Biotechnological production of bio-based long-chain dicarboxylic acids with oleogenious yeasts

Long-chain α,ω-dicarboxylic acids (DCAs) are versatile chemical intermediates of industrial importance used as building blocks for the production of polymers, lubricants, or adhesives. The majority of industrial long-chain DCAs is produced from petro-chemical resources. An alternative is their biotechnological production from renewable materials like plant oil fatty acids by microbial fermentation using oleogenious yeasts. Oleogenious yeasts are natural long-chain DCA producers, which have to be genetically engineered for high-yield DCA production. Although, some commercialized fermentation processes using engineered yeasts are reported, bio-based long-chain DCAs are still far from being a mass product. Further progress in bioprocess engineering and rational strain design is necessary to advance their further commercialization. The present article reviews the basic strategies, as well as novel approaches in the strain design of oleogenious yeasts, such as the combination of traditional metabolic engineering with system biology strategies for high-yield long-chain DCA production. Therefore a detailed overview of the involved metabolic processes for the biochemical long-chain DCA synthesis is given.     

Microbial n‐butanol production from Clostridia to non‐Clostridial hosts

In the context of the global objective of shifting from petroleum to a biomass‐based economy, the research on fermentative strategies to produce alternative biofuels and chemicals has become a predominant field of study. Microorganisms, because of their substrate versatility and metabolic efficiency, are promising to partially support our increasing needs for materials and fuels, opening up scenarios for the use of alternative sources, including wastes. Butanol is a very attractive molecule since it can be seen both as a chemical platform and as a fuel. Today, it is principally derived from petroleum, but it also represents the final product of a microbial fermentation. Although Clostridia are the natural and traditional organisms employed in butanol production, systematic approaches to improve production and resistance traits are currently impeded by a lack of characterization and genetic tools. This is the main reason why, besides their optimizations, a significant and growing amount of research is centered on the engineering of alternative robust cell factories capable of elevated production, possibly combined with higher tolerance. Here, we review the most recent advances in n‐butanol production in non‐Clostridial microbial hosts, including not only other prokaryotic but also eukaryotic microorganisms, which might eventually be seen as second‐generation hosts.     

A comprehensive review of microbial electrochemical systems as a platform technology

Microbial electrochemical systems (MESs) use microorganisms to covert the chemical energy stored in biodegradable materials to direct electric current and chemicals. Compared to traditional treatment-focused, energy-intensive environmental technologies, this emerging technology offers a new and transformative solution for integrated waste treatment and energy and resource recovery, because it offers a flexible platform for both oxidation and reduction reaction oriented processes. All MESs share one common principle in the anode chamber, in which biodegradable substrates, such as waste materials, are oxidized and generate electrical current. In contrast, a great variety of applications have been developed by utilizing this in situ current, such as direct power generation (microbial fuel cells, MFCs), chemical production (microbial electrolysis cells, MECs; microbial electrosynthesis, MES), or water desalination (microbial desalination cells, MDCs). Different from previous reviews that either focus on one function or a specific application aspect, this article provides a comprehensive and quantitative review of all the different functions or system constructions with different acronyms developed so far from the MES platform and summarizes nearly 50 corresponding systems to date. It also provides discussions on the future development of this promising yet early-stage technology.     

New strategies for combating multidrug-resistant bacteria

Antibiotic resistance is a problem that continues to challenge the healthcare sector. In particular, multidrug resistance is now common in familiar pathogens such as Staphylococcus aureus and Mycobacterium tuberculosis, as well as emerging pathogens such as Acinetobacter baumannii. New antibiotics and new therapeutic strategies are needed to address this challenge. Advances in identifying new sources of antibiotic natural products and expanding antibiotic chemical diversity are providing chemical leads for new drugs. Inhibitors of resistance mechanisms and microbial virulence are orthogonal strategies that are also generating new chemicals that can extend the life of existing antibiotics. This new chemistry, coupled with a growing understanding of the mechanisms, origins and distribution of antibiotic resistance, position us to tackle the challenges of antibiotic resistance in the 21st century.     

Molecular engineering of antimicrobial peptides: microbial targets,peptide motifs and translation opportunities

The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.     

Information about transmission opportunities triggers a life-history switch in a parasite

Many microbial pathogens can switch to new hosts or adopt alternative transmission routes as environmental conditions change, displaying unexpected flexibility in their infection pathways and often causing emerging diseases. In contrast, parasitic worms that must develop through a fixed series of host species appear less likely to show phenotypic plasticity in their transmission pathways. Here, I demonstrate experimentally that a trematode parasite, Coitocaecum parvum, can accelerate its development and rapidly reach precocious maturity in its crustacean intermediate host in the absence of chemical cues emanating from its fish definitive host. Juvenile trematodes can also mature precociously when the mortality rate of their intermediate hosts is increased. Eggs produced by precocious adults hatch into viable larvae, capable of pursuing the parasite's life cycle. In the absence of chemical cues from fish hosts, the size of eggs released by precocious trematodes in their intermediate hosts becomes more variable, possibly indicating a bet-hedging strategy. These results illustrate that parasitic worms with complex life cycles have development and transmission strategies that are more plastic than commonly believed, allowing them to skip one host in their cycle when they perceive limited opportunities for transmission.     

A trait-based approach for modelling microbial litter decomposition

Trait-based models are an emerging tool in ecology with the potential to link community dynamics, environmental responses and ecosystem processes. These models represent complex communities by defining taxa with trait combinations derived from prior distributions that may be constrained by trade-offs. Herein I develop a model that links microbial community composition with physiological and enzymatic traits to predict litter decomposition rates. This approach allows for trade-offs among traits that represent alternative microbial strategies for resource acquisition. The model predicts that optimal strategies depend on the level of enzyme production in the whole community, which determines resource availability and decomposition rates. There is also evidence for facilitation and competition among microbial taxa that co-occur on decomposing litter. These interactions vary with community investment in extracellular enzyme production and the magnitude of trade-offs affecting enzyme biochemical traits. The model accounted for 69% of the variation in decomposition rates of 15 Hawaiian litter types and up to 26% of the variation in enzyme activities. By explicitly representing diversity, trait-based models can predict ecosystem processes based on functional trait distributions in a community. The model developed herein illustrates that traits influencing microbial enzyme production are some of the key controls on litter decomposition rates.     

抗病原菌植物基因工程进展

植物病原菌给农林生产带来巨大的损失,植物基因工程在培育抗病原菌植物方面是传统育种技术的补充和发展,短短几年,在抗细菌和抗真菌植物基因工程方面出现了一些全新的成功策略,这些范例都是针对病原菌的生理结构、致病机理及与植物的相互关系。本文概括论述了这些策略的基本思路并对其局限性加以探讨。随着植物病理学、植物分子生物学和病原菌分子生物学的研究进展,新的抗性策略将会出现。     

The re-emerging role of microbial natural products in antibiotic discovery

New classes of antibacterial compounds are urgently needed to respond to the high frequency of occurrence of resistances to all major classes of known antibiotics. Microbial natural products have been for decades one of the most successful sources of drugs to treat infectious diseases but today, the emerging unmet clinical need poses completely new challenges to the discovery of novel candidates with the desired properties to be developed as antibiotics. While natural products discovery programs have been gradually abandoned by the big pharma, smaller biotechnology companies and research organizations are taking over the lead in the discovery of novel antibacterials. Recent years have seen new approaches and technologies being developed and integrated in a multidisciplinary effort to further exploit microbial resources and their biosynthetic potential as an untapped source of novel molecules. New strategies to isolate novel species thought to be uncultivable, and synthetic biology approaches ranging from genome mining of microbial strains for cryptic biosynthetic pathways to their heterologous expression have been emerging in combination with high throughput sequencing platforms, integrated bioinformatic analysis, and on-site analytical detection and dereplication tools for novel compounds. These different innovative approaches are defining a completely new framework that is setting the bases for the future discovery of novel chemical scaffolds that should foster a renewed interest in the identification of novel classes of natural product antibiotics from the microbial world.     

Microbial production of small peptide: pathway engineering and synthetic biology

Small peptides are a group of natural products with low molecular weights and complex structures. The diverse structures of small peptides endow them with broad bioactivities and suggest their potential therapeutic use in the medical field. The remaining challenge is methods to address the main limitations, namely (i) the low amount of available small peptides from natural sources, and (ii) complex processes required for traditional chemical synthesis. Therefore, harnessing microbial cells as workhorse appears to be a promising approach to synthesize these bioactive peptides. As an emerging engineering technology, synthetic biology aims to create standard, well-characterized and controllable synthetic systems for the biosynthesis of natural products. In this review, we describe the recent developments in the microbial production of small peptides. More importantly, synthetic biology approaches are considered for the production of small peptides, with an emphasis on chassis cells, the evolution of biosynthetic pathways, strain improvements and fermentation.     

Inducible cell lysis systems in microbial production of bio-based chemicals

The release of products from microbial cells is an essential process for industrial scale production of bio-based chemicals. However, traditional methods of cell lysis, e.g., mechanical disruption, chemical solvent extraction, and immobilized enzyme degradation, account for a large share of the total production cost. Thus, an efficient cell lysis system is required to lower the cost. This review has focused on our current knowledge of two cell lysis systems, bacteriophage holin–endolysin system, and lipid enzyme hydrolysis system. These systems are controlled by conditionally inducible regulatory apparatus and applied in microbial production of fatty acids and polyhydroxyalkanoates. Moreover, toxin–antitoxin system is also suggested as alternative for its potential applications in cell lysis. Compared with traditional methods of cell disruption, the inducible cell lysis systems are more economically feasible and easier to control and show a promising perspective in industrial production of bio-based chemicals.     

Estimation of Aedes aegypti (Diptera: Culicidae) population size and adult male survival in an urban area in Panama

Traditional mosquito control strategies rely heavily on the use of chemical insecticides. However, concerns about the efficiency of traditional control methods, environmental impact and emerging pesticide resistance have highlighted the necessity for developing innovative tools for mosquito control. Some novel strategies, including release of insects carrying a dominant lethal gene (RIDL^®), rely on the sustained release of modified male mosquitoes and therefore benefit from a thorough understanding of the biology of the male of the species. In this report we present the results of a mark-release-recapture study aimed at: (i) establishing the survival in the field of laboratory-reared, wild-type male Aedes aegypti and (b) estimating the size of the local adult Ae. aegypti population. The study took place in Panama, a country where recent increases in the incidence and severity of dengue cases have prompted health authorities to evaluate alternative strategies for vector control. Results suggest a life expectancy of 2.3 days for released male mosquitoes (confidence interval: 1.78-2.86). Overall, the male mosquito population was estimated at 58 males/ha (range 12-81 males/ha), which can be extrapolated to an average of 0.64 pupae/person for the study area. The practical implications of these results are discussed.     

Strategies for efficient and economical 2,3-butanediol production: new trends in this field

2,3-Butanediol (2,3-BD) is a promising bulk chemical with a potentially wide range of applications e.g., in the manufacture of printing inks, perfumes, synthetic rubber, fumigants, antifreeze agents, fuel additives, foodstuffs and pharmaceuticals. Its high heating value and ability to increase the octane number of fuels make 2,3-BD a promising drop-in fuel. It can also be converted to methyl-ethyl ketone (MEK), which is considered an effective liquid fuel additive. After combination with MEK and hydrogenation reaction, 2,3-BD can be converted to octane, which is used to produce high-quality aviation fuel. Currently 2,3-BD is mainly produced on an industrial scale by chemical methods. However, microbiological production of 2,3-BD offers a less expensive and more environmentally friendly alternative to traditional synthesis. This alcohol is generated from hexoses and pentoses mainly by bacterial strains of the genera Klebsiella, Bacillus, Serratia, and Enterobacter, which can convert waste products (such as glycerol and agricultural residues) and excess biomass (such as wood hydrolysates) to 2,3-BD. Recently, a significant improvement in microbial production has been achieved by the screening of efficient natural microbial strains, the application of alternative cost-effective substrates, and the genetic improvement of microbial producers. Furthermore, Klebsiella strains, which are regarded the most efficient natural 2,3-BD producers, have been subjected to genetic modifications aiming at the removal of pathogenic factors and the development of avirulent strains that could be used for the safe production of the diol. This review summarizes existing knowledge and experience concerning various strategies for efficient and economical microbial production of 2,3-BD.     

Transition metal catalyzed methods for site-selective protein modification

The broad utility of protein bioconjugates has created a need for new and diverse strategies for site-selective protein modification. In particular, chemical reactions that target alternative amino acid side chains or unnatural functional groups are emerging as a valuable complement to more commonly used lysine- and cysteine-based strategies. Considering their widespread use in organic synthesis, reactions catalyzed by transition metals could provide a particularly powerful set of transformations for the continued expansion of the bioconjugation toolkit. Recent efforts to apply transition metal catalysis to protein modification have resulted in new methods for protein cross-linking, tryptophan modification, tyrosine modification, reductive amination of protein amines, and unnatural amino acid labeling. These strategies have substantially expanded the synthetic flexibility of protein modification, and thus the range of applications for which bioconjugates can be used in chemical biology and materials science.     

Recent advances in biotechnological production of 2-phenylethanol

2-Phenylethanol (2-PE) is an important aromatic alcohol with a rose-like fragrance. It has been widely applied in the cosmetic, perfume, and food industries and is mainly produced by chemical synthesis. An alternative method for the production of natural flavors and fragrances is the microbial transformation process, which is attracting increasing attention because it is an environmentally friendly process and the products are considered “natural”. The production of 2-PE from L-phenylalanine by biotransformation is possible through the Ehrlich pathway and considerable progress has been made in the development of this process. The present report reviews recent advances in biotechnological production of 2-PE, with emphasis on the strategies used to increase production and the applications of in situ product removal techniques. Future research should focus on product scale-up and product recovery processes for the industrialization of microbial processes.     

宏基因组学在纤维素酶研究中的应用进展

纤维素酶能降解纤维素,被广泛应用于生物修复、食品加工、化工合成等领域,开发高活力、广底物、耐高温高碱等极端条件的新型纤维素酶具有重要意义。宏基因组学以特定环境样品中微生物的基因组总和为研究对象,避开传统的微生物分离培养过程,为基因资源的开发、利用提供了新技术。文中结合本课题组的研究工作,综述了利用宏基因组学获取纤维素酶的策略,同时着重介绍利用宏基因组学从动物胃肠道、土壤等环境中获取纤维素酶的研究。     

From Metchnikoff to Monsanto and beyond: the path of microbial control

In 125 years since Metchnikoff proposed the use of Metarhizium anisopliae to control the wheat cockchafer and brought about the first field trials, microbial control has progressed from the application of naturalists' observations to biotechnology and precision delivery. This review highlights major milestones in its evolution and presents a perspective on its current direction. Fungal pathogens, the most eye-catching agents, dominated the early period, but major mycological control efforts for chinch bugs and citrus pests in the US had questionable success, and interest waned. The discoveries of Bacillus popilliae and Bacillus thuringiensis began the era of practical and commercially viable microbial control. A program to control the Japanese beetle in the US led to the discovery of both B. popilliae and Steinernema glaseri, the first nematode used as a microbial control agent. Viral insect control became practical in the latter half of the 20th century, and the first registration was obtained with the Heliothis nuclear polyhedrosis virus in 1975. Now strategies are shifting for microbial control. While Bt transgenic crops are now planted on millions of hectares, the successes of more narrowly defined microbial control are mainly in small niches. Commercial enthusiasm for traditional microbial control agents has been unsteady in recent years. The prospects of microbial insecticide use on vast areas of major crops are now viewed more realistically. Regulatory constraints, activist resistance, benign and efficacious chemicals, and limited research funding all drive changes in focus. Emphasis is shifting to monitoring, conservation, integration with chemical pesticides, and selection of favorable venues such as organic agriculture and countries that have low costs, mild regulatory climates, modest chemical inputs, and small scale farming.     

Microbial synthetic biology for human therapeutics

The emerging field of synthetic biology holds tremendous potential for developing novel drugs to treat various human conditions. The current study discusses the scope of synthetic biology for human therapeutics via microbial approach. In this context, synthetic biology aims at designing, engineering and building new microbial synthetic cells that do not pre-exist in nature as well as re-engineer existing microbes for synthesis of therapeutic products. It is expected that the construction of novel microbial genetic circuitry for human therapeutics will greatly benefit from the data generated by ??omics?? approaches and multidisciplinary nature of synthetic biology. Development of novel antimicrobial drugs and vaccines by engineering microbial systems are a promising area of research in the field of synthetic biology for human theragnostics. Expression of plant based medicinal compounds in the microbial system using synthetic biology tools is another avenue dealt in the present study. Additionally, the study suggest that the traditional medicinal knowledge can do value addition for developing novel drugs in the microbial systems using synthetic biology tools. The presented work envisions the success of synthetic biology for human therapeutics via microbial approach in a holistic manner. Keeping this in view, various legal and socio-ethical concerns emerging from the use of synthetic biology via microbial approach such as patenting, biosafety and biosecurity issues have been touched upon in the later sections.     

未来食品的低碳生物制造

受到人口增长过快、社会经济发展水平不平衡、人口老龄化和不健康饮食方式等影响,人类面临着食品和营养缺乏、部分人群中营养相关疾病高发等问题。同时,社会低碳发展的需求呼唤一种可持续的食物供给模式。因此,既能满足消费者口感和营养需求,又是绿色可持续食物供给模式的技术,例如功能糖、人造肉等未来食品技术,受到了广泛的关注。近年,新兴的生物制造技术及产品得到了迅猛发展,将会支撑形成绿色、低碳的未来食品产业,引发传统生产模式的深刻变革,是新兴生物经济的重大战略发展方向。本文聚焦于未来食品——功能糖、微生物蛋白及人造肉等关键辅配料的生物制造技术研究,追踪其在细胞工厂构建、工业环境下菌种测试与过程优化和衍生产品开发等研究的最新进展,展望未来的发展趋势,旨在为微生物制造未来食品的产业发展提供指导。