Current Opinion in Biotechnology

Improving yield by exploiting mechanisms underlying natural variation of photosynthesis.

Publication Date: 2012 Jan 30 PMID: 22296828
Authors: Lawson, T. - Kramer, D. M. - Raines, C. A.
Journal: Curr Opin Biotechnol

Increasing photosynthesis in C3 species has been identified as an approach to increase the yield of crop plants. Most of our knowledge of photosynthetic performance has come from studies in which plants were grown in controlled growth conditions but plants in natural environments have to cope with unpredictable and rapidly changing conditions. Plants adapt to the light environment in which they grow and this is demonstrated by the differences in anatomy and morphology of leaves in sun and shade leaves. Superimposed on this are the dynamic responses of plants to rapid changes in the light environment that occur throughout the day. Application of next generation sequencing (NGS), QTL analysis and innovative phenomic screening can provide information to underpin approaches for breeding of higher yielding crop plants.

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Synthetic signaling networks for therapeutic applications.

Publication Date: 2012 Jan 27 PMID: 22285057
Authors: Aurand, T. C. - Russell, M. S. - March, J. C.
Journal: Curr Opin Biotechnol

Synthetic signaling networks contain exogenous, modified, or rationally designed components involved in sending, receiving, and processing information from the environment and other cells. Advances in the input, output, and processing elements for such networks hold promise towards developing new therapies and prophylactics for disease. Therapeutic synthetic signaling systems are still in their infancy, but are progressing into mouse models of disease and even into clinical trials. As signaling technology matures, we will see an increase in implanted and ingested cellular therapies capable of autonomously diagnosing and treating disease. These technologies have the potential to reduce some of the burden on both patients and clinicians, contributing to more efficient and eventually personalized medicine.

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New and emerging analytical techniques for marine biotechnology.

Publication Date: 2012 Jan 18 PMID: 22265377
Authors: Burgess, J. G.
Journal: Curr Opin Biotechnol

Marine biotechnology is the industrial, medical or environmental application of biological resources from the sea. Since the marine environment is the most biologically and chemically diverse habitat on the planet, marine biotechnology has, in recent years delivered a growing number of major therapeutic products, industrial and environmental applications and analytical tools. These range from the use of a snail toxin to develop a pain control drug, metabolites from a sea squirt to develop an anti-cancer therapeutic, and marine enzymes to remove bacterial biofilms. In addition, well known and broadly used analytical techniques are derived from marine molecules or enzymes, including green fluorescence protein gene tagging methods and heat resistant polymerases used in the polymerase chain reaction. Advances in bacterial identification, metabolic profiling and physical handling of cells are being revolutionised by techniques such as mass spectrometric analysis of bacterial proteins. Advances in instrumentation and a combination of these physical advances with progress in proteomics and bioinformatics are accelerating our ability to harness biology for commercial gain. Single cell Raman spectroscopy and microfluidics are two emerging techniques which are also discussed elsewhere in this issue. In this review, we provide a brief survey and update of the most powerful and rapidly growing analytical techniques as used in marine biotechnology, together with some promising examples of less well known earlier stage methods which may make a bigger impact in the future.

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Innovation at the intersection of synthetic and systems biology.

Publication Date: 2012 Jan 19 PMID: 22265125
Authors: Lanza, A. M. - Crook, N. C. - Alper, H. S.
Journal: Curr Opin Biotechnol

The promises of modern biotechnology hinge upon the hope that we can understand microscopic cellular complexity and in doing so create novel function. In this regard, the fields of systems and synthetic biology are important for accelerating both our understanding of biological systems and our ability to quantitatively engineer cells. At the nexus of these two fields is a unique synergy that can help attain these goals. Thus, the next greatest advances in biology and biotechnology are arising at the intersection of the top-down systems approach and the bottom-up synthetic approach. Collectively, these developments enable the precise control of cellular state for systems studies and the discovery of novel parts, control strategies, and interactions for the design of robust synthetic function. This review seeks to highlight this activity as well as provide a perspective for future directions. Combining these efforts can provide novel insights into cellular function and lead to robust, novel synthetic design.

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Engineering C(4) photosynthetic regulatory networks.

Publication Date: 2012 Jan 17 PMID: 22261559
Authors: Weissmann, S. - Brutnell, T. P.
Journal: Curr Opin Biotechnol

C(4) photosynthesis is a complex metabolic pathway responsible for carbon fixation in major feed, food and bioenergy crops. Although many enzymes driving this pathway have been identified, regulatory mechanisms underlying this system remain elusive. C(4) photosynthesis contributes to photosynthetic efficiency in major bioenergy crops such as sugarcane, Miscanthus, switchgrass, maize and sorghum, and international efforts are underway to engineer C(4) photosynthesis into C(3) crops. A fundamental understanding of the C(4) network is thus needed. New experimental and informatics methods can facilitate the accumulation and analysis of high-throughput data to define components of the C(4) system. The use of new model plants, closely related to C(4) crops, will also contribute to our understanding of the mechanisms that regulate this complex and important pathway.

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Re-engineering of carbon fixation in plants - challenges for plant biotechnology to improve yields in a high-CO(2) world.

Publication Date: 2012 Jan 17 PMID: 22261558
Authors: Peterhansel, C. - Offermann, S.
Journal: Curr Opin Biotechnol

Source and sink strength control plant carbon gain and yield. Source strength was recently engineered by modifying the large subunit of Rubisco, replacing the small subunit, and creating improved thermostable Rubisco activases. This technological breakthrough makes Rubisco engineering feasible at last. Enhancement of leaf transitory starch synthesis or induction of artificial sinks in leaves increased biomass and yield. Importantly, such approaches also had a positive feedback on source strength. In addition, novel targets for the improvement of carbon gain in crops have been identified that are especially relevant in the light of climate change.

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Imaging plants dynamics in heterogenic environments.

Publication Date: 2012 Jan 16 PMID: 22257752
Authors: Fiorani, F. - Rascher, U. - Jahnke, S. - Schurr, U.
Journal: Curr Opin Biotechnol

Noninvasive imaging sensors and computer vision approaches are key technologies to quantify plant structure, physiological status, and performance. Today, imaging sensors exploit a wide range of the electromagnetic spectrum, and they can be deployed to measure a growing number of traits, also in heterogenic environments. Recent advances include the possibility to acquire high-resolution spectra by imaging spectroscopy and classify signatures that might be informative of plant development, nutrition, health, and disease. Three-dimensional (3D) reconstruction of surfaces and volume is of particular interest, enabling functional and mechanistic analyses. While taking pictures is relatively easy, quantitative interpretation often remains challenging and requires integrating knowledge of sensor physics, image analysis, and complex traits characterizing plant phenotypes.

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Strategies to mitigate N(2)O emissions from biological nitrogen removal systems.

Publication Date: 2012 Jan 13 PMID: 22244791
Authors: Desloover, J. - Vlaeminck, S. E. - Clauwaert, P. - Verstraete, W. - Boon, N.
Journal: Curr Opin Biotechnol

N(2)O emissions from the biological treatment of sewage, manure, landfill leachates and industrial effluents have gained considerable interest among policy makers and environmental scientists. Estimated global emission rates from these sources can contribute up to 10% of the anthropogenic N(2)O emissions. Particularly at the level of a treatment plant, the N(2)O impact can be very significant and reach up to 80% of the operational CO(2) footprint. Imperfect nitritation by an imbalance in the two-step nitritation metabolism of ammonia-oxidizing bacteria is considered as the main contributor to N(2)O production with hydroxylamine and particularly nitrite as key precursors. Monitoring of these compounds is warranted to understand and abate N(2)O emissions. Mitigation strategies should also comprise optimizations of the process parameters as well as bio-augmentative approaches empowered to restore the functional capacity and to deal with unwanted accumulation of intermediates. These strategies require validation for their effectiveness and costs at full-scale.

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Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli.

Publication Date: 2012 Jan 13 PMID: 22244790
Authors: Yuzawa, S. - Kim, W. - Katz, L. - Keasling, J. D.
Journal: Curr Opin Biotechnol

Heterologous production of polyketide compounds, an important class of natural products with complex chemical structures, was first demonstrated with Streptomyces parvulus in 1984. Although Streptomyces strains are good first options for heterologous polyketide biosynthesis, their slow growth kinetics prompt other hosts to also be considered. Escherichia coli provides key elements of an ideal host in terms of the growth rate, culture conditions, and available recombinant DNA tools. Here we review the current status and potential for metabolic engineering of polyketides in E. coli.

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Integrating C(4) photosynthesis into C(3) crops to increase yield potential.

Publication Date: 2012 Jan 13 PMID: 22244789
Authors: Covshoff, S. - Hibberd, J. M.
Journal: Curr Opin Biotechnol

The growth rate of the human population is faster than improvements in crop yields. To feed people in the future, multiple strategies are required. One proposed approach is to raise the yield potential of C(3) crops by modifying photosynthesis to the more efficient C(4) pathway. Owing to complex changes associated with C(4) photosynthesis, it is no understatement to define this conversion as one of the Grand Challenges for Biology in the 21st Century. Here we outline the challenges of installing a C(4) system and assess how new approaches and knowledge may help achieve this goal.

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Systems and synthetic metabolic engineering for amino acid production - the heartbeat of industrial strain development.

Publication Date: 2012 Jan 13 PMID: 22244788
Authors: Becker, J. - Wittmann, C.
Journal: Curr Opin Biotechnol

With a world market of more than four million tons per year, l-amino acids are among the most important products in industrial biotechnology. The recent years have seen a tremendous progress in the development of tailor-made strains for such products, intensively driven from systems metabolic engineering, which upgrades strain engineering into a concept of optimization on a global scale. This concept seems especially valuable for efficient amino acid production, demanding for a global modification of pathway fluxes - a challenge with regard to the high complexity of the underlying metabolism, superimposed by various layers of metabolic and transcriptional control.

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Prebiotics in foods.

Publication Date: 2012 Jan 12 PMID: 22244693
Authors: Charalampopoulos, D. - Rastall, R. A.
Journal: Curr Opin Biotechnol

A wealth of information has been gathered over the past 15 years on prebiotics through experimental, animal and human studies, with the aim to understand the mechanism of actions and elucidate their beneficial health effects to the human host. Significant amount of evidence exists for their ability to increase the bioavailability of minerals and stimulate the immune system, although there is less clear evidence so far for their prophylactic or therapeutic role in gastrointestinal infections. Moreover, the effect of the food delivery vehicle on the efficacy of prebiotics is an area that has been hardly investigated. Besides their beneficial effects, prebiotics influence the textural and organoleptic properties of the food products, such as dairy and baked products. To do this however, they need to be stable during food processing, in particular under conditions of high temperature and low pH.

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When single cell technology meets omics, the new toolbox of analytical biotechnology is emerging.

Publication Date: 2012 Jan 11 PMID: 22244690
Authors: Huang, W. E. - Zhou, J.
Journal: Curr Opin Biotechnol

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Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression.

Publication Date: 2012 Jan 9 PMID: 22237017
Authors: Rao, C. V.
Journal: Curr Opin Biotechnol

Despite substantial progress in synthetic biology, we still lack the ability to engineer anything as complex as Nature has. One of the many reasons is that we lack the requisite tools for independently controlling the expression of multiple genes in parallel. While our toolbox is still spare, the situation is rapidly changing. This opinion discusses some recent approaches and open challenges in designing orthogonal regulators of gene expression in bacteria.

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Recent advances in genetic code engineering in Escherichia coli.

Publication Date: 2012 Jan 9 PMID: 22237016
Authors: Hoesl, M. G. - Budisa, N.
Journal: Curr Opin Biotechnol

The expansion of the genetic code is gradually becoming a core discipline in Synthetic Biology. It offers the best possible platform for the transfer of numerous chemical reactions and processes from the chemical synthetic laboratory into the biochemistry of living cells. The incorporation of biologically occurring or chemically synthesized non-canonical amino acids into recombinant proteins and even proteomes via reprogrammed protein translation is in the heart of these efforts. Orthogonal pairs consisting of aminoacyl-tRNA synthetase and its cognate tRNA proved to be a general tool for the assignment of certain codons of the genetic code with a maximum degree of chemical liberty. Here, we highlight recent developments that should provide a solid basis for the development of generalist tools enabling a controlled variation of chemical composition in proteins and even proteomes. This will take place in the frame of a greatly expanded genetic code with emancipated codons liberated from the current function or with totally new coding units.

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DNA-based assembly lines and nanofactories.

Publication Date: 2012 Jan 9 PMID: 22237015
Authors: Simmel, F. C.
Journal: Curr Opin Biotechnol

With the invention of the DNA origami technique, DNA self-assembly has reached a new level of sophistication. DNA can now be used to arrange molecules and other nanoscale components into almost arbitrary geometries-in two and even three dimensions and with nanometer precision. One exciting prospect is the realization of dynamic systems based on DNA, in which chemical reactions are precisely controlled by the spatial arrangement of components, ultimately resulting in nanoscale analogs of molecular assembly lines or 'nanofactories'. This review will discuss recent progress toward this goal, ranging from DNA-templated synthesis over artificial DNA-based enzyme cascades to first examples of 'molecular robots'.

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From genomics to metagenomics.

Publication Date: 2012 Jan 5 PMID: 22227326
Authors: Desai, N. - Antonopoulos, D. - Gilbert, J. A. - Glass, E. M. - Meyer, F.
Journal: Curr Opin Biotechnol

Next-generation sequencing has changed metagenomics. However, sequencing DNA is no longer the bottleneck, rather, the bottleneck is computational analysis and also interpretation. Computational cost is the obvious issue, as is tool limitations, considering most of the tools we routinely use have been built for clonal genomics or are being adapted to microbial communities. The current trend in metagenomics analysis is toward reducing computational costs through improved algorithms and through analysis strategies. Data sharing and interoperability between tools are critical, since computation for metagenomic datasets is very high.

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Metabolically versatile large-genome prokaryotes.

Publication Date: 2012 Jan 6 PMID: 22226959
Authors: Guieysse, B. - Wuertz, S.
Journal: Curr Opin Biotechnol

Although versatile microorganisms are critical in industrial applications where the ability to cope with change and carry out complex tasks is needed, very little is in fact known about the evolutionary and ecological meanings of versatility in prokaryotes. Testing the hypothesis that a large genome size is a prerequisite for versatility in prokaryotes, we found that putatively versatile prokaryotes are phylogenetically and ecologically diverse and indeed include many well known and commercially relevant versatile microorganisms. Despite individual differences in metabolic abilities, a common trait of large-genome prokaryotes appears that they have gained their large genomes as an evolutionary response to nutrient-scarce and/or variable environments. This insight seriously questions the ability of traditional microbiology methods to isolate versatile prokaryotes and casts doubt on the ecological relevance of knowledge based on the study of specialists.

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Molecular motors for DNA translocation in prokaryotes.

Publication Date: 2012 Jan 6 PMID: 22226958
Authors: Allemand, J. F. - Maier, B. - Smith, D. E.
Journal: Curr Opin Biotechnol

DNA transport is an essential life process. From chromosome separation during cell division or sporulation, to DNA virus ejection or encapsidation, to horizontal gene transfer, it is ubiquitous in all living organisms. Directed DNA translocation is often energetically unfavorable and requires an active process that uses energy, namely the action of molecular motors. In this review we present recent advances in the understanding of three molecular motors involved in DNA transport in prokaryotes, paying special attention to recent studies using single-molecule techniques. We first discuss DNA transport during cell division, then packaging of DNA in phage capsids, and then DNA import during bacterial transformation.

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