1
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Farmer M, Rajasabhai R, Tarpeh W, Tyo K, Wells G. Meta-omic profiling reveals ubiquity of genes encoding for the nitrogen-rich biopolymer cyanophycin in activated sludge microbiomes. Front Microbiol 2023; 14:1287491. [PMID: 38033562 PMCID: PMC10687191 DOI: 10.3389/fmicb.2023.1287491] [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: 09/01/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Recovering nitrogen (N) from municipal wastewater is a promising approach to prevent nutrient pollution, reduce energy use, and transition toward a circular N bioeconomy, but remains a technologically challenging endeavor. Existing N recovery techniques are optimized for high-strength, low-volume wastewater. Therefore, developing methods to concentrate dilute N from mainstream wastewater will bridge the gap between existing technologies and practical implementation. The N-rich biopolymer cyanophycin is a promising candidate for N bioconcentration due to its pH-tunable solubility characteristics and potential for high levels of accumulation. However, the cyanophycin synthesis pathway is poorly explored in engineered microbiomes. In this study, we analyzed over 3,700 publicly available metagenome assembled genomes (MAGs) and found that the cyanophycin synthesis gene cphA was ubiquitous across common activated sludge bacteria. We found that cphA was present in common phosphorus accumulating organisms (PAO) Ca. 'Accumulibacter' and Tetrasphaera, suggesting potential for simultaneous N and P bioconcentration in the same organisms. Using metatranscriptomic data, we confirmed the expression of cphA in lab-scale bioreactors enriched with PAO. Our findings suggest that cyanophycin synthesis is a ubiquitous metabolic activity in activated sludge microbiomes. The possibility of combined N and P bioconcentration could lower barriers to entry for N recovery, since P concentration by PAO is already a widespread biotechnology in municipal wastewater treatment. We anticipate this work to be a starting point for future evaluations of combined N and P bioaccumulation, with the ultimate goal of advancing widespread adoption of N recovery from municipal wastewater.
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Affiliation(s)
- McKenna Farmer
- Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Rashmi Rajasabhai
- Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - William Tarpeh
- Chemical Engineering, Stanford University, Stanford, CA, United States
| | - Keith Tyo
- Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
| | - George Wells
- Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
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2
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Wang Z, Wang YW, Kasuga T, Hassler H, Lopez-Giraldez F, Dong C, Yarden O, Townsend JP. Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa. Mol Ecol 2023. [PMID: 37843462 DOI: 10.1111/mec.17168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
The origin of new genes has long been a central interest of evolutionary biologists. However, their novelty means that they evade reconstruction by the classical tools of evolutionary modelling. This evasion of deep ancestral investigation necessitates intensive study of model species within well-sampled, recently diversified, clades. One such clade is the model genus Neurospora, members of which lack recent gene duplications. Several Neurospora species are comprehensively characterized organisms apt for studying the evolution of lineage-specific genes (LSGs). Using gene synteny, we documented that 78% of Neurospora LSG clusters are located adjacent to the telomeres featuring extensive tracts of non-coding DNA and duplicated genes. Here, we report several instances of LSGs that are likely from regional rearrangements and potentially from gene rebirth. To broadly investigate the functions of LSGs, we assembled transcriptomics data from 68 experimental data points and identified co-regulatory modules using Weighted Gene Correlation Network Analysis, revealing that LSGs are widely but peripherally involved in known regulatory machinery for diverse functions. The ancestral status of the LSG mas-1, a gene with roles in cell-wall integrity and cellular sensitivity to antifungal toxins, was investigated in detail alongside its genomic neighbours, indicating that it arose from an ancient lysophospholipase precursor that is ubiquitous in lineages of the Sordariomycetes. Our discoveries illuminate a "rummage region" in the N. crassa genome that enables the formation of new genes and functions to arise via gene duplication and relocation, followed by fast mutation and recombination facilitated by sequence repeats and unconstrained non-coding sequences.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Takao Kasuga
- College of Biological Sciences, University of California, Davis, Davis, California, USA
| | - Hayley Hassler
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | | | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
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3
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Tenenbaum D, Inlow K, Friedman LJ, Cai A, Gelles J, Kondev J. RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons. Proc Natl Acad Sci U S A 2023; 120:e2301402120. [PMID: 37459525 PMCID: PMC10372574 DOI: 10.1073/pnas.2301402120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/19/2023] [Indexed: 07/20/2023] Open
Abstract
DNA transcription initiates after an RNA polymerase (RNAP) molecule binds to the promoter of a gene. In bacteria, the canonical picture is that RNAP comes from the cytoplasmic pool of freely diffusing RNAP molecules. Recent experiments suggest the possible existence of a separate pool of polymerases, competent for initiation, which freely slide on the DNA after having terminated one round of transcription. Promoter-dependent transcription reinitiation from this pool of posttermination RNAP may lead to coupled initiation at nearby operons, but it is unclear whether this can occur over the distance and timescales needed for it to function widely on a bacterial genome in vivo. Here, we mathematically model the hypothesized reinitiation mechanism as a diffusion-to-capture process and compute the distances over which significant interoperon coupling can occur and the time required. These quantities depend on molecular association and dissociation rate constants between DNA, RNAP, and the transcription initiation factor σ70; we measure these rate constants using single-molecule experiments in vitro. Our combined theory/experimental results demonstrate that efficient coupling can occur at physiologically relevant σ70 concentrations and on timescales appropriate for transcript synthesis. Coupling is efficient over terminator-promoter distances up to ∼1,000 bp, which includes the majority of terminator-promoter nearest neighbor pairs in the Escherichia coli genome. The results suggest a generalized mechanism that couples the transcription of nearby operons and breaks the paradigm that each binding of RNAP to DNA can produce at most one messenger RNA.
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Affiliation(s)
- Debora Tenenbaum
- Department of Biochemistry, Brandeis University, Waltham, MA02453
- Department of Physics, Brandeis University, Waltham, MA02453
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Koe Inlow
- Department of Biochemistry, Brandeis University, Waltham, MA02453
| | | | - Anthony Cai
- Department of Biochemistry, Brandeis University, Waltham, MA02453
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, MA02453
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA02453
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4
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Tenenbaum D, Inlow K, Friedman L, Cai A, Gelles J, Kondev J. RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.528045. [PMID: 36798213 PMCID: PMC9934669 DOI: 10.1101/2023.02.10.528045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
DNA transcription initiates after an RNA polymerase (RNAP) molecule binds to the promoter of a gene. In bacteria, the canonical picture is that RNAP comes from the cytoplasmic pool of freely diffusing RNAP molecules. Recent experiments suggest the possible existence of a separate pool of polymerases, competent for initiation, which freely slide on the DNA after having terminated one round of transcription. Promoter-dependent transcription reinitiation from this pool of post-termination RNAP may lead to coupled initiation at nearby operons, but it is unclear whether this can occur over the distance- and time-scales needed for it to function widely on a bacterial genome in vivo. Here, we mathematically model the hypothesized reinitiation mechanism as a diffusion-to-capture process and compute the distances over which significant inter-operon coupling can occur and the time required. These quantities depend on previously uncharacterized molecular association and dissociation rate constants between DNA, RNAP and the transcription initiation factor σ 70 ; we measure these rate constants using single-molecule experiments in vitro. Our combined theory/experimental results demonstrate that efficient coupling can occur at physiologically relevant σ 70 concentrations and on timescales appropriate for transcript synthesis. Coupling is efficient over terminator-promoter distances up to ∼ 1, 000 bp, which includes the majority of terminator-promoter nearest neighbor pairs in the E. coli genome. The results suggest a generalized mechanism that couples the transcription of nearby operons and breaks the paradigm that each binding of RNAP to DNA can produce at most one messenger RNA. SIGNIFICANCE STATEMENT After transcribing an operon, a bacterial RNA polymerase can stay bound to DNA, slide along it, and reini-tiate transcription of the same or a different operon. Quantitative single-molecule biophysics experiments combined with mathematical theory demonstrate that this reinitiation process can be quick and efficient over gene spacings typical of a bacterial genome. Reinitiation may provide a mechanism to orchestrate the transcriptional activities of groups of nearby operons.
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Affiliation(s)
- Debora Tenenbaum
- Department of Biochemistry, Brandeis University, Waltham, MA, United States
- Department of Physics, Brandeis University, Waltham, MA, United States
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Koe Inlow
- Department of Biochemistry, Brandeis University, Waltham, MA, United States
| | - Larry Friedman
- Department of Biochemistry, Brandeis University, Waltham, MA, United States
| | - Anthony Cai
- Department of Biochemistry, Brandeis University, Waltham, MA, United States
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, MA, United States
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA, United States
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5
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Yu L, Cao Q, Chen W, Yang N, Yang CG, Ji Q, Wu M, Bae T, Lan L. A novel copper-sensing two-component system for inducing Dsb gene expression in bacteria. Sci Bull (Beijing) 2022; 67:198-212. [PMID: 36546013 DOI: 10.1016/j.scib.2021.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/15/2021] [Accepted: 03/01/2021] [Indexed: 01/06/2023]
Abstract
In nature, bacteria must sense copper and tightly regulate gene expression to evade copper toxicity. Here, we identify a new copper-responsive two-component system named DsbRS in the important human pathogen Pseudomonas aeruginosa; in this system, DsbS is a sensor histidine kinase, and DsbR, its cognate response regulator, directly induces the transcription of genes involved in protein disulfide bond formation (Dsb) (i.e., the dsbDEG operon and dsbB). In the absence of copper, DsbS acts as a phosphatase toward DsbR, thus blocking the transcription of Dsb genes. In the presence of copper, the metal ion directly binds to the sensor domain of DsbS, and the Cys82 residue plays a critical role in this process. The copper-binding behavior appears to inhibit the phosphatase activity of DsbS, leading to the activation of DsbR. The copper resistance of the dsbRS knock-out mutant is restored by the ectopic expression of the dsbDEG operon, which is a DsbRS major target. Strikingly, cognates of the dsbRS-dsbDEG pair are widely distributed across eubacteria. In addition, a DsbR-binding site, which contains the consensus sequence 5'-TTA-N8-TTAA-3', is detected in the promoter region of dsbDEG homologs in these species. These findings suggest that the regulation of Dsb genes by DsbRS represents a novel mechanism by which bacterial cells cope with copper stress.
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Affiliation(s)
- Liang Yu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qiao Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weizhong Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Nana Yang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cai-Guang Yang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota, Grand Forks ND 58203-9037, USA
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary IN 46408, USA
| | - Lefu Lan
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai 201203, China.
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6
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Dautt-Castro M, Jijón-Moreno S, Gómez-Hernández N, del Carmen González-López M, Hernández-Hernández EJ, Rosendo-Vargas MM, Rebolledo-Prudencio OG, Casas-Flores S. New Insights on the Duality of Trichoderma as a Phytopathogen Killer and a Plant Protector Based on an Integrated Multi-omics Perspective. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Hill AM, Rybarski JR, Hu K, Finkelstein IJ, Wilke CO. Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets. JOURNAL OF OPEN SOURCE SOFTWARE 2021; 6:3678. [PMID: 35445164 PMCID: PMC9017871 DOI: 10.21105/joss.03678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gene clusters are sets of co-localized, often contiguous genes that together perform specific functions, many of which are relevant to biotechnology. There is a need for software tools that can extract candidate gene clusters from vast amounts of available genomic data. Therefore, we developed Opfi: a modular pipeline for identification of arbitrary gene clusters in assembled genomic or metagenomic sequences. Opfi contains functions for annotation, de-deduplication, and visualization of putative gene clusters. It utilizes a customizable rule-based filtering approach for selection of candidate systems that adhere to user-defined criteria. Opfi is implemented in Python, and is available on the Python Package Index and on Bioconda (Grüning et al., 2018).
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Affiliation(s)
- Alexis M Hill
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - James R Rybarski
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Kuang Hu
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Claus O Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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8
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Sharma V, Kaur R, Salwan R. Streptomyces: host for refactoring of diverse bioactive secondary metabolites. 3 Biotech 2021; 11:340. [PMID: 34221811 DOI: 10.1007/s13205-021-02872-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
Microbial secondary metabolites are intensively explored due to their demands in pharmaceutical, agricultural and food industries. Streptomyces are one of the largest sources of secondary metabolites having diverse applications. In particular, the abundance of secondary metabolites encoding biosynthetic gene clusters and presence of wobble position in Streptomyces strains make it potential candidate as a native or heterologous host for secondary metabolite production including several cryptic gene clusters expression. Here, we have discussed the developments in Streptomyces strains genome mining, its exploration as a suitable host and application of synthetic biology for refactoring genetic systems for developing chassis for enhanced as well as novel secondary metabolites with reduced genome and cleaned background.
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Affiliation(s)
- Vivek Sharma
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Randhir Kaur
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Richa Salwan
- College of Horticulture and Forestry, Dr YS Parmar University of Horticulture and Forestry, Neri, Hamirpur, Himachal Pradesh 177001 India
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9
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McCarthy DM, Medford JI. Quantitative and Predictive Genetic Parts for Plant Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2020; 11:512526. [PMID: 33123175 PMCID: PMC7573182 DOI: 10.3389/fpls.2020.512526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Plant synthetic biology aims to harness the natural abilities of plants and to turn them to new purposes. A primary goal of plant synthetic biology is to produce predictable and programmable genetic circuits from simple regulatory elements and well-characterized genetic components. The number of available DNA parts for plants is increasing, and the methods for rapid quantitative characterization are being developed, but the field of plant synthetic biology is still in its early stages. We here describe methods used to describe the quantitative properties of genetic components needed for plant synthetic biology. Once the quantitative properties and transfer function of a variety of genetic parts are known, computers can select the optimal components to assemble into functional devices, such as toggle switches and positive feedback circuits. However, while the variety of circuits and traits that can be put into plants are limitless, doing synthetic biology in plants poses unique challenges. Plants are composed of differentiated cells and tissues, each representing potentially unique regulatory or developmental contexts to introduced synthetic genetic circuits. Further, plants have evolved to be highly sensitive to environmental influences, such as light or temperature, any of which can affect the quantitative function of individual parts or whole circuits. Measuring the function of plant components within the context of a plant cell and, ideally, in a living plant, will be essential to using these components in gene circuits with predictable function. Mathematical modeling will be needed to account for the variety of contexts a genetic part will experience in different plant tissues or environments. With such understanding in hand, it may be possible to redesign plant traits to serve human and environmental needs.
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10
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Schwaiger KN, Voit A, Dobiašová H, Luley C, Wiltschi B, Nidetzky B. Plasmid Design for Tunable Two-Enzyme Co-Expression Promotes Whole-Cell Production of Cellobiose. Biotechnol J 2020; 15:e2000063. [PMID: 32668097 DOI: 10.1002/biot.202000063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/16/2020] [Indexed: 12/30/2022]
Abstract
Catalyst development for biochemical cascade reactions often follows a "whole-cell-approach" in which a single microbial cell is made to express all required enzyme activities. Although attractive in principle, the approach can encounter limitations when efficient overall flux necessitates precise balancing between activities. This study shows an effective integration of major design strategies from synthetic biology to a coherent development of plasmid vectors, enabling tunable two-enzyme co-expression in E. coli, for whole-cell-production of cellobiose. An efficient transformation of sucrose and glucose into cellobiose by a parallel (countercurrent) cascade of disaccharide phosphorylases requires the enzyme co-expression to cope with large differences in specific activity of cellobiose phosphorylase (14 U mg-1 ) and sucrose phosphorylase (122 U mg-1 ). Mono- and bicistronic co-expression strategies controlling transcription, transcription-translation coupling or plasmid replication are analyzed for effect on activity and stable producibility of the whole-cell-catalyst. A key role of bom (basis of mobility) for plasmid stability dependent on the ori is reported and the importance of RBS (ribosome binding site) strength is demonstrated. Whole cell catalysts show high specific rates (460 µmol cellobiose min-1 g-1 dry cells) and performance metrics (30 g L-1 ; ∼82% yield; 3.8 g L-1 h-1 overall productivity) promising for cellobiose production.
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Affiliation(s)
- Katharina N Schwaiger
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria
| | - Alena Voit
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria
| | - Hana Dobiašová
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria
| | - Christiane Luley
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria
| | - Birgit Wiltschi
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria
| | - Bernd Nidetzky
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010, Graz, Austria.,Institute of Biotechnology and Biochemical Engineering, TU Graz, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
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11
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Mo XH, Zhang H, Wang TM, Zhang C, Zhang C, Xing XH, Yang S. Establishment of CRISPR interference in Methylorubrum extorquens and application of rapidly mining a new phytoene desaturase involved in carotenoid biosynthesis. Appl Microbiol Biotechnol 2020; 104:4515-4532. [PMID: 32215707 DOI: 10.1007/s00253-020-10543-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 02/04/2023]
Abstract
The methylotrophic bacterium Methylorubrum extorquens AM1 holds a great potential of a microbial cell factory in producing high value chemicals with methanol as the sole carbon and energy source. However, many gene functions remain unknown, hampering further rewiring of metabolic networks. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been demonstrated to be a robust tool for gene knockdown in diverse organisms. In this study, we developed an efficient CRISPRi system through optimizing the promoter strength of Streptococcus pyogenes-derived deactivated cas9 (dcas9). When the dcas9 and sgRNA were respectively controlled by medium PR/tetO and strong PmxaF-g promoters, dynamic repression efficacy of cell growth through disturbing a central metabolism gene glyA was achieved from 41.9 to 96.6% dependent on the sgRNA targeting sites. Furthermore, the optimized CRISPRi system was shown to effectively decrease the abundance of exogenous fluorescent protein gene mCherry over 50% and to reduce the expression of phytoene desaturase gene crtI by 97.7%. We then used CRISPRi technology combined with 26 sgRNAs pool to rapidly discover a new phytoene desaturase gene META1_3670 from 2470 recombinant mutants. The gene function was further verified through gene deletion and complementation as well as phylogenetic tree analysis. In addition, we applied CRISPRi to repress the transcriptional level of squalene-hopene cyclase gene shc involved in hopanoid biosynthesis by 64.9%, which resulted in enhancing 1.9-fold higher of carotenoid production without defective cell growth. Thus, the CRISPRi system developed here provides a useful tool in mining functional gene of M. extorquens as well as in biotechnology for producing high-valued chemicals from methanol. KEY POINTS: Developing an efficient CRISPRi to knockdown gene expression in C1-utilizing bacteria CRISPRi combined with sgRNAs pool to rapidly discover a new phytoene desaturase gene Improvement of carotenoid production by repressing a competitive pathway.
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Affiliation(s)
- Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Hui Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Tian-Min Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Chong Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Cong Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, 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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12
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Genome Sequence of Streptomyces cavourensis 1AS2a, a Rhizobacterium Isolated from the Brazilian Cerrado Biome. Microbiol Resour Announc 2019; 8:8/18/e00065-19. [PMID: 31048389 PMCID: PMC6498222 DOI: 10.1128/mra.00065-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces cavourensis strain 1AS2a, isolated from wheat rhizosphere in the Brazilian Neotropical savanna, exhibits strong antimicrobial activities. Its genome comprises 7,600,475 bp with 6,590 open reading frames (ORFs) that reveal 30 biosynthetic gene clusters (BGCs). It provides a genetic basis for further research of the potential of this strain for the production of antimicrobial compounds.
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13
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Schaub AJ, Moreno GO, Zhao S, Truong HV, Luo R, Tsai SC. Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases. Methods Enzymol 2019; 622:375-409. [PMID: 31155062 PMCID: PMC7197764 DOI: 10.1016/bs.mie.2019.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Various computational methodologies can be applied to enzymological studies on enzymes in the fatty acid, polyketide, and non-ribosomal peptide biosynthetic pathways. These multi-domain complexes are called fatty acid synthases, polyketide synthases, and non-ribosomal peptide synthetases. These mega-synthases biosynthesize chemically diverse and complex bioactive molecules, with the intermediates being chauffeured between catalytic partners via a carrier protein. Recent efforts have been made to engineer these systems to expand their product diversity. A major stumbling block is our poor understanding of the transient protein-protein and protein-substrate interactions between the carrier protein and its many catalytic partner domains and product intermediates. The innate reactivity of pathway intermediates in two major classes of polyketide synthases has frustrated our mechanistic understanding of these interactions during the biosynthesis of these natural products, ultimately impeding the engineering of these systems for the generation of engineered natural products. Computational techniques described in this chapter can aid data interpretation or used to generate testable models of these experimentally intractable transient interactions, thereby providing insight into key interactions that are difficult to capture otherwise, with the potential to expand the diversity in these systems.
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Affiliation(s)
- Andrew J Schaub
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Gabriel O Moreno
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Shiji Zhao
- Mathematical, Computational and Systems Biology Program, Center for Complex Biological Systems, University of California, Irvine, CA, United States
| | - Hau V Truong
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, CA, United States.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, Pharmaceutical Sciences, University of California, Irvine, CA, United States.
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14
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Polyprotein strategy for stoichiometric assembly of nitrogen fixation components for synthetic biology. Proc Natl Acad Sci U S A 2018; 115:E8509-E8517. [PMID: 30061389 PMCID: PMC6130400 DOI: 10.1073/pnas.1804992115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The requirement of maintaining balanced expression of a large number of gene products represents a major challenge to the engineering of nitrogen fixation in cereal crops, necessitating reiterative combinatorial assembly cycles to optimize monocistronic gene expression. In this study, we have explored a “fuse-and-cleave” virus-derived polyprotein strategy to reduce gene numbers and achieve balanced expression of protein components required for nitrogenase biosynthesis and activity. After testing and regrouping assemblies on the basis of expression profiles, cleavage patterns, and activity, 14 essential genes were selectively assembled into 5 giant genes that enable growth on dinitrogen. This strategy has potential advantages, not only for transferring nitrogen fixation to plants, but also for the engineering of other complex systems of profound agronomic and ecological importance. Re-engineering of complex biological systems (CBS) is an important goal for applications in synthetic biology. Efforts have been made to simplify CBS by refactoring a large number of genes with rearranged polycistrons and synthetic regulatory circuits. Here, a posttranslational protein-splicing strategy derived from RNA viruses was exploited to minimize gene numbers of the classic nitrogenase system, where the expression stoichiometry is particularly important. Operon-based nif genes from Klebsiella oxytoca were regrouped into giant genes either by fusing genes together or by expressing polyproteins that are subsequently cleaved with Tobacco Etch Virus protease. After several rounds of selection based on protein expression levels and tolerance toward a remnant C-terminal ENLYFQ-tail, a system with only five giant genes showed optimal nitrogenase activity and supported diazotrophic growth of Escherichia coli. This study provides an approach for efficient translation from an operon-based system into a polyprotein-based assembly that has the potential for portable and stoichiometric expression of the complex nitrogenase system in eukaryotic organisms.
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15
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Abstract
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry—biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function.
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Affiliation(s)
- Caleb J. Bashor
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
| | - James J. Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
- Harvard–MIT Program in Health Sciences and Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
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16
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Kerfeld CA. A bioarchitectonic approach to the modular engineering of metabolism. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0387. [PMID: 28808103 DOI: 10.1098/rstb.2016.0387] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2017] [Indexed: 01/13/2023] Open
Abstract
Dissociating the complexity of metabolic processes into modules is a shift in focus from the single gene/gene product to functional and evolutionary units spanning the scale of biological organization. When viewing the levels of biological organization through this conceptual lens, modules are found across the continuum: domains within proteins, co-regulated groups of functionally associated genes, operons, metabolic pathways and (sub)cellular compartments. Combining modules as components or subsystems of a larger system typically leads to increased complexity and the emergence of new functions. By virtue of their potential for 'plug and play' into new contexts, modules can be viewed as units of both evolution and engineering. Through consideration of lessons learned from recent efforts to install new metabolic modules into cells and the emerging understanding of the structure, function and assembly of protein-based organelles, bacterial microcompartments, a structural bioengineering approach is described: one that builds from an architectural vocabulary of protein domains. This bioarchitectonic approach to engineering cellular metabolism can be applied to microbial cell factories, used in the programming of members of synthetic microbial communities or used to attain additional levels of metabolic organization in eukaryotic cells for increasing primary productivity and as the foundation of a green economy.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.
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Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA .,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.,Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA
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17
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Heinsch SC, Das SR, Smanski MJ. Simulation Modeling to Compare High-Throughput, Low-Iteration Optimization Strategies for Metabolic Engineering. Front Microbiol 2018. [PMID: 29535690 PMCID: PMC5835107 DOI: 10.3389/fmicb.2018.00313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Increasing the final titer of a multi-gene metabolic pathway can be viewed as a multivariate optimization problem. While numerous multivariate optimization algorithms exist, few are specifically designed to accommodate the constraints posed by genetic engineering workflows. We present a strategy for optimizing expression levels across an arbitrary number of genes that requires few design-build-test iterations. We compare the performance of several optimization algorithms on a series of simulated expression landscapes. We show that optimal experimental design parameters depend on the degree of landscape ruggedness. This work provides a theoretical framework for designing and executing numerical optimization on multi-gene systems.
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Affiliation(s)
- Stephen C. Heinsch
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
- Bioinformatics and Computational Biology Program, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
| | - Siba R. Das
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
| | - Michael J. Smanski
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
- Bioinformatics and Computational Biology Program, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
- *Correspondence: Michael J. Smanski,
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18
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Casini A, Chang FY, Eluere R, King AM, Young EM, Dudley QM, Karim A, Pratt K, Bristol C, Forget A, Ghodasara A, Warden-Rothman R, Gan R, Cristofaro A, Borujeni AE, Ryu MH, Li J, Kwon YC, Wang H, Tatsis E, Rodriguez-Lopez C, O’Connor S, Medema MH, Fischbach MA, Jewett MC, Voigt C, Gordon DB. A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology. J Am Chem Soc 2018; 140:4302-4316. [DOI: 10.1021/jacs.7b13292] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Arturo Casini
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Fang-Yuan Chang
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Raissa Eluere
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Andrew M. King
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Eric M. Young
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Quentin M. Dudley
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty Karim
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Katelin Pratt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Cassandra Bristol
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Anthony Forget
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Amar Ghodasara
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Robert Warden-Rothman
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Rui Gan
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexander Cristofaro
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Amin Espah Borujeni
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Min-Hyung Ryu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Jian Li
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Yong-Chan Kwon
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - He Wang
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Evangelos Tatsis
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | - Sarah O’Connor
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Michael A. Fischbach
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Bioengineering and Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, California 94305, United States
| | - Michael C. Jewett
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher Voigt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - D. Benjamin Gordon
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
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19
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Katzke N, Knapp A, Loeschcke A, Drepper T, Jaeger KE. Novel Tools for the Functional Expression of Metagenomic DNA. Methods Mol Biol 2017; 1539:159-196. [PMID: 27900689 DOI: 10.1007/978-1-4939-6691-2_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Functional expression of genes from metagenomic libraries is limited by various factors including inefficient transcription and/or translation of target genes as well as improper folding and assembly of the corresponding proteins caused by the lack of appropriate chaperones and cofactors. It is now well accepted that the use of different expression hosts of distinct phylogeny and physiology can dramatically increase the rate of success. In the following chapter, we therefore describe tools and protocols allowing for the comparative heterologous expression of genes in five bacterial expression hosts, namely Escherichia coli, Pseudomonas putida, Bacillus subtilis, Burkholderia glumae, and Rhodobacter capsulatus. Different broad-host-range shuttle vectors are described that allow activity-based screening of metagenomic DNA in these bacteria. Furthermore, we describe the newly developed transfer-and-expression system TREX which comprises genetic elements essential to allow for expression of large clusters of functionally coupled genes in different microbial species.
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Affiliation(s)
- Nadine Katzke
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich GmbH, Heinrich-Heine-University Düsseldorf, 52426, Jülich, Germany.
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20
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Abstract
Bacterial genomes encode the biosynthetic potential to produce hundreds of thousands of complex molecules with diverse applications, from medicine to agriculture and materials. Accessing these natural products promises to reinvigorate drug discovery pipelines and provide novel routes to synthesize complex chemicals. The pathways leading to the production of these molecules often comprise dozens of genes spanning large areas of the genome and are controlled by complex regulatory networks with some of the most interesting molecules being produced by non-model organisms. In this Review, we discuss how advances in synthetic biology--including novel DNA construction technologies, the use of genetic parts for the precise control of expression and for synthetic regulatory circuits--and multiplexed genome engineering can be used to optimize the design and synthesis of pathways that produce natural products.
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21
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Sharma S, Shrivastava N. Renaissance in phytomedicines: promising implications of NGS technologies. PLANTA 2016; 244:19-38. [PMID: 27002972 DOI: 10.1007/s00425-016-2492-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.
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Affiliation(s)
- Sonal Sharma
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India
- Nirma University, Ahmedabad, Gujarat, India
| | - Neeta Shrivastava
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India.
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22
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Medford JI, Prasad A. Towards programmable plant genetic circuits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:139-148. [PMID: 27297052 DOI: 10.1111/tpj.13235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 06/06/2023]
Abstract
Synthetic biology enables the construction of genetic circuits with predictable gene functions in plants. Detailed quantitative descriptions of the transfer function or input-output function for genetic parts (promoters, 5' and 3' untranslated regions, etc.) are collected. These data are then used in computational simulations to determine their robustness and desired properties, thereby enabling the best components to be selected for experimental testing in plants. In addition, the process forms an iterative workflow which allows vast improvement to validated elements with sub-optimal function. These processes enable computational functions such as digital logic in living plants and follow the pathway of technological advances which took us from vacuum tubes to cell phones.
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Affiliation(s)
- June I Medford
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ashok Prasad
- School of Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA
- Department of Biological and Chemical Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO, 80523, USA
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23
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Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol 2016. [PMID: 27084023 DOI: 10.1128/aem.01055-01016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
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Affiliation(s)
- Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Matthew B Crook
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Evangelia D Kouri
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | | | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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24
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Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol 2016; 82:3698-3710. [PMID: 27084023 PMCID: PMC4907175 DOI: 10.1128/aem.01055-16] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
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Affiliation(s)
- Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Matthew B Crook
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Evangelia D Kouri
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | | | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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25
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Kerfeld CA, Melnicki MR. Assembly, function and evolution of cyanobacterial carboxysomes. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:66-75. [PMID: 27060669 DOI: 10.1016/j.pbi.2016.03.009] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 05/19/2023]
Abstract
All cyanobacteria contain carboxysomes, RuBisCO-encapsulating bacterial microcompartments that function as prokaryotic organelles. The two carboxysome types, alpha and beta, differ fundamentally in components, assembly, and species distribution. Alpha carboxysomes share a highly-conserved gene organization, with evidence of horizontal gene transfer from chemoautotrophic proteobacteria to the picocyanobacteria, and seem to co-assemble shells concomitantly with aggregation of cargo enzymes. In contrast, beta carboxysomes assemble an enzymatic core first, with an encapsulation peptide playing a critical role in formation of the surrounding shell. Based on similarities in assembly, and phylogenetic analysis of the pentameric shell protein conserved across all bacterial microcompartments, beta carboxysomes appear to be more closely related to the microcompartments of heterotrophic bacteria (metabolosomes) than to alpha carboxysomes, which appear deeply divergent. Beta carboxysomes can be found in the basal cyanobacterial clades that diverged before the ancestor of the chloroplast and have recently been shown to be able to encapsulate functional RuBisCO enzymes resurrected from ancestrally-reconstructed sequences, consistent with an ancient origin. Alpha and beta carboxysomes are not only distinct units of evolution, but are now emerging as genetic/metabolic modules for synthetic biology; heterologous expression and redesign of both the shell and the enzymatic core have recently been achieved.
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Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Matthew R Melnicki
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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26
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Complete Genome Sequence of Streptomyces venezuelae ATCC 15439, Producer of the Methymycin/Pikromycin Family of Macrolide Antibiotics, Using PacBio Technology. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00337-16. [PMID: 27151802 PMCID: PMC4859184 DOI: 10.1128/genomea.00337-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the complete genome sequence of Streptomyces venezuelae ATCC 15439, a producer of the methymycin/pikromycin family of macrolide antibiotics and a model host for natural product studies, obtained exclusively using PacBio sequencing technology. The 9.03-Mbp genome harbors 8,775 genes and 11 polyketide and nonribosomal peptide natural product gene clusters.
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27
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Cock PJA, Chilton JM, Grüning B, Johnson JE, Soranzo N. NCBI BLAST+ integrated into Galaxy. Gigascience 2015; 4:39. [PMID: 26336600 PMCID: PMC4557756 DOI: 10.1186/s13742-015-0080-7] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 08/18/2015] [Indexed: 01/29/2023] Open
Abstract
Background The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST into Galaxy was a natural step for sequence comparison workflows. Findings The command line NCBI BLAST+ tool suite was wrapped for use within Galaxy. Appropriate datatypes were defined as needed. The integration of the BLAST+ tool suite into Galaxy has the goal of making common BLAST tasks easy and advanced tasks possible. Conclusions This project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide. Several examples of applications are described here.
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Affiliation(s)
- Peter J A Cock
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - John M Chilton
- Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant St. SE, 55455 Minneapolis, MN USA
| | - Björn Grüning
- Department of Computer Science, Albert-Ludwigs-University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110 Germany
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant St. SE, 55455 Minneapolis, MN USA
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28
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Reen FJ, Romano S, Dobson ADW, O'Gara F. The Sound of Silence: Activating Silent Biosynthetic Gene Clusters in Marine Microorganisms. Mar Drugs 2015; 13:4754-83. [PMID: 26264003 PMCID: PMC4557003 DOI: 10.3390/md13084754] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 06/05/2015] [Accepted: 07/27/2015] [Indexed: 12/14/2022] Open
Abstract
Unlocking the rich harvest of marine microbial ecosystems has the potential to both safeguard the existence of our species for the future, while also presenting significant lifestyle benefits for commercial gain. However, while significant advances have been made in the field of marine biodiscovery, leading to the introduction of new classes of therapeutics for clinical medicine, cosmetics and industrial products, much of what this natural ecosystem has to offer is locked in, and essentially hidden from our screening methods. Releasing this silent potential represents a significant technological challenge, the key to which is a comprehensive understanding of what controls these systems. Heterologous expression systems have been successful in awakening a number of these cryptic marine biosynthetic gene clusters (BGCs). However, this approach is limited by the typically large size of the encoding sequences. More recently, focus has shifted to the regulatory proteins associated with each BGC, many of which are signal responsive raising the possibility of exogenous activation. Abundant among these are the LysR-type family of transcriptional regulators, which are known to control production of microbial aromatic systems. Although the environmental signals that activate these regulatory systems remain unknown, it offers the exciting possibility of evoking mimic molecules and synthetic expression systems to drive production of potentially novel natural products in microorganisms. Success in this field has the potential to provide a quantum leap forward in medical and industrial bio-product development. To achieve these new endpoints, it is clear that the integrated efforts of bioinformaticians and natural product chemists will be required as we strive to uncover new and potentially unique structures from silent or cryptic marine gene clusters.
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Affiliation(s)
- F Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
| | - Stefano Romano
- BIOMERIT Research Centre, School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
| | - Alan D W Dobson
- School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork-National University of Ireland, Cork, Ireland.
- School of Biomedical Sciences, Curtin University, Perth WA 6845, Australia.
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29
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Papoutsakis ET. Reassessing the Progress in the Production of Advanced Biofuels in the Current Competitive Environment and Beyond: What Are the Successes and Where Progress Eludes Us and Why. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01695] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Eleftherios T. Papoutsakis
- Molecular Biotechnology Laboratory, Department of Chemical & Biomolecular Engineering, Department of Biological Sciences & the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
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30
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Lagomarsino MC, Espéli O, Junier I. From structure to function of bacterial chromosomes: Evolutionary perspectives and ideas for new experiments. FEBS Lett 2015; 589:2996-3004. [PMID: 26171924 DOI: 10.1016/j.febslet.2015.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 12/11/2022]
Abstract
The link between chromosome structure and function is a challenging open question because chromosomes in vivo are highly dynamic and arduous to manipulate. Here, we examine several promising approaches to tackle this question specifically in bacteria, by integrating knowledge from different sources. Toward this end, we first provide a brief overview of experimental tools that have provided insights into the description of the bacterial chromosome, including genetic, biochemical and fluorescence microscopy techniques. We then explore the possibility of using comparative genomics to isolate functionally important features of chromosome organization, exploiting the fact that features shared between phylogenetically distant bacterial species reflect functional significance. Finally, we discuss possible future perspectives from the field of experimental evolution. Specifically, we propose novel experiments in which bacteria could be screened and selected on the basis of the structural properties of their chromosomes.
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Affiliation(s)
| | - Olivier Espéli
- CIRB-Collège de France, CNRS UMR 7241, INSERM U1050, Paris, France
| | - Ivan Junier
- Laboratoire Adaptation et Pathogénie des Micro-organismes - UMR 5163, Université Grenoble 1, CNRS, BP 170, F-38042 Grenoble Cedex 9, France; Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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31
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Aussignargues C, Paasch BC, Gonzalez-Esquer R, Erbilgin O, Kerfeld CA. Bacterial microcompartment assembly: The key role of encapsulation peptides. Commun Integr Biol 2015; 8:e1039755. [PMID: 26478774 PMCID: PMC4594438 DOI: 10.1080/19420889.2015.1039755] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/03/2015] [Accepted: 04/06/2015] [Indexed: 12/14/2022] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles used by a broad range of bacteria to segregate and optimize metabolic reactions. Their functions are diverse, and can be divided into anabolic (carboxysome) and catabolic (metabolosomes) processes, depending on their cargo enzymes. The assembly pathway for the β-carboxysome has been characterized, revealing that biogenesis proceeds from the inside out. The enzymes coalesce into a procarboxysome, followed by encapsulation in a protein shell that is recruited to the procarboxysome by a short (∼17 amino acids) extension on the C-terminus of one of the encapsulated proteins. A similar extension is also found on the N- or C-termini of a subset of metabolosome core enzymes. These encapsulation peptides (EPs) are characterized by a primary structure predicted to form an amphipathic α-helix that interacts with shell proteins. Here, we review the features, function and widespread occurrence of EPs among metabolosomes, and propose an expanded role for EPs in the assembly of diverse BMCs.
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Affiliation(s)
| | - Bradley C Paasch
- DOE Plant Research Laboratory; Michigan State University ; East Lansing, MI USA
| | | | - Onur Erbilgin
- Department of Plant and Microbial Biology; University of California, Berkeley ; Berkeley, CA USA
| | - Cheryl A Kerfeld
- DOE Plant Research Laboratory; Michigan State University ; East Lansing, MI USA ; Department of Plant and Microbial Biology; University of California, Berkeley ; Berkeley, CA USA ; Physical Biosciences Division; Lawrence Berkeley National Laboratory ; Berkeley, CA USA ; Berkeley Synthetic Biology Institute ; Berkeley, CA USA
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32
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Fine-tuning of ecaA and pepc gene expression increases succinic acid production in Escherichia coli. Appl Microbiol Biotechnol 2015; 99:8575-86. [DOI: 10.1007/s00253-015-6734-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 05/04/2015] [Accepted: 05/27/2015] [Indexed: 12/20/2022]
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Abstract
![]()
Synthetic cell therapy is a field
that has broad potential for
future applications in human disease treatment. Next generation therapies
will consist of engineered bacterial strains capable of diagnosing
disease, producing and delivering therapeutics, and controlling their
numbers to meet containment and safety concerns. A thorough understanding
of the microbial ecology of the human body and the interaction of
the microbes with the immune system will benefit the choice of an
appropriate chassis that engrafts stably and interacts productively
with the resident community in specific body niches.
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Affiliation(s)
- Jan Claesen
- Department of Bioengineering
and Therapeutic Sciences and the California Institute for Quantitative
Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Michael A. Fischbach
- Department of Bioengineering
and Therapeutic Sciences and the California Institute for Quantitative
Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
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34
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Richter TKS, Hughes CC, Moore BS. Sioxanthin, a novel glycosylated carotenoid, reveals an unusual subclustered biosynthetic pathway. Environ Microbiol 2014; 17:2158-71. [PMID: 25329237 DOI: 10.1111/1462-2920.12669] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/26/2014] [Accepted: 10/12/2014] [Indexed: 01/30/2023]
Abstract
Members of the marine actinomycete genus Salinispora constitutively produce a characteristic orange pigment during vegetative growth. Contrary to the understanding of widespread carotenoid biosynthesis pathways in bacteria, Salinispora carotenoid biosynthesis genes are not confined to a single cluster. Instead, bioinformatic and genetic investigations confirm that four regions of the Salinispora tropica CNB-440 genome, consisting of two gene clusters and two independent genes, contribute to the in vivo production of a single carotenoid. This compound, namely (2'S)-1'-(β-D-glucopyranosyloxy)-3',4'-didehydro-1',2'-dihydro-φ,ψ-caroten-2'-ol, is novel and has been given the trivial name 'sioxanthin'. Sioxanthin is a C40 -carotenoid, glycosylated on one end of the molecule and containing an aryl moiety on the opposite end. Glycosylation is unusual among actinomycete carotenoids, and sioxanthin joins a rare group of carotenoids with polar and non-polar head groups. Gene sequence homology predicts that the sioxanthin biosynthetic pathway is present in all of the Salinispora as well as other members of the family Micromonosporaceae. Additionally, this study's investigations of clustering of carotenoid biosynthetic genes in heterotrophic bacteria show that a non-clustered genome arrangement is more common than previously suggested, with nearly half of the investigated genomes showing a non-clustered architecture.
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Affiliation(s)
- Taylor K S Richter
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Chambers C Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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35
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Functional optimization of gene clusters by combinatorial design and assembly. Nat Biotechnol 2014; 32:1241-9. [PMID: 25419741 DOI: 10.1038/nbt.3063] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 10/07/2014] [Indexed: 01/21/2023]
Abstract
Large microbial gene clusters encode useful functions, including energy utilization and natural product biosynthesis, but genetic manipulation of such systems is slow, difficult and complicated by complex regulation. We exploit the modularity of a refactored Klebsiella oxytoca nitrogen fixation (nif) gene cluster (16 genes, 103 parts) to build genetic permutations that could not be achieved by starting from the wild-type cluster. Constraint-based combinatorial design and DNA assembly are used to build libraries of radically different cluster architectures by varying part choice, gene order, gene orientation and operon occupancy. We construct 84 variants of the nifUSVWZM operon, 145 variants of the nifHDKY operon, 155 variants of the nifHDKYENJ operon and 122 variants of the complete 16-gene pathway. The performance and behavior of these variants are characterized by nitrogenase assay and strand-specific RNA sequencing (RNA-seq), and the results are incorporated into subsequent design cycles. We have produced a fully synthetic cluster that recovers 57% of wild-type activity. Our approach allows the performance of genetic parts to be quantified simultaneously in hundreds of genetic contexts. This parallelized design-build-test-learn cycle, which can access previously unattainable regions of genetic space, should provide a useful, fast tool for genetic optimization and hypothesis testing.
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36
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Axen SD, Erbilgin O, Kerfeld CA. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol 2014; 10:e1003898. [PMID: 25340524 PMCID: PMC4207490 DOI: 10.1371/journal.pcbi.1003898] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/09/2014] [Indexed: 01/21/2023] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications. Some enzymatic transformations have undesirable side reactions, produce toxic or volatile intermediates, or are inefficient; these shortcomings can be alleviated through their sequestration with their substrates in a confined space, as in the membrane-bound organelles of eukaryotes. Recently, it was discovered that bacteria also form organelles–bacterial microcompartments (BMCs)–composed of a protein shell that surrounds functionally related enzymes. BMCs long evaded detection because they typically form only in the presence of the substrate they metabolize, and they can only be visualized by electron microscopy. A few BMCs have been experimentally characterized; they have diverse functions in CO2 fixation, pathogenesis, and niche colonization. While the encapsulated enzymes differ among functionally distinct BMCs, the shell architecture is conserved. This enables their detection computationally, as genes for shell proteins are typically nearby genes for the encapsulated enzymes. We developed a novel algorithm to comprehensively identify and categorize BMCs in sequenced bacterial genomes. We show that BMCs are often encoded adjacent to genes that play supporting roles to the organelle's function. Our results provide the first glimpse of the extent of BMC metabolic diversity and will inform design of genetic modules encoding BMCs for introduction of new metabolic functions in a plug-and-play approach.
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Affiliation(s)
- Seth D. Axen
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Onur Erbilgin
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Cheryl A. Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Berkeley Synthetic Biology Institute, Berkeley, California, United States of America
- * E-mail: ,
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37
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Oßwald C, Zipf G, Schmidt G, Maier J, Bernauer HS, Müller R, Wenzel SC. Modular construction of a functional artificial epothilone polyketide pathway. ACS Synth Biol 2014; 3:759-72. [PMID: 23654254 DOI: 10.1021/sb300080t] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Natural products of microbial origin continue to be an important source of pharmaceuticals and agrochemicals exhibiting potent activities and often novel modes of action. Due to their inherent structural complexity chemical synthesis is often hardly possible, leaving fermentation as the only viable production route. In addition, the pharmaceutical properties of natural products often need to be optimized for application by sophisticated medicinal chemistry and/or biosynthetic engineering. The latter requires a detailed understanding of the biosynthetic process and genetic tools to modify the producing organism that are often unavailable. Consequently, heterologous expression of complex natural product pathways has been in the focus of development over recent years. However, piecing together existing DNA cloned from natural sources and achieving efficient expression in heterologous circuits represent several limitations that can be addressed by synthetic biology. In this work we have redesigned and reassembled the 56 kb epothilone biosynthetic gene cluster from Sorangium cellulosum for expression in the high GC host Myxococcus xanthus. The codon composition was adapted to a modified codon table for M. xanthus, and unique restriction sites were simultaneously introduced and others eliminated from the sequence in order to permit pathway assembly and future interchangeability of modular building blocks from the epothilone megasynthetase. The functionality of the artificial pathway was demonstrated by successful heterologous epothilone production in M. xanthus at significant yields that have to be improved in upcoming work. Our study sets the stage for future engineering of epothilone biosynthesis and production optimization using a highly flexible assembly strategy.
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Affiliation(s)
- Corina Oßwald
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical
Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, Saarbrücken,
Germany
| | | | | | - Josef Maier
- IStLS, Information Services to Life Science, Oberndorf a.N., Germany
| | | | - Rolf Müller
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical
Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, Saarbrücken,
Germany
| | - Silke C. Wenzel
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical
Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical
Biotechnology, Saarland University, Saarbrücken,
Germany
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38
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Junier I. Conserved patterns in bacterial genomes: a conundrum physically tailored by evolutionary tinkering. Comput Biol Chem 2014; 53 Pt A:125-33. [PMID: 25239779 DOI: 10.1016/j.compbiolchem.2014.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 11/17/2022]
Abstract
The proper functioning of bacteria is encoded in their genome at multiple levels or scales, each of which is constrained by specific physical forces. At the smallest spatial scales, interatomic forces dictate the folding and function of proteins and nucleic acids. On longer length scales, stochastic forces emerging from the thermal jiggling of proteins and RNAs impose strong constraints on the organization of genes along chromosomes, more particularly in the context of the building of nucleoprotein complexes and the operational mode of regulatory agents. At the cellular level, transcription, replication and cell division activities generate forces that act on both the internal structure and cellular location of chromosomes. The overall result is a complex multi-scale organization of genomes that reflects the evolutionary tinkering of bacteria. The goal of this review is to highlight avenues for deciphering this complexity by focusing on patterns that are conserved among evolutionarily distant bacteria. To this end, I discuss three different organizational scales: the protein structures, the chromosomal organization of genes and the global structure of chromosomes.
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Affiliation(s)
- Ivan Junier
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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39
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Liebl W, Angelov A, Juergensen J, Chow J, Loeschcke A, Drepper T, Classen T, Pietruszka J, Ehrenreich A, Streit WR, Jaeger KE. Alternative hosts for functional (meta)genome analysis. Appl Microbiol Biotechnol 2014; 98:8099-109. [PMID: 25091044 DOI: 10.1007/s00253-014-5961-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/25/2022]
Abstract
Microorganisms are ubiquitous on earth, often forming complex microbial communities in numerous different habitats. Most of these organisms cannot be readily cultivated in the laboratory using standard media and growth conditions. However, it is possible to gain access to the vast genetic, enzymatic, and metabolic diversity present in these microbial communities using cultivation-independent approaches such as sequence- or function-based metagenomics. Function-based analysis is dependent on heterologous expression of metagenomic libraries in a genetically amenable cloning and expression host. To date, Escherichia coli is used in most cases; however, this has the drawback that many genes from heterologous genomes and complex metagenomes are expressed in E. coli either at very low levels or not at all. This review emphasizes the importance of establishing alternative microbial expression systems consisting of different genera and species as well as customized strains and vectors optimized for heterologous expression of membrane proteins, multigene clusters encoding protein complexes or entire metabolic pathways. The use of alternative host-vector systems will complement current metagenomic screening efforts and expand the yield of novel biocatalysts, metabolic pathways, and useful metabolites to be identified from environmental samples.
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Affiliation(s)
- Wolfgang Liebl
- Lehrstuhl für Mikrobiologie, Technische Universität München, Emil-Ramann-Str. 4, 85654, Freising, Germany,
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40
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Brophy JAN, Voigt CA. Principles of genetic circuit design. Nat Methods 2014; 11:508-20. [PMID: 24781324 DOI: 10.1038/nmeth.2926] [Citation(s) in RCA: 566] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/18/2014] [Indexed: 12/17/2022]
Abstract
Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.
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Affiliation(s)
- Jennifer A N Brophy
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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41
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Medema MH, Takano E, Breitling R. Detecting sequence homology at the gene cluster level with MultiGeneBlast. Mol Biol Evol 2013; 30:1218-23. [PMID: 23412913 PMCID: PMC3670737 DOI: 10.1093/molbev/mst025] [Citation(s) in RCA: 245] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The genes encoding many biomolecular systems and pathways are genomically organized in operons or gene clusters. With MultiGeneBlast, we provide a user-friendly and effective tool to perform homology searches with operons or gene clusters as basic units, instead of single genes. The contextualization offered by MultiGeneBlast allows users to get a better understanding of the function, evolutionary history, and practical applications of such genomic regions. The tool is fully equipped with applications to generate search databases from GenBank or from the user’s own sequence data. Finally, an architecture search mode allows searching for gene clusters with novel configurations, by detecting genomic regions with any user-specified combination of genes. Sources, precompiled binaries, and a graphical tutorial of MultiGeneBlast are freely available from http://multigeneblast.sourceforge.net/.
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Affiliation(s)
- Marnix H Medema
- Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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42
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Regulation of internal promoters in a zinc-responsive operon is influenced by transcription from upstream promoters. J Bacteriol 2013; 195:1285-93. [PMID: 23316045 DOI: 10.1128/jb.01488-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the cyanobacterium Anabaena sp. strain PCC 7120 (also known as Nostoc sp. strain PCC 7120), a zinc-responsive operon (all4725-all4721) has been described, which contains 4 distinct promoters. The two most upstream ones bind Zur with high affinity, whereas the other two do not or do so with a very low affinity. In this paper, a detailed characterization of the four promoters is presented, showing that all four were induced by metal depletion, and they were constitutively derepressed in a zur mutant, despite the two downstream promoters not being direct targets for this regulator. Crucially, induction by metal depletion of the two downstream promoters was abrogated when transcription initiated at the upstream promoters was interrupted by a polar insertion midway in the operon. In contrast, insertion of a nitrogen-responsive promoter at a roughly similar position provoked the two downstream promoters to adopt a regulatory pattern mimicking that of the inserted promoter. Thus, regulation of the two downstream promoters is apparently influenced by transcription from promoters upstream. Evidence is presented indicating that the activity of the two downstream promoters is kept basal in Anabaena by repression. A regulatory model compatible with these results is proposed, where promoters controlled by repression in bacterial operons may be subjected to a hierarchical regulation depending on their position in the operon. According to this model, internal promoters may respond to stimuli governing the activity of promoters upstream by an indirect regulation and to specific stimuli by a direct regulation.
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43
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Fast AG, Papoutsakis ET. Stoichiometric and energetic analyses of non-photosynthetic CO2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals. Curr Opin Chem Eng 2012. [DOI: 10.1016/j.coche.2012.07.005] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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44
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Synthetic biotechnology to study and engineer ribosomal bottromycin biosynthesis. ACTA ACUST UNITED AC 2012; 19:1278-87. [PMID: 23021914 DOI: 10.1016/j.chembiol.2012.08.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/03/2012] [Accepted: 08/09/2012] [Indexed: 12/23/2022]
Abstract
Bottromycins represent a promising class of antibiotics binding to the therapeutically unexploited A-site of the bacterial ribosome. By inhibiting translation they are active against clinically important pathogens, such as vancomycin-resistant Enterococci. Structurally, bottromycins are heavily modified peptides exhibiting various unusual biosynthetic features. To set the stage for compound modification and yield optimization, we identified the biosynthetic gene cluster, used synthetic biotechnology approaches to establish and improve heterologous production, and generated analogs by pathway genetic engineering. We unambiguously identified three radical SAM methyltransferase-encoding genes required for various methylations at unactivated carbons yielding tert-butyl valine, methyl-proline, and β-methyl-phenylalanine residues, plus a gene involved in aspartate methyl-ester formation. Evidence for the formation of the exo-thiazole unit and for a macrocyclodehydration mechanism leading to amidine ring formation is provided.
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Abstract
The parameters in a complex synthetic gene network must be extensively tuned before the network functions as designed. Here, we introduce a simple and general approach to rapidly tune gene networks in Escherichia coli using hypermutable simple sequence repeats embedded in the spacer region of the ribosome binding site. By varying repeat length, we generated expression libraries that incrementally and predictably sample gene expression levels over a 1,000-fold range. We demonstrate the utility of the approach by creating a bistable switch library that programmatically samples the expression space to balance the two states of the switch, and we illustrate the need for tuning by showing that the switch's behavior is sensitive to host context. Further, we show that mutation rates of the repeats are controllable in vivo for stability or for targeted mutagenesis--suggesting a new approach to optimizing gene networks via directed evolution. This tuning methodology should accelerate the process of engineering functionally complex gene networks.
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Abstract
Metabolism is a highly interconnected web of chemical reactions that power life. Though the stoichiometry of metabolism is well understood, the multidimensional aspects of metabolic regulation in time and space remain difficult to define, model and engineer. Complex metabolic conversions can be performed by multiple species working cooperatively and exchanging metabolites via structured networks of organisms and resources. Within cells, metabolism is spatially regulated via sequestration in subcellular compartments and through the assembly of multienzyme complexes. Metabolic engineering and synthetic biology have had success in engineering metabolism in the first and second dimensions, designing linear metabolic pathways and channeling metabolic flux. More recently, engineering of the third dimension has improved output of engineered pathways through isolation and organization of multicell and multienzyme complexes. This review highlights natural and synthetic examples of three-dimensional metabolism both inter- and intracellularly, offering tools and perspectives for biological design.
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Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci U S A 2012; 109:7085-90. [PMID: 22509035 DOI: 10.1073/pnas.1120788109] [Citation(s) in RCA: 252] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial genes associated with a single trait are often grouped in a contiguous unit of the genome known as a gene cluster. It is difficult to genetically manipulate many gene clusters because of complex, redundant, and integrated host regulation. We have developed a systematic approach to completely specify the genetics of a gene cluster by rebuilding it from the bottom up using only synthetic, well-characterized parts. This process removes all native regulation, including that which is undiscovered. First, all noncoding DNA, regulatory proteins, and nonessential genes are removed. The codons of essential genes are changed to create a DNA sequence as divergent as possible from the wild-type (WT) gene. Recoded genes are computationally scanned to eliminate internal regulation. They are organized into operons and placed under the control of synthetic parts (promoters, ribosome binding sites, and terminators) that are functionally separated by spacer parts. Finally, a controller consisting of genetic sensors and circuits regulates the conditions and dynamics of gene expression. We applied this approach to an agriculturally relevant gene cluster from Klebsiella oxytoca encoding the nitrogen fixation pathway for converting atmospheric N(2) to ammonia. The native gene cluster consists of 20 genes in seven operons and is encoded in 23.5 kb of DNA. We constructed a "refactored" gene cluster that shares little DNA sequence identity with WT and for which the function of every genetic part is defined. This work demonstrates the potential for synthetic biology tools to rewrite the genetics encoding complex biological functions to facilitate access, engineering, and transferability.
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A retrosynthetic biology approach to therapeutics: from conception to delivery. Curr Opin Biotechnol 2012; 23:948-56. [PMID: 22475981 DOI: 10.1016/j.copbio.2012.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 03/09/2012] [Accepted: 03/13/2012] [Indexed: 01/08/2023]
Abstract
De novo biosynthetic pathways are designed, assembled and optimized to produce high-value compounds such as drugs and chemical building blocks from renewable resources. Microorganisms are used as synthetic platforms of systems biology where biochemical pathways are engineered into the host metabolic network. Retrosynthetic biology offers a creative pathway design concept that has gained interest because of its potential to identify novel metabolic ways for therapeutic production. Retrosynthetic biology uses the backward search of retrosynthetic analysis to devise and optimize tailor-made pathways. The retrosynthetic process can be seamlessly integrated into a complete circuitry system for therapeutic applications where production, sensing and delivery act as constitutive interconnecting parts. The aim of this review is to highlight recent efforts toward synthetic design for therapeutic development.
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Göbel U. Meeting report: Synthetic DNA - Writing with the Letters of Life: January 24, 2012, Frankfurt, Germany. Biotechnol J 2012; 7:471-2. [PMID: 22461398 DOI: 10.1002/biot.201200113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The one-day meeting on Synthetic DNA (January 24, 2012) organized by and held at the DECHEMA in Frankfurt attracted about 100 participants from academia and industry interested in synthesizing DNA and its applications in synthetic biology. In recent years the cost for synthetic DNA reduced from 7€/bp to 0.35€/bp which has opened up many new possibilities for molecular biology. You can purchase the gene, cDNA, oligo library or full vector specifically for a particular expression host and apply synthetic biology principles to produce or create new drugs, vaccines or any other biotechnological products. There are, however, great concerns within society to produce organisms that do not exist in nature, and the potential misuse of them. Adressing these concerns and to use a clear terminology that do not cause misunderstandings are important issues within the field, which were also discussed at this meeting.
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