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2.
Nat Commun ; 10(1): 2142, 2019 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-31086174

RESUMO

Metabolic engineers endeavor to create a bio-based manufacturing industry using microbes to produce fuels, chemicals, and medicines. Plant natural products (PNPs) are historically challenging to produce and are ubiquitous in medicines, flavors, and fragrances. Engineering PNP pathways into new hosts requires finding or modifying a suitable host to accommodate the pathway, planning and implementing a biosynthetic route to the compound, and discovering or engineering enzymes for missing steps. In this review, we describe recent developments in metabolic engineering at the level of host, pathway, and enzyme, and discuss how the field is approaching ever more complex biosynthetic opportunities.


Assuntos
Produtos Biológicos/metabolismo , Engenharia Metabólica/métodos , Microrganismos Geneticamente Modificados/metabolismo , Plantas/metabolismo , Vias Biossintéticas/genética , Enzimas/genética , Enzimas/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Engenharia Metabólica/tendências , Microrganismos Geneticamente Modificados/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Biologia Sintética/métodos , Biologia Sintética/tendências
4.
Nanoscale ; 11(10): 4130-4146, 2019 Mar 07.
Artigo em Inglês | MEDLINE | ID: mdl-30793729

RESUMO

The organization of enzymes into different subcellular compartments is essential for correct cell function. Protein-based cages are a relatively recently discovered subclass of structurally dynamic cellular compartments that can be mimicked in the laboratory to encapsulate enzymes. These synthetic structures can then be used to improve our understanding of natural protein-based cages, or as nanoreactors in industrial catalysis, metabolic engineering, and medicine. Since the function of natural protein-based cages is related to their three-dimensional structure, it is important to determine this at the highest possible resolution if viable nanoreactors are to be engineered. Cryo-electron microscopy (cryo-EM) is ideal for undertaking such analyses within a feasible time frame and at near-native conditions. This review describes how three-dimensional cryo-EM is used in this field and discusses its advantages. An overview is also given of the nanoreactors produced so far, their structure, function, and applications.


Assuntos
Microscopia Crioeletrônica , Enzimas Imobilizadas , Engenharia Metabólica , Nanotecnologia , Microscopia Crioeletrônica/instrumentação , Microscopia Crioeletrônica/métodos , Enzimas Imobilizadas/química , Enzimas Imobilizadas/ultraestrutura , Humanos , Engenharia Metabólica/instrumentação , Engenharia Metabólica/métodos , Engenharia Metabólica/tendências , Nanotecnologia/instrumentação , Nanotecnologia/métodos , Nanotecnologia/tendências , Retratos como Assunto
6.
Microb Biotechnol ; 12(2): 200-209, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30793487

RESUMO

The harmful effects of pollution from the massive and widespread use of fossil fuels have led various organizations and governments to search for alternative energy sources. To address this, a new energy bioprocess is being developed that utilizes non-edible lignocellulose - the only sustainable source of organic carbon in nature. In this mini-review, we consider the potential use of synthetic biology to develop new-to-nature pathways for the biosynthesis of chemicals that are currently synthesized using classical industrial approaches. The number of industrial processes based on starch or lignocellulose is still very modest. Advances in the area require the development of more efficient approaches to deconstruct plant materials, better exploitation of the catalytic potential of prokaryotes and lower eukaryotes and the identification of new and useful genes for product synthesis. Further research and progress is urgently needed in order for government and industry to achieve the major milestone of transitioning 30% of the total industry to renewable sources by 2050.


Assuntos
Biocombustíveis/microbiologia , Biotecnologia/métodos , Lignina/metabolismo , Engenharia Metabólica/métodos , Amido/metabolismo , Biotecnologia/tendências , Engenharia Metabólica/tendências
7.
World J Microbiol Biotechnol ; 35(2): 33, 2019 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-30706208

RESUMO

Cell metabolism in living organisms is largely regulated at the transcriptional level, and the promoters are regarded as basic regulatory elements responsible for transcription initiation. Promoter engineering is an important technique to regulate gene expression and optimize metabolite biosynthesis in metabolic engineering and synthetic biology. The rational and precise control of gene expression in the multi-gene pathways can significantly affect the metabolic flux distribution and maximize the production of specific metabolites. Thus, many efforts have been made to identify natural promoters, construct inducible or hybrid promoters, and design artificial promoters for fine-tuning specific gene expression at the transcriptional level and improving production levels of the metabolites of interest. In this review, we will briefly introduce the architecture and function of both prokaryotic and eukaryotic promoters, and provide an overview of several major approaches for promoter engineering. The recent achievements and advances by promoter engineering for the optimization of metabolite biosynthetic pathways in multiple widely-used model microorganism, including Escherichia coli, Corynebacterium glutamicum and Saccharomyces cerevisiae, will also be extensively discussed.


Assuntos
Corynebacterium glutamicum/genética , Escherichia coli/genética , Engenharia Metabólica , Regiões Promotoras Genéticas , Saccharomyces cerevisiae/genética , Corynebacterium glutamicum/metabolismo , Escherichia coli/metabolismo , Engenharia Metabólica/tendências , Saccharomyces cerevisiae/metabolismo , Biologia Sintética/tendências
9.
Microb Biotechnol ; 12(1): 44-47, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30484965

RESUMO

Recombinant proteins are essential for biotechnology. Here we review some of the key points for improving the production of heterologous proteins, and what can be the future of the field.


Assuntos
Bactérias/genética , Bactérias/metabolismo , Biotecnologia/métodos , Engenharia Metabólica/métodos , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Biotecnologia/tendências , Engenharia Metabólica/tendências
11.
Biotechnol Adv ; 37(1): 91-108, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30521853

RESUMO

Single enzyme systems or engineered microbial hosts have been used for decades but the notion of assembling multiple enzymes into cell-free synthetic pathways is a relatively new development. The extensive possibilities that stem from this synthetic concept makes it a fast growing and potentially high impact field for biomanufacturing fine and platform chemicals, pharmaceuticals and biofuels. However, the translation of individual single enzymatic reactions into cell-free multi-enzyme pathways is not trivial. In reality, the kinetics of an enzyme pathway can be very inadequate and the production of multiple enzymes can impose a great burden on the economics of the process. We examine here strategies for designing synthetic pathways and draw attention to the requirements of substrates, enzymes and cofactor regeneration systems for improving the effectiveness and sustainability of cell-free biocatalysis. In addition, we comment on methods for the immobilisation of members of a multi-enzyme pathway to enhance the viability of the system. Finally, we focus on the recent development of integrative tools such as in silico pathway modelling and high throughput flux analysis with the aim of reinforcing their indispensable role in the future of cell-free biocatalytic pathways for biomanufacturing.


Assuntos
Sistema Livre de Células/metabolismo , Enzimas/metabolismo , Engenharia Metabólica/tendências , Biologia Sintética , Biocatálise , Sistema Livre de Células/química , Simulação por Computador , Enzimas/química , Enzimas/genética , Humanos , Cinética , Compostos Orgânicos/química , Compostos Orgânicos/metabolismo
12.
Biotechnol Adv ; 37(4): 538-568, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30339871

RESUMO

While the widespread reliance on fossil fuels is driven by their low cost and relative abundance, this fossil-based economy has been deemed unsustainable and, therefore, the adoption of sustainable and environmentally compatible energy sources is on the horizon. Biorefinery is an emerging approach that integrates metabolic engineering, synthetic biology, and systems biology principles for the development of whole-cell catalytic platforms for biomanufacturing. Due to the high degree of reduction and low cost, glycerol, either refined or crude, has been recognized as an ideal feedstock for the production of value-added biologicals, though microbial dissimilation of glycerol sometimes can be difficult particularly under anaerobic conditions. While strain development for glycerol biorefinery is widely reported in the literature, few, if any, commercialized bioprocesses have been developed as a result, such that engineering of glycerol metabolism in microbial hosts remains an untapped opportunity in biomanufacturing. Here we review the recent progress made in engineering microbial hosts for the production of biofuels, diols, organic acids, biopolymers, and specialty chemicals from glycerol. We begin with a broad outline of the major pathways for fermentative and respiratory glycerol dissimilation and key end metabolites, and then focus our analysis on four key genera of bacteria known to naturally dissimilate glycerol, i.e. Klebsiella, Citrobacter, Clostridium, and Lactobacillus, in addition to Escherichia coli, and systematically review the progress made toward engineering these microorganisms for glycerol biorefinery. We also identify the major biotechnological and bioprocessing advantages and disadvantages of each genus, and bottlenecks limiting the production of target metabolites from glycerol in engineered strains. Our analysis culminates in the development of potential strategies to overcome the current technical limitations identified for commonly employed strains, with an outlook on the suitability of different hosts for the production of key metabolites and avenues for their future development into biomanufacturing platforms.


Assuntos
Biocombustíveis , Biotecnologia/tendências , Glicerol/química , Engenharia Metabólica/tendências , Escherichia coli/química , Escherichia coli/genética , Fermentação , Biologia Sintética
14.
Microb Biotechnol ; 12(1): 98-124, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-29926529

RESUMO

The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.


Assuntos
Bactérias/genética , Bactérias/metabolismo , Biotecnologia/métodos , Engenharia Metabólica/métodos , Biotecnologia/tendências , Engenharia Metabólica/tendências , Biologia Sintética/métodos
15.
Biotechnol Adv ; 37(4): 519-529, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30576717

RESUMO

Filamentous fungi, as the main producers of lignocellulolytic enzymes in industry, need to be engineered to improve the economy of large-scale lignocellulose conversion. Investigation of the cellular processes involved in lignocellulolytic enzyme production, as well as optimization of enzyme mixtures for higher hydrolysis efficiency, have provided effective targets for the engineering of lignocellulolytic fungi. Recently, the development of efficient genetic manipulation systems in several lignocellulolytic fungi opens up the possibility of systems engineering of these strains. Here, we review the recent progresses made in the engineering of lignocellulolytic fungi and highlight the research gaps in this area.


Assuntos
Enzimas/química , Fungos/genética , Lignina/química , Engenharia Metabólica/tendências , Biomassa , Celulase/química , Enzimas/genética , Fungos/química , Hidrólise , Lignina/genética
16.
Biotechnol Adv ; 37(2): 271-283, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30553928

RESUMO

Numerous metabolic engineering strategies have allowed yeasts to efficiently assimilate xylose, the second most abundant sugar component of lignocellulosic biomass. During the investigation of xylose utilization by yeasts, a global rewiring of metabolic networks upon xylose cultivation has been captured, as opposed to a pattern of glucose repression. A clear understanding of the xylose-induced metabolic reprogramming in yeast would shed light on the optimization of yeast-based bioprocesses to produce biofuels and chemicals using xylose. In this review, we delved into the characteristics of yeast xylose metabolism, and potential benefits of using xylose as a carbon source to produce various biochemicals with examples. Transcriptomic and metabolomic patterns of xylose-grown yeast cells were distinct from those on glucose-a conventional sugar of industrial biotechnology-and the gap might lead to opportunities to produce biochemicals efficiently. Indeed, limited glycolytic metabolic fluxes during xylose utilization could result in enhanced production of metabolites whose biosynthetic pathways compete for precursors with ethanol fermentation. Also, alleviation of glucose repression on cytosolic acetyl coenzyme A (acetyl-CoA) synthesis, and respiratory energy metabolism during xylose utilization enhanced production of acetyl-CoA derivatives. Consideration of singular properties of xylose metabolism, such as redox cofactor imbalance between xylose reductase and xylitol dehydrogenase, is necessary to maximize these positive xylose effects. This review argues the importance and benefits of xylose utilization as not only a way of expanding a substrate range, but also an effective environmental perturbation for the efficient production of advanced biofuels and chemicals in yeasts.


Assuntos
Biocombustíveis/microbiologia , Vias Biossintéticas/genética , Engenharia Metabólica/tendências , Xilose/metabolismo , Acetilcoenzima A/metabolismo , Aldeído Redutase/química , Fermentação , Glucose/metabolismo , Metabolômica/tendências , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Transcriptoma/genética , Xilose/química
17.
Metab Eng ; 50: 156-172, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30367967

RESUMO

Expanding the concept of cell-free biology, implemented both with purified components and crude extracts, is continuing to deepen our appreciation of biological fundamentals while enlarging the range of applications. We are no longer intimidated by the complexity of crude extracts and complicated reaction systems with hundreds of active components, and, instead, coordinately activate and inactivate metabolic processes to focus and expand the capabilities of natural biological processes. This, in turn, dramatically increases the range of benefits offered by new products, both natural and supernatural, that were previously infeasible and/or unimaginable. This overview of cell-free metabolic engineering provides a broad range of examples and insights to guide and motivate continued research that will further expand fundamental understanding and beneficial applications. However, this survey also reveals how far we are from fully unlocking the potential offered by natural and engineered biological components and systems. This is an exciting conclusion, but metabolic engineering by itself is not sufficient. Going forward, innovative metabolic engineering must be intimately combined with creative process engineering to fully realize potential contributions toward a sustainable global civilization.


Assuntos
Engenharia Metabólica/métodos , Engenharia Metabólica/tendências
18.
FEMS Microbiol Lett ; 365(20)2018 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-30169822

RESUMO

Recent advances in DNA synthesis and computer science have enabled the de novo design of biosynthetic pathways. Numerous computational tools are currently available for searching biosynthetic pathways and ranking them on the basis of multiple criteria for installation into microbial chassis strains. This new framework allows the design of artificial biosynthetic pathways without expert knowledge of the specific biochemical reactions involved. Moreover, genetic apparatuses with quantitative and predictable properties enable rational construction of gene circuits. Thus, our ability to construct microbial cells specialized for bio-production is accelerating. However, many synthetic biology tools have not yet been fully applied to metabolic engineering owing to the lack of interdisciplinary collaboration between metabolic engineers and synthetic biologists. Therefore, we have focused on discussing how synthetic biology tools can be applied to de novo design of biosynthetic pathways.


Assuntos
Biocombustíveis , Vias Biossintéticas/genética , Engenharia Metabólica/métodos , Compostos Orgânicos/metabolismo , Biologia Sintética/métodos , Engenharia Metabólica/tendências , Biologia Sintética/tendências
19.
Appl Microbiol Biotechnol ; 102(22): 9541-9548, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30238143

RESUMO

The oleaginous yeast Yarrowia lipolytica is widely used for the production of both bulk and fine chemicals, including organic acids, fatty acid-derived biofuels and chemicals, polyunsaturated fatty acids, single-cell proteins, terpenoids, and other valuable products. Consequently, it is becoming increasingly popular for metabolic engineering applications. Multiple gene manipulation tools including URA blast, Cre/LoxP, and transcription activator-like effector nucleases (TALENs) have been developed for metabolic engineering in Y. lipolytica. However, the low efficiency and time-consuming procedures involved in these methods hamper further research. The emergence of the CRISPR/Cas system offers a potential solution for these problems due to its high efficiency, ease of operation, and time savings, which can significantly accelerate the genomic engineering of Y. lipolytica. In this review, we summarize the research progress on the development of CRISPR/Cas systems for Y. lipolytica, including Cas9 proteins and sgRNA expression strategies, as well as gene knock-out/knock-in and repression/activation applications. Finally, the most promising and tantalizing future prospects in this area are highlighted.


Assuntos
Engenharia Metabólica/métodos , Yarrowia/genética , Yarrowia/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sistemas CRISPR-Cas , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Engenharia Metabólica/tendências
20.
Trends Biotechnol ; 36(12): 1219-1229, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30262405

RESUMO

The consistent increase in the global population, estimated to reach 9 billion people by 2050, poses a serious challenge for the achievement of global food security. Therefore, the need to feed an increasing world population and to respond adequately to the effects of climate change must be urgently considered. Progress may be achieved by applying knowledge of molecular and genetic mechanisms to create and/or improve agricultural and industrial processes. We highlight the importance of crops (wheat, maize, rice, rapeseed, and soybean) to the development of sustainable agriculture and agrobiotechnology in the EU and discuss possible solutions for ensuring food security, while also considering their social acceptance.


Assuntos
Agricultura/métodos , Criação de Animais Domésticos/métodos , Biotecnologia/métodos , Abastecimento de Alimentos/métodos , Engenharia Metabólica/métodos , Crescimento Demográfico , Agricultura/tendências , Criação de Animais Domésticos/tendências , Biotecnologia/tendências , Humanos , Engenharia Metabólica/tendências
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