: 10.1128/aem.02094-22] [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: 12/10/2022] [Accepted: 04/21/2023] [Indexed: 05/16/2023] Open
Abstract
Pseudomonas aeruginosa possesses three type VI secretion systems (T6SSs) that are involved in interspecies competition, internalization into epithelial cells, and virulence. Host-derived mucin glycans regulate the T6SSs through RetS, and attacks from other species activate the H1-T6SS. However, other environmental signals that control the T6SSs remain to be explored. Previously, we determined PitA to be a constitutive phosphate transporter, whose mutation reduces the intracellular phosphate concentration. Here, we demonstrate that mutation in the pitA gene increases the expression of the H2- and H3-T6SS genes and enhances bacterial uptake by A549 cells. We further found that mutation of pitA results in activation of the quorum sensing (QS) systems, which contributes to the upregulation of the H2- and H3-T6SS genes. Overexpression of the phosphate transporter complex genes pstSCAB or knockdown of the phosphate starvation response regulator gene phoB in the ΔpitA mutant reduces the expression of the QS genes and subsequently the H2- and H3-T6SS genes and bacterial internalization. Furthermore, growth of wild-type PA14 in a low-phosphate medium results in upregulation of the QS and H2- and H3-T6SS genes and bacterial internalization compared to those in cells grown in a high-phosphate medium. Deletion of the phoB gene abolished the differences in the expression of the QS and T6SS genes as well as bacterial internalization in the low- and high- phosphate media. Overall, our results elucidate the mechanism of PitA-mediated regulation on the QS system and H2- and H3-T6SSs and reveal a novel pathway that regulates the T6SSs in response to phosphate starvation. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogenic bacterium that causes acute and chronic infections in humans. The type VI secretion systems (T6SSs) have been shown to associate with chronic infections. Understanding the mechanism used by the bacteria to sense environmental signals and regulate virulence factors will provide clues for developing novel effective treatment strategies. Here, we demonstrate a relationship between a phosphate transporter and the T6SSs and reveal a novel regulatory pathway that senses phosphate limitation and controls bacterial virulence factors in P. aeruginosa.
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Affiliation(s)
- Xinrui Zhao
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Congjuan Xu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Junze Qu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
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3
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Tanniche I, Nazem-Bokaee H, Scherr DM, Schlemmer S, Senger RS. A novel synthetic sRNA promoting protein overexpression in cell-free systems. Biotechnol Prog 2023; 39:e3324. [PMID: 36651906 DOI: 10.1002/btpr.3324] [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: 06/02/2022] [Revised: 10/31/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Bacterial small RNAs (sRNAs) that regulate gene expression have been engineered for uses in synthetic biology and metabolic engineering. Here, we designed a novel non-Hfq-dependent sRNA scaffold that uses a modifiable 20 nucleotide antisense binding region to target mRNAs selectively and influence protein expression. The system was developed for regulation of a fluorescent reporter in vivo using Escherichia coli, but the system was found to be more responsive and produced statistically significant results when applied to protein synthesis using in vitro cell-free systems (CFS). Antisense binding sequences were designed to target not only translation initiation regions but various secondary structures in the reporter mRNA. Targeting a high-energy stem loop structure and the 3' end of mRNA yielded protein expression knock-downs that approached 70%. Notably, targeting a low-energy stem structure near a potential RNase E binding site led to a statistically significant 65% increase in protein expression (p < 0.05). These results were not obtainable in vivo, and the underlying mechanism was translated from the reporter system to achieve better than 75% increase in recombinant diaphorase expression in a CFS. It is possible the designs developed here can be applied to improve/regulate expression of other proteins in a CFS.
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Affiliation(s)
- Imen Tanniche
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
- School of Plant & Environmental Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Hadi Nazem-Bokaee
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
- CSIRO, Black Mountain Science & Innovation Park, Canberra, Australia
| | - David M Scherr
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Sara Schlemmer
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Ryan S Senger
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia, USA
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia, USA
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4
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Kitagawa W, Hata M. Development of Efficient Genome-Reduction Tool Based on Cre/ loxP System in Rhodococcus erythropolis. Microorganisms 2023; 11:microorganisms11020268. [PMID: 36838232 PMCID: PMC9959502 DOI: 10.3390/microorganisms11020268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Rhodococcus has been extensively studied for its excellent ability to degrade artificial chemicals and its capability to synthesize biosurfactants and antibiotics. In recent years, studies have attempted to use Rhodococcus as a gene expression host. Various genetic tools, such as plasmid vectors, transposon mutagenesis, and gene disruption methods have been developed for use in Rhodococcus; however, no effective method has been reported for performing large-size genome reduction. Therefore, the present study developed an effective plasmid-curing method using the levansucrase-encoding sacB gene and a simple two-step genome-reduction method using a modified Cre/loxP system. For the results, R. erythropolis JCM 2895 was used as the model; a mutant strain that cured all four plasmids and deleted seven chromosomal regions was successfully obtained in this study. The total DNA deletion size was >600 kb, which corresponds mostly to 10% of the genome size. Using this method, a genome-structure-stabilized and unfavorable gene/function-lacking host strain can be created in Rhodococcus. This genetic tool will help develop and improve Rhodococcus strains for various industrial and environmental applications.
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Affiliation(s)
- Wataru Kitagawa
- Bioproduction Research Institute, National Institute of Advanced Industrial and Technology (AIST), Sapporo 062-8517, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
- Correspondence:
| | - Miyako Hata
- Bioproduction Research Institute, National Institute of Advanced Industrial and Technology (AIST), Sapporo 062-8517, Japan
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5
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Hogan AM, Cardona ST. Gradients in gene essentiality reshape antibacterial research. FEMS Microbiol Rev 2022; 46:fuac005. [PMID: 35104846 PMCID: PMC9075587 DOI: 10.1093/femsre/fuac005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 02/03/2023] Open
Abstract
Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.
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Affiliation(s)
- Andrew M Hogan
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Silvia T Cardona
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
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6
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Yamamoto K, Yamamoto N, Ayukawa S, Yasutake Y, Ishiya K, Nakashima N. Scaffold size-dependent effect on the enhanced uptake of antibiotics and other compounds by Escherichia coli and Pseudomonas aeruginosa. Sci Rep 2022; 12:5609. [PMID: 35379875 PMCID: PMC8980104 DOI: 10.1038/s41598-022-09635-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/24/2022] [Indexed: 11/29/2022] Open
Abstract
The outer membrane of Gram-negative bacteria functions as an impermeable barrier to foreign compounds. Thus, modulating membrane transport can contribute to improving susceptibility to antibiotics and efficiency of bioproduction reactions. In this study, the cellular uptake of hydrophobic and large-scaffold antibiotics and other compounds in Gram-negative bacteria was investigated by modulating the homolog expression of bamB encoding an outer membrane lipoprotein and tolC encoding an outer membrane efflux protein via gene deletion and gene silencing. The potential of deletion mutants for biotechnological applications, such as drug screening and bioproduction, was also demonstrated. Instead of being subjected to gene deletion, wild-type bacterial cells were treated with cell-penetrating peptide conjugates of a peptide nucleic acid (CPP-PNA) against bamB and tolC homologs as antisense agents. Results revealed that the single deletion of bamB and tolC in Escherichia coli increased the uptake of large- and small-scaffold hydrophobic compounds, respectively. A bamB-and-tolC double deletion mutant had a higher uptake efficiency for certain antibiotics and other compounds with high hydrophobicity than each single deletion mutant. The CPP-PNA treated E. coli and Pseudomonas aeruginosa cells showed high sensitivity to various antibiotics. Therefore, these gene deletion and silencing approaches can be utilized in therapeutic and biotechnological fields.
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Affiliation(s)
- Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, 062-8517, Japan
| | - Nao Yamamoto
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Shotaro Ayukawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, 062-8517, Japan
| | - Yoshiaki Yasutake
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, 062-8517, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, 169-8555, Japan
| | - Koji Ishiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, 062-8517, Japan
| | - Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, 062-8517, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
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7
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Lauro C, Colarusso A, Calvanese M, Parrilli E, Tutino ML. Conditional gene silencing in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Res Microbiol 2022; 173:103939. [DOI: 10.1016/j.resmic.2022.103939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
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8
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Fujita S, Tsumori Y, Makino Y, Saito M, Kawano M. Development of multiplexing gene silencing system using conditionally induced polycistronic synthetic antisense RNAs in Escherichia coli. Biochem Biophys Res Commun 2021; 556:163-170. [PMID: 33845307 DOI: 10.1016/j.bbrc.2021.03.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/28/2021] [Indexed: 11/16/2022]
Abstract
Although efficient methods of gene silencing have been established in eukaryotes, many different techniques are still used in bacteria due to the lack of a standardized tool. Here, we developed a convenient and efficient method to downregulate the expression of a specific gene using ∼140 nucleotide RNA with a 24-nucleotide antisense region from an arabinose-inducible expression plasmid by taking Escherichia coli lacZ and phoA genes encoding β-galactosidase and alkaline phosphatase, respectively, as target genes to evaluate the model. We examined the antisense RNA (asRNA) design, including targeting position, uORF stability elements at the 5'-end, and Hfq-binding module at the 3'-end, and inducer amount required to obtain effective experimental conditions for gene silencing. Furthermore, we constructed multiplexed dual-acting asRNA genes in the plasmid, which were transcribed as polycistronic RNA and were able to knockdown multiple target genes simultaneously. We observed the highest inhibition level of 98.6% when lacZ was targeted using the pMKN104 asRNA expression plasmid, containing a five times stronger PBAD -10 promoter sequence with no requirement of the Hfq protein for repression. These features allow the system to be utilized as an asRNA expression platform in many bacteria, besides E. coli, for gene regulation.
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Affiliation(s)
- Shouta Fujita
- Laboratory of Gene Regulation Study, Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Yutaka Tsumori
- Laboratory of Gene Regulation Study, Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Yuko Makino
- Laboratory of Gene Regulation Study, Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Mineki Saito
- Department of Microbiology, Kawasaki Medical School, Kurashiki, Japan
| | - Mitsuoki Kawano
- Department of Human Nutrition, Faculty of Contemporary Life Science, Chugokugakuen University, Okayama, Japan.
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9
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Nikolay R, Hilal T, Schmidt S, Qin B, Schwefel D, Vieira-Vieira CH, Mielke T, Bürger J, Loerke J, Amikura K, Flügel T, Ueda T, Selbach M, Deuerling E, Spahn CMT. Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization. Mol Cell 2021; 81:1200-1215.e9. [PMID: 33639093 DOI: 10.1016/j.molcel.2021.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 11/11/2020] [Accepted: 02/02/2021] [Indexed: 01/13/2023]
Abstract
Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. In this study, we analyze physiologic prokaryotic ribosome biogenesis by isolating bona fide pre-50S subunits from an Escherichia coli strain with the biogenesis factor ObgE, affinity tagged at its native gene locus. Our integrative structural approach reveals a network of interacting biogenesis factors consisting of YjgA, RluD, RsfS, and ObgE on the immature pre-50S subunit. In addition, our study provides mechanistic insight into how the GTPase ObgE, in concert with other biogenesis factors, facilitates the maturation of the 50S functional core and reveals both conserved and divergent evolutionary features of ribosome biogenesis between prokaryotes and eukaryotes.
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Affiliation(s)
- Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Tarek Hilal
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Freie Universität Berlin, Research Centre for Electron Microscopy, Fabeckstr. 36a, 14195 Berlin, Germany
| | - Sabine Schmidt
- Molekulare Mikrobiologie, Universität Konstanz, Konstanz, Germany
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - David Schwefel
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Carlos H Vieira-Vieira
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Faculty of Life Sciences, Humboldt Universität zu Berlin, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Kazuaki Amikura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, FSB-401, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Timo Flügel
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, FSB-401, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Elke Deuerling
- Molekulare Mikrobiologie, Universität Konstanz, Konstanz, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
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10
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Abstract
CRISPR-Cas systems have been engineered as powerful tools to control gene expression in bacteria. The most common strategy relies on the use of Cas effectors modified to bind target DNA without introducing DNA breaks. These effectors can either block the RNA polymerase or recruit it through activation domains. Here, we discuss the mechanistic details of how Cas effectors can modulate gene expression by blocking transcription initiation or acting as transcription roadblocks. CRISPR-Cas tools can be further engineered to obtain fine-tuned control of gene expression or target multiple genes simultaneously. Several caveats in using these tools have also been revealed, including off-target effects and toxicity, making it important to understand the design rules of engineered CRISPR-Cas effectors in bacteria. Alternatively, some types of CRISPR-Cas systems target RNA and could be used to block gene expression at the posttranscriptional level. Finally, we review applications of these tools in high-throughput screens and the progress and challenges in introducing CRISPR knockdown to other species, including nonmodel bacteria with industrial or clinical relevance. A deep understanding of how CRISPR-Cas systems can be harnessed to control gene expression in bacteria and build powerful tools will certainly open novel research directions.
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Affiliation(s)
- Antoine Vigouroux
- Synthetic Biology, Institut Pasteur, Paris, France
- Microbial Morphogenesis and Growth, Institut Pasteur, Paris, France
| | - David Bikard
- Synthetic Biology, Institut Pasteur, Paris, France
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11
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Murai R, Kiyoshi K, Yoshida N. Effect of Target Gene Silencing on Calcite Single Crystal Formation by Thermophilic Bacterium Geobacillus thermoglucosidasius NY05. Curr Microbiol 2019; 76:1298-1305. [PMID: 31428805 DOI: 10.1007/s00284-019-01756-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 08/09/2019] [Indexed: 10/26/2022]
Abstract
Geobacillus thermoglucosidasius NY05 catalyzes calcite single crystal formation at 60 °C by using acetate and calcium. Endospores are embedded at the central part of the calcite single crystal and carbon atoms in the calcite lattice are derived from acetate carbon. Here, we synthesized 21-mer antisense DNA oligonucleotides targeting sporulation transcription factor, acetate-CoA ligase, isocitrate lyase, and malate synthase G mRNAs and evaluated the effect of these oligonucleotides on calcite formation in G. thermoglucosidasius NY05. G. thermoglucosidasius NY05 cells containing antisense DNA oligonucleotides targeting sporulation transcription factor, acetate-CoA ligase, isocitrate lyase, and malate synthase G mRNAs had reduced calcite single crystal formation by 18.7, 50.6, 55.7, and 82.3%, respectively, compared with cells without antisense DNA oligonucleotides. These results support that calcite formation needs endospores as the nucleus to grow, and carbon dioxide generated from acetate, which is metabolized via the glyoxylate pathway and glucogenesis, is supplied to the crystal lattice.
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Affiliation(s)
- Rie Murai
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki, 889-2192, Japan
| | - Keiji Kiyoshi
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki, 889-2192, Japan
| | - Naoto Yoshida
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki, 889-2192, Japan.
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12
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Advances in engineered trans-acting regulatory RNAs and their application in bacterial genome engineering. J Ind Microbiol Biotechnol 2019; 46:819-830. [PMID: 30887255 DOI: 10.1007/s10295-019-02160-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022]
Abstract
Small noncoding RNAs, a large class of ancient posttranscriptional regulators, are increasingly recognized and utilized as key modulators of gene expression in a broad range of microorganisms. Owing to their small molecular size and the central role of Watson-Crick base pairing in defining their interactions, structure and function, numerous diverse types of trans-acting RNA regulators that are functional at the DNA, mRNA and protein levels have been experimentally characterized. It has become increasingly clear that most small RNAs play critical regulatory roles in many processes and are, therefore, considered to be powerful tools for genetic engineering and synthetic biology. The trans-acting regulatory RNAs accelerate this ability to establish potential framework for genetic engineering and genome-scale engineering, which allows RNA structure characterization, easier to design and model compared to DNA or protein-based systems. In this review, we summarize recent advances in engineered trans-acting regulatory RNAs that are used in bacterial genome-scale engineering and in novel cellular capabilities as well as their implementation in wide range of biotechnological, biological and medical applications.
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Construction of artificial micro-aerobic metabolism for energy- and carbon-efficient synthesis of medium chain fatty acids in Escherichia coli. Metab Eng 2019; 53:1-13. [PMID: 30684584 DOI: 10.1016/j.ymben.2019.01.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 01/18/2019] [Accepted: 01/23/2019] [Indexed: 02/06/2023]
Abstract
Medium-chain (C6-C10) chemicals are important components of fuels, commodities and fine chemicals. Numerous exciting achievements have proven reversed β-oxidation cycle as a promising platform to synthesize these chemicals. However, under native central carbon metabolism, energetic and redox constraints limit the efficient operation of reversed β-oxidation cycle. Current fermentative platform has to use different chemically and energetically inefficient ways for acetyl-CoA and NADH biosynthesis, respectively. The characteristics such as supplementation of additional acetate and formate or high ATP requirement makes this platform incompatible with large-scale production. Here, an artificial micro-aerobic metabolism for energy and carbon-efficient conversion of glycerol to MCFAs was constructed to present solutions towards these barriers. After evaluating numerous bacteria pathways under micro-aerobic conditions, one synthetic metabolic step enabling biosynthesis of acetyl-CoA and NADH simultaneously, without any energy cost and additional carbon requirement, and reducing loss of carbon to carbon dioxide-emitting reactions, was conceived and successfully constructed. The pyruvate dehydrogenase from Enterococcus faecalis was identified and biochemically characterized, demonstrating the most suitable characteristics. Furthermore, the carbon and energy metabolism in Escherichia coli was rewired by the clustered regularly interspaced short palindromic repeats interference system, inhibiting native fermentation pathways outcompeting this synthetic step. The present engineered strain exhibited a 15.7-fold increase in MCFA titer compared with that of the initial strain, and produced 15.67 g/L MCFAs from the biodiesel byproduct glycerol in 3-L bioreactor without exogenous feed of acetate or formate, representing the highest MCFA titer reported to date. This work demonstrates this artificial micro-aerobic metabolism has the potential to enable the cost-effective, large-scale production of fatty acids and other value-added reduced chemicals.
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14
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Yao R, Li J, Feng L, Zhang X, Hu H. 13C metabolic flux analysis-guided metabolic engineering of Escherichia coli for improved acetol production from glycerol. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:29. [PMID: 30805028 PMCID: PMC6373095 DOI: 10.1186/s13068-019-1372-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/06/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Bioprocessing offers a sustainable and green approach to manufacture various chemicals and materials. Development of bioprocesses requires transforming common producer strains to cell factories. 13C metabolic flux analysis (13C-MFA) can be applied to identify relevant targets to accomplish the desired phenotype, which has become one of the major tools to support systems metabolic engineering. In this research, we applied 13C-MFA to identify bottlenecks in the bioconversion of glycerol into acetol by Escherichia coli. Valorization of glycerol, the main by-product of biodiesel, has contributed to the viability of biofuel economy. RESULTS We performed 13C-MFA and measured intracellular pyridine nucleotide pools in a first-generation acetol producer strain (HJ06) and a non-producer strain (HJ06C), and identified that engineering the NADPH regeneration is a promising target. Based on this finding, we overexpressed nadK encoding NAD kinase or pntAB encoding membrane-bound transhydrogenase either individually or in combination with HJ06, obtaining HJ06N, HJ06P and HJ06PN. The step-wise approach resulted in increasing the acetol titer from 0.91 g/L (HJ06) to 2.81 g/L (HJ06PN). To systematically characterize and the effect of mutation(s) on the metabolism, we also examined the metabolomics and transcriptional levels of key genes in four strains. The pool sizes of NADPH, NADP+ and the NADPH/NADP+ ratio were progressively increased from HJ06 to HJ06PN, demonstrating that the sufficient NADPH supply is critical for acetol production. Flux distribution was optimized towards acetol formation from HJ06 to HJ06PN: (1) The carbon partitioning at the DHAP node directed gradually more carbon from the lower glycolytic pathway through the acetol biosynthetic pathway; (2) The transhydrogenation flux was constantly increased. In addition, 13C-MFA showed the rigidity of upper glycolytic pathway, PP pathway and the TCA cycle to support growth. The flux patterns were supported by most metabolomics data and gene expression profiles. CONCLUSIONS This research demonstrated how 13C-MFA can be applied to drive the cycles of design, build, test and learn implementation for strain development. This succeeding engineering strategy can also be applicable for rational design of other microbial cell factories.
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Affiliation(s)
- Ruilian Yao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Jiawei Li
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Lei Feng
- Instrumental Analysis Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
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Yang Y, Wang J, Zhang R, Yan Y. Antisense RNA Elements for Downregulating Expression. Methods Mol Biol 2019; 1927:23-35. [PMID: 30788783 DOI: 10.1007/978-1-4939-9142-6_3] [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: 06/09/2023]
Abstract
Antisense RNA (asRNA) technology is an important tool for downregulating gene expression. When applying this strategy, the asRNA interference efficiency is determined by several elements including scaffold design, loop size, and relative abundance. Here, we take the Escherichia coli gene fabD encoding malonyl-CoA-[acyl-carrier-protein] transacylase as an example to describe the asRNA design with reliable and controllable interference efficiency. Real-time PCR and fluorescence assay methods are introduced to detect the interference efficiency at RNA level and protein level, respectively.
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Affiliation(s)
- Yaping Yang
- College of Engineering, University of Georgia, Athens, GA, USA
| | - Jian Wang
- College of Engineering, University of Georgia, Athens, GA, USA
| | - Ruihua Zhang
- College of Engineering, University of Georgia, Athens, GA, USA
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA, USA.
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16
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Jing P, Cao X, Lu X, Zong H, Zhuge B. Modification of an engineered Escherichia coli by a combined strategy of deleting branch pathway, fine-tuning xylose isomerase expression, and substituting decarboxylase to improve 1,2,4-butanetriol production. J Biosci Bioeng 2018; 126:547-552. [DOI: 10.1016/j.jbiosc.2018.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/10/2018] [Accepted: 05/24/2018] [Indexed: 12/18/2022]
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Abstract
As the transcriptional and post-transcriptional regulators of gene expression, small RNAs (sRNAs) play important roles in every domain of life in organisms. It has been discovered gradually that bacteria possess multiple means of gene regulation using RNAs. They have been continuously used as model organisms for photosynthesis, metabolism, biotechnology, evolution, and nitrogen fixation for many decades. Cyanobacteria, one of the most ancient life forms, constitute all kinds of photoautotrophic bacteria and exist in almost any environment on this planet. It is believed that a complex RNA-based regulatory mechanism functions in cyanobacteria to help them adapt to changes and stresses in diverse environments. Although lagging far behind other model microorganisms, such as yeast and Escherichia coli, more and more non-coding regulatory sRNAs have been recognized in cyanobacteria during the past decades. In this article, by focusing on cyanobacterial sRNAs, the approaches for detection and targeting of sRNAs will be summarized, four major mechanisms and regulatory functions will be generalized, eight types of cis-encoded sRNA and four types of trans-encoded sRNAs will be reviewed in detail, and their possible physiological functions will be further discussed.
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Affiliation(s)
- Jinlu Hu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Qiang Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan, China.,University of the Chinese Academy of Sciences, Beijing, China
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18
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Tao S, Qian Y, Wang X, Cao W, Ma W, Chen K, Ouyang P. Regulation of ATP levels in Escherichia coli using CRISPR interference for enhanced pinocembrin production. Microb Cell Fact 2018; 17:147. [PMID: 30227873 PMCID: PMC6142380 DOI: 10.1186/s12934-018-0995-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/11/2018] [Indexed: 01/07/2023] Open
Abstract
Background Microbial biosynthesis of natural products holds promise for preclinical studies and treating diseases. For instance, pinocembrin is a natural flavonoid with important pharmacologic characteristics and is widely used in preclinical studies. However, high yield of natural products production is often limited by the intracellular cofactor level, including adenosine triphosphate (ATP). To address this challenge, tailored modification of ATP concentration in Escherichia coli was applied in efficient pinocembrin production. Results In the present study, a clustered regularly interspaced short palindromic repeats (CRISPR) interference system was performed for screening several ATP-related candidate genes, where metK and proB showed its potential to improve ATP level and increased pinocembrin production. Subsequently, the repression efficiency of metK and proB were optimized to achieve the appropriate levels of ATP and enhancing the pinocembrin production, which allowed the pinocembrin titer increased to 102.02 mg/L. Coupled with the malonyl-CoA engineering and optimization of culture and induction condition, a final pinocembrin titer of 165.31 mg/L was achieved, which is 10.2-fold higher than control strains. Conclusions Our results introduce a strategy to approach the efficient biosynthesis of pinocembrin via ATP level strengthen using CRISPR interference. Furthermore coupled with the malonyl-CoA engineering and induction condition have been optimized for pinocembrin production. The results and engineering strategies demonstrated here would hold promise for the ATP level improvement of other flavonoids by CRISPRi system, thereby facilitating other flavonoids production. Electronic supplementary material The online version of this article (10.1186/s12934-018-0995-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sha Tao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Ying Qian
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Weijia Cao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Weichao Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China.
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
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Pokhrel AR, Nguyen HT, Dhakal D, Chaudhary AK, Sohng JK. Implication of orphan histidine kinase (OhkAsp) in biosynthesis of doxorubicin and daunorubicin in Streptomyces peucetius ATCC 27952. Microbiol Res 2018; 214:37-46. [DOI: 10.1016/j.micres.2018.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/18/2018] [Accepted: 05/09/2018] [Indexed: 12/30/2022]
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20
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Peters G, Maertens J, Lammertyn J, De Mey M. Exploring of the feature space of de novo developed post-transcriptional riboregulators. PLoS Comput Biol 2018; 14:e1006170. [PMID: 30118473 PMCID: PMC6114898 DOI: 10.1371/journal.pcbi.1006170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 08/29/2018] [Accepted: 04/30/2018] [Indexed: 11/23/2022] Open
Abstract
Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered regularly interspaced short palindromic repeats technology. Despite this clear advantage, no clear general design principles are available to de novo develop repressing riboregulators, limiting the availability and the reliable development of these type of riboregulators. Here, to overcome this lack of knowledge on the functionality of repressing riboregulators, translation inhibiting RNAs are developed from scratch. These de novo developed riboregulators explore features related to thermodynamical and structural factors previously attributed to translation initiation modulation. In total, 12 structural and thermodynamic features were defined of which six features were retained after removing correlations from an in silico generated riboregulator library. From this translation inhibiting RNA library, 18 riboregulators were selected using a experimental design and subsequently constructed and co-expressed with two target untranslated regions to link the translation inhibiting RNA features to functionality. The pure riboregulators in the design of experiments showed repression down to 6% of the original protein expression levels, which could only be partially explained by a ordinary least squares regression model. To allow reliable forward engineering, a partial least squares regression model was constructed and validated to link the properties of translation inhibiting RNA riboregulators to gene repression. In this model both structural and thermodynamic features were important for efficient gene repression by pure riboregulators. This approach enables a more reliable de novo forward engineering of effective pure riboregulators, which further expands the RNA toolbox for gene expression modulation. To allow reliable forward engineering of microbial cell factories, various metabolic engineering efforts rely on RNA-based technology. As such, programmable riboregulators allow dynamic control over gene expression. However, no clear design principles exist for de novo developed repressing riboregulators, which limits their applicability. Here, various engineering principles are identified and computationally explored. Subsequently, various design criteria are used in an experimental design, which were explored in an in vivo study. This resulted in a regression model that enables a more reliable computational design of repression small RNAs.
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Affiliation(s)
- Gert Peters
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | | | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
- * E-mail:
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21
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Sun T, Li S, Song X, Diao J, Chen L, Zhang W. Toolboxes for cyanobacteria: Recent advances and future direction. Biotechnol Adv 2018; 36:1293-1307. [DOI: 10.1016/j.biotechadv.2018.04.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/09/2018] [Accepted: 04/26/2018] [Indexed: 12/20/2022]
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22
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Newman SL, Will WR, Libby SJ, Fang FC. The curli regulator CsgD mediates stationary phase counter-silencing of csgBA in Salmonella Typhimurium. Mol Microbiol 2018; 108:101-114. [PMID: 29388265 DOI: 10.1111/mmi.13919] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 12/23/2022]
Abstract
Integration of horizontally acquired genes into transcriptional networks is essential for the regulated expression of virulence in bacterial pathogens. In Salmonella enterica, expression of such genes is repressed by the nucleoid-associated protein H-NS, which recognizes and binds to AT-rich DNA. H-NS-mediated silencing must be countered by other DNA-binding proteins to allow expression under appropriate conditions. Some genes that can be transcribed by RNA polymerase (RNAP) associated with the alternative sigma factor σS or the housekeeping sigma factor σ70 in vitro appear to be preferentially transcribed by σS in the presence of H-NS, suggesting that σS may act as a counter-silencer. To determine whether σS directly counters H-NS-mediated silencing and whether co-regulation by H-NS accounts for the σS selectivity of certain promoters, we examined the csgBA operon, which is required for curli fimbriae expression and is known to be regulated by both H-NS and σS . Using genetics and in vitro biochemical analyses, we found that σS is not directly required for csgBA transcription, but rather up-regulates csgBA via an indirect upstream mechanism. Instead, the biofilm master regulator CsgD directly counter-silences the csgBA promoter by altering the DNA-protein complex structure to disrupt H-NS-mediated silencing in addition to directing the binding of RNAP.
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Affiliation(s)
- S L Newman
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - W R Will
- Department of Microbiology, University of Washington, Seattle WA, USA
| | - S J Libby
- Department of Microbiology, University of Washington, Seattle WA, USA
| | - F C Fang
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.,Department of Microbiology, University of Washington, Seattle WA, USA
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23
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Sun T, Li S, Song X, Pei G, Diao J, Cui J, Shi M, Chen L, Zhang W. Re-direction of carbon flux to key precursor malonyl-CoA via artificial small RNAs in photosynthetic Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:26. [PMID: 29441124 PMCID: PMC5798194 DOI: 10.1186/s13068-018-1032-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/23/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Photosynthetic cyanobacteria have attracted a significant attention as promising chassis to produce renewable fuels and chemicals due to their capability to utilizing solar energy and CO2. Notably, the enhancing supply of key precursors like malonyl-CoA would benefit the production of many bio-compounds. Nevertheless, the lacking of genetic tools in cyanobacteria, especially the knockdown strategies for essential pathways, has seriously restricted the attempts to re-direct carbon flux from the central carbohydrate metabolism to the synthesis of bioproducts. RESULTS Aiming at developing new genetic tools, two small RNA regulatory tools are reported for the model cyanobacterium Synechocystis sp. PCC6803, based on paired termini RNAs as well as the exogenous Hfq chaperone and MicC scaffold (Hfq-MicC) previously developed in Escherichia coli. Both regulatory tools functioned well in regulating exogenous reporter gene lacZ and endogenous glgC gene in Synechocystis sp. PCC6803, achieving a downregulation of gene expression up to 90% compared with wildtype. In addition, the Hfq-MicC tool was developed to simultaneously regulate multiple genes related to essential fatty acids biosynthesis, which led to decreased fatty acids content by 11%. Furthermore, aiming to re-direct the carbon flux, the Hfq-MicC tool was utilized to interfere the competing pathway of malonyl-CoA, achieving an increased intracellular malonyl-CoA abundance up to 41% (~ 698.3 pg/mL/OD730 nm) compared to the wildtype. Finally, the Hfq-MicC system was further modified into an inducible system based on the theophylline-inducible riboswitch. CONCLUSIONS In this study, two small RNA regulatory tools for manipulating essential metabolic pathways and re-directing carbon flux are reported for Synechocystis sp. PCC6803. The work introduces efficient and valuable metabolic regulatory strategies for photosynthetic cyanobacteria.
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Affiliation(s)
- Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Shubin Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Xinyu Song
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Guangsheng Pei
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Jinjin Diao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Jinyu Cui
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Mengliang Shi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, People’s Republic of China
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Improving metabolic efficiency of the reverse beta-oxidation cycle by balancing redox cofactor requirement. Metab Eng 2017; 44:313-324. [PMID: 29122703 DOI: 10.1016/j.ymben.2017.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/29/2017] [Accepted: 11/04/2017] [Indexed: 12/15/2022]
Abstract
Previous studies have made many exciting achievements on pushing the functional reversal of beta-oxidation cycle (r-BOX) to more widespread adoption for synthesis of a wide variety of fuels and chemicals. However, the redox cofactor requirement for the efficient operation of r-BOX remains unclear. In this work, the metabolic efficiency of r-BOX for medium-chain fatty acid (C6-C10, MCFA) production was optimized by redox cofactor engineering. Stoichiometric analysis of the r-BOX pathway and further experimental examination identified NADH as a crucial determinant of r-BOX process yield. Furthermore, the introduction of formate dehydrogenase from Candida boidinii using fermentative inhibitor byproduct formate as a redox NADH sink improved MCFA titer from initial 1.2g/L to 3.1g/L. Moreover, coupling of increasing the supply of acetyl-CoA with NADH to achieve fermentative redox balance enabled product synthesis at maximum titers. To this end, the acetate re-assimilation pathway was further optimized to increase acetyl-CoA availability associated with the new supply of NADH. It was found that the acetyl-CoA synthetase activity and intracellular ATP levels constrained the activity of acetate re-assimilation pathway, and 4.7g/L of MCFA titer was finally achieved after alleviating these two limiting factors. To the best of our knowledge, this represented the highest titer reported to date. These results demonstrated that the key constraint of r-BOX was redox imbalance and redox engineering could further unleash the lipogenic potential of this cycle. The redox engineering strategies could be applied to acetyl-CoA-derived products or other bio-products requiring multiple redox cofactors for biosynthesis.
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25
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Vazquez-Anderson J, Mihailovic MK, Baldridge KC, Reyes KG, Haning K, Cho SH, Amador P, Powell WB, Contreras LM. Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions. Nucleic Acids Res 2017; 45:5523-5538. [PMID: 28334800 PMCID: PMC5435917 DOI: 10.1093/nar/gkx115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/14/2017] [Indexed: 11/17/2022] Open
Abstract
Current approaches to design efficient antisense RNAs (asRNAs) rely primarily on a thermodynamic understanding of RNA–RNA interactions. However, these approaches depend on structure predictions and have limited accuracy, arguably due to overlooking important cellular environment factors. In this work, we develop a biophysical model to describe asRNA–RNA hybridization that incorporates in vivo factors using large-scale experimental hybridization data for three model RNAs: a group I intron, CsrB and a tRNA. A unique element of our model is the estimation of the availability of the target region to interact with a given asRNA using a differential entropic consideration of suboptimal structures. We showcase the utility of this model by evaluating its prediction capabilities in four additional RNAs: a group II intron, Spinach II, 2-MS2 binding domain and glgC 5΄ UTR. Additionally, we demonstrate the applicability of this approach to other bacterial species by predicting sRNA–mRNA binding regions in two newly discovered, though uncharacterized, regulatory RNAs.
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Affiliation(s)
- Jorge Vazquez-Anderson
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
| | - Mia K Mihailovic
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
| | - Kevin C Baldridge
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
| | - Kristofer G Reyes
- Department of Operations Research and Financial Engineering, Princeton University, Sherrerd Hall, Charlton St., Princeton, NJ 08544, USA
| | - Katie Haning
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
| | - Seung Hee Cho
- Institute for Cellular & Molecular Biology, The University of Texas at Austin, 2500 Speedway, Stop A4800, Austin, TX 78712, USA
| | - Paul Amador
- Institute for Cellular & Molecular Biology, The University of Texas at Austin, 2500 Speedway, Stop A4800, Austin, TX 78712, USA
| | - Warren B Powell
- Department of Operations Research and Financial Engineering, Princeton University, Sherrerd Hall, Charlton St., Princeton, NJ 08544, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA
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Hennessy RC, Phippen CBW, Nielsen KF, Olsson S, Stougaard P. Biosynthesis of the antimicrobial cyclic lipopeptides nunamycin and nunapeptin by Pseudomonas fluorescens strain In5 is regulated by the LuxR-type transcriptional regulator NunF. Microbiologyopen 2017; 6. [PMID: 28782279 PMCID: PMC5727362 DOI: 10.1002/mbo3.516] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/30/2017] [Accepted: 06/13/2017] [Indexed: 12/02/2022] Open
Abstract
Nunamycin and nunapeptin are two antimicrobial cyclic lipopeptides (CLPs) produced by Pseudomonas fluorescens In5 and synthesized by nonribosomal synthetases (NRPS) located on two gene clusters designated the nun–nup regulon. Organization of the regulon is similar to clusters found in other CLP‐producing pseudomonads except for the border regions where putative LuxR‐type regulators are located. This study focuses on understanding the regulatory role of the LuxR‐type‐encoding gene nunF in CLP production of P. fluorescens In5. Functional analysis of nunF coupled with liquid chromatography–high‐resolution mass spectrometry (LC‐HRMS) showed that CLP biosynthesis is regulated by nunF. Quantitative real‐time PCR analysis indicated that transcription of the NRPS genes catalyzing CLP production is strongly reduced when nunF is mutated indicating that nunF is part of the nun–nup regulon. Swarming and biofilm formation was reduced in a nunF knockout mutant suggesting that these CLPs may also play a role in these phenomena as observed in other pseudomonads. Fusion of the nunF promoter region to mCherry showed that nunF is strongly upregulated in response to carbon sources indicating the presence of a fungus suggesting that environmental elicitors may also influence nunF expression which upon activation regulates nunamycin and nunapeptin production required for the growth inhibition of phytopathogens.
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Affiliation(s)
- Rosanna C Hennessy
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Kristian F Nielsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Stefan Olsson
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fujian, China
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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Dong X, Jin Y, Ming D, Li B, Dong H, Wang L, Wang T, Wang D. CRISPR/dCas9-mediated inhibition of gene expression in Staphylococcus aureus. J Microbiol Methods 2017; 139:79-86. [PMID: 28522389 DOI: 10.1016/j.mimet.2017.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/09/2017] [Accepted: 05/15/2017] [Indexed: 12/27/2022]
Abstract
The understanding of the genetic mechanism of Staphylococcus aureus requires efficient tools, however, genetic manipulation in S. aureus is always laborious and time-consuming. Here we proposed a novel CRISPR/dCas9 interference method for the rapid knockdown of target genes. Furthermore, multiple genes can be repressed simultaneously by using this method.
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Affiliation(s)
- Xiaoyun Dong
- Department of Pharmacology, College of Basic Medical Science, Jilin University, Changchun, China
| | - Yingli Jin
- Department of Pharmacology, College of Basic Medical Science, Jilin University, Changchun, China.
| | - Di Ming
- Department of Biochemistry and Molecular Biology, College of Animal Science, Jilin University, Changchun, China
| | - Bangbang Li
- Department of Pharmacology, College of Basic Medical Science, Jilin University, Changchun, China
| | - Haisi Dong
- Department of Biochemistry and Molecular Biology, College of Animal Science, Jilin University, Changchun, China
| | - Lin Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China.
| | - Tiedong Wang
- Department of Biochemistry and Molecular Biology, College of Animal Science, Jilin University, Changchun, China.
| | - Dacheng Wang
- Department of Biochemistry and Molecular Biology, College of Animal Science, Jilin University, Changchun, China.
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Rational modular design of metabolic network for efficient production of plant polyphenol pinosylvin. Sci Rep 2017; 7:1459. [PMID: 28469159 PMCID: PMC5431097 DOI: 10.1038/s41598-017-01700-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/29/2017] [Indexed: 11/08/2022] Open
Abstract
Efficient biosynthesis of the plant polyphenol pinosylvin, which has numerous applications in nutraceuticals and pharmaceuticals, is necessary to make biological production economically viable. To this end, an efficient Escherichia coli platform for pinosylvin production was developed via a rational modular design approach. Initially, different candidate pathway enzymes were screened to construct de novo pinosylvin pathway directly from D-glucose. A comparative analysis of pathway intermediate pools identified that this initial construct led to the intermediate cinnamic acid accumulation. The pinosylvin synthetic pathway was then divided into two new modules separated at cinnamic acid. Combinatorial optimization of transcriptional and translational levels of these two modules resulted in a 16-fold increase in pinosylvin titer. To further improve the concentration of the limiting precursor malonyl-CoA, the malonyl-CoA synthesis module based on clustered regularly interspaced short palindromic repeats interference was assembled and optimized with other two modules. The final pinosylvin titer was improved to 281 mg/L, which was the highest pinosylvin titer even directly from D-glucose without any additional precursor supplementation. The rational modular design approach described here could bolster our capabilities in synthetic biology for value-added chemical production.
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Wu J, Zhang X, Xia X, Dong M. A systematic optimization of medium chain fatty acid biosynthesis via the reverse beta-oxidation cycle in Escherichia coli. Metab Eng 2017; 41:115-124. [PMID: 28392294 DOI: 10.1016/j.ymben.2017.03.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/15/2017] [Accepted: 03/30/2017] [Indexed: 12/24/2022]
Abstract
Medium-chain fatty acids (MCFAs, 6-10 carbons) are valuable precursors to many industrial biofuels and chemicals, recently engineered reversal of the β-oxidation (r-BOX) cycle has been proposed as a potential platform for efficient synthesis of MCFAs. Previous studies have made many exciting achievements on functionally characterizing four core enzymes of this r-BOX cycle. However, the information about bottleneck nodes in this cycle is elusive. Here, a quantitative assessment of the inherent limitations of this cycle was conducted to capitalize on its potential. The selection of the core β-oxidation reversal enzymes in conjunction with acetyl-CoA synthetase endowed the ability to synthesize about 1g/L MCFAs. Furthermore, a gene dosage experiment was developed to identify two rate-limiting enzymes (acetyl-CoA synthetase and thiolase). The de novo pathway was then separated into two modules at thiolase and MCFA production titer increased to 2.8g/L after evaluating different construct environments. Additionally, the metabolism of host organism was reprogrammed to the desired biochemical product by the clustered regularly interspaced short palindromic repeats interference system, resulted in a final MCFA production of 3.8g/L. These findings described here identified the inherent limitations of r-BOX cycle and further unleashed the lipogenic potential of this cycle, thus paving the way for the development of a bacterial platform for microbial production of high-value oleo-chemicals from low-value carbons in a sustainable and environmentally friendly manner.
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Affiliation(s)
- Junjun Wu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu 210095, China
| | - Xia Zhang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu 210095, China
| | - Xiudong Xia
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210095, China
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu 210095, China.
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30
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Wu J, Zhou P, Zhang X, Dong M. Efficient de novo synthesis of resveratrol by metabolically engineered Escherichia coli. J Ind Microbiol Biotechnol 2017; 44:1083-1095. [PMID: 28324236 DOI: 10.1007/s10295-017-1937-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/12/2017] [Indexed: 12/18/2022]
Abstract
Resveratrol has been the subject of numerous scientific investigations due to its health-promoting activities against a variety of diseases. However, developing feasible and efficient microbial processes remains challenging owing to the requirement of supplementing expensive phenylpropanoic precursors. Here, various metabolic engineering strategies were developed for efficient de novo biosynthesis of resveratrol. A recombinant malonate assimilation pathway from Rhizobium trifolii was introduced to increase the supply of the key precursor malonyl-CoA and simultaneously, the clustered regularly interspaced short palindromic repeats interference system was explored to down-regulate fatty acid biosynthesis pathway to inactivate the malonyl-CoA consumption pathway. Down-regulation of fabD, fabH, fabB, fabF, fabI increased resveratrol production by 80.2, 195.6, 170.3, 216.5 and 123.7%, respectively. Furthermore, the combined effect of these genetic perturbations was investigated, which increased the resveratrol titer to 188.1 mg/L. Moreover, the efficiency of this synthetic pathway was improved by optimizing the expression level of the rate-limiting enzyme TAL based on reducing mRNA structure of 5' region. This further increased the final resveratrol titer to 304.5 mg/L. The study described here paves the way to the development of a simple and economical process for microbial production of resveratrol.
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Affiliation(s)
- Junjun Wu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu, People's Republic of China.,Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Peng Zhou
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu, People's Republic of China.,Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xia Zhang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu, People's Republic of China.,Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu, People's Republic of China. .,Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, Jiangsu, People's Republic of China.
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31
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Pan X, Dong Y, Fan Z, Liu C, Xia B, Shi J, Bai F, Jin Y, Cheng Z, Jin S, Wu W. In vivo Host Environment Alters Pseudomonas aeruginosa Susceptibility to Aminoglycoside Antibiotics. Front Cell Infect Microbiol 2017; 7:83. [PMID: 28352614 PMCID: PMC5348532 DOI: 10.3389/fcimb.2017.00083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/02/2017] [Indexed: 01/06/2023] Open
Abstract
During host infection, Pseudomonas aeruginosa coordinately regulates the expression of numerous genes to adapt to the host environment while counteracting host clearance mechanisms. As infected patients take antibiotics, the invading bacteria encounter antibiotics in the host milieu. P. aeruginosa is highly resistant to antibiotics due to multiple chromosomally encoded resistant determinants. And numerous in vitro studies have demonstrated the regulatory mechanisms of antibiotic resistance related genes in response to antibiotics. However, it is not well-known how host environment affects bacterial response to antibiotics. In this study, we found that P. aeruginosa cells directly isolated from mice lungs displayed higher susceptibility to tobramycin than in vitro cultured bacteria. In vitro experiments demonstrated that incubation with A549 and differentiated HL60 (dHL60) cells sensitized P. aeruginosa to tobramycin. Further studies revealed that reactive oxygen species produced by the host cells contributed to the increased bacterial susceptibility. At the same concentration of tobramycin, presence of A549 and dHL60 cells resulted in higher expression of heat shock proteins, which are known inducible by tobramycin. Further analyses revealed decreased membrane potential upon incubation with the host cells and modification of lipopolysaccharide, which contributed to the increased susceptibility to tobramycin. Therefore, our results demonstrate that contact with host cells increased bacterial susceptibility to tobramycin.
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Affiliation(s)
- Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University Tianjin, China
| | - Yuanyuan Dong
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University Tianjin, China
| | - Zheng Fan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University Tianjin, China
| | - Chang Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University Tianjin, China
| | - Bin Xia
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University Tianjin, China
| | - Jing Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University Tianjin, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy and Life Sciences, Nankai University Tianjin, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University Tianjin, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University Tianjin, China
| | - Shouguang Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China; Department of Molecular Genetics and Microbiology, College of Medicine, University of FloridaGainesville, FL, USA
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University Tianjin, China
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Metabolic engineering of Escherichia coli W3110 for the production of L-methionine. J Ind Microbiol Biotechnol 2016; 44:75-88. [PMID: 27844169 DOI: 10.1007/s10295-016-1870-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/06/2016] [Indexed: 12/13/2022]
Abstract
In this study, we constructed an L-methionine-producing recombinant strain from wild-type Escherichia coli W3110 by metabolic engineering. To enhance the carbon flux to methionine and derepression met regulon, thrBC, lysA, and metJ were deleted in turn. Methionine biosynthesis obstacles were overcome by overexpression of metA Fbr (Fbr, Feedback resistance), metB, and malY under control of promoter pN25. Recombinant strain growth and methionine production were further improved by attenuation of metK gene expression through replacing native promoter by metK84p. Blocking the threonine pathway by deletion of thrBC or thrC was compared. Deletion of thrC showed faster growth rate and higher methionine production. Finally, metE, metF, and metH were overexpressed to enhance methylation efficiency. Compared with the original strain E. coli W3110, the finally obtained Me05 (pETMAFbr-B-Y/pKKmetH) improved methionine production from 0 to 0.65 and 5.62 g/L in a flask and a 15-L fermenter, respectively.
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Wu J, Zhang X, Zhou J, Dong M. Efficient biosynthesis of (2S)-pinocembrin from d-glucose by integrating engineering central metabolic pathways with a pH-shift control strategy. BIORESOURCE TECHNOLOGY 2016; 218:999-1007. [PMID: 27450982 DOI: 10.1016/j.biortech.2016.07.066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 05/06/2023]
Abstract
Microbial fermentations promise to revolutionize the conventional extraction of (2S)-pinocembrin from natural plant sources. Previously an Escherichia coli fermentation system was developed for one-step (2S)-pinocembrin production. However, this fermentation platform need supplementation of expensive malonyl-CoA precursor malonate and requires morpholinopropane sulfonate to provide buffering capacity. Here, a clustered regularly interspaced short palindromic repeats interference was constructed to efficiently channel carbon flux toward malonyl-CoA. By exploring the effects of different culture pH on microbial fermentation, it was found that high pH values favored upstream pathway catalysis, while low pH values favored downstream pathway catalysis. Based on this theory, a two-stage pH control strategy was proposed. The pH was controlled at 7.0 during 0-10h, and was shifted to 6.5 after 10h. Finally, the (2S)-pinocembrin titers increased to 525.8mg/L. These results were attained in minimal medium without additional precursor supplementation, thus offering opportunities for industrial scale low-cost production of flavonoids.
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Affiliation(s)
- Junjun Wu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210095, China
| | - Xia Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210095, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210095, China.
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Stepwise modular pathway engineering of Escherichia coli for efficient one-step production of (2S)-pinocembrin. J Biotechnol 2016; 231:183-192. [DOI: 10.1016/j.jbiotec.2016.06.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/26/2016] [Accepted: 06/09/2016] [Indexed: 12/17/2022]
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Lu X, Ji G, Zong H, Zhuge B. The role of budABC on 1,3-propanediol and 2,3-butanediol production from glycerol in Klebsiella pneumoniae CICIM B0057. Bioengineered 2016; 7:439-444. [PMID: 27439015 DOI: 10.1080/21655979.2016.1169355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
1,3-propanediol (1,3-PD) is an important compound from which many others can be synthesized. 2,3-butanediol (BDO) is the key by-product in the biosynthesis of 1,3-PD from glycerol, but it impedes its downstream purification. In Klebsiella, the budA, budB and budC genes encode enzymes that are responsible for the synthesis of BDO. In this study, 3 individual antisense RNAs were designed to repress the expression and hence activity of BudA-C. Compared with the parent strains, the activities of BudB and BudC were reduced by 60.5% and 70.5%, respectively, and the mRNA level of budA was reduced by 70%. Decreased BudC activity had no effect on cell growth or carbon distribution. However, reduced BudA and BudB activity decreased the BDO concentration by 35% and led to a 10% increase in the yield of 1,3-PD. This result suggests the activities of BudA and BudB could be key factors in the production of BDO from glycerol in Klebsiella. This study provides a deeper understanding of the role of budABC in glycerol metabolism in Klebsiella.
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Affiliation(s)
- Xinyao Lu
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Guangjian Ji
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Hong Zong
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Bin Zhuge
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi, Jiangsu , China
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Peters G, Coussement P, Maertens J, Lammertyn J, De Mey M. Putting RNA to work: Translating RNA fundamentals into biotechnological engineering practice. Biotechnol Adv 2015; 33:1829-44. [PMID: 26514597 DOI: 10.1016/j.biotechadv.2015.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/13/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
Abstract
Synthetic biology, in close concert with systems biology, is revolutionizing the field of metabolic engineering by providing novel tools and technologies to rationally, in a standardized way, reroute metabolism with a view to optimally converting renewable resources into a broad range of bio-products, bio-materials and bio-energy. Increasingly, these novel synthetic biology tools are exploiting the extensive programmable nature of RNA, vis-à-vis DNA- and protein-based devices, to rationally design standardized, composable, and orthogonal parts, which can be scaled and tuned promptly and at will. This review gives an extensive overview of the recently developed parts and tools for i) modulating gene expression ii) building genetic circuits iii) detecting molecules, iv) reporting cellular processes and v) building RNA nanostructures. These parts and tools are becoming necessary armamentarium for contemporary metabolic engineering. Furthermore, the design criteria, technological challenges, and recent metabolic engineering success stories of the use of RNA devices are highlighted. Finally, the future trends in transforming metabolism through RNA engineering are critically evaluated and summarized.
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Affiliation(s)
- Gert Peters
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Pieter Coussement
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jo Maertens
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jeroen Lammertyn
- BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, 3001 Louvain, Belgium
| | - Marjan De Mey
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli. Sci Rep 2015; 5:13477. [PMID: 26323217 PMCID: PMC4555050 DOI: 10.1038/srep13477] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/20/2015] [Indexed: 12/11/2022] Open
Abstract
The limited supply of intracellular malonyl-CoA in Escherichia coli impedes the biological synthesis of polyketides, flavonoids and biofuels. Here, a clustered regularly interspaced short palindromic repeats (CRISPR) interference system was constructed for fine-tuning central metabolic pathways to efficiently channel carbon flux toward malonyl-CoA. Using synthetic sgRNA to silence candidate genes, genes that could increase the intracellular malonyl-CoA level by over 223% were used as target genes. The efficiencies of repression of these genes were tuned to achieve appropriate levels so that the intracellular malonyl-CoA level was enhanced without significantly altering final biomass accumulation (the final OD600 decreased by less than 10%). Based on the results, multiple gene repressing was successful in approaching the limit of the amount of malonyl-CoA needed to produce the plant-specific secondary metabolite (2S)-naringenin. By coupling the genetic modifications to cell growth, the combined effects of these genetic perturbations increased the final (2S)-naringenin titer to 421.6 mg/L, which was 7.4-fold higher than the control strain. The strategy described here could be used to characterize genes that are essential for cell growth and to develop E. coli as a well-organized cell factory for producing other important products that require malonyl-CoA as a precursor.
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Silencing of Essential Genes within a Highly Coordinated Operon in Escherichia coli. Appl Environ Microbiol 2015; 81:5650-9. [PMID: 26070674 DOI: 10.1128/aem.01444-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/08/2015] [Indexed: 01/13/2023] Open
Abstract
Essential bacterial genes located within operons are particularly challenging to study independently because of coordinated gene expression and the nonviability of knockout mutants. Essentiality scores for many operon genes remain uncertain. Antisense RNA (asRNA) silencing or in-frame gene disruption of genes may help establish essentiality but can lead to polar effects on genes downstream or upstream of the target gene. Here, the Escherichia coli ribF-ileS-lspA-fkpB-ispH operon was used to evaluate the possibility of independently studying an essential gene using expressed asRNA and target gene overexpression to deregulate coupled expression. The gene requirement for growth in conditional silencing strains was determined by the relationship of target mRNA reduction with growth inhibition as the minimum transcript level required for 50% growth (MTL50). Mupirocin and globomycin, the protein inhibitors of IleS and LspA, respectively, were used in sensitization assays of strains containing both asRNA-expressing and open reading frame-expressing plasmids to examine deregulation of the overlapping ileS-lspA genes. We found upstream and downstream polar silencing effects when either ileS or lspA was silenced, indicating coupled expression. Weighted MTL50 values (means and standard deviations) of ribF, ileS, and lspA were 0.65 ± 0.18, 0.64 ± 0.06, and 0.76 ± 0.10, respectively. However, they were not significantly different (P = 0.71 by weighted one-way analysis of variance). The gene requirement for ispH could not be determined due to insufficient growth reduction. Mupirocin and globomycin sensitization experiments indicated that ileS-lspA expression could not be decoupled. The results highlight the inherent challenges associated with genetic analyses of operons; however, coupling of essential genes may provide opportunities to improve RNA-silencing antimicrobials.
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Massaiu I, Pasotti L, Casanova M, Politi N, Zucca S, Cusella De Angelis MG, Magni P. Quantification of the gene silencing performances of rationally-designed synthetic small RNAs. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:107-23. [PMID: 26279705 DOI: 10.1007/s11693-015-9177-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/12/2015] [Accepted: 07/27/2015] [Indexed: 11/30/2022]
Abstract
Small RNAs (sRNAs) are genetic tools for the efficient and specific tuning of target genes expression in bacteria. Inspired by naturally occurring sRNAs, recent works proposed the use of artificial sRNAs in synthetic biology for predictable repression of the desired genes. Their potential was demonstrated in several application fields, such as metabolic engineering and bacterial physiology studies. Guidelines for the rational design of novel sRNAs have been recently proposed. According to these guidelines, in this work synthetic sRNAs were designed, constructed and quantitatively characterized in Escherichia coli. An sRNA targeting the reporter gene RFP was tested by measuring the specific gene silencing when RFP was expressed at different transcription levels, under the control of different promoters, in different strains, and in single-gene or operon architecture. The sRNA level was tuned by using plasmids maintained at different copy numbers. Results demonstrated that RFP silencing worked as expected in an sRNA and mRNA expression-dependent fashion. A mathematical model was used to support sRNA characterization and to estimate an efficiency-related parameter that can be used to compare the performance of the designed sRNA. Gene silencing was also successful when RFP was placed in a two-gene synthetic operon, while the non-target gene (GFP) in the operon was not considerably affected. Finally, silencing was evaluated for another designed sRNA targeting the endogenous lactate dehydrogenase gene. The quantitative study performed in this work elucidated interesting performance-related and context-dependent features of synthetic sRNAs that will strongly support predictable gene silencing in disparate basic or applied research studies.
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Affiliation(s)
- Ilaria Massaiu
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Lorenzo Pasotti
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Michela Casanova
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Nicolò Politi
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Susanna Zucca
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | | | - Paolo Magni
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
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41
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Paired-termini antisense RNA mediated inhibition of DoxR in Streptomyces peucetius ATCC 27952. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0810-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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Metabolic engineering of Escherichia coli to enhance acetol production from glycerol. Appl Microbiol Biotechnol 2015; 99:7945-52. [PMID: 26078109 DOI: 10.1007/s00253-015-6732-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/17/2015] [Accepted: 05/27/2015] [Indexed: 12/22/2022]
Abstract
Acetol, a C3 keto alcohol, is an important intermediate used to produce polyols and acrolein. To enhance acetol production from glycerol by Escherichia coli, a mutant (HJ02) was constructed by replacing the native glpK gene with the allele from E. coli Lin 43 and overexpression of yqhD, which encodes aldehyde oxidoreductase YqhD that converts methylglyoxal to acetol. Compared to the control strain without the glpK replacement, HJ02 had 5.5 times greater acetol production and a 53.4 % higher glycerol consumption rate. Then, glucose was added as a co-substrate to enhance NADPH availability and the ptsG gene was deleted in HJ02 (HJ04) to alleviate carbon catabolite repression, which led to a 30 % increase in the NADPH level and NADPH/NADP(+). Consequently, HJ04 accumulated up to 1.20 g/L of acetol, which is 69.0 % higher than that of HJ02. Furthermore, the gapA gene in HJ04 was silenced by antisense RNA (HJ05) to further enhance acetol production. The acetol concentration produced by HJ05 reached 1.82 g/L, which was 2.1 and 1.5 times higher than that of HJ02 and HJ04.Real-time PCR analysis indicates that glucose catabolism was rerouted from glycolysis to the oxidative pentose phosphate pathway in HJ05.
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Chaudhary AK, Na D, Lee EY. Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs. Biotechnol Adv 2015; 33:914-30. [PMID: 26027891 DOI: 10.1016/j.biotechadv.2015.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/27/2015] [Accepted: 05/27/2015] [Indexed: 12/11/2022]
Abstract
Due to global crises such as pollution and depletion of fossil fuels, sustainable technologies based on microbial cell-factories have been garnering great interest as an alternative to chemical factories. The development of microbial cell-factories is imperative in cutting down the overall manufacturing cost. Thus, diverse metabolic engineering strategies and engineering tools have been established to obtain a preferred genotype and phenotype displaying superior productivity. However, these tools are limited to only a handful of genes with permanent modification of a genome and significant labor costs, and this is one of the bottlenecks associated with biofactory construction. Therefore, a groundbreaking rapid and high-throughput engineering tool is needed for efficient construction of microbial cell-factories. During the last decade, copious small noncoding RNAs (ncRNAs) have been discovered in bacteria. These are involved in substantial regulatory roles like transcriptional and post-transcriptional gene regulation by modulating mRNA elongation, stability, or translational efficiency. Because of their vulnerability, ncRNAs can be used as another layer of conditional control over gene expression without modifying chromosomal sequences, and hence would be a promising high-throughput tool for metabolic engineering. Here, we review successful design principles and applications of ncRNAs for high-throughput metabolic engineering or physiological studies of diverse industrially important microorganisms.
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Affiliation(s)
- Amit Kumar Chaudhary
- Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do 446-701, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea.
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do 446-701, Republic of Korea.
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Yang Y, Lin Y, Li L, Linhardt RJ, Yan Y. Regulating malonyl-CoA metabolism via synthetic antisense RNAs for enhanced biosynthesis of natural products. Metab Eng 2015; 29:217-226. [PMID: 25863265 DOI: 10.1016/j.ymben.2015.03.018] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/18/2015] [Accepted: 03/31/2015] [Indexed: 01/14/2023]
Abstract
Malonyl-CoA is the building block for fatty acid biosynthesis and also a precursor to various pharmaceutically and industrially valuable molecules, such as polyketides and biopolymers. However, intracellular malonyl-CoA is usually maintained at low levels, which poses great challenges to efficient microbial production of malonyl-CoA derived molecules. Inactivation of the malonyl-CoA consumption pathway to increase its intracellular availability is not applicable, since it is usually lethal to microorganisms. In this work, we employ synthetic antisense RNAs (asRNAs) to conditionally down-regulate fatty acid biosynthesis and achieve malonyl-CoA enrichment in Escherichia coli. The optimized asRNA constructs with a loop-stem structure exhibit high interference efficiency up to 80%, leading to a 4.5-fold increase in intracellular malonyl-CoA concentration when fabD gene expression is inhibited. Strikingly, this strategy allows the improved production of natural products 4-hydroxycoumarin, resveratrol, and naringenin by 2.53-, 1.70-, and 1.53-fold in E. coli, respectively. In addition, down-regulation of other fab genes including fabH, fabB, and fabF also leads to remarkable increases in 4-hydroxycoumarin production. This study demonstrates a novel strategy to enhance intracellular malonyl-CoA and indicates the effectiveness of asRNA as a powerful tool for use in metabolic engineering.
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Affiliation(s)
- Yaping Yang
- College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Yuheng Lin
- College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Lingyun Li
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Yajun Yan
- BioChemical Engineering Program, College of Engineering, University of Georgia, Athens, GA 30602, USA.
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Abstract
ABSTRACT
The scientific and technical ambition of contemporary synthetic biology is the engineering of biological objects with a degree of predictability comparable to those made through electric and industrial manufacturing. To this end, biological parts with given specifications are sequence-edited, standardized, and combined into devices, which are assembled into complete systems. This goal, however, faces the customary context dependency of biological ingredients and their amenability to mutation. Biological orthogonality (i.e., the ability to run a function in a fashion minimally influenced by the host) is thus a desirable trait in any deeply engineered construct. Promiscuous conjugative plasmids found in environmental bacteria have evolved precisely to autonomously deploy their encoded activities in a variety of hosts, and thus they become excellent sources of basic building blocks for genetic and metabolic circuits. In this article we review a number of such reusable functions that originated in environmental plasmids and keep their properties and functional parameters in a variety of hosts. The properties encoded in the corresponding sequences include
inter alia
origins of replication, DNA transfer machineries, toxin-antitoxin systems, antibiotic selection markers, site-specific recombinases, effector-dependent transcriptional regulators (with their cognate promoters), and metabolic genes and operons. Several of these sequences have been standardized as BioBricks and/or as components of the SEVA (Standard European Vector Architecture) collection. Such formatting facilitates their physical composability, which is aimed at designing and deploying complex genetic constructs with new-to-nature properties.
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Ferreira E, Giménez R, Cañas MA, Aguilera L, Aguilar J, Badia J, Baldomà L. Glyceraldehyde-3-phosphate dehydrogenase is required for efficient repair of cytotoxic DNA lesions in Escherichia coli. Int J Biochem Cell Biol 2015; 60:202-12. [PMID: 25603270 DOI: 10.1016/j.biocel.2015.01.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 12/04/2014] [Accepted: 01/12/2015] [Indexed: 01/07/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a multifunctional protein with diverse biological functions in human cells. In bacteria, moonlighting GAPDH functions have only been described for the secreted protein in pathogens or probiotics. At the intracellular level, we previously reported the interaction of Escherichia coli GAPDH with phosphoglycolate phosphatase, a protein involved in the metabolism of the DNA repair product 2-phosphoglycolate, thus suggesting a putative role of GAPDH in DNA repair processes. Here, we provide evidence that GAPDH is required for the efficient repair of DNA lesions in E. coli. We show that GAPDH-deficient cells are more sensitive to bleomycin or methyl methanesulfonate. In cells challenged with these genotoxic agents, GAPDH deficiency results in reduced cell viability and filamentous growth. In addition, the gapA knockout mutant accumulates a higher number of spontaneous abasic sites and displays higher spontaneous mutation frequencies than the parental strain. Pull-down experiments in different genetic backgrounds show interaction between GAPDH and enzymes of the base excision repair pathway, namely the AP-endonuclease Endo IV and uracil DNA glycosylase. This finding suggests that GAPDH is a component of a protein complex dedicated to the maintenance of genomic DNA integrity. Our results also show interaction of GAPDH with the single-stranded DNA binding protein. This interaction may recruit GAPDH to the repair sites and implicates GAPDH in DNA repair pathways activated by profuse DNA damage, such as homologous recombination or the SOS response.
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Affiliation(s)
- Elaine Ferreira
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Rosa Giménez
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - María Alexandra Cañas
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Laura Aguilera
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Juan Aguilar
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Josefa Badia
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Laura Baldomà
- Departament de Bioquímica i Biología Molecular, Institut de Biomedicina de la Universitat de Barcelona, Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain.
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Thermoadaptation-directed enzyme evolution in an error-prone thermophile derived from Geobacillus kaustophilus HTA426. Appl Environ Microbiol 2014; 81:149-58. [PMID: 25326311 DOI: 10.1128/aem.02577-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. In this study, we constructed an error-prone strain of the thermophile Geobacillus kaustophilus HTA426 and investigated thermoadaptation-directed enzyme evolution using the strain. A mutation frequency assay using the antibiotics rifampin and streptomycin revealed that G. kaustophilus had substantially higher mutability than Escherichia coli and Bacillus subtilis. The predominant mutations in G. kaustophilus were A · T→G · C and C · G→T · A transitions, implying that the high mutability of G. kaustophilus was attributable in part to high-temperature-associated DNA damage during growth. Among the genes that may be involved in DNA repair in G. kaustophilus, deletions of the mutSL, mutY, ung, and mfd genes markedly enhanced mutability. These genes were subsequently deleted to construct an error-prone thermophile that showed much higher (700- to 9,000-fold) mutability than the parent strain. The error-prone strain was auxotrophic for uracil owing to the fact that the strain was deficient in the intrinsic pyrF gene. Although the strain harboring Bacillus subtilis pyrF was also essentially auxotrophic, cells became prototrophic after 2 days of culture under uracil starvation, generating B. subtilis PyrF variants with an enhanced half-denaturation temperature of >10°C. These data suggest that this error-prone strain is a promising host for thermoadaptation-directed evolution to generate thermostable variants from thermolabile enzymes.
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48
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Fine-Tuning of the Fatty Acid Pathway by Synthetic Antisense RNA for Enhanced (2S)-Naringenin Production from l-Tyrosine in Escherichia coli. Appl Environ Microbiol 2014; 80:7283-92. [PMID: 25239896 DOI: 10.1128/aem.02411-14] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/12/2014] [Indexed: 12/26/2022] Open
Abstract
Malonyl coenzyme A (malonyl-CoA) is an important precursor for the synthesis of natural products, such as polyketides and flavonoids. The majority of this cofactor often is consumed for producing fatty acids and phospholipids, leaving only a small amount of cellular malonyl-CoA available for producing the target compound. The tuning of malonyl-CoA into heterologous pathways yields significant phenotypic effects, such as growth retardation and even cell death. In this study, fine-tuning of the fatty acid pathway in Escherichia coli with antisense RNA (asRNA) to balance the demands on malonyl-CoA for target-product synthesis and cell health was proposed. To establish an efficient asRNA system, the relationship between sequence and function for asRNA was explored. It was demonstrated that the gene-silencing effect of asRNA could be tuned by directing asRNA to different positions in the 5'-UTR (untranslated region) of the target gene. Based on this principle, the activity of asRNA was quantitatively tailored to balance the need for malonyl-CoA in cell growth and the production of the main flavonoid precursor, (2S)-naringenin. Appropriate inhibitory efficiency of the anti-fabB/fabF asRNA improved the production titer by 431% (391 mg/liter). Therefore, the strategy presented in this study provided a useful tool for the fine-tuning of endogenous gene expression in bacteria.
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Mitsudome Y, Takahama M, Hirose J, Yoshida N. The use of nano-sized acicular material, sliding friction, and antisense DNA oligonucleotides to silence bacterial genes. AMB Express 2014; 4:70. [PMID: 25401071 PMCID: PMC4230895 DOI: 10.1186/s13568-014-0070-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/15/2014] [Indexed: 11/15/2022] Open
Abstract
Viable bacterial cells impaled with a single particle of a nano-sized acicular material formed when a mixture containing the cells and the material was exposed to a sliding friction field between polystyrene and agar gel; hereafter, we refer to these impaled cells as penetrons. We have used nano-sized acicular material to establish a novel method for bacterial transformation. Here, we generated penetrons that carried antisense DNA adsorbed on nano-sized acicular material (α-sepiolite) by providing sliding friction onto the surface of agar gel; we then investigated whether penetron formation was applicable to gene silencing techniques. Antisense DNA was artificially synthesized as 15 or 90mer DNA oligonucleotides based on the sequences around the translation start codon of target mRNAs. Mixtures of bacterial cells with antisense DNA adsorbed on α-sepiolite were stimulated by sliding friction on the surface of agar gel for 60 s. Upon formation of Escherichia coli penetrons, β-lactamase and β-galactosidase expression was evaluated by counting the numbers of colonies formed on LB agar containing ampicillin and by measuring β-galactosidase activity respectively. The numbers of ampicillin resistant colonies and the β-galactosidase activity derived from penetrons bearing antisense DNA (90mer) was repressed to 15% and 25%, respectively, of that of control penetrons which lacked antisense DNA. Biphenyl metabolite, ring cleavage yellow compound produced by Pseudomonas pseudoalcaligenes penetron treated with antisense oligonucleotide DNA targeted to bphD increased higher than that lacking antisense DNA. This result indicated that expression of bphD in P. pseudoalcaligenes penetrons was repressed by antisense DNA that targeted bphD mRNA. Sporulation rates of Bacillus subtilis penetrons treated with antisense DNA (15mer) targeted to spo0A decreased to 24.4% relative to penetrons lacking antisense DNA. This novel method of gene silencing has substantial promise for elucidation of gene function in bacterial species that have been refractory to experimental introduction of exogenous DNA.
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50
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Nakashima N, Akita H, Hoshino T. Establishment of a novel gene expression method, BICES (biomass-inducible chromosome-based expression system), and its application to the production of 2,3-butanediol and acetoin. Metab Eng 2014; 25:204-14. [PMID: 25108217 DOI: 10.1016/j.ymben.2014.07.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/23/2014] [Accepted: 07/29/2014] [Indexed: 11/17/2022]
Abstract
In this study, we describe a novel method for producing valuable chemicals from glucose and xylose in Escherichia coli. The notable features in our method are avoidance of plasmids and expensive inducers for foreign gene expression to reduce production costs; foreign genes are knocked into the chromosome, and their expression is induced with xylose that is present in most biomass feedstock. As loci for the gene knock-in, lacZYA and some pseudogenes are chosen to minimize unexpected effects of the knock-in on cell physiology. The promoter of xylF is inducible with xylose and is combined with the T7 RNA polymerase-T7 promoter system to ensure strong gene expression. This expression system was named BICES (biomass-inducible chromosome-based expression system). As examples of BICES application, 2,3-butanediol and acetoin were successfully produced from glucose and xylose, and the maximal concentrations reached 54gL(-1) [99.6% in (R,S)-form] and 31gL(-1), respectively. 2,3-Butanediol and acetoin are industrially important chemicals that are, at present, produced primarily through petrochemical processes. To demonstrate usability of BICES in practical situations, we produced these chemicals from a saccharified cedar solution. From these results, we can conclude that BICES is suitable for practical production of valuable chemicals from biomass.
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Affiliation(s)
- Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan; Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Hironaga Akita
- Biomass Refinery Research Center, National Institute of Advanced Industrial Sciences and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Tamotsu Hoshino
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan; Biomass Refinery Research Center, National Institute of Advanced Industrial Sciences and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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