Expression and export: recombinant protein production systems for Aspergillus

Several Aspergillus species, in particular Aspergillus niger and Aspergillus oryzae, are widely used as protein production hosts in various biotechnological applications. In order to improve the expression and secretion of recombinant proteins in these filamentous fungi, several novel genetic engineering strategies have been developed in recent years. This review describes state-of-the-art genetic manipulation technologies used for strain improvement, as well as recent advances in designing the most appropriate engineering strategy for a particular protein production process. Furthermore, current developments in identifying bottlenecks in the protein production and secretion pathways are described and novel approaches to overcome these limitations are introduced. An appropriate combination of expression vectors and optimized host strains will provide cell factories customized for each production process and expand the great potential of Aspergilli as biotechnology workhorses to more complex multi-step industrial applications.     

空间生物技术研究与应用动态

由于空间生物技术潜在重大社会和经济效益。加强探索空间生物技术的发展。目前已经成为空间科学技术发展的重点之一。我国的空间技术在系列应用卫星成功发展的基础上,已将进入到更先进的载人飞船阶段。我国的科技人员将会有更多的机会,更好的条件在空间开展生物技术的研究。以促进其发展和应用,造福于人类,本文简要地介绍了空间发展生物技术的优越性。空间生物技术发展的热点和趋势,以及空间生物技术硬件发展的动态。     

From genomics to post-genomics in Aspergillus

Genome sequence data has recently become available for certain Aspergillus species. We consider the transition from genomics to a post-genomic era in Aspergillus, describing resources and methodologies available to underpin research efforts. Advances in our understanding of the fundamental biology of the Aspergilli, together with applications within the biotechnology and medical fields, are anticipated.     

The greening of biotechnology: the growth of the US biotechnology industry

The growth and advancement of biotechnology worldwide has been the focus of many studies, and at the heart of this advancement has been a new industry of small biotechnology firms in the United States. Since the early 1970s more than 300 small companies have been founded in the United States to work with the new technologies of genetic engineering, monoclonal antibody production, and in related areas. In addition, many major corporations in the United States have sought entry into biotechnology. Hundreds of new companies have been founded to interact with the biotechnology firms and large corporations, supplying reagents, equipment, fermentation expertise and serving a variety of other ancillary functions. Nowhere else in the world has a biotechnology industry been initiated to such a large degree. Today, the average US biotechnology firm is six to seven years old. The current state of the US biotechnology industry, historical perspectives, major trends and some future outlooks will be described below.     

White biotechnology: differences in US and EU approaches?

Several predominantly political movements advocate white, or industrial, biotechnology as a means to alleviate economic, ecological and societal problems in petroleum-dependent industrialized nations worldwide. US and European approaches differ significantly and we believe that, in the long-term, only economic drivers will be able to bring about the broad use of renewable resources and a bio-based economy. As long as the cost of fossil fuel and feedstock for key chemicals have not passed their respective critical thresholds, industrial biotechnology and its products will need political support and funding, particularly in the energy and bulk-chemicals sectors. Other uses of industrial biotechnology, however, such as biocatalytic conversions of fine and specialty chemicals and the manufacture of high-value products, such as nutriceuticals, cosmeceuticals and performance chemicals offer dynamic growth opportunities both for established chemical industries, as well as emerging entrepreneurial enterprises.     

Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics

Filamentous fungi and yeast from the genera Saccharomyces, Penicillium, Aspergillus, and Fusarium are well known for their impact on our life as pathogens, involved in food spoilage by degradation or toxin contamination, and also for their wide use in biotechnology for the production of beverages, chemicals, pharmaceuticals, and enzymes. The genomes of these eukaryotic micro-organisms range from about 6000 genes in yeasts (S. cerevisiae) to more than 10,000 genes in filamentous fungi (Aspergillus sp.). Yeast and filamentous fungi are expected to share much of their primary metabolism; therefore much understanding of the central metabolism and regulation in less-studied filamentous fungi can be learned from comparative metabolite profiling and metabolomics of yeast and filamentous fungi. Filamentous fungi also have a very active and diverse secondary metabolism in which many of the additional genes present in fungi, compared with yeast, are likely to be involved. Although the 'blueprint' of a given organism is represented by the genome, its behaviour is expressed as its phenotype, i.e. growth characteristics, cell differentiation, response to the environment, the production of secondary metabolites and enzymes. Therefore the profile of (secondary) metabolites--fungal chemodiversity--is important for functional genomics and in the search for new compounds that may serve as biotechnology products. Fungal chemodiversity is, however, equally efficient for identification and classification of fungi, and hence a powerful tool in fungal taxonomy. In this paper, the use of metabolite profiling is discussed for the identification and classification of yeasts and filamentous fungi, functional analysis or discovery by integration of high performance analytical methodology, efficient data handling techniques and core concepts of species, and intelligent screening. One very efficient approach is direct infusion Mass Spectrometry (diMS) integrated with automated data handling, but a full metabolic picture requires the combination of several different analytical techniques.     

Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays

DNA microarray technology has become an important research tool for microbiology and biotechnology as it allows for comprehensive DNA and RNA analyses to characterize genetic diversity and gene expression in a genome-wide manner. DNA microarrays have been applied extensively to study the biology of many bacteria including Mycobacterium tuberculosis, but only recently have they been used for the related high-GC Gram-positive Corynebacterium glutamicum, which is widely used for biotechnological amino acid production. Besides the design and generation of microarrays as well as their use in hybridization experiments and subsequent data analysis, recent applications of DNA microarray technology in C. glutamicum including the characterization of ribose-specific gene expression and the valine stress response will be described. Emerging perspectives of functional genomics to enlarge our insight into fundamental biology of C. glutamicum and their impact on applied biotechnology will be discussed.     

Search and discovery strategies for biotechnology: the paradigm shift.

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.     

Fungal secretomes—nature’s toolbox for white biotechnology

Adapting their metabolism to varying carbon and nitrogen sources, saprophytic fungi produce an arsenal of extracellular enzymes, the secretome, which allows for an efficient degradation of lignocelluloses and further biopolymers. Based on fundamental advances in electrophoretic, chromatographic, and mass spectrometric techniques on the one hand and the availability of annotated fungal genomes and sophisticated bioinformatic software tools on the other hand, a detailed analysis of fungal secretomes has become feasible. While a number of reports on ascomycetous secretomes of, e.g., Aspergillus, Trichoderma, and Fusarium species are already available, studies on basidiomycetes have been mainly focused on the two model organisms Phanerochaete chrysosporium and Coprinopsis cinerea so far. Though an impressive number and diversity of fungal biocatalysts has been revealed by secretome analyses, the identity and function of many extracellular proteins still remains to be elucidated. A comprehensive understanding of the qualitative and quantitative composition of fungal secretomes, together with their synergistic actions and kinetic expression profiles, will allow for the development of optimized enzyme cocktails for white biotechnology.     

国外动物生物技术研究和产业化趋势分析

生物技术在全世界范围取得了飞速的进展,与此同时其应用和产业化在各国政府、科研机构和生物技术公司的大力参与和激烈竞争中也逐步加快,预计它将成为许多国家经济的重要支柱产业之一。一些重大生物研究项目如人类基因组计划、克隆技术等开始引起公众的广泛注意。综述了２０世纪９０ 来动物生物技术的发展状况,对基因组研究、转基因动物、克隆技术和细胞培养等重要研究方向作了介绍和分析。     

Commercial development of microalgal biotechnology: from the test tube to the marketplace

While humans have taken limited advantage of natural populations of microalgae for centuries (Nostoc in Asia and Spirulina in Africa and North America for sustenance), it is only recently that we have come to realize the potential of microalgal biotechnology. Microalgal biotechnology has the potential to produce a vast array of products including foodstuffs, industrial chemicals, compounds with therapeutic applications and bioremediation solutions from a virtually untapped source. From an industrial (i.e. commercial) perspective, the goal of microalgal biotechnology is to make money by developing marketable products. For such a business to succeed the following steps must be taken: identify a desirable metabolite and a microalga that produces and accumulates the desired metabolite, establish a large-scale production process for the desired metabolite, and market the desired metabolite. So far, the commercial achievements of microalgal biotechnology have been modest. Microalgae that produce dozens of desirable metabolites have been identified. Aided by high throughput screening technology even more leads will become available. However, the successes in large-scale production and product marketing have been few. We will discuss those achievements and difficulties from the industrial point of view by considering examples from industry, specially our own experience at Mera Pharmaceuticals.     

Industrial biotechnology: Tools and applications

Industrial biotechnology involves the use of enzymes and microorganisms to produce value-added chemicals from renewable sources. Because of its association with reduced energy consumption, greenhouse gas emissions, and waste generation, industrial biotechnology is a rapidly growing field. Here we highlight a variety of important tools for industrial biotechnology, including protein engineering, metabolic engineering, synthetic biology, systems biology, and downstream processing. In addition, we show how these tools have been successfully applied in several case studies, including the production of 1, 3-propanediol, lactic acid, and biofuels. It is expected that industrial biotechnology will be increasingly adopted by chemical, pharmaceutical, food, and agricultural industries.     

Aspergillus niger contains the cryptic phylogenetic species A. awamori

Aspergillus section Nigri is an important group of species for food and medical mycology, and biotechnology. The Aspergillus niger 'aggregate' represents its most complicated taxonomic subgroup containing eight morphologically indistinguishable taxa: A. niger, Aspergillus tubingensis, Aspergillus acidus, Aspergillus brasiliensis, Aspergillus costaricaensis, Aspergillus lacticoffeatus, Aspergillus piperis, and Aspergillus vadensis. Aspergillus awamori, first described by Nakazawa, has been compared taxonomically with other black aspergilli and recently it has been treated as a synonym of A. niger. Phylogenetic analyses of sequences generated from portions of three genes coding for the proteins β-tubulin (benA), calmodulin (CaM), and the translation elongation factor-1 alpha (TEF-1α) of a population of A. niger strains isolated from grapes in Europe revealed the presence of a cryptic phylogenetic species within this population, A. awamori. Morphological, physiological, ecological and chemical data overlap occurred between A. niger and the cryptic A. awamori, however the splitting of these two species was also supported by AFLP analysis of the full genome. Isolates in both phylospecies can produce the mycotoxins ochratoxin A and fumonisin B?, and they also share the production of pyranonigrin A, tensidol B, funalenone, malformins, and naphtho-γ-pyrones. In addition, sequence analysis of four putative A. awamori strains from Japan, used in the koji industrial fermentation, revealed that none of these strains belong to the A. awamori phylospecies.     

Analysis and prediction of gene splice sites in four Aspergillus genomes

Several Aspergillus fungal genomic sequences have been published, with many more in progress. Obviously, it is essential to have high-quality, consistently annotated sets of proteins from each of the genomes, in order to make meaningful comparisons. We have developed a dedicated, publicly available, splice site prediction program called NetAspGene, for the genus Aspergillus. Gene sequences from Aspergillus fumigatus, the most common mould pathogen, were used to build and test our model. Compared to many animals and plants, Aspergillus contains smaller introns; thus we have applied a larger window size on single local networks for training, to cover both donor and acceptor site information. We have applied NetAspGene to other Aspergilli, including Aspergillus nidulans, Aspergillus oryzae, and Aspergillus niger. Evaluation with independent data sets reveal that NetAspGene performs substantially better splice site prediction than other available tools. NetAspGene will be very helpful for the study in Aspergillus splice sites and especially in alternative splicing. A webpage for NetAspGene is publicly available at http://www.cbs.dtu.dk/services/NetAspGene.     

Improving the politics of biotechnological innovations in food security and other sustainable development goals

The unwarranted interference of some environmental non-governmental organisations (ENGOs) in decision-making over genetically modified (GM) crops has prompted calls for politics to be removed from the regulatory governance of these products. However, regulatory systems are inevitably political because their purpose is to decide whether the use of particular products will help or hinder the delivery of public policy objectives. ENGOs are most able to interfere in regulatory decision-making when policy objectives and decision-making criteria are vague, making the process vulnerable to disruption by organisations that have a distinct agenda. Making regulatory decision-making about GM crops and other green biotechnology more resistant to interference therefore requires better politics not the removal of politics. Better politics begins with political leadership making a case for green biotechnology in achieving food security and other sustainable development goals. Such a policy must involve making political choices and cannot be outsourced to science. Other aspects of better politics include regulatory reform to set policy aims and decision-making criteria that encourage innovation as well as control risk, and engagement with civil society that discusses the values behind attitudes to the application of green biotechnology. In short, green biotechnology for sustainable development needs better politics to counter well-organised opposition, to encourage innovation, and to build the trust of civil society for these policies. Removing politics from regulatory governance would be a gift to ENGOs that are opposed to the use of biotechnology.

     

Diffusion of synthetic biology: a challenge to biosafety

One of the main aims of synthetic biology is to make biology easier to engineer. Major efforts in synthetic biology are made to develop a toolbox to design biological systems without having to go through a massive research and technology process. With this “de-skilling” agenda, synthetic biology might finally unleash the full potential of biotechnology and spark a wave of innovation, as more and more people have the necessary skills to engineer biology. But this ultimate domestication of biology could easily lead to unprecedented safety challenges that need to be addressed: more and more people outside the traditional biotechnology community will create self-replicating machines (life) for civil and defence applications, “biohackers” will engineer new life forms at their kitchen table; and illicit substances will be produced synthetically and much cheaper. Such a scenario is a messy and dangerous one, and we need to think about appropriate safety standards now.