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Ashwath P, Sannejal AD. A quest to the therapeutic arsenal: Novel strategies to combat multidrug-resistant bacteria. Curr Gene Ther 2021; 22:79-88. [PMID: 33874870 DOI: 10.2174/1566523221666210419084836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/24/2021] [Accepted: 03/09/2021] [Indexed: 11/22/2022]
Abstract
The increasing resistance of the disease-causing pathogens to antimicrobial drugs is a public health concern and a socio-economic burden. The emergence of multi-drug resistant strains has made it harder to treat and combat infectious diseases with available conventional antibiotics. There are currently few effective therapeutic regimens for the successful prevention of infections caused by drug-resistant microbes. The various alternative strategies used in the recent past to decrease and limit antibiotic resistance in pathogens include bacteriophages, vaccines, anti-biofilm peptides, and antimicrobial peptides. However, in this review, we focus on the novel and robust molecular approach of antisense RNA (asRNA) technology and the clustered regulatory interspaced short palindromic repeat (CRISPR)-based antibiotic therapy, which can be exploited to selectively eradicate the drug-resistant bacterial strain in a sequence-specific fashion establishing opportunities in the treatment of multi-drug resistant related infections.
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Affiliation(s)
- Priyanka Ashwath
- Nitte (Deemed to be University), Nitte University Centre for Science Education & Research (NUCSER), Mangaluru. India
| | - Akhila Dharnappa Sannejal
- Nitte (Deemed to be University), Nitte University Centre for Science Education & Research (NUCSER), Mangaluru. India
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Application of a Pyruvate-Producing Escherichia coli Strain LAFCPCPt-accBC-aceE: A Case Study for d-Lactate Production. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6030070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pyruvate, a potential precursor of various chemicals, is one of the fundamental chemicals produced by the fermentation process. We previously reported a pyruvate-producing Escherichia coli strain LAFCPCPt-accBC-aceE (PYR) that has the potential to be applied to the industrial production of pyruvate. In this study, the availability of the PYR strain for the production of pyruvate-derivative chemicals was evaluated using a d-lactate-producing strain (LAC) based on the PYR strain. The LAC strain expresses a d-lactate dehydrogenase-encoding gene from Lactobacillus bulgaricus under the control of a T7 expression system. The d-lactate productivity of the LAC strain was further improved by limiting aeration and changing the induction period for the expression of d-lactate dehydrogenase-encoding gene expression. Under combined conditions, the LAC strain produced d-lactate at 21.7 ± 1.4 g·L−1, which was compatible with the pyruvate production by the PYR strain (26.1 ± 0.9 g·L−1). These results suggest that we have succeeded in the effective conversion of pyruvate to d-lactate in the LAC strain, demonstrating the wide versatility of the parental PYR strain as basal strain for various chemicals production.
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Perche F, Le Gall T, Montier T, Pichon C, Malinge JM. Cardiolipin-Based Lipopolyplex Platform for the Delivery of Diverse Nucleic Acids into Gram-Negative Bacteria. Pharmaceuticals (Basel) 2019; 12:ph12020081. [PMID: 31141930 PMCID: PMC6630428 DOI: 10.3390/ph12020081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Abstract
Antibiotic resistance is a growing public health concern. Because only a few novel classes of antibiotics have been developed in the last 40 years, such as the class of oxazolidinones, new antibacterial strategies are urgently needed [1]. Nucleic acid-based antibiotics are a new type of antimicrobials. However, free nucleic acids cannot spontaneously cross the bacterial cell wall and membrane;consequently, their intracellular delivery into bacteria needs to be assisted. Here, we introduce an original lipopolyplex system named liposome polymer nucleic acid (LPN), capable of versatile nucleic acid delivery into bacteria. We characterized LPN formed with significant therapeutic nucleic acids: 11 nt antisense single-stranded (ss) DNA and double-stranded (ds) DNA of 15 and 95 base pairs (bp), 9 kbp plasmid DNA (pDNA), and 1,000 nt ssRNA. All these complexes were efficiently internalized by two different bacterial species, i.e., Escherichia coli and Pseudomonas aeruginosa, as shown by flow cytometry. Consistent with intracellular delivery, LPN prepared with an antisense oligonucleotide and directed against an essential gene, induced specific and important bacterial growth inhibition likely leading to a bactericidal effect. Our findings indicate that LPN is a versatile platform for efficient delivery of diverse nucleic acids into Gram-negative bacteria.
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Affiliation(s)
- Federico Perche
- Centre de Biophysique Moléculaire, UPR4301 CNRS, Rue Charles Sadron Orléans CEDEX 02, France.
| | - Tony Le Gall
- Unité INSERM 1078, Faculté de Médecine, Université de Bretagne Occidentale, Université Européenne de Bretagne, 22 avenue Camille Desmoulins, 29238 Brest CEDEX 3, France.
| | - Tristan Montier
- Unité INSERM 1078, Faculté de Médecine, Université de Bretagne Occidentale, Université Européenne de Bretagne, 22 avenue Camille Desmoulins, 29238 Brest CEDEX 3, France.
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, UPR4301 CNRS, Rue Charles Sadron Orléans CEDEX 02, France.
| | - Jean-Marc Malinge
- Centre de Biophysique Moléculaire, UPR4301 CNRS, Rue Charles Sadron Orléans CEDEX 02, France.
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Koopal B, Kruis AJ, Claassens NJ, Nobrega FL, van der Oost J. Incorporation of a Synthetic Amino Acid into dCas9 Improves Control of Gene Silencing. ACS Synth Biol 2019; 8:216-222. [PMID: 30668910 DOI: 10.1021/acssynbio.8b00347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The CRISPR-Cas9 nuclease has been repurposed as a tool for gene repression (CRISPRi). This catalytically dead Cas9 (dCas9) variant inhibits transcription by blocking either initiation or elongation by the RNA polymerase complex. Conditional control of dCas9-mediated repression has been achieved with inducible promoters that regulate the expression of the dcas9 gene. However, as dCas9-mediated gene silencing is very efficient, even slightly leaky dcas9 expression leads to significant background levels of repression of the target gene. In this study, we report on the development of optimized control of dCas9-mediated silencing through additional regulation at the translation level. We have introduced the TAG stop codon in the dcas9 gene in order to insert a synthetic amino acid, l-biphenylalanine (BipA), at a permissive site in the dCas9 protein. In the absence of BipA, a nonfunctional, truncated dCas9 is produced, but when BipA is present, the TAG codon is translated resulting in a functional, full-length dCas9 protein. This synthetic, BipA-containing dCas9 variant (dCas9-BipA) could still fully repress gene transcription. Comparison of silencing mediated by dCas9 to dCas9-BipA revealed a 14-fold reduction in background repression by the latter system. The here developed proof-of-principle system thus reduces unwanted background levels of gene silencing, allowing for tight and timed control of target gene expression.
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Affiliation(s)
- Balwina Koopal
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Aleksander J. Kruis
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Nico J. Claassens
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Franklin L. Nobrega
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Novel Three-Component Phenazine-1-Carboxylic Acid 1,2-Dioxygenase in Sphingomonas wittichii DP58. Appl Environ Microbiol 2017; 83:AEM.00133-17. [PMID: 28188209 DOI: 10.1128/aem.00133-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/06/2017] [Indexed: 11/20/2022] Open
Abstract
Phenazine-1-carboxylic acid, the main component of shenqinmycin, is widely used in southern China for the prevention of rice sheath blight. However, the fate of phenazine-1-carboxylic acid in soil remains uncertain. Sphingomonas wittichii DP58 can use phenazine-1-carboxylic acid as its sole carbon and nitrogen sources for growth. In this study, dioxygenase-encoding genes, pcaA1A2, were found using transcriptome analysis to be highly upregulated upon phenazine-1-carboxylic acid biodegradation. PcaA1 shares 68% amino acid sequence identity with the large oxygenase subunit of anthranilate 1,2-dioxygenase from Rhodococcus maanshanensis DSM 44675. The dioxygenase was coexpressed in Escherichia coli with its adjacent reductase-encoding gene, pcaA3, and ferredoxin-encoding gene, pcaA4, and showed phenazine-1-carboxylic acid consumption. The dioxygenase-, ferredoxin-, and reductase-encoding genes were expressed in Pseudomonas putida KT2440 or E. coli BL21, and the three recombinant proteins were purified. A phenazine-1-carboxylic acid conversion capability occurred in vitro only when all three components were present. However, P. putida KT2440 transformed with pcaA1A2 obtained phenazine-1-carboxylic acid degradation ability, suggesting that phenazine-1-carboxylic acid 1,2-dioxygenase has low specificities for its ferredoxin and reductase. This was verified by replacing PcaA3 with RedA2 in the in vitro enzyme assay. High-performance liquid chromatography-mass spectrometry (HPLC-MS) and nuclear magnetic resonance (NMR) analysis showed that phenazine-1-carboxylic acid was converted to 1,2-dihydroxyphenazine through decarboxylation and hydroxylation, indicating that PcaA1A2A3A4 constitutes the initial phenazine-1-carboxylic acid 1,2-dioxygenase. This study fills a gap in our understanding of the biodegradation of phenazine-1-carboxylic acid and illustrates a new dioxygenase for decarboxylation.IMPORTANCE Phenazine-1-carboxylic acid is widely used in southern China as a key fungicide to prevent rice sheath blight. However, the degradation characteristics of phenazine-1-carboxylic acid and the environmental consequences of the long-term application are not clear. S. wittichii DP58 can use phenazine-1-carboxylic acid as its sole carbon and nitrogen sources. In this study, a three-component dioxygenase, PcaA1A2A3A4, was determined to be the initial dioxygenase for phenazine-1-carboxylic acid degradation in S. wittichii DP58. Phenazine-1-carboxylic acid was converted to 1,2-dihydroxyphenazine through decarboxylation and hydroxylation. This finding may help us discover the pathway for phenazine-1-carboxylic acid degradation.
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Neuhaus K, Landstorfer R, Simon S, Schober S, Wright PR, Smith C, Backofen R, Wecko R, Keim DA, Scherer S. Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP. BMC Genomics 2017; 18:216. [PMID: 28245801 PMCID: PMC5331693 DOI: 10.1186/s12864-017-3586-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 02/13/2017] [Indexed: 12/14/2022] Open
Abstract
Background While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA. Results Based on their low RCV, 150 novel non-translated EHEC transcripts were identified as putative ncRNAs, representing both antisense and intergenic transcripts, 74 of which had expressed homologs in E. coli MG1655. Bioinformatics analysis predicted statistically significant target regulons for 15 of the intergenic transcripts; experimental analysis revealed 4-fold or higher differential expression of 46 novel ncRNA in different growth media. Out of 329 annotated EHEC ncRNAs, 52 showed an RCV similar to protein-coding genes, of those, 16 had RIBOseq patterns matching annotated genes in other enterobacteriaceae, and 11 seem to possess a Shine-Dalgarno sequence, suggesting that such ncRNAs may encode small proteins instead of being solely non-coding. To support that the RIBOseq signals are reflecting translation, we tested the ribosomal-footprint covered ORF of ryhB and found a phenotype for the encoded peptide in iron-limiting condition. Conclusion Determination of the RCV is a useful approach for a rapid first-step differentiation between bacterial ncRNAs and small mRNAs. Further, many known ncRNAs may encode proteins as well. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3586-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Klaus Neuhaus
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany. .,Core Facility Microbiome/NGS, ZIEL Institute for Food & Health, Weihenstephaner Berg 3, D-85354, Freising, Germany.
| | - Richard Landstorfer
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany
| | - Svenja Simon
- Informatik und Informationswissenschaft, Universität Konstanz, D-78457, Konstanz, Germany
| | - Steffen Schober
- Institut für Nachrichtentechnik, Universität Ulm, Albert-Einstein-Allee 43, D-89081, Ulm, Germany
| | - Patrick R Wright
- Bioinformatics Group, Department of Computer Science and BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, University of Freiburg, D-79110, Freiburg, Germany
| | - Cameron Smith
- Bioinformatics Group, Department of Computer Science and BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, University of Freiburg, D-79110, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science and BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, University of Freiburg, D-79110, Freiburg, Germany
| | - Romy Wecko
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany
| | - Daniel A Keim
- Informatik und Informationswissenschaft, Universität Konstanz, D-78457, Konstanz, Germany
| | - Siegfried Scherer
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany
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Akita H, Nakashima N, Hoshino T. Pyruvate production using engineered Escherichia coli. AMB Express 2016; 6:94. [PMID: 27718215 PMCID: PMC5055523 DOI: 10.1186/s13568-016-0259-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/28/2016] [Indexed: 12/24/2022] Open
Abstract
Pyruvate plays an essential role in the central carbon metabolism of multiple organisms and is used as a raw material in the chemical, biochemical and pharmaceutical industries. To meet demand, large amounts of pyruvate are produced through fermentation processes. Here we describe a simple and efficient method for producing pyruvate in Escherichia coli. To stop carbon flux from pyruvate to fatty acids, the accBC genes, which encode the enzyme that catalyzes the first step of fatty acid biosynthesis and is essential for vegetative growth, were manipulated within the genome; its native promoter was replaced with the tetracycline (or doxycycline)-regulated promoter and the corresponding transcriptional regulator genes. The resulting strain grew normally in the presence of doxycycline, but showed poor growth upon withdrawal of doxycycline. Using this strain, we developed a high pyruvate producing strain (strain LAFCPCPt-accBC-aceE), in which the tetracycline-regulated promoter was also introduced upstream of aceE, and the ackA-pta, adhE, cra, ldhA, pflB and poxB genes were deleted. After determining the optimal culture conditions for this strain, the final pyruvate concentration reached 26.1 g L-1 after 72 h with a theoretical yield of 55.6 %. These levels are high enough to indicate that the developed strain has the potential for application to industrial production of pyruvate.
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8
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Tools and Principles for Microbial Gene Circuit Engineering. J Mol Biol 2016; 428:862-88. [DOI: 10.1016/j.jmb.2015.10.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 12/26/2022]
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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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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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Bacterial production of isobutanol without expensive reagents. Appl Microbiol Biotechnol 2014; 99:991-9. [DOI: 10.1007/s00253-014-6173-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 10/24/2022]
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13
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Saeedinia AR, Zeinoddini M, Soleimani M, Sadeghizadeh M. A new method for simultaneous gene deletion and down-regulation in Brucella melitensis Rev.1. Microbiol Res 2014; 170:114-23. [PMID: 25249309 DOI: 10.1016/j.micres.2014.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 08/17/2014] [Accepted: 08/24/2014] [Indexed: 10/24/2022]
Abstract
In this study, our aim was to integrate an antisense expression cassette in bacterial chromosome for providing a long-term expression down-regulation in a bid to develop a new approach for simultaneous deletion and down-regulation of target genes in bacterial system. Therefore, we were used this approach for simultaneous deletion of the perosamine synthetase (per) gene and down-regulation of the virB1 expression in Brucella melitensis Rev.1. The per gene, which is one of the LPS O-chain coding genes, was replaced by homologous recombination with an antisense virB1 expression cassette together with kanamycin resistance cassette (kan(R)). Deletion of the per gene was characterized by PCR analysis and DNA sequencing. The expression of antisense virB1 cassette was confirmed by RT-PCR. Down-regulation of the virB1 mRNA expression was quantified by real-time RT-PCR using virB1 specific primers relative to the groEL reference gene. The survival rate of mutant strain was evaluated by CFU count in the BALB/c mice. The virB1 mRNA expression was down-regulated on average 10-fold in mutant strain as compared to parental strain. The loss of per gene function and decrease of the virB1 mRNA expression resulted in reduced entry and survival of the mutant Rev.1 strain in BALB/c mice splenocytes. We propose that this method can be used for simultaneous regulation of multiple genes expression.
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Affiliation(s)
- Ali Reza Saeedinia
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box: 14115-175, Tehran, Iran.
| | - Mehdi Zeinoddini
- Department of Genetics, Science and Biotechnology Research Center, Mallek-Ashtar University of Technology, P.O. Box: 15875-1774, Tehran, Iran.
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box: 14115-111, Tehran, Iran.
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box: 14115-175, Tehran, Iran.
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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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15
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Nakashima N, Miyazaki K. Bacterial cellular engineering by genome editing and gene silencing. Int J Mol Sci 2014; 15:2773-93. [PMID: 24552876 PMCID: PMC3958881 DOI: 10.3390/ijms15022773] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/27/2014] [Accepted: 01/28/2014] [Indexed: 12/18/2022] Open
Abstract
Genome editing is an important technology for bacterial cellular engineering, which is commonly conducted by homologous recombination-based procedures, including gene knockout (disruption), knock-in (insertion), and allelic exchange. In addition, some new recombination-independent approaches have emerged that utilize catalytic RNAs, artificial nucleases, nucleic acid analogs, and peptide nucleic acids. Apart from these methods, which directly modify the genomic structure, an alternative approach is to conditionally modify the gene expression profile at the posttranscriptional level without altering the genomes. This is performed by expressing antisense RNAs to knock down (silence) target mRNAs in vivo. This review describes the features and recent advances on methods used in genomic engineering and silencing technologies that are advantageously used for bacterial cellular engineering.
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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.
| | - Kentaro Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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