Bio-mining the microbial treasures of the ocean: new natural products

The biological resources of the oceans have been exploited since ancient human history, mainly by catching fish and harvesting algae. Research on natural products with special emphasis on marine animals and also algae during the last decades of the 20th century has revealed the importance of marine organisms as producers of substances useful for the treatment of human diseases. Though a large number of bioactive substances have been identified, some many years ago, only recently the first drugs from the oceans were approved. Quite astonishingly, the immense diversity of microbes in the marine environments and their almost untouched capacity to produce natural products and therefore the importance of microbes for marine biotechnology was realized on a broad basis by the scientific communities only recently. This has strengthened worldwide research activities dealing with the exploration of marine microorganisms for biotechnological applications, which comprise the production of bioactive compounds for pharmaceutical use, as well as the development of other valuable products, such as enzymes, nutraceuticals and cosmetics. While the focus in these fields was mainly on marine bacteria, also marine fungi now receive growing attention. Although culture-dependent studies continue to provide interesting new chemical structures with biological activities at a high rate and represent highly promising approaches for the search of new drugs, exploration and use of genomic and metagenomic resources are considered to further increase this potential. Many efforts are made for the sustainable exploration of marine microbial resources. Large culture collections specifically of marine bacteria and marine fungi are available. Compound libraries of marine natural products, even of highly purified substances, were established. The expectations into the commercial exploitation of marine microbial resources has given rise to numerous institutions worldwide, basic research facilities as well as companies. In Europe, recent activities have initiated a dynamic development in marine biotechnology, though concentrated efforts on marine natural product research are rare. One of these activities is represented by the Kieler Wirkstoff-Zentrum KiWiZ, which was founded in 2005 in Kiel (Germany).     

Realizing the promises of marine biotechnology

High-quality research in the field of marine biotechnology is one of the key-factors for successful innovation in exploiting the vast diversity of marine life. However, fascinating scientific research with promising results and claims on promising potential applications (e.g. for pharmaceuticals, nutritional supplements, (feed-)products for aquaculture and bioremediation solutions) is not the only factor to realise the commercial applications of marine biotechnology. What else is needed to exploit the promising potential of marine biotechnology and to create new industrial possibilities? In the study project 'Ocean Farming-Sustainable exploitation of marine organisms', we explore the possibilities of marine organisms to fulfill needs, such as safe and healthy food, industrial (raw) materials and renewable energy in a sustainable way. One of the three design groups is envisioning the future of strong land-based 'marine' market chains. Marine biotechnology is one of the foci of attention in this design group. This article provides a model of future-oriented thinking in which a variety of experts actively participate.     

Microalgae as bioreactors

Microalgae already serve as a major natural source of valuable macromolecules including carotenoids, long-chain polyunsaturated fatty acids and phycocolloids. As photoautotrophs, their simple growth requirements make these primitive plants potentially attractive bioreactor systems for the production of high-value heterologous proteins. The difficulty of producing stable transformants has meant that the field of transgenic microalgae is still in its infancy. Nonetheless, several species can now be routinely transformed and algal biotechnology companies have begun to explore the possibilities of synthesizing recombinant therapeutic proteins in microalgae and the engineering of metabolic pathways to produce increased levels of desirable compounds. In this review, we compare the current commercially viable bioreactor systems, outline recent progress in microalgal biotechnology and transformation, and discuss the potential of microalgae as bioreactors for the production of heterologous proteins.     

Advances in genetic engineering of marine algae

Algae are a component of bait sources for animal aquaculture, and they produce abundant valuable compounds for the chemical industry and human health. With today's fast growing demand for algae biofuels and the profitable market for cosmetics and pharmaceuticals made from algal natural products, the genetic engineering of marine algae has been attracting increasing attention as a crucial systemic technology to address the challenge of the biomass feedstock supply for sustainable industrial applications and to modify the metabolic pathway for the more efficient production of high-value products. Nevertheless, to date, only a few marine algae species can be genetically manipulated. In this article, an updated account of the research progress in marine algal genomics is presented along with methods for transformation. In addition, vector construction and gene selection strategies are reviewed. Meanwhile, a review on the progress of bioreactor technologies for marine algae culture is also revisited.     

Free Marine Natural Products Databases for Biotechnology and Bioengineering

Marine organisms and micro‐organisms are a source of natural compounds with unique chemical features. These chemical properties are useful for the discovery of new functions and applications of marine natural products (MNPs). To extensively exploit the potential implementations of MNPs, they are gathered in chemical databases that allow their study and screening for applications of biotechnological interest. However, the classification of MNPs is currently poor in generic chemical databases. The present availability of free‐access‐focused MNP databases is scarce and the molecular diversity of these databases is still very low when compared to the paid‐access ones. In this review paper, the current scenario of free‐access MNP databases is presented as well as the hindrances involved in their development, mainly compound dereplication. Examples and opportunities for using freely accessible MNP databases in several important areas of biotechnology are also assessed. The scope of this paper is, as well, to notify the latent potential of these information sources for the discovery and development of new MNPs in biotechnology, and push future efforts to develop a public domain MNP database freely available for the scientific community.     

化学生态学在海洋污损生物防除中的应用

在海洋环境中,许多海洋生物都能产生对环境无危害的、具有防污活性的次生代谢产物以保护自身的洁净,利于自身的生存.用化学生态学的方法从海洋生物中提取天然防除物质成为近年来解决海洋污损生物问题的新思路,其目标是寻找高效无毒的防污材料取代原有的对海洋环境有严重危害的化学合成防污材料.虽然目前对提取生物的次生代谢产物的防污机理还所知甚少,但不少从海洋生物中获得的天然产物已显示出良好的防污活性.要解决污损生物防污问题,还需对天然产物的作用机制、生态学效应、天然产物与涂料的结合、控制和释放及野外实验进行更加深入的研究与探讨.     

Photosynthetic marine organisms as a source of anticancer compounds

Since early human history, plants have served as the most important source of medicinal natural products, and even in the “synthetic age” the majority of lead compounds for pharmaceutical development remain of plant origin. In the marine realm, algae and seagrasses were amongst the first organisms investigated by marine natural products scientists on their quest for novel pharmaceutical compounds. Forty years after the pioneering work in the field of marine drug discovery began, the biodiversity of marine organisms investigated as potential sources of anticancer, anti-inflammatory, and antibiotic compounds has increased tremendously. Nonetheless, marine plants are still an important source of novel secondary metabolites with interesting biomedical properties. The present review focuses on the antitumour properties of compounds isolated from marine algae, phytoplankton, mangroves, seagrasses, or cordgrasses. Compounds produced by marine epi- or endophytic fungi are also discussed.     

Heterologous production of secondary metabolites as pharmaceuticals in <Emphasis Type="Italic">Saccharomyces</Emphasis> <Emphasis Type="Italic">cerevisiae</Emphasis>

Heterologous expression of genes involved in the biosynthesis of various products is of increasing interest in biotechnology and in drug research and development. Microbial cells are most appropriate for this purpose. Availability of more microbial genomic sequences in recent years has greatly facilitated the elucidation of metabolic and regulatory networks and helped gain overproduction of desired metabolites or create novel production of commercially important compounds. Saccharomyces cerevisiae, as one of the most intensely studied eukaryotic model organisms with a rich density of knowledge detailing its genetics, biochemistry, physiology, and large-scale fermentation performance, can be capitalized upon to enable a substantial increase in the industrial application of this yeast. In this review, we describe recent efforts made to produce commercial secondary metabolites in Saccharomyces cerevisiae as pharmaceuticals. As natural products are increasingly becoming the center of attention of the pharmaceutical and nutraceutical industries, such as naringenin, coumarate, artemisinin, taxol, amorphadiene and vitamin C, the use of S. cerevisiae for their production is only expected to expand in the future, further allowing the biosynthesis of novel molecular structures with unique properties.     

源于海洋真菌的抗肿瘤天然产物

海洋真菌因其特殊的生存环境和代谢机制而具有产生新型生物活性物质的潜力。近年来随着对海洋微生物研究的深入,从海洋真菌中发现了越来越多的具有抗肿瘤活性且结构新颖的天然产物。这些海洋真菌有的分离自海水、海泥或海洋沉积物,有的来自于海洋生物体。本文综述了近几年来从海洋真菌中分离得到的抗肿瘤天然产物的研究状况。     

海洋真菌抗污损活性天然产物研究

黏附于海洋船舶或人工设施表面的污损生物给人类海洋生产活动与生态环境带来诸多不利影响.将具有抗污损活性的化合物开发成防污涂料是目前防治海洋生物污损的最常用手段之一.而大量传统有机金属防污剂因其严重毒副作用被禁用,亟须开发高效、环境友好型抗污损涂料.海洋真菌能够产生大量结构新颖、作用机制独特的高效、低毒/无毒抗污损活性次级...     

High-value products from microalgae—their development and commercialisation

Microalgae (including the cyanobacteria) are established commercial sources of high-value chemicals such as β-carotene, astaxanthin, docosahexaenoic acid, eicosahexaenoic acid, phycobilin pigments and algal extracts for use in cosmetics. Microalgae are also increasingly playing a role in cosmaceuticals, nutraceuticals and functional foods. In the last few years, there has been renewed interest in microalgae as commercial sources of these and other high-value compounds, driven in part by the attempts to develop commercially viable biofuels from microalgae. This paper briefly reviews the main existing and potential high-value products which can be derived from microalgae and considers their commercial development with a particular focus on the various aspects which need to be considered on the path to commercialisation, using the experience gained in the commercialisation of existing algae products. These considerations include the existing and potential market size and market characteristics of the product, competition by chemically synthesised products or by ‘natural’ compounds from other organisms such as fungi, bacteria, higher plants, etc., product quality requirements and assurance, and the legal and regulatory environment.     

Highlights of marine invertebrate-derived biosynthetic products: their biomedical potential and possible production by microbial associants

Coral reefs are among the most productive marine ecosystems and are the source of a large group of structurally unique biosynthetic products. Annual reviews of marine natural products continue to illustrate that the most prolific source of bioactive compounds consist of coral reef invertebrates-sponges, ascidians, mollusks, and bryozoans. This account examines recent milestone developments pertaining to compounds from invertebrates designated as therapeutic leads for biomedical discovery. The focus is on the secondary metabolites, their inspirational structural scaffolds and the possible role of micro-organism associants in their biosynthesis. Also important are the increasing concerns regarding the collection of reef invertebrates for the discovery process. The case examples considered here will be useful to insure that future research to unearth bioactive invertebrate-derived compounds will be carried out in a sustainable and environmentally conscious fashion. Our account begins with some observations pertaining to the natural history of these organisms. Many still believe that a serious obstacle to the ultimate development of a marine natural product isolated from coral reef invertebrates is the problem of compound supply. Recent achievements through total synthesis can now be drawn on to forcefully cast this myth aside. The tools of semisynthesis of complex natural products or insights from SAR efforts to simplify an active pharmacophore are at hand and demand discussion. Equally exciting is the prospect that invertebrate-associated micro-organisms may represent the next frontier to accelerate the development of high priority therapeutic candidates. Currently in the United States there are two FDA approved marine-derived therapeutic drugs and two others that are often cited as being marine-inspired. This record will be examined first followed by an analysis of a dozen of our favorite examples of coral reef invertebrate natural products having therapeutic potential. The record of using complex scaffolds of marine invertebrate products as the starting point for development will be reviewed by considering eight case examples. The potential promise of developing invertebrate-derived micro-organisms as the starting point for further exploration of therapeutically relevant structures is considered. Also significant is the circumstance that there are some 14 sponge-derived compounds that are available to facilitate fundamental biological investigations.     

Marine bioprocess engineering: the missing link to commercialization

Success of US biotechnology has been and continues to be dependent on new discoveries and their timely transformation into useful products through bioprocess engineering and a systems approach. Bioprocess engineering is an essential element of ‘generic applied’ or ‘precompetitive’ research. For marine biotechnology, like biopharmaceutical biotechnology, bioprocess engineering represents the key. The many hundreds of tantalizing bioactive compounds discovered and isolated from varied marine organisms over the past decades have led to only minimal commercialization due to the limited availability of the compounds in question. To address international competitiveness and the revitalization of key US industries, the National Science Foundation launched the Engineering Research Centers Program in the mid 1980s. The essential feature of this program is a partnership among academia, industry and the government to develop next-generation technology through cutting-edge research, relevant education and innovative technology transfer. MarBEC (Marine Bioproducts Engineering Center) is a recently established multi-disciplinary engineering-science cooperative effort of the University of Hawaii and the University of California at Berkeley. Additional partners include three federal laboratories—Argonne National Laboratory, the Edgewood Research, Development and Engineering Center and the Eastern Regional Research Center of the US Department of Agriculture—and the Bishop Museum. MarBEC's research program consists of four major thrusts: Production Systems; Marine Bioproducts and Bioresources; Separation and Conversion; and Bioproduct Formulation.     

Lessons learned from the transformation of natural product discovery to a genome-driven endeavor

Natural product discovery is currently undergoing a transformation from a phenotype-driven field to a genotype-driven one. The increasing availability of genome sequences, coupled with improved techniques for identifying biosynthetic gene clusters, has revealed that secondary metabolomes are strikingly vaster than previously thought. New approaches to correlate biosynthetic gene clusters with the compounds they produce have facilitated the production and isolation of a rapidly growing collection of what we refer to as “reverse-discovered” natural products, in analogy to reverse genetics. In this review, we present an extensive list of reverse-discovered natural products and discuss seven important lessons for natural product discovery by genome-guided methods: structure prediction, accurate annotation, continued study of model organisms, avoiding genome-size bias, genetic manipulation, heterologous expression, and potential engineering of natural product analogs.     

Some results and prospects of studies in the area of marine biochemistry and biotechnology]

Recent studies on bioactive metabolites from marine macro- and microorganisms are reviewed with 83 refs. Structures of new sulphated and glycosylated secondary metabolites, which have been reported to have antifungal, immunomodulatory, and cytotoxic properties, are given. Some peculiarities of biosynthesis of natural compounds in marine organisms are revealed. It was shown that some natural products, isolated earlier from sponges, are produced by microbial symbionts. Different physiological activities associated with 8000 marine microbial (mainly symbiotic) strains are discussed as well as some prospects of marine biochemistry and biotechnology development.     

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.     

Trends in the Discovery of New Marine Natural Products from Invertebrates over the Last Two Decades – Where and What Are We Bioprospecting?

It is acknowledged that marine invertebrates produce bioactive natural products that may be useful for developing new drugs. By exploring untapped geographical sources and/or novel groups of organisms one can maximize the search for new marine drugs to treat human diseases. The goal of this paper is to analyse the trends associated with the discovery of new marine natural products from invertebrates (NMNPI) over the last two decades. The analysis considers different taxonomical levels and geographical approaches of bioprospected species. Additionally, this research is also directed to provide new insights into less bioprospected taxa and world regions. In order to gather the information available on NMNPI, the yearly-published reviews of Marine Natural Products covering 1990-2009 were surveyed. Information on source organisms, specifically taxonomical information and collection sites, was assembled together with additional geographical information collected from the articles originally describing the new natural product. Almost 10000 NMNPI were discovered since 1990, with a pronounced increase between decades. Porifera and Cnidaria were the two dominant sources of NMNPI worldwide. The exception was polar regions where Echinodermata dominated. The majority of species that yielded the new natural products belong to only one class of each Porifera and Cnidaria phyla (Demospongiae and Anthozoa, respectively). Increased bioprospecting efforts were observed in the Pacific Ocean, particularly in Asian countries that are associated with the Japan Biodiversity Hotspot and the Kuroshio Current. Although results show comparably less NMNPI from polar regions, the number of new natural products per species is similar to that recorded for other regions. The present study provides information to future bioprospecting efforts addressing previously unexplored taxonomic groups and/or regions. We also highlight how marine invertebrates, which in some cases have no commercial value, may become highly valuable in the ongoing search for new drugs from the sea.     

Mini-review: Marine natural products and their synthetic analogs as antifouling compounds: 2009–2014

This review covers 214 marine natural compounds and 23 of their synthetic analogs, which were discovered and/or synthesized from mid-2009 to August 2014. The antifouling (AF) compounds reported have medium to high bioactivity (with a threshold of EC₅₀ < 15.0 mg ml^?1). Among these compounds, 82 natural compounds were identified as new structures. All the compounds are marine-derived, demonstrating that marine organisms are prolific and promising sources of natural products that may be developed as environmentally friendly antifoulants. However, this mini-review excludes more than 200 compounds that were also reported as AF compounds but with rather weak bioactivity during the same period. Also excluded are terrestrial-derived AF compounds reported during the last five years. A brief discussion on current challenges in AF compound research is also provided to reflect the authors’ own views in terms of future research directions.     

Outlook in the application of Chlamydomonas reinhardtii chloroplast as a platform for recombinant protein production

Microalgae, also called microphytes, are a vast group of microscopic photosynthetic organisms living in aquatic ecosystems. Microalgae have attracted the attention of biotechnology industry as a platform for extracting natural products with high commercial value. During last decades, microalgae have been also used as cost-effective and easily scalable platform for the production of recombinant proteins with medical and industrial applications. Most progress in this field has been made with Chlamydomonas reinhardtii as a model organism mainly because of its simple life cycle, well-established genetics and ease of cultivation. However, due to the scarcity of existing infrastructure for commercial production and processing together with relatively low product yields, no recombinant products from C. reinhardtii have gained approval for commercial production and most of them are still in research and development. In this review, we focus on the chloroplast of C. reinhardtii as an algal recombinant expression platform and compare its advantages and disadvantages to other currently used expression systems. We then discuss the strategies for engineering the chloroplast of C. reinhardtii to produce recombinant cells and present a comprehensive overview of works that have used this platform for the expression of high-value products.     

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.