MicrobiologyBytes

Marine natural products are a continued focus for drug discovery and have provided many important therapeutic agents. Lead compounds with biomedical potential have been isolated from marine invertebrates, bacteria, and fungi. Each year numerous compounds with an array of biological activities are reported, but to-date only 13 molecules have entered into the clinical pipeline. Four molecules have been approved for clinical use, one of which is approved only in the EU. The approved molecules include two nucleosides based on sponge-derived nucleosides, a cone snail peptide, and a metabolite isolated from a tunicate. Marine microbes have received growing attention as the sources for bioactive metabolites and have great potential to increase the number of marine natural products in clinical trials. The sustainable and economic supply of the active pharmaceutical ingredient is often easier to achieve for compounds produced through microbial fermentation approaches versus the cultivation of slower growing macroorganisms.

Marine natural products provide an excellent opportunity to study diverse and unique compounds not readily accessible from any other source leading to expansion of the pharmaceutical pipeline. Marine microbes can produce unique compounds covering new chemical space, and the utility of marine natural products is expanding beyond its original role in identification of new prototype drug leads into fields of study involving sustainable supplies of unique molecules using biosynthesis in conjunction with synthesis. Perhaps the greatest impact marine natural products has played is in revealing that unexplored and previously inaccessible chemical space can contribute to growth in the pharmaceutical pipeline. Improved methodologies in fermentation technologies, biosynthesis, and synthesis provide opportunities to both create and supply drug leads that would not be available by any single method independently. As a result pharmaceutical biotechnology in the future is certain to provide increasingly sophisticated molecular architecture assembled using biosynthesis and synthesis in concert.

The expanding role of marine microbes in pharmaceutical development. Curr Opin Biotechnol. Oct 16 2010
Marine microbes have received growing attention as sources of bioactive metabolites and offer a unique opportunity to both increase the number of marine natural products in clinical trials as well as expedite their development. This review focuses specifically on those molecules currently in the clinical pipeline that are established or highly likely to be produced by bacteria based on expanding circumstantial evidence. We also include an example of how compounds from harmful algal blooms may yield both tools for measuring environmental change as well as leads for pharmaceutical development. An example of the karlotoxin class of compounds isolated from the dinoflagellate Karlodinium veneficum reveals a significant environmental impact in the form of massive fish kills, but also provides opportunities to construct new molecules for the control of cancer and serum cholesterol assisted by tools associated with rational drug design.

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• Biofilms Use Chemical Weapons
• New Approach for the Discovery of Antibiotics
• Predator and Prey

Wolbachia pipientis is an intracellular maternally-inherited bacterial symbiont of invertebrates that is very common in insects, including a number of mosquito species. It can manipulate host reproduction in several ways, including cytoplasmic incompatibility, whereby certain crosses are rendered effectively sterile. Females that are uninfected produce infertile eggs when they mate with males that carry Wolbachia, while there is a “rescue” effect in Wolbachia-infected embryos such that infected females can reproduce successfully with any males. Therefore uninfected females suffer a frequency-dependent reproductive disadvantage. Wolbachia is able to rapidly invade populations using this powerful mechanism

Malaria is one of the world’s most devastating diseases, particularly in Africa, and new control strategies are desperately needed. Here we show that the presence of Wolbachia bacteria inhibits the development of a malaria parasite in the most important Anopheles mosquito species of Africa. In addition it shows that the presence of Wolbachia results in the switching on of immune genes that are known to affect development of many species of malaria parasite. When added to the lifespan-shortening effects of this particular strain of Wolbachia, and the general ability of Wolbachia to spread through insect populations, this study provides a stimulus for the development of Wolbachia-based malaria control methods. It also provides new insights into the wide range of effects of Wolbachia in insects.

Wolbachia Stimulates Immune Gene Expression and Inhibits Plasmodium Development in Anopheles gambiae. (2010) PLoS Pathog 6(10): e1001143. doi:10.1371/journal.ppat.1001143
The over-replicating wMelPop strain of the endosymbiont Wolbachia pipientis has recently been shown to be capable of inducing immune upregulation and inhibition of pathogen transmission in Aedes aegypti mosquitoes. In order to examine whether comparable effects would be seen in the malaria vector Anopheles gambiae, transient somatic infections of wMelPop were created by intrathoracic inoculation. Upregulation of six selected immune genes was observed compared to controls, at least two of which (LRIM1 and TEP1) influence the development of malaria parasites. A stably infected An. gambiae cell line also showed increased expression of malaria-related immune genes. Highly significant reductions in Plasmodium infection intensity were observed in the wMelPop-infected cohort, and using gene knockdown, evidence for the role of TEP1 in this phenotype was obtained. Comparing the levels of upregulation in somatic and stably inherited wMelPop infections in Ae. aegypti revealed that levels of upregulation were lower in the somatic infections than in the stably transinfected line; inhibition of development of Brugia filarial nematodes was nevertheless observed in the somatic wMelPop infected females. Thus we consider that the effects observed in An. gambiae are also likely to be more pronounced if stably inherited wMelPop transinfections can be created, and that somatic infections of Wolbachia provide a useful model for examining effects on pathogen development or dissemination. The data are discussed with respect to the comparative effects on malaria vectorial capacity of life shortening and direct inhibition of Plasmodium development that can be produced by Wolbachia.

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• Wolbachia
• Wolbachia could combat dengue fever
• Bacterial sequences in invertebrate genomes

Viruses are obligate intracellular parasites which have evolved as natural, biological delivery vehicles. This makes them an attractive choice of vector for various clinical gene therapy applications. Human adenoviruses (Ad) are currently the most widely used viral vectors for gene therapy for several reasons; their basic biology has been studied extensively, the viral genome can accommodate large heterologous transgene insertions, they readily infect quiescent and dividing cells, they can be amplified to high titers and they have previously been shown to be relatively safe for use in humans. The family Adenoviridae consists of five genera, including genus Mastadenovirus and genus Aviadenovirus, which infect mammals and birds respectively. The Adenoviridae are non-enveloped, icosahedral virions which contain a linear, monopartite, double-stranded DNA genome approximately 36 kb in size. As of now, there are at least 55 different human adenoviruses which can be distinguished on the basis of their serological cross-reactivity, hemagglutinating properties or according to their phylogenetic sequence similarity. The adenovirus vector most commonly used for clinical trials and experimental gene therapy applications is species C adenovirus, HAdV-C5 (referred to as Ad5 in this review).

Tropism-Modification Strategies for Targeted Gene Delivery Using Adenoviral Vectors. Viruses 2010, 2(10), 2290-2355 doi:10.3390/v2102290
Achieving high efficiency, targeted gene delivery with adenoviral vectors is a long-standing goal in the field of clinical gene therapy. To achieve this, platform vectors must combine efficient retargeting strategies with detargeting modifications to ablate native receptor binding (i.e. CAR/integrins/heparan sulfate proteoglycans) and “bridging” interactions. “Bridging” interactions refer to coagulation factor binding, namely coagulation factor X (FX), which bridges hepatocyte transduction in vivo through engagement with surface expressed heparan sulfate proteoglycans (HSPGs). These interactions can contribute to the off-target sequestration of Ad5 in the liver and its characteristic dose-limiting hepatotoxicity, thereby significantly limiting the in vivo targeting efficiency and clinical potential of Ad5-based therapeutics. To date, various approaches to retargeting adenoviruses (Ad) have been described. These include genetic modification strategies to incorporate peptide ligands (within fiber knob domain, fiber shaft, penton base, pIX or hexon), pseudotyping of capsid proteins to include whole fiber substitutions or fiber knob chimeras, pseudotyping with non-human Ad species or with capsid proteins derived from other viral families, hexon hypervariable region (HVR) substitutions and adapter-based conjugation/crosslinking of scFv, growth factors or monoclonal antibodies directed against surface-expressed target antigens. In order to maximize retargeting, strategies which permit detargeting from undesirable interactions between the Ad capsid and components of the circulatory system (e.g. coagulation factors, erythrocytes, pre-existing neutralizing antibodies), can be employed simultaneously. Detargeting can be achieved by genetic ablation of native receptor-binding determinants, ablation of “bridging interactions” such as those which occur between the hexon of Ad5 and coagulation factor X (FX), or alternatively, through the use of polymer-coated “stealth” vectors which avoid these interactions. Simultaneous retargeting and detargeting can be achieved by combining multiple genetic and/or chemical modifications.

Related:

• Adenovirus vectors – new genes, new vaccines

On the 11th October at the Society for Applied Microbiology hosted a lecture by Proffessor Willy Verstraete on Microbial Resource Management. Here’s the blurb:

In the 21st century, we are faced with a set of challenges: from climate change to the need for renewable energy sources, the threat of new pandemics and the general demise in environmental quality. The role of micro-organisms in each of these challenges is crucially important and to fully understand how microbes play a part, we must better explore our microbial resources as they currently exist – in culture collections or at evolved environmental sites. We need to develop key strategies to deal with microbial communities, instead of thinking in terms of haphazard assemblages of species. A pragmatic approach to this problem is proposed in this lecture, making use of current developments in molecular methods. Also, a list of potential environmental biotech solutions which are appropriate to the current market economy are presented. By upgrading the services of microbial communities through implementing Microbial Resource Management (MRM) and combining these communities with novel technology, we can indeed address these challenges.

And here’s the lecture:

Fungi reproduce both sexually and asexually, producing a vast array of structures which have evolved over time to suit habitat and in some cases host. These structures are of great economic importance to society. Approximately 48% of the world’s food crop yield is lost due to plant diseases, of which the majority are caused by fungi. For most fungal diseases, the primary sources of inoculum are sexual and/or asexual spores. As well as economic losses, fungi can have positive economic benefits for agriculture, such as biocontrol of plant diseases. Numerous fungi have been successfully developed as biocontrol agents (BCAs) of plant diseases and the majority of these are sold as spore preparations.

The global fungal BCA market is dominated by species of the ubiquitous ascomycete Trichoderma. In general, commercial preparations of Trichoderma spp. for biological control consist of bulk-produced conidia (asexual spores), but good biocontrol activity in the environment relies upon the fungus remaining vegetative, and thus antagonistically active. The ideal Trichoderma BCA produces ample conidia in a cost-effective manner during production and maintains long periods of vigorous vegetative growth during usage. Understanding the factors that control this morphogenic switch from mycelia to conidia is integral to biocontrol research. Over 50 years of studies on conidiation in the genus have established Trichoderma as a model for asexual reproduction in fungi. This review presents what is known about the physiological responses of Trichoderma to the environmental cues that induce conidiation, and provides insights into the molecular basis of these responses, including an examination of the signal transduction pathways which link environmental signals to physiological outputs. Understanding species-specific differences in metabolic adaptations to the environment should assist biocontrol design and implementation. Knowledge of the appropriate conditions for maximal yields of viable spores would likely reduce production costs. Knowledge of survivability and vigour within a complex environment could enable targeting of biocontrol strains to the soil or foliar condition appropriate for their species. It may also be possible to create designer BCAs which incorporate desired traits through protoplast fusion or genetic modification.

Reproduction without sex: conidiation in the filamentous fungus Trichoderma. Microbiology 2010 156: 2887-2900
Trichoderma spp. have served as models for asexual reproduction in filamentous fungi for over 50 years. Physical stimuli, such as light exposure and mechanical injury to the mycelium, trigger conidiation; however, conidiogenesis itself is a holistic response determined by the cell’s metabolic state, as influenced by the environment and endogenous biological rhythms. Key environmental parameters are the carbon and nitrogen status and the C:N ratio, the ambient pH and the level of calcium ions. Recent advances in our understanding of the molecular biology of this fungus have revealed a conserved mechanism of environmental perception through the White Collar orthologues BLR-1 and BLR-2. Also implicated in the molecular regulation are the PacC pathways and the conidial regulator VELVET. Signal transduction cascades which link environmental signals to physiological outputs have also been revealed.

Related:

• Bacterial endophytes
• High Tech Fungi

High-throughput sequencing is an umbrella term applied to new sequencing technologies that deliver sequence data hundreds or thousands times more cheaply and speedily than traditional approaches. Three competing technologies have achieved widespread uptake: the Roche 454 platform, the Solexa/Illumina platform and Life Technologies SOLiD platform.

Genome sequencing has already transformed the study of microbial pathogens. For the first time, sequencing on a genomic scale now falls within the technical capability of the average university department and within the financial envelope of a modest research grant. Now that bacterial genomes can be sequenced in days or weeks rather than months or years, microbial genomics is at last poised to make a direct impact in clinical diagnostics, epidemiology and infection control. High-throughput sequencing also stands to revolutionise our view of the host response to infection and vaccination.

High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Curr Opin Microbiol. Sep 13 2010
High-throughput sequencing is sweeping through clinical microbiology, transforming our discipline in its wake. It is already providing an enhanced view of pathogen biology through rapid and inexpensive whole-genome sequencing and more sophisticated applications such as RNA-seq. It also promises to deliver high-resolution genomic epidemiology as the ultimate typing method for bacteria. However, the most revolutionary effect of this ‘disruptive technology’ is likely to be creation of a novel sequence-based, culture-independent diagnostic microbiology that incorporates microbial community profiling, metagenomics and single-cell genomics. We should prepare for the coming ‘technological singularity’ in sequencing, when this technology becomes so fast and so cheap that it threatens to out-compete existing diagnostic and typing methods in microbiology.

Related:

• Structural and functional analysis of virus siRNAs
• Metagenomic Analysis of Human Diarrhoea

Mycobacterium tuberculosis is a remarkably successful human pathogen. The interaction with the human host is complex and much remains unknown. Recent advances in systems biology have allowed the integration of data from humans and animal models into computational approaches. For example, mathematical models provide a platform for in silico manipulation of host-pathogen interactions to gain insight into this infection across temporal and biologic scales. This article reviews recent studies on global approaches toward identifying comprehensive responses of both host and bacillus during infection, and the potential for incorporation of these data into many types of useful computational systems. Systems biology approaches provide a unique opportunity to study interventions that may improve therapy and vaccines against this major killer.

Tuberculosis: global approaches to a global disease. Curr Opin Biotechnol. Jul 14 2010

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• Cough!
• Origin and spread of Mycobacterium tuberculosis

The immune system of plants can be unstable in the face of rapidly evolving micro-organisms, and pathogens that can evade recognition can spread with alarming speed through a plant population. In this article in Microbiology Today, Gail Preston and Dawn Arnold ask, what is the reason for this inherent instability, and how can disease control be improved?

Plants, unlike animals, lack an adaptive immune system that allows them to recognize and defend against novel pathogenic micro-organisms. Instead they rely on a heritable, innate immune system in which plant receptors recognize the presence or activity of microbial molecules known as elicitors. Plants exposed to infection can increase the effectiveness of their immune system by increasing the speed and strength of their defence mechanisms. However, pathogens that have the ability to evade recognition can spread rapidly through plant populations. The instability of receptor-dependent resistance in the face of rapid microbial evolution creates one of the most fundamental challenges in plant breeding. In this article we discuss why receptordependent resistance breaks down in the face of pathogen evolution and consider whether knowledge of pathogen evolution can provide insights to improve disease control.

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Related:

• Toxins for microbial attack and plant defence
• Bacteriophages for plant disease control

This article reviews recent research on Rift Valley fever virus (RVFV) infection, encompassing four main areas: epidemiology and outbreak prediction, viral pathogenesis, human diagnostics and therapeutics, and vaccine and therapeutic candidates. RVFV continues to extend its range in Africa and the Middle East. Better definition of RVFV-related clinical syndromes and human risk factors for severe disease, combined with early-warning systems based on remote-sensing, simplified rapid diagnostics, and tele-epidemiology, hold promise for earlier deployment of effective outbreak control measures. Advances in understanding of viral replication pathways and host cell-related pathogenesis suggest means for antiviral therapeutics and for more effective vaccination strategies based on genetically engineered virus strains or subunit vaccines. RVFV is a significant health and economic burden in many areas of Africa, and remains a serious threat to other parts of the world. Development of more effective methods for RVFV outbreak prevention and control remains a global health priority.

Advances in Rift Valley fever research: insights for disease prevention. Curr Opin Infect Dis. Jul 6 2010 doi: 10.1097/QCO.0b013e32833c3da6