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Lautenschläger N, Schmidt K, Schiffer C, Wulff TF, Hahnke K, Finstermeier K, Mansour M, Elsholz AKW, Charpentier E. Expanding the genetic toolbox for the obligate human pathogen Streptococcus pyogenes. Front Bioeng Biotechnol 2024; 12:1395659. [PMID: 38911550 PMCID: PMC11190166 DOI: 10.3389/fbioe.2024.1395659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/06/2024] [Indexed: 06/25/2024] Open
Abstract
Genetic tools form the basis for the study of molecular mechanisms. Despite many recent advances in the field of genetic engineering in bacteria, genetic toolsets remain scarce for non-model organisms, such as the obligatory human pathogen Streptococcus pyogenes. To overcome this limitation and enable the straightforward investigation of gene functions in S. pyogenes, we have developed a comprehensive genetic toolset. By adapting and combining different tools previously applied in other Gram-positive bacteria, we have created new replicative and integrative plasmids for gene expression and genetic manipulation, constitutive and inducible promoters as well as fluorescence reporters for S. pyogenes. The new replicative plasmids feature low- and high-copy replicons combined with different resistance cassettes and a standardized multiple cloning site for rapid cloning procedures. We designed site-specific integrative plasmids and verified their integration by nanopore sequencing. To minimize the effect of plasmid integration on bacterial physiology, we screened publicly available RNA-sequencing datasets for transcriptionally silent sites. We validated this approach by designing the integrative plasmid pSpy0K6 targeting the transcriptionally silent gene SPy_1078. Analysis of the activity of different constitutive promoters indicated a wide variety of strengths, with the lactococcal promoter P 23 showing the strongest activity and the synthetic promoter P xylS2 showing the weakest activity. Further, we assessed the functionality of three inducible regulatory elements including a zinc- and an IPTG-inducible promoter as well as an erythromycin-inducible riboswitch that showed low-to-no background expression and high inducibility. Additionally, we demonstrated the applicability of two codon-optimized fluorescent proteins, mNeongreen and mKate2, as reporters in S. pyogenes. We therefore adapted the chemically defined medium called RPMI4Spy that showed reduced autofluorescence and enabled efficient signal detection in plate reader assays and fluorescence microscopy. Finally, we developed a plasmid-based system for genome engineering in S. pyogenes featuring the counterselection marker pheS*, which enabled the scarless deletion of the sagB gene. This new toolbox simplifies previously laborious genetic manipulation procedures and lays the foundation for new methodologies to study gene functions in S. pyogenes, leading to a better understanding of its virulence mechanisms and physiology.
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Affiliation(s)
| | - Katja Schmidt
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Thomas F. Wulff
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Karin Hahnke
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Moïse Mansour
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
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2
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Zhang Z, Huo J, Velo J, Zhou H, Flaherty A, Saier MH. Comprehensive Characterization of fucAO Operon Activation in Escherichia coli. Int J Mol Sci 2024; 25:3946. [PMID: 38612757 PMCID: PMC11011485 DOI: 10.3390/ijms25073946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Wildtype Escherichia coli cells cannot grow on L-1,2-propanediol, as the fucAO operon within the fucose (fuc) regulon is thought to be silent in the absence of L-fucose. Little information is available concerning the transcriptional regulation of this operon. Here, we first confirm that fucAO operon expression is highly inducible by fucose and is primarily attributable to the upstream operon promoter, while the fucO promoter within the 3'-end of fucA is weak and uninducible. Using 5'RACE, we identify the actual transcriptional start site (TSS) of the main fucAO operon promoter, refuting the originally proposed TSS. Several lines of evidence are provided showing that the fucAO locus is within a transcriptionally repressed region on the chromosome. Operon activation is dependent on FucR and Crp but not SrsR. Two Crp-cAMP binding sites previously found in the regulatory region are validated, where the upstream site plays a more critical role than the downstream site in operon activation. Furthermore, two FucR binding sites are identified, where the downstream site near the first Crp site is more important than the upstream site. Operon transcription relies on Crp-cAMP to a greater degree than on FucR. Our data strongly suggest that FucR mainly functions to facilitate the binding of Crp to its upstream site, which in turn activates the fucAO promoter by efficiently recruiting RNA polymerase.
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Affiliation(s)
- Zhongge Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0116, USA; (J.H.); (J.V.); (A.F.)
| | | | | | | | | | - Milton H. Saier
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0116, USA; (J.H.); (J.V.); (A.F.)
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3
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Zhu L, Song Y, Ma S, Yang S. Heterologous production of 3-hydroxypropionic acid in Methylorubrum extorquens by introducing the mcr gene via a multi-round chromosomal integration system based on cre-lox71/lox66 and transposon. Microb Cell Fact 2024; 23:5. [PMID: 38172868 PMCID: PMC10763676 DOI: 10.1186/s12934-023-02275-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND AND AIM Reprogramming microorganisms to enhance the production of metabolites is a part of contemporary synthetic biology, which relies on the availability of genetic tools to successfully manipulate the bacteria. Methylorubrum extorquens AM1 is a platform microorganism used to convert C1 compounds into various value-added products. However, the repertoire of available plasmids to conveniently and quickly fine-tune the expression of multiple genes in this strain is extremely limited compared with other model microorganisms such as Escherichia coli. Thus, this study aimed to integrate existing technologies, such as transposon-mediated chromosomal integration and cre-lox-mediated recombination, to achieve the diversified expression of target genes through multiple chromosomal insertions in M. extorquens AM1. RESULTS A single plasmid toolkit, pSL-TP-cre-km, containing a miniHimar1 transposon and an inducible cre-lox71/lox66 system, was constructed and characterized for its multiple chromosomal integration capacity. A co-transcribed mcr-egfp cassette [for the production of 3-hydroxypropionic acid (3-HP) and a reporting green fluorescent protein] was added to construct pTP-cre-mcr-egfp for evaluating its utility in mediating the expression of heterologous genes, resulting in the production of 3-HP with a titer of 34.7-55.2 mg/L by two chromosomal integration copies. Furthermore, in association with the expression of plasmid-based mcr, 3-HP production increased to 65.5-92.4 mg/L. CONCLUSIONS This study used a multi-round chromosomal integration system based on cre-lox71/lox66 and a transposon to construct a single constructed vector. A heterologous mcr gene was introduced through this vector, and high expression of 3-hydroxypropionic acid was achieved in M. extorquens. This study provided an efficient genetic tool for manipulating M. extorquens, which not only help increase the expression of heterologous genes in M. extorquens but also provide a reference for strains lacking genetic manipulation vectors.
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Affiliation(s)
- Liping Zhu
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.
| | - Yazhen Song
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Shunan Ma
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Song Yang
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China.
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4
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Kruse L, Loeschcke A, de Witt J, Wierckx N, Jaeger K, Thies S. Halopseudomonas species: Cultivation and molecular genetic tools. Microb Biotechnol 2024; 17:e14369. [PMID: 37991430 PMCID: PMC10832565 DOI: 10.1111/1751-7915.14369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
The Halopseudomonas species, formerly classified as Pseudomonas pertucinogena lineage, form a unique phylogenetic branch within the Pseudomonads. Most strains have recently been isolated from challenging habitats including oil- or metal-polluted sites, deep sea, and intertidal zones, suggesting innate resilience to physical and chemical stresses. Despite their comparably small genomes, these bacteria synthesise several biomolecules with biotechnological potential and a role in the degradation of anthropogenic pollutants has been suggested for some Halopseudomonads. Until now, these bacteria are not readily amenable to existing cultivation and cloning methods. We addressed these limitations by selecting four Halopseudomonas strains of particular interest, namely H. aestusnigri, H. bauzanensis, H. litoralis, and H. oceani to establish microbiological and molecular genetic methods. We found that C4 -C10 dicarboxylic acids serve as viable carbon sources in both complex and mineral salt cultivation media. We also developed plasmid DNA transfer protocols and assessed vectors with different origins of replication and promoters inducible with isopropyl-β-d-thiogalactopyranoside, l-arabinose, and salicylate. Furthermore, we have demonstrated the simultaneous genomic integration of expression cassettes into one and two attTn7 integration sites. Our results provide a valuable toolbox for constructing robust chassis strains and highlight the biotechnological potential of Halopseudomonas strains.
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Affiliation(s)
- Luzie Kruse
- Institute of Molecular Enzyme TechnologyHeinrich Heine UniversityDüsseldorfGermany
| | - Anita Loeschcke
- Institute of Molecular Enzyme TechnologyHeinrich Heine UniversityDüsseldorfGermany
| | - Jan de Witt
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyJülichGermany
| | - Nick Wierckx
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyJülichGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich Heine UniversityDüsseldorfGermany
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyJülichGermany
| | - Stephan Thies
- Institute of Molecular Enzyme TechnologyHeinrich Heine UniversityDüsseldorfGermany
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5
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Systematic metabolic engineering of Escherichia coli for the enhanced production of cinnamaldehyde. Metab Eng 2023; 76:63-74. [PMID: 36639020 DOI: 10.1016/j.ymben.2023.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Cinnamaldehyde (CAD) derived from cinnamon bark has received much attention for its potential as a nematicide and food additive. Previously, we have succeeded in developing an Escherichia coli strain (YHP05) capable of synthesizing cinnamaldehyde; however, the production titer (75 mg/L) was not sufficient for commercialization. Herein, to develop an economical and sustainable production bioprocess, we further engineered the YHP05 strain for non-auxotrophic, antibiotic-free, inducer-free hyperproduction of CAD using systematic metabolic engineering. First, the conversion of trans-cinnamic acid (t-CA) to CAD was improved by the co-expression of carboxylic acid reductase and phosphopantetheinyl transferase (PPTase) genes. Second, to prevent the spontaneous conversion of CAD to cinnamyl alcohol, 10 endogenous reductase and dehydrogenase genes were deleted. Third, all expression cassettes were integrated into the chromosomal DNA using an auto-inducible system for antibiotic- and inducer-free production. Subsequently, to facilitate CAD production, available pools of cofactors (NADPH, CoA, and ATP) were increased, and acetate pathways were deleted. With the final antibiotic-, plasmid-, and inducer-free strain (H-11MPmR), fed-batch cultivations combined with in situ product recovery (ISPR) were performed, and the production titer of CAD as high as 3.8 g/L could be achieved with 49.1 mg/L/h productivity, which is the highest CAD titer ever reported.
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6
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Hsu SY, Lee J, Sychla A, Smanski MJ. Rational search of genetic design space for a heterologous terpene metabolic pathway in Streptomyces. Metab Eng 2023; 77:1-11. [PMID: 36863605 DOI: 10.1016/j.ymben.2023.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/05/2023] [Accepted: 02/22/2023] [Indexed: 03/04/2023]
Abstract
Modern tools in DNA synthesis and assembly give genetic engineers control over the nucleotide-level design of complex, multi-gene systems. Systematic approaches to explore genetic design space and optimize the performance of genetic constructs are lacking. Here we explore the application of a five-level Plackett-Burman fractional factorial design to improve the titer of a heterologous terpene biosynthetic pathway in Streptomyces. A library of 125 engineered gene clusters encoding the production of diterpenoid ent-atiserenoic acid (eAA) via the methylerythritol phosphate pathway was constructed and introduced into Streptomyces albidoflavus J1047 for heterologous expression. The eAA production titer varied within the library by over two orders of magnitude and host strains showed unexpected and reproducible colony morphology phenotypes. Analysis of Plackett-Burman design identified expression of dxs, the gene encoding the first and the flux-controlling enzyme, having the strongest impact on eAA titer, but with a counter-intuitive negative correlation between dxs expression and eAA production. Finally, simulation modeling was performed to determine how several plausible sources of experimental error/noise and non-linearity impact the utility of Plackett-Burman analyses.
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Affiliation(s)
- Szu-Yi Hsu
- Department of Biochemistry, Molecular Biology, and Biophysics, USA; Biotechnology Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jihaeng Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, USA; Biotechnology Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Adam Sychla
- Department of Biochemistry, Molecular Biology, and Biophysics, USA; Biotechnology Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Michael J Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, USA; Biotechnology Institute, University of Minnesota, Saint Paul, MN, 55108, USA.
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7
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Overexpression of a Thermostable α-Amylase through Genome Integration in Bacillus subtilis. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A carbohydrate binding module 68 (CBM68) of pullulanase from Anoxybacillus sp. LM18-11 was used to enhance the secretory expression of a thermostable α-amylase (BLA702) in Bacillus subtilis, through an atypical secretion pathway. The extracellular activity of BLA702 guided by CBM68 was 1248 U/mL, which was 12.6 and 7.2 times higher than that of BLA702 guided by its original signal peptide and the endogenous signal peptide LipA, respectively. A single gene knockout strain library containing 51 genes encoding macromolecular transporters was constructed to detect the effect of each transporter on the secretory expression of CBM68-BLA702. The gene knockout strain 0127 increased the extracellular amylase activity by 2.5 times. On this basis, an engineered strain B. subtilis 0127 (AmyE::BLA702-NprB::CBM68-BLA702-PrsA) was constructed by integrating BLA702 and CBM68-BLA702 at the AmyE and NprB sites in the genome of B. subtilis 0127, respectively. The molecular chaperone PrsA was overexpressed, to reduce the inclusion body formation of the recombinant enzymes. The highest extracellular amylase activity produced by B. subtilis 0127 (AmyE::BLA702-NprB::CBM68-BLA702-PrsA) was 3745.7 U/mL, which was a little lower than that (3825.4 U/mL) of B. subtilis 0127 (pMAC68-BLA702), but showing a better stability of passage. This newly constructed strain has potential for the industrial production of BLA702.
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8
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Ye B, Tao Q, Yan X. A transposon system for random insertion of a gene expression cassette into the chromosome of Bacillus subtilis. J Biotechnol 2023; 361:66-73. [PMID: 36494011 DOI: 10.1016/j.jbiotec.2022.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Bacillus subtilis is a robust industrial workhorse for the production of heterologous proteins. Chromosomal integration-based protein production has advantages over plasmid-based methods. Considering that the expression level of a gene is affected by its location in the chromosome, it is important to find an optimal integration site for the gene to be expressed. This work establishes a method for random insertion of a gene expression cassette into chromosomes, enabling the screening of optimal integration sites for high-level protein production. Specifically, a gene expression cassette and a chloromycetin-resistance marker are assembled into a transposon. This transposon is inserted between the promoter and the ribosomal binding site of the zeocin-resistance marker in the chromosome, which blocks the transcription of the zeocin-resistance gene. Transposase Himar1-mediated transposition of this transposon activates the zeocin-resistance marker, which can be selected on plates containing both chloromycetin and zeocin. The transposition frequency was over 10-5. This method was used to select proper insertion sites for the expression cassette of methyl parathion hydrolase (MPH). Compared with the common integration site amyE, the expression level of MPH was increased up to 50 % at the yjbH site.
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Affiliation(s)
- Bin Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China; Institute of Microbe and Host Health, College of Agriculture and Forestry, Linyi University, Linyi, Shandong 276000, PR China
| | - Qing Tao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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9
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Anderson ME, Smith JL, Grossman AD. Multiple mechanisms for overcoming lethal over-initiation of DNA replication. Mol Microbiol 2022; 118:426-442. [PMID: 36053906 PMCID: PMC9825946 DOI: 10.1111/mmi.14976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/14/2022] [Accepted: 08/25/2022] [Indexed: 01/12/2023]
Abstract
DNA replication is highly regulated and primarily controlled at the step of initiation. In bacteria, the replication initiator DnaA and the origin of replication oriC are the primary targets of regulation. Perturbations that increase or decrease replication initiation can cause a decrease in cell fitness. We found that multiple mechanisms, including an increase in replication elongation and a decrease in replication initiation, can compensate for lethal over-initiation. We found that in Bacillus subtilis, under conditions of rapid growth, loss of yabA, a negative regulator of replication initiation, caused a synthetic lethal phenotype when combined with the dnaA1 mutation that also causes replication over-initiation. We isolated several classes of suppressors that restored viability to dnaA1 ∆yabA double mutants. Some suppressors (relA, nrdR) stimulated replication elongation. Others (dnaC, cshA) caused a decrease in replication initiation. One class of suppressors decreased replication initiation in the dnaA1 ∆yabA mutant by causing a decrease in the amount of the replicative helicase, DnaC. We found that decreased levels of helicase in otherwise wild-type cells were sufficient to decrease replication initiation during rapid growth, indicating that the replicative helicase is limiting for replication initiation. Our results highlight the multiple mechanisms cells use to regulate DNA replication.
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Affiliation(s)
- Mary E. Anderson
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Janet L. Smith
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Alan D. Grossman
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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10
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Moschner C, Wedd C, Bakshi S. The context matrix: Navigating biological complexity for advanced biodesign. Front Bioeng Biotechnol 2022; 10:954707. [PMID: 36082163 PMCID: PMC9445834 DOI: 10.3389/fbioe.2022.954707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/29/2022] [Indexed: 12/05/2022] Open
Abstract
Synthetic biology offers many solutions in healthcare, production, sensing and agriculture. However, the ability to rationally engineer synthetic biosystems with predictable and robust functionality remains a challenge. A major reason is the complex interplay between the synthetic genetic construct, its host, and the environment. Each of these contexts contains a number of input factors which together can create unpredictable behaviours in the engineered biosystem. It has become apparent that for the accurate assessment of these contextual effects a more holistic approach to design and characterisation is required. In this perspective article, we present the context matrix, a conceptual framework to categorise and explore these contexts and their net effect on the designed synthetic biosystem. We propose the use and community-development of the context matrix as an aid for experimental design that simplifies navigation through the complex design space in synthetic biology.
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11
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Bernhards CB, Liem AT, Berk KL, Roth PA, Gibbons HS, Lux MW. Putative Phenotypically Neutral Genomic Insertion Points in Prokaryotes. ACS Synth Biol 2022; 11:1681-1685. [PMID: 35271248 PMCID: PMC9016761 DOI: 10.1021/acssynbio.1c00531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
The barriers to effective
genome editing in diverse prokaryotic
organisms have been falling at an accelerated rate. As editing becomes
easier in more organisms, quickly identifying genomic locations to
insert new genetic functions without disrupting organism fitness becomes
increasingly useful. When the insertion is noncoding DNA for applications
such as information storage or barcoding, a neutral insertion point
can be especially important. Here we describe an approach to identify
putatively neutral insertion sites in prokaryotes. An algorithm (targetFinder)
finds convergently transcribed genes with gap sizes within a specified
range, and looks for annotations within the gaps. We report putative
editing targets for 10 common synthetic biology chassis organisms,
including coverage of available RNA-seq data, and provide software
to apply to others. We further experimentally evaluate the neutrality
of six identified targets in Escherichia coli through
insertion of a DNA barcode. We anticipate this information and the
accompanying tool will prove useful for synthetic biologists seeking
neutral insertion points for genome editing.
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Affiliation(s)
- Casey B. Bernhards
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
- Excet, Inc., Springfield, Virginia 22150, United States
| | - Alvin T. Liem
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
- DCS Corporation, Belcamp, Maryland 21017, United States
| | - Kimberly L. Berk
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Pierce A. Roth
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
- DCS Corporation, Belcamp, Maryland 21017, United States
| | - Henry S. Gibbons
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Matthew W. Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
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12
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Falkenberg KB, Mol V, de la Maza Larrea AS, Pogrebnyakov I, Nørholm MHH, Nielsen AT, Jensen SI. The ProUSER2.0 Toolbox: Genetic Parts and Highly Customizable Plasmids for Synthetic Biology in Bacillus subtilis. ACS Synth Biol 2021; 10:3278-3289. [PMID: 34793671 DOI: 10.1021/acssynbio.1c00130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Versatile DNA assembly standards and compatible, well-characterized part libraries are essential tools for creating effective designs in synthetic biology. However, to date, vector standards for Gram-positive hosts have limited flexibility. As a result, users often revert to PCR-based methods for building the desired genetic constructs. These methods are inherently prone to introducing mutations, which is problematic considering vector backbone parts are often left unsequenced in cloning workflows. To circumvent this, we present the ProUSER2.0 toolbox: a standardized vector platform for building both integrative and replicative shuttle vectors forBacillus subtilis. The ProUSER2.0 vectors consist of a ProUSER cassette for easy and efficient insertion of cargo sequences and six exchangeable modules. Furthermore, the standard is semicompatible with several previously developed standards, allowing the user to utilize the parts developed for these. To provide parts for the toolbox, seven novel integration sites and six promoters were thoroughly characterized in B. subtilis. Finally, the capacity of the ProUSER2.0 system was demonstrated through the construction of signal peptide libraries for two industrially relevant proteins. Altogether, the ProUSER2.0 toolbox is a powerful and flexible framework for use in B. subtilis.
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Affiliation(s)
- Kristoffer Bach Falkenberg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Viviënne Mol
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Arrate Sainz de la Maza Larrea
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Ivan Pogrebnyakov
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Morten H. H. Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, Kongens Lyngby 2800, Denmark
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13
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Zhou C, Yang G, Zhang L, Zhang H, Zhou H, Lu F. Construction of an alkaline protease overproducer strain based on Bacillus licheniformis 2709 using an integrative approach. Int J Biol Macromol 2021; 193:1449-1456. [PMID: 34742839 DOI: 10.1016/j.ijbiomac.2021.10.208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
Bacillus licheniformis 2709 is a potential cell factory for the production of alkaline protease AprE, which has important value in industrial application but still lacks sufficient production capacity. To address this problem, we investigated the effects of the secretory viscous materials on the synthesis of AprE, which might seriously affect the industrial fermentation. Furthermore, an iterative chromosomal integration strategy at various chromosomal loci was implemented to achieve stable high-level expression of AprE in B. licheniformis 2709. The host was genetically modified by disrupting the native pgs cluster controlling the biosynthesis of viscous poly-glutamic acid identified in the study by GC/MS, generating a mutant with significantly higher biomass and better bioreactor performance. We further enhanced the expression of alkaline protease by integrating two additional aprE expression cassettes into the genome, generating the integration mutant BL ∆UEP-3 with three aprE expression cassettes, whose AprE enzyme activity in shake flasks reached 25,736 ± 997 U/mL, which was 136% higher than that of the original strain, while the aprE transcription level increased 4.05 times. Thus, an AprE high-yielding strain with excellent fermentation traits was engineered, which was more suitable for bulk-production. Finally, the AprE titer was further increased in a 5-L fermenter, reaching 57,763 ± 1039 U/mL. In summary, genetic modification is an enabling technology for enhancing enzyme production by eliminating the unfavorable characteristics of the host and optimizing the expression of aprE through iterative chromosomal integration. We believe that the protocol developed in this study provides a valuable reference for chromosomal overexpression of proteins or bioactive molecules in other Bacillus species.
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Affiliation(s)
- Cuixia Zhou
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Guangcheng Yang
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China.
| | - Lei Zhang
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China
| | - Huitu Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Huiying Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China.
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14
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Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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15
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The spatial position effect: synthetic biology enters the era of 3D genomics. Trends Biotechnol 2021; 40:539-548. [PMID: 34607694 DOI: 10.1016/j.tibtech.2021.09.001] [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: 07/23/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022]
Abstract
Microbial cell factories are critical to achieving green biomanufacturing. A position effect occurs when a synthetic gene circuit is expressed from different positions in the chassis strain genome. Here, we propose the concept of the 'spatial position effect,' which uses technologies in 3D genomics to reveal the spatial structure characteristics of the 3D genome of the chassis. On this basis, we propose to rationally design the integration sites of synthetic gene circuits, use reporter genes for preliminary screening, and integrate synthetic gene circuits into promising sites for further experiments. This approach can produce stable and efficient chassis strains for green biomanufacturing. The proposed spatial position effect brings synthetic biology into the era of 3D genomics.
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16
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Appelbaum M, Schweder T. Metabolic Engineering of
Bacillus
– New Tools, Strains, and Concepts. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Nagy C, Thiel K, Mulaku E, Mustila H, Tamagnini P, Aro EM, Pacheco CC, Kallio P. Comparison of alternative integration sites in the chromosome and the native plasmids of the cyanobacterium Synechocystis sp. PCC 6803 in respect to expression efficiency and copy number. Microb Cell Fact 2021; 20:130. [PMID: 34246263 PMCID: PMC8272380 DOI: 10.1186/s12934-021-01622-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Synechocystis sp. PCC 6803 provides a well-established reference point to cyanobacterial metabolic engineering as part of basic photosynthesis research, as well as in the development of next-generation biotechnological production systems. This study focused on expanding the current knowledge on genomic integration of expression constructs in Synechocystis, targeting a range of novel sites in the chromosome and in the native plasmids, together with established loci used in literature. The key objective was to obtain quantitative information on site-specific expression in reference to replicon copy numbers, which has been speculated but never compared side by side in this host. Results An optimized sYFP2 expression cassette was successfully integrated in two novel sites in Synechocystis chromosome (slr0944; sll0058) and in all four endogenous megaplasmids (pSYSM/slr5037-slr5038; pSYSX/slr6037; pSYSA/slr7023; pSYSG/slr8030) that have not been previously evaluated for the purpose. Fluorescent analysis of the segregated strains revealed that the expression levels between the megaplasmids and chromosomal constructs were very similar, and reinforced the view that highest expression in Synechocystis can be obtained using RSF1010-derived replicative vectors or the native small plasmid pCA2.4 evaluated in comparison. Parallel replicon copy number analysis by RT-qPCR showed that the expression from the alternative loci is largely determined by the gene dosage in Synechocystis, thereby confirming the dependence formerly proposed based on literature. Conclusions This study brings together nine different integrative loci in the genome of Synechocystis to demonstrate quantitative differences between target sites in the chromosome, the native plasmids, and a RSF1010-based replicative expression vector. To date, this is the most comprehensive comparison of alternative integrative sites in Synechocystis, and provides the first direct reference between expression efficiency and replicon gene dosage in the context. In the light of existing literature, the findings support the view that the small native plasmids can be notably more difficult to target than the chromosome or the megaplasmids, and that the RSF1010-derived vectors may be surprisingly well maintained under non-selective culture conditions in this cyanobacterial host. Altogether, the work broadens our views on genomic integration and the rational use of different integrative loci versus replicative plasmids, when aiming at expressing heterologous genes in Synechocystis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01622-2.
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Affiliation(s)
- Csaba Nagy
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Kati Thiel
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Edita Mulaku
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Henna Mustila
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Paula Tamagnini
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007, Porto, Portugal
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Catarina C Pacheco
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Pauli Kallio
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland.
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18
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Redondo A, Wood D, Amaral S, Ferré J, Goti D, Bertran J. Production of Toxoplasma gondii Recombinant Antigens in Genome-Edited Escherichia coli. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821020137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Biggs BW, Bedore SR, Arvay E, Huang S, Subramanian H, McIntyre EA, Duscent-Maitland CV, Neidle EL, Tyo KEJ. Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1. Nucleic Acids Res 2020; 48:5169-5182. [PMID: 32246719 PMCID: PMC7229861 DOI: 10.1093/nar/gkaa167] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/20/2020] [Accepted: 03/04/2020] [Indexed: 01/10/2023] Open
Abstract
One primary objective of synthetic biology is to improve the sustainability of chemical manufacturing. Naturally occurring biological systems can utilize a variety of carbon sources, including waste streams that pose challenges to traditional chemical processing, such as lignin biomass, providing opportunity for remediation and valorization of these materials. Success, however, depends on identifying micro-organisms that are both metabolically versatile and engineerable. Identifying organisms with this combination of traits has been a historic hindrance. Here, we leverage the facile genetics of the metabolically versatile bacterium Acinetobacter baylyi ADP1 to create easy and rapid molecular cloning workflows, including a Cas9-based single-step marker-less and scar-less genomic integration method. In addition, we create a promoter library, ribosomal binding site (RBS) variants and test an unprecedented number of rationally integrated bacterial chromosomal protein expression sites and variants. At last, we demonstrate the utility of these tools by examining ADP1’s catabolic repression regulation, creating a strain with improved potential for lignin bioprocessing. Taken together, this work highlights ADP1 as an ideal host for a variety of sustainability and synthetic biology applications.
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Affiliation(s)
- Bradley W Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Biotechnology Training Program, Northwestern University, Evanston, IL 60208, USA
| | - Stacy R Bedore
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Erika Arvay
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Biotechnology Training Program, Northwestern University, Evanston, IL 60208, USA
| | - Shu Huang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Harshith Subramanian
- Master of Science in Biotechnology Program, Northwestern University, Evanston, IL 60208, USA
| | - Emily A McIntyre
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | | | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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20
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Krogh TJ, Franke A, Møller-Jensen J, Kaleta C. Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes - Observing Strong Local Effects of Nucleoid Structure on Gene Regulation. Front Microbiol 2020; 11:2002. [PMID: 32983020 PMCID: PMC7491251 DOI: 10.3389/fmicb.2020.02002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/29/2020] [Indexed: 11/13/2022] Open
Abstract
Both intrinsic and extrinsic mechanisms regulating bacterial expression have been elucidated and described, however, such studies have mainly focused on local effects on the two-dimensional structure of the prokaryote genome while long-range as well as spatial interactions influencing gene expression are still only poorly understood. In this paper, we investigate the association between co-expression and distance between genes, using RNA-seq data at multiple growth phases in order to illuminate whether such conserved patterns are an indication of a gene regulatory mechanism relevant for prokaryotic cell proliferation, adaption, and evolution. We observe recurrent sinusoidal patterns in correlation of pairwise expression as function of genomic distance and rule out that these are caused by transcription-induced supercoiling gradients, gene clustering in operons, or association with regulatory transcription factors (TFs). By comparing spatial proximity for pairs of genomic bins with their correlation of pairwise expression, we further observe a high co-expression proportional with the spatial proximity. Based on these observations, we propose that the observed patterns are related to nucleoid structure as a product of transcriptional spilling, where genes actively influence transcription of spatially proximal genes through increases within shared local pools of RNA polymerases (RNAP), and actively spilling transcription onto neighboring genes.
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Affiliation(s)
- Thøger Jensen Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University Kiel, Kiel, Germany
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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21
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Developing rapid growing Bacillus subtilis for improved biochemical and recombinant protein production. Metab Eng Commun 2020; 11:e00141. [PMID: 32874915 PMCID: PMC7452210 DOI: 10.1016/j.mec.2020.e00141] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 12/28/2022] Open
Abstract
Bacillus subtilis is a model Gram-positive bacterium, which has been widely used as industrially important chassis in synthetic biology and metabolic engineering. Rapid growth of chassis is beneficial for shortening the fermentation period and enhancing production of target product. However, engineered B. subtilis with faster growth phenotype is lacking. Here, fast-growing B. subtilis were constructed through rational gene knockout and adaptive laboratory evolution using wild type strain B. subtilis 168 (BS168) as starting strain. Specifically, strains BS01, BS02, and BS03 were obtained through gene knockout of oppD, hag, and flgD genes, respectively, resulting 15.37%, 24.18% and 36.46% increases of specific growth rate compared with BS168. Next, strains A28 and A40 were obtained through adaptive laboratory evolution, whose specific growth rates increased by 39.88% and 43.53% compared to BS168, respectively. Then these two methods were combined via deleting oppD, hag, and flgD genes respectively on the basis of evolved strain A40, yielding strain A4003 with further 7.76% increase of specific growth rate, reaching 0.75 h-1 in chemical defined M9 medium. Finally, bioproduction efficiency of intracellular product (ribonucleic acid, RNA), extracellular product (acetoin), and recombinant proteins (green fluorescent protein (GFP) and ovalbumin) by fast-growing strain A4003 was tested. And the production of RNA, acetoin, GFP, and ovalbumin increased 38.09%, 5.40%, 9.47% and 19.79% using fast-growing strain A4003 as chassis compared with BS168, respectively. The developed fast-growing B. subtilis strains and strategies used for developing these strains should be useful for improving bioproduction efficiency and constructing other industrially important bacterium with faster growth phenotype. Fast-growing Bacillus subtilis were constructed through rational gene knockout and adaptive laboratory evolution. Specific growth rate of engineered B. subtilis increased 53.06% compared with B. subtilis 168, reaching 0.75 h-1 in M9 medium. Production of RNA, acetoin, and ovalbumin increased 38.09%, 5.40%, and 19.79% using fast-growing strain as chassis.
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22
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Evaluation of chromosomal insertion loci in the Pseudomonas putida KT2440 genome for predictable biosystems design. Metab Eng Commun 2020; 11:e00139. [PMID: 32775199 PMCID: PMC7398981 DOI: 10.1016/j.mec.2020.e00139] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/02/2020] [Accepted: 07/15/2020] [Indexed: 01/27/2023] Open
Abstract
The development of Pseudomonas strains for industrial production of fuels and chemicals will require the integration of heterologous genes and pathways into the chromosome. Finding the most appropriate integration site to maximize strain performance is an essential part of the strain design process. We characterized seven chromosomal loci in Pseudomonas putida KT2440 for integration of a fluorescent protein expression construct. Insertion in five of the loci did not affect growth rate, but fluorescence varied by up to 27-fold. Three sites displaying a diversity of phenotypes with the fluorescent reporter were also chosen for the integration of a gene encoding a muconate importer. Depending on the integration locus, expression of the importer varied by approximately 3-fold and produced significant phenotypic differences. This work demonstrates the impact of the integration location on host viability, gene expression, and overall strain performance. Pseudomonas putida KT2440 chromosomal loci were characterized as potential insertion targets for heterologous genes. Integration location had a significant effect on heterologous protein expression and host phenotype. The identification of an appropriate chromosomal insertion location is essential to optimize genetic engineering design.
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23
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Zhao Y, Yao Z, Ploessl D, Ghosh S, Monti M, Schindler D, Gao M, Cai Y, Qiao M, Yang C, Cao M, Shao Z. Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories. ACS Synth Biol 2020; 9:1736-1752. [PMID: 32396718 DOI: 10.1021/acssynbio.0c00123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We broadened the usage of DNA transposon technology by demonstrating its capacity for the rapid creation of expression libraries for long biochemical pathways, which is beyond the classical application of building genome-scale knockout libraries in yeasts. This strategy efficiently leverages the readily available fine-tuning impact provided by the diverse transcriptional environment surrounding each random integration locus. We benchmark the transposon-mediated integration against the nonhomologous end joining-mediated strategy. The latter strategy was demonstrated for achieving pathway random integration in other yeasts but is associated with a high false-positive rate in the absence of a high-throughput screening method. Our key innovation of a nonreplicable circular DNA platform increased the possibility of identifying top-producing variants to 97%. Compared to the classical DNA transposition protocol, the design of a nonreplicable circular DNA skipped the step of counter-selection for plasmid removal and thus not only reduced the time required for the step of library creation from 10 to 5 d but also efficiently removed the "transposition escapers", which undesirably represented almost 80% of the entire population as false positives. Using one endogenous product (i.e., shikimate) and one heterologous product (i.e., (S)-norcoclaurine) as examples, we presented a streamlined procedure to rapidly identify high-producing variants with titers significantly higher than the reported data in the literature. We selected Scheffersomyces stipitis, a representative nonconventional yeast, as a demo, but the strategy can be generalized to other nonconventional yeasts. This new exploration of transposon technology, therefore, adds a highly versatile tool to accelerate the development of novel species as microbial cell factories for producing value-added chemicals.
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Affiliation(s)
- Yuxin Zhao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Zhanyi Yao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Saptarshi Ghosh
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Marco Monti
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Daniel Schindler
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Yizhi Cai
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Chao Yang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa, United States
- Bioeconomy Institute, Iowa State University, Ames, Iowa, United States
- Interdepartmental Microbiology Program, Iowa State University, Ames, Iowa, United States
- The Ames Laboratory, Ames, Iowa, United States
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24
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Lato DF, Golding GB. Spatial Patterns of Gene Expression in Bacterial Genomes. J Mol Evol 2020; 88:510-520. [PMID: 32506154 PMCID: PMC7324424 DOI: 10.1007/s00239-020-09951-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/08/2020] [Indexed: 01/06/2023]
Abstract
Gene expression in bacteria is a remarkably controlled and intricate process impacted by many factors. One such factor is the genomic position of a gene within a bacterial genome. Genes located near the origin of replication generally have a higher expression level, increased dosage, and are often more conserved than genes located farther from the origin of replication. The majority of the studies involved with these findings have only noted this phenomenon in a single gene or cluster of genes that was re-located to pre-determined positions within a bacterial genome. In this work, we look at the overall expression levels from eleven bacterial data sets from Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti. We have confirmed that gene expression tends to decrease when moving away from the origin of replication in majority of the replicons analysed in this study. This study sheds light on the impact of genomic location on molecular trends such as gene expression and highlights the importance of accounting for spatial trends in bacterial molecular analysis.
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Affiliation(s)
- Daniella F Lato
- Department of Biology, McMaster Univeristy, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada
| | - G Brian Golding
- Department of Biology, McMaster Univeristy, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada.
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25
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Zhou C, Zhou H, Li D, Zhang H, Wang H, Lu F. Optimized expression and enhanced production of alkaline protease by genetically modified Bacillus licheniformis 2709. Microb Cell Fact 2020; 19:45. [PMID: 32093734 PMCID: PMC7041084 DOI: 10.1186/s12934-020-01307-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/12/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Bacillus licheniformis 2709 is extensively applied as a host for the high-level production of heterologous proteins, but Bacillus cells often possess unfavorable wild-type properties, such as production of viscous materials and foam during fermentation, which seriously influenced the application in industrial fermentation. How to develop it from a soil bacterium to a super-secreting cell factory harboring less undomesticated properties always plays vital role in industrial production. Besides, the optimal expression pattern of the inducible enzymes like alkaline protease has not been optimized by comparing the transcriptional efficiency of different plasmids and genomic integration sites in B. licheniformis. RESULT Bacillus licheniformis 2709 was genetically modified by disrupting the native lchAC genes related to foaming and the eps cluster encoding the extracellular mucopolysaccharide via a markerless genome-editing method. We further optimized the expression of the alkaline protease gene (aprE) by screening the most efficient expression system among different modular plasmids and genomic loci. The results indicated that genomic expression of aprE was superior to plasmid expression and finally the transcriptional level of aprE greatly increased 1.67-fold through host optimization and chromosomal integration in the vicinity of the origin of replication, while the enzyme activity significantly improved 62.19% compared with the wild-type alkaline protease-producing strain B. licheniformis. CONCLUSION We successfully engineered an AprE high-yielding strain free of undesirable properties and its fermentation traits could be applied to bulk-production by host genetic modification and expression optimization. In summary, host optimization is an enabling technology for improving enzyme production by eliminating the harmful traits of the host and optimizing expression patterns. We believe that these strategies can be applied to improve heterologous protein expression in other Bacillus species.
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Affiliation(s)
- Cuixia Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Road, Tianjin Economic-Technological Development Area, Tianjin 022, 300457, People's Republic of China
| | - Huiying Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Road, Tianjin Economic-Technological Development Area, Tianjin 022, 300457, People's Republic of China
| | - Dengke Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Road, Tianjin Economic-Technological Development Area, Tianjin 022, 300457, People's Republic of China
| | - Huitu Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Road, Tianjin Economic-Technological Development Area, Tianjin 022, 300457, People's Republic of China.
| | - Hongbin Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Road, Tianjin Economic-Technological Development Area, Tianjin 022, 300457, People's Republic of China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Road, Tianjin Economic-Technological Development Area, Tianjin 022, 300457, People's Republic of China.
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Egbert RG, Rishi HS, Adler BA, McCormick DM, Toro E, Gill RT, Arkin AP. A versatile platform strain for high-fidelity multiplex genome editing. Nucleic Acids Res 2019; 47:3244-3256. [PMID: 30788501 PMCID: PMC6451135 DOI: 10.1093/nar/gkz085] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/13/2018] [Accepted: 02/09/2019] [Indexed: 12/01/2022] Open
Abstract
Precision genome editing accelerates the discovery of the genetic determinants of phenotype and the engineering of novel behaviors in organisms. Advances in DNA synthesis and recombineering have enabled high-throughput engineering of genetic circuits and biosynthetic pathways via directed mutagenesis of bacterial chromosomes. However, the highest recombination efficiencies have to date been reported in persistent mutator strains, which suffer from reduced genomic fidelity. The absence of inducible transcriptional regulators in these strains also prevents concurrent control of genome engineering tools and engineered functions. Here, we introduce a new recombineering platform strain, BioDesignER, which incorporates (i) a refactored λ-Red recombination system that reduces toxicity and accelerates multi-cycle recombination, (ii) genetic modifications that boost recombination efficiency, and (iii) four independent inducible regulators to control engineered functions. These modifications resulted in single-cycle recombineering efficiencies of up to 25% with a 7-fold increase in recombineering fidelity compared to the widely used recombineering strain EcNR2. To facilitate genome engineering in BioDesignER, we have curated eight context-neutral genomic loci, termed Safe Sites, for stable gene expression and consistent recombination efficiency. BioDesignER is a platform to develop and optimize engineered cellular functions and can serve as a model to implement comparable recombination and regulatory systems in other bacteria.
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Affiliation(s)
- Robert G Egbert
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Harneet S Rishi
- Biophysics Graduate Group, University of California - Berkeley, Berkeley, CA 94720, USA.,Designated Emphasis Program in Computational and Genomic Biology, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Benjamin A Adler
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California - Berkeley, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Dylan M McCormick
- Department of Bioengineering, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Esteban Toro
- Department of Bioengineering, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California - Berkeley, Berkeley, CA 94720, USA
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27
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Watzlawick H, Altenbuchner J. Multiple integration of the gene ganA into the Bacillus subtilis chromosome for enhanced β-galactosidase production using the CRISPR/Cas9 system. AMB Express 2019; 9:158. [PMID: 31571017 PMCID: PMC6768931 DOI: 10.1186/s13568-019-0884-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 09/21/2019] [Indexed: 01/18/2023] Open
Abstract
The ganA gene from Bacillus subtilis encoding a β-galactosidase for degradation of the galactomannan was integrated in different loci of the B. subtilis chromosome employing the CRISPR/Cas9 system. Hereby a total of five copies of ganA cassettes in which the ganA gene was fused with the glucitol-promoter were inserted in the recipient chromosome wherein hypothetical, sporulation and protease genes were deleted. The strain with five copies of ganA expression cassette showed a β-galactosidase activity similar to the one with the same gene on a pUB110 derived multi-copy plasmid and under the same regulatory control of the glucitol promoter and GutR activator. The production of β-galactosidase in the strain with the multi-copy plasmid decreased rapidly when growth was performed under induced conditions and without antibiotic selection. In contrast, the strain with the five copies of ganA in the chromosome produced β-galactosidase for at least 40 generations. This demonstrates that the CRISPR/Cas9 system is a valuable and easy tool for constructing stable producer strains. The bigger efforts that are needed for the multiple target gene integration into the chromosome compared to cloning in expression vectors were justified by the higher stability of the target genes and the lack of antibiotic resistance genes.
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28
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Pinto D, Vecchione S, Wu H, Mauri M, Mascher T, Fritz G. Engineering orthogonal synthetic timer circuits based on extracytoplasmic function σ factors. Nucleic Acids Res 2019; 46:7450-7464. [PMID: 29986061 PMCID: PMC6101570 DOI: 10.1093/nar/gky614] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/26/2018] [Indexed: 01/02/2023] Open
Abstract
The rational design of synthetic regulatory circuits critically hinges on the availability of orthogonal and well-characterized building blocks. Here, we focus on extracytoplasmic function (ECF) σ factors, which are the largest group of alternative σ factors and hold extensive potential as synthetic orthogonal regulators. By assembling multiple ECF σ factors into regulatory cascades of varying length, we benchmark the scalability of the approach, showing that these ‘autonomous timer circuits’ feature a tuneable time delay between inducer addition and target gene activation. The implementation of similar timers in Escherichia coli and Bacillus subtilis shows strikingly convergent circuit behavior, which can be rationalized by a computational model. These findings not only reveal ECF σ factors as powerful building blocks for a rational, multi-layered circuit design, but also suggest that ECF σ factors are universally applicable as orthogonal regulators in a variety of bacterial species.
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Affiliation(s)
- Daniela Pinto
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062 Dresden, Germany
| | - Stefano Vecchione
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Hao Wu
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Marco Mauri
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062 Dresden, Germany
| | - Georg Fritz
- LOEWE-Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35032 Marburg, Germany
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29
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Synthetic Biology Toolbox and Chassis Development in Bacillus subtilis. Trends Biotechnol 2019; 37:548-562. [DOI: 10.1016/j.tibtech.2018.10.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 12/24/2022]
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30
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Targeted and Repetitive Chromosomal Integration Enables High-Level Heterologous Gene Expression in Lactobacillus casei. Appl Environ Microbiol 2019; 85:AEM.00033-19. [PMID: 30824448 DOI: 10.1128/aem.00033-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/23/2019] [Indexed: 12/18/2022] Open
Abstract
Lactobacillus casei is a potential cell factory for the production of enzymes and bioactive molecules using episomal plasmids, which suffer from genetic instability. While chromosomal integration strategies can provide genetic stability of recombinant proteins, low expression yields limit their application. To address this problem, we developed a two-step integration strategy in Lb. casei by combination of the LCABL_13040-50-60 recombineering system (comprised of LCABL_1340, LCABL_13050, and LCABL_13060) with the Cre/loxP site-specific recombination system, with an efficiency of ∼3.7 × 103 CFU/µg DNA. A gfp gene was successfully integrated into six selected chromosomal sites, and the relative fluorescence intensities (RFUs) of the resulting integrants varied up to ∼3.7-fold depending on the integrated site, among which the LCABL_07270 site gfp integration showed the highest RFU. However, integrants with gfp gene(s) integrated into the LCABL_07270 site showed various RFUs, ranging from 993 ± 89 to 7,289 ± 564 and corresponding to 1 to 13.68 ± 1.08 copies of gfp gene integration. Moreover, the integrant with 13.68 ± 1.08 copies of the gfp gene had a more stable RFU after 63 generations compared to that of a plasmid-engineered strain. To investigate the feasibility of this system for bioactive molecules with high expression levels, the fimbrial adhesin gene, faeG, from Escherichia coli was tested and successfully integrated into the LCABL_07270 site with 5.51 ± 0.25 copies, and the integrated faeG achieved stable expression. All results demonstrate that this two-step integration system could achieve a high yield of heterologous gene expression by repetitive integration at a targeted chromosomal location in Lb. casei IMPORTANCE Lactic acid bacteria (LAB), including Lactobacillus casei, have the potential for overexpression of heterologous proteins, such as bioactive molecules and enzymes. However, traditional genetic tools for expression of these proteins show genetic instability or low yields of the desired product. In this study, we provide a procedure for repetitive integration of genes at various chromosomal locations, achieving high-level and stable expression of proteins in Lb. casei without selective pressure. The protocol developed in this study provides an essential reference for chromosomal overexpression of proteins or bioactive molecules in LAB.
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31
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Li L, Liu X, Wei K, Lu Y, Jiang W. Synthetic biology approaches for chromosomal integration of genes and pathways in industrial microbial systems. Biotechnol Adv 2019; 37:730-745. [PMID: 30951810 DOI: 10.1016/j.biotechadv.2019.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
Abstract
Industrial biotechnology is reliant on native pathway engineering or foreign pathway introduction for efficient biosynthesis of target products. Chromosomal integration, with intrinsic genetic stability, is an indispensable step for reliable expression of homologous or heterologous genes and pathways in large-scale and long-term fermentation. With advances in synthetic biology and CRISPR-based genome editing approaches, a wide variety of novel enabling technologies have been developed for single-step, markerless, multi-locus genomic integration of large biochemical pathways, which significantly facilitate microbial overproduction of chemicals, pharmaceuticals and other value-added biomolecules. Notably, the newly discovered homology-mediated end joining strategy could be widely applicable for high-efficiency genomic integration in a number of homologous recombination-deficient microbes. In this review, we explore the fundamental principles and characteristics of genomic integration, and highlight the development and applications of targeted integration approaches in the three representative industrial microbial systems, including Escherichia coli, actinomycetes and yeasts.
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Affiliation(s)
- Lei Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaocao Liu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Keke Wei
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, 200232, China.
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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32
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Extracytoplasmic Function σ Factors Can Be Implemented as Robust Heterologous Genetic Switches in Bacillus subtilis. iScience 2019; 13:380-390. [PMID: 30897511 PMCID: PMC6426705 DOI: 10.1016/j.isci.2019.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/14/2019] [Accepted: 03/01/2019] [Indexed: 02/06/2023] Open
Abstract
In bacteria, the promoter specificity of RNA polymerase is determined by interchangeable σ subunits. Extracytoplasmic function σ factors (ECFs) form the largest and most diverse family of alternative σ factors, and their suitability for constructing genetic switches and circuits was already demonstrated. However, a systematic study on how genetically determined perturbations affect the behavior of these switches is still lacking, which impairs our ability to predict their behavior in complex circuitry. Here, we implemented four ECF switches in Bacillus subtilis and comprehensively characterized their robustness toward genetic perturbations, including changes in copy number, protein stability, or antisense transcription. All switches show characteristic dose-response behavior that varies depending on the individual ECF-promoter pair. Most perturbations had performance costs. Although some general design rules could be derived, a detailed characterization of each ECF switch before implementation is recommended to understand and thereby accommodate its individual behavior. Four heterologous ECF-based genetic switches were implemented in Bacillus subtilis Each ECF switch was excessively modified and comprehensively evaluated The robustness to genetic perturbations differed significantly between switches B. subtilis has a narrow phylogenetic acceptance range for heterologous ECFs
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33
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Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile. Antimicrob Agents Chemother 2019; 63:AAC.01363-18. [PMID: 30455241 DOI: 10.1128/aac.01363-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/04/2018] [Indexed: 01/08/2023] Open
Abstract
Clostridium difficile is a potentially lethal gut pathogen that causes nosocomial and community-acquired infections. Limited treatment options and reports of reduced susceptibility to current treatment emphasize the necessity for novel antimicrobials. The DNA polymerase of Gram-positive organisms is an attractive target for the development of antimicrobials. ACX-362E [N 2-(3,4-dichlorobenzyl)-7-(2-[1-morpholinyl]ethyl)guanine; MorE-DCBG] is a DNA polymerase inhibitor in preclinical development as a novel therapeutic against C. difficile infection. This synthetic purine shows preferential activity against C. difficile PolC over those of other organisms in vitro and is effective in an animal model of C. difficile infection. In this study, we have determined its efficacy against a large collection of clinical isolates. At concentrations below the MIC, the presumed slowing (or stalling) of replication forks due to ACX-362E leads to a growth defect. We have determined the transcriptional response of C. difficile to replication inhibition and observed an overrepresentation of upregulated genes near the origin of replication in the presence of PolC inhibitors, but not when cells were subjected to subinhibitory concentrations of other antibiotics. This phenomenon can be explained by a gene dosage shift, as we observed a concomitant increase in the ratio between origin-proximal and terminus-proximal gene copy number upon exposure to PolC inhibitors. Moreover, we show that certain genes differentially regulated under PolC inhibition are controlled by the origin-proximal general stress response regulator sigma factor B. Together, these data suggest that genome location both directly and indirectly determines the transcriptional response to replication inhibition in C. difficile.
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34
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Hantke I, Schäfer H, Janczikowski A, Turgay K. YocM a small heat shock protein can protect Bacillus subtilis cells during salt stress. Mol Microbiol 2018; 111:423-440. [PMID: 30431188 DOI: 10.1111/mmi.14164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2018] [Indexed: 12/17/2022]
Abstract
Small heat shock proteins (sHsp) occur in all domains of life. By interacting with misfolded or aggregated proteins these chaperones fulfill a protective role in cellular protein homeostasis. Here, we demonstrate that the sHsp YocM of the Gram-positive model organism Bacillus subtilis is part of the cellular protein quality control system with a specific role in salt stress response. In the absence of YocM the survival of salt shocked cells is impaired, and increased levels of YocM protect B. subtilis exposed to heat or salt. We observed a salt and heat stress-induced localization of YocM to intracellular protein aggregates. Interestingly, purified YocM appears to accelerate protein aggregation of different model substrates in vitro. In addition, the combined presence of YocM and chemical chaperones, which accumulate in salt stressed cells, can facilitate in vitro a synergistic protective effect on protein misfolding. Therefore, the beneficial role of YocM during salt stress could be related to a mutual functional relationship with chemical chaperones and adds a new possible functional aspect to sHsp chaperone activities.
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Affiliation(s)
- Ingo Hantke
- Institut für Mikrobiologie der Universität Hannover, Leibniz-Universität Hannover, Hannover, Germany
| | - Heinrich Schäfer
- Institut für Mikrobiologie der Universität Hannover, Leibniz-Universität Hannover, Hannover, Germany
| | - Armgard Janczikowski
- Institut für Mikrobiologie der Universität Hannover, Leibniz-Universität Hannover, Hannover, Germany
| | - Kürşad Turgay
- Institut für Mikrobiologie der Universität Hannover, Leibniz-Universität Hannover, Hannover, Germany
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35
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Advances and prospects of Bacillus subtilis cellular factories: From rational design to industrial applications. Metab Eng 2018; 50:109-121. [DOI: 10.1016/j.ymben.2018.05.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/02/2018] [Accepted: 05/10/2018] [Indexed: 01/29/2023]
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36
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Krogh TJ, Møller-Jensen J, Kaleta C. Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes. Front Microbiol 2018; 9:2019. [PMID: 30210483 PMCID: PMC6119826 DOI: 10.3389/fmicb.2018.02019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
The bacterial nucleoid is highly condensed and forms compartment-like structures within the cell. Much attention has been devoted to investigating the dynamic topology and organization of the nucleoid. In contrast, the specific nucleoid organization, and the relationship between nucleoid structure and function is often neglected with regard to importance for adaption to changing environments and horizontal gene acquisition. In this review, we focus on the structure-function relationship in the bacterial nucleoid. We provide an overview of the fundamental properties that shape the chromosome as a structured yet dynamic macromolecule. These fundamental properties are then considered in the context of the living cell, with focus on how the informational flow affects the nucleoid structure, which in turn impacts on the genetic output. Subsequently, the dynamic living nucleoid will be discussed in the context of evolution. We will address how the acquisition of foreign DNA impacts nucleoid structure, and conversely, how nucleoid structure constrains the successful and sustainable chromosomal integration of novel DNA. Finally, we will discuss current challenges and directions of research in understanding the role of chromosomal architecture in bacterial survival and adaptation.
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Affiliation(s)
- Thøger J Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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37
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Abstract
The ability of bacterial cells to adjust their gene expression program in response to environmental perturbation is often critical for their survival. Recent experimental advances allowing us to quantitatively record gene expression dynamics in single cells and in populations coupled with mathematical modeling enable mechanistic understanding on how these responses are shaped by the underlying regulatory networks. Here, we review how the combination of local and global factors affect dynamical responses of gene regulatory networks. Our goal is to discuss the general principles that allow extrapolation from a few model bacteria to less understood microbes. We emphasize that, in addition to well-studied effects of network architecture, network dynamics are shaped by global pleiotropic effects and cell physiology.
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Affiliation(s)
- David L Shis
- Department of Biosciences, Rice University, Houston, Texas 77005, USA;
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, USA; .,Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| | - Oleg A Igoshin
- Department of Biosciences, Rice University, Houston, Texas 77005, USA; .,Department of Bioengineering, Rice University, Houston, Texas 77005, USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
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38
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Gyulev IS, Willson BJ, Hennessy RC, Krabben P, Jenkinson ER, Thomas GH. Part by Part: Synthetic Biology Parts Used in Solventogenic Clostridia. ACS Synth Biol 2018; 7:311-327. [PMID: 29186949 DOI: 10.1021/acssynbio.7b00327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solventogenic Clostridia are of interest to the chemical industry because of their natural ability to produce chemicals such as butanol, acetone and ethanol from diverse feedstocks. Their use as whole cell factories presents multiple metabolic engineering targets that could lead to improved sustainability and profitability of Clostridium industrial processes. However, engineering efforts have been held back by the scarcity of genetic and synthetic biology tools. Over the past decade, genetic tools to enable transformation and chromosomal modifications have been developed, but the lack of a broad palette of synthetic biology parts remains one of the last obstacles to the rapid engineered improvement of these species for bioproduction. We have systematically reviewed existing parts that have been used in the modification of solventogenic Clostridia, revealing a narrow range of empirically chosen and nonengineered parts that are in current use. The analysis uncovers elements, such as promoters, transcriptional terminators and ribosome binding sites where increased fundamental knowledge is needed for their reliable use in different applications. Together, the review provides the most comprehensive list of parts used and also presents areas where an improved toolbox is needed for full exploitation of these industrially important bacteria.
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Affiliation(s)
- Ivan S. Gyulev
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Benjamin J. Willson
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Rosanna C. Hennessy
- Department
of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Preben Krabben
- Green Biologics Limited, Milton Park, Abingdon, Oxfordshire OX14 4RU, United Kingdom
| | | | - Gavin H. Thomas
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
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39
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DeLorenzo DM, Rottinghaus AG, Henson WR, Moon TS. Molecular Toolkit for Gene Expression Control and Genome Modification in Rhodococcus opacus PD630. ACS Synth Biol 2018; 7:727-738. [PMID: 29366319 DOI: 10.1021/acssynbio.7b00416] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rhodococcus opacus PD630 is a non-model Gram-positive bacterium that possesses desirable traits for lignocellulosic biomass conversion. In particular, it has a relatively rapid growth rate, exhibits genetic tractability, produces high quantities of lipids, and can tolerate and consume toxic lignin-derived aromatic compounds. Despite these unique, industrially relevant characteristics, R. opacus has been underutilized because of a lack of reliable genetic parts and engineering tools. In this work, we developed a molecular toolbox for reliable gene expression control and genome modification in R. opacus. To facilitate predictable gene expression, a constitutive promoter library spanning ∼45-fold in output was constructed. To improve the characterization of available plasmids, the copy numbers of four heterologous and nine endogenous plasmids were determined using quantitative PCR. The molecular toolbox was further expanded by screening a previously unreported antibiotic resistance marker (HygR) and constructing a curable plasmid backbone for temporary gene expression (pB264). Furthermore, a system for genome modification was devised, and three neutral integration sites were identified using a novel combination of transcriptomic data, genomic architecture, and growth rate analysis. Finally, the first reported system for targeted, tunable gene repression in Rhodococcus was developed by utilizing CRISPR interference (CRISPRi). Overall, this work greatly expands the ability to manipulate and engineer R. opacus, making it a viable new chassis for bioproduction from renewable feedstocks.
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Affiliation(s)
- Drew M. DeLorenzo
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Austin G. Rottinghaus
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - William R. Henson
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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40
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Jeong DE, So Y, Park SY, Park SH, Choi SK. Random knock-in expression system for high yield production of heterologous protein in Bacillus subtilis. J Biotechnol 2017; 266:50-58. [PMID: 29229542 DOI: 10.1016/j.jbiotec.2017.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 12/07/2017] [Accepted: 12/07/2017] [Indexed: 10/18/2022]
Abstract
Chromosome-integrated recombinant protein expression in bacteria has advantages for the stable maintenance of genes without any use of antibiotics during large-scale fermentation. Even though different levels of gene expression were reported, depending upon their chromosomal position in bacterial species, only a limited number of integration sites have been used in B. subtilis. In this study, we randomly integrated the GFP and AprE expression cassettes into the B. subtilis genome to determine integration sites that can produce a high yield of heterologous protein expression. Our mariner transposon-based expression cassette integration system was able to find integration sites, which can produce up to 2.9-fold and 1.5-fold increased expression of intracellular GFP and extracellular AprE, respectively, compared to the common integration site amyE. By analyzing the location of integration sites, we observed an adjacent promoter effect, gene dosage effect, and gene knock-out effect all complexly contributing to the increased level of integrated gene expression. Besides obtaining a high yield of heterologous protein expression, our system can also provide a wide-range of expression to expand the systematic application for steady-state metabolic protein production.
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Affiliation(s)
- Da-Eun Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Younju So
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Soo-Young Park
- Genofocus Inc., 65 Techno 1-ro, Yuseong-gu, Daejeon 34014, Republic of Korea
| | - Seung-Hwan Park
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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41
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Bacillus SEVA siblings: A Golden Gate-based toolbox to create personalized integrative vectors for Bacillus subtilis. Sci Rep 2017; 7:14134. [PMID: 29074996 PMCID: PMC5658365 DOI: 10.1038/s41598-017-14329-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/06/2017] [Indexed: 02/02/2023] Open
Abstract
Bacillus subtilis combines natural competence for genetic transformation with highly efficient homologous recombination. These features allow using vectors that integrate into the genome via double homologous recombination. So far, their utilization is restricted by the fixed combination of resistance markers and integration loci, as well as species- or strain-specific regions of homology. To overcome these limitations, we developed a toolbox for the creation of personalized Bacillus vectors in a standardized manner with a focus on fast and easy adaptation of the sequences specifying the integration loci. We based our vector toolkit on the Standard European Vector Architecture (SEVA) to allow the usage of their vector parts. The Bacillus SEVA siblings are assembled via efficient one-pot Golden Gate reactions from four entry parts with the choice of four different enzymes. The toolbox contains seven Bacillus resistance markers, two Escherichia coli origins of replication, and a free choice of integration loci. Vectors can be customized with a cargo, before or after vector assembly, and could be used in different B. subtilis strains and potentially beyond. Our adaptation of the SEVA-standard provides a powerful and standardized toolkit for the convenient creation of personalized Bacillus vectors.
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Decoene T, De Paepe B, Maertens J, Coussement P, Peters G, De Maeseneire SL, De Mey M. Standardization in synthetic biology: an engineering discipline coming of age. Crit Rev Biotechnol 2017; 38:647-656. [PMID: 28954542 DOI: 10.1080/07388551.2017.1380600] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited. PURPOSE In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed. CONCLUSION Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.
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Affiliation(s)
- Thomas Decoene
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | - Brecht De Paepe
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | - Jo Maertens
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | | | - Gert Peters
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | - Sofie L De Maeseneire
- b InBio.be, Centre for Industrial Biotechnology and Biocatalysis, Ghent University , Ghent , Belgium
| | - Marjan De Mey
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
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Overproduction of Rummeliibacillus pycnus arginase with multi-copy insertion of the arg R.pyc cassette into the Bacillus subtilis chromosome. Appl Microbiol Biotechnol 2017; 101:6039-6048. [DOI: 10.1007/s00253-017-8355-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/19/2017] [Accepted: 05/20/2017] [Indexed: 01/29/2023]
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Englaender JA, Jones JA, Cress BF, Kuhlman TE, Linhardt RJ, Koffas MAG. Effect of Genomic Integration Location on Heterologous Protein Expression and Metabolic Engineering in E. coli. ACS Synth Biol 2017; 6:710-720. [PMID: 28055177 DOI: 10.1021/acssynbio.6b00350] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chromosomal integration offers a selection-free alternative to DNA plasmids for expression of foreign proteins and metabolic pathways. Episomal plasmid DNA is convenient but has drawbacks including increased metabolic burden and the requirement for selection in the form of antibiotics. E. coli has long been used for the expression of foreign proteins and for the production of valuable metabolites by expression of complete metabolic pathways. The gene encoding the fluorescent reporter protein mCherry was integrated into four genomic loci on the E. coli chromosome to measure protein expression at each site. Expression levels ranged from 25% to 500% compared to the gene expressed on a high-copy plasmid. Modular expression of DNA is one of the most commonly used methods for optimizing metabolite production by metabolic engineering. By combining a recently developed method for integration of large synthetic DNA constructs into the genome, we were able to integrate two foreign pathways into the same four genomic loci. We have demonstrated that only one of the genomic loci resulted in the production of violacein, and that all four loci produced trans-cinnamic acid from the TAL pathway.
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Affiliation(s)
- Jacob A Englaender
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - J Andrew Jones
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Department of Chemistry, Hamilton College , Clinton, New York 13323, United States
| | - Brady F Cress
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Thomas E Kuhlman
- Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Carl. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Robert J Linhardt
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Mattheos A G Koffas
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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Schwartz C, Shabbir-Hussain M, Frogue K, Blenner M, Wheeldon I. Standardized Markerless Gene Integration for Pathway Engineering in Yarrowia lipolytica. ACS Synth Biol 2017; 6:402-409. [PMID: 27989123 DOI: 10.1021/acssynbio.6b00285] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The yeast Yarrowia lipolytica is a promising microbial host due to its native capacity to produce lipid-based chemicals. Engineering stable production strains requires genomic integration of modified genes, avoiding episomal expression that requires specialized media to maintain selective pressures. Here, we develop a CRISPR-Cas9-based tool for targeted, markerless gene integration into the Y. lipolytica genome. A set of genomic loci was screened to identify sites that were accepting of gene integrations without impacting cell growth. Five sites were found to meet these criteria. Expression levels from a GFP expression cassette were consistent when inserted into AXP, XPR2, A08, and D17, with reduced expression from MFE1. The standardized tool is comprised of five pairs of plasmids (one homologous donor plasmid and a CRISPR-Cas9 expression plasmid), with each pair targeting gene integration into one of the characterized sites. To demonstrate the utility of the tool we rapidly engineered a semisynthetic lycopene biosynthesis pathway by integrating four different genes at different loci. The capability to integrate multiple genes without the need for marker recovery and into sites with known expression levels will enable more rapid and reliable pathway engineering in Y. lipolytica.
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Affiliation(s)
- Cory Schwartz
- Chemical
and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Murtaza Shabbir-Hussain
- Chemical
and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Keith Frogue
- Chemical
and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Mark Blenner
- Chemical
and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Ian Wheeldon
- Chemical
and Environmental Engineering, University of California, Riverside, California 92521, United States
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Towards improved butanol production through targeted genetic modification of Clostridium pasteurianum. Metab Eng 2017; 40:124-137. [PMID: 28119139 PMCID: PMC5367854 DOI: 10.1016/j.ymben.2017.01.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/18/2017] [Accepted: 01/20/2017] [Indexed: 11/23/2022]
Abstract
Declining fossil fuel reserves, coupled with environmental concerns over their continued extraction and exploitation have led to strenuous efforts to identify renewable routes to energy and fuels. One attractive option is to convert glycerol, a by-product of the biodiesel industry, into n-butanol, an industrially important chemical and potential liquid transportation fuel, using Clostridium pasteurianum. Under certain growth conditions this Clostridium species has been shown to predominantly produce n-butanol, together with ethanol and 1,3-propanediol, when grown on glycerol. Further increases in the yields of n-butanol produced by C. pasteurianum could be accomplished through rational metabolic engineering of the strain. Accordingly, in the current report we have developed and exemplified a robust tool kit for the metabolic engineering of C. pasteurianum and used the system to make the first reported in-frame deletion mutants of pivotal genes involved in solvent production, namely hydA (hydrogenase), rex (Redox response regulator) and dhaBCE (glycerol dehydratase). We were, for the first time in C. pasteurianum, able to eliminate 1,3-propanediol synthesis and demonstrate its production was essential for growth on glycerol as a carbon source. Inactivation of both rex and hydA resulted in increased n-butanol titres, representing the first steps towards improving the utilisation of C. pasteurianum as a chassis for the industrial production of this important chemical.
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Wu XL, Li BZ, Zhang WZ, Song K, Qi H, Dai JB, Yuan YJ. Genome-wide landscape of position effects on heterogeneous gene expression in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:189. [PMID: 28729884 PMCID: PMC5516366 DOI: 10.1186/s13068-017-0872-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 07/11/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Integration of heterogeneous genes is widely applied in synthetic biology and metabolic engineering. However, knowledge about the effect of integrative position on gene expression remains limited. RESULTS We established a genome-wide landscape of position effect on gene expression in Saccharomyces cerevisiae. The expression cassette of red fluorescence protein (RFP) gene was constructed and inserted at 1044 loci, which were scattered uniformly in the yeast genome. Due to the different integrative loci on the genome, the maximum relative intensity of RFP is more than 13-fold over the minimum. Plots of the number of strains to RFP relative intensity showed normal distribution, indicating significant position effect on gene expression in yeast. Furthermore, changing the promoters or reporter genes, as well as carbon sources, revealed little consequences on reporter gene expression, indicating chromosomal location is the major determinant of reporter gene expression. CONCLUSIONS We have examined the position effects to integration genes expression in large number loci around whole genome in S. cerevisiae. The results could guide the design of integration loci for exogenous genes and pathways to maximize their expression in metabolic engineering.
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Affiliation(s)
- Xiao-Le Wu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Wen-Zheng Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Kai Song
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Hao Qi
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Jun-biao Dai
- Key Laboratory of Industrial Biocatalysis (Ministry of Education) and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 People’s Republic of China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
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Slager J, Veening JW. Hard-Wired Control of Bacterial Processes by Chromosomal Gene Location. Trends Microbiol 2016; 24:788-800. [PMID: 27364121 PMCID: PMC5034851 DOI: 10.1016/j.tim.2016.06.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/31/2016] [Accepted: 06/08/2016] [Indexed: 12/23/2022]
Abstract
Bacterial processes, such as stress responses and cell differentiation, are controlled at many different levels. While some factors, such as transcriptional regulation, are well appreciated, the importance of chromosomal gene location is often underestimated or even completely neglected. A combination of environmental parameters and the chromosomal location of a gene determine how many copies of its DNA are present at a given time during the cell cycle. Here, we review bacterial processes that rely, completely or partially, on the chromosomal location of involved genes and their fluctuating copy numbers. Special attention will be given to the several different ways in which these copy-number fluctuations can be used for bacterial cell fate determination or coordination of interdependent processes in a bacterial cell.
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Affiliation(s)
- Jelle Slager
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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