Secrets of a covalent interaction for biomaterials and biotechnology: SpyTag and SpyCatcher.
Abstract SpyTag is a short peptide that forms an isopeptide bond upon encountering its protein partner SpyCatcher. This covalent peptide interaction is a simple and powerful tool for bioconjugation and extending what protein architectures are accessible. Here we review the origin and mechanism of SpyTag/SpyCatcher, focusing on recent innovative applications. Ligation of targeting-antibody with antigen provided a simple route to vaccine generation. SpyRings, from head-to-tail cyclisation, gave major enhancements in enzyme resilience. Linking multiple SpyCatchers gave dendrimers for T-cell activation or Spy networks...
Source: Current Opinion in Chemical Biology - October 27, 2015 Category: Biochemistry Authors: Reddington SC, Howarth M Tags: Curr Opin Chem Biol Source Type: research

Detection and identification of protein citrullination in complex biological systems.
Abstract Protein citrullination is a post-translational modification of arginine that is catalyzed by the Protein Arginine Deiminase (PAD) family of enzymes. Aberrantly increased citrullination is associated with a host of inflammatory diseases and cancer and PAD inhibitors have shown remarkable efficacy in a range of diseases including rheumatoid arthritis, lupus, atherosclerosis, and ulcerative colitis. In rheumatoid arthritis, citrullinated proteins serve as key antigens for rheumatoid arthritis-associated autoantibodies. These data suggest that citrullinated proteins may serve more generally as biomarkers of s...
Source: Current Opinion in Chemical Biology - October 27, 2015 Category: Biochemistry Authors: Clancy KW, Weerapana E, Thompson PR Tags: Curr Opin Chem Biol Source Type: research

How specific is CRISPR/Cas9 really?
Abstract The specificity of RNA-guided nucleases has gathered considerable interest as they become broadly applied to basic research and therapeutic development. Reports of the simple generation of animal models and genome engineering of cells raised questions about targeting precision. Conflicting early reports led the field to believe that CRISPR/Cas9 system was promiscuous, leading to a variety of strategies for improving specificity and increasingly sensitive methods to detect off-target events. However, other studies have suggested that CRISPR/Cas9 is a highly specific genome-editing tool. This review will fo...
Source: Current Opinion in Chemical Biology - October 23, 2015 Category: Biochemistry Authors: O'Geen H, Yu AS, Segal DJ Tags: Curr Opin Chem Biol Source Type: research

Three steps forward, two steps back: mechanistic insights into the assembly and disassembly of the SNARE complex.
Abstract Membrane fusion is a tightly controlled process in all eukaryotic cell types. The SNARE family of proteins is required for fusion throughout the exocytic and endocytic trafficking pathways. SNAREs on a transport vesicle interact with the cognate SNAREs on the target membrane, forming an incredibly stable SNARE complex that provides energy for the membranes to fuse, although many aspects of the mechanism remain elusive. Recent advances in single-molecule and high-resolution structural methods provide exciting new insights into how SNARE complexes assemble, including measurements of assembly energetics and ...
Source: Current Opinion in Chemical Biology - October 22, 2015 Category: Biochemistry Authors: Bombardier JP, Munson M Tags: Curr Opin Chem Biol Source Type: research

Synthetic biology for microbial production of lipid-based biofuels.
Abstract The risks of maintaining current CO2 emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO2 produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. We further discuss engineering strategies to optimize engineered bios...
Source: Current Opinion in Chemical Biology - October 16, 2015 Category: Biochemistry Authors: d'Espaux L, Mendez-Perez D, Li R, Keasling JD Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Opportunities and challenges in synthetic biology.
PMID: 26456417 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - October 8, 2015 Category: Biochemistry Authors: Chang MC, Zhao H Tags: Curr Opin Chem Biol Source Type: research

Chemically induced dimerization: reversible and spatiotemporal control of protein function in cells.
u YW Abstract Small-molecule perturbation of biological systems is able to tackle biological problems that are not accessible by classical genetic interference methods. Chemically induced dimerization (CID) has been used as a valuable tool to study various biological processes. Recent years have seen tremendous progress in the development of orthogonal and reversible CID systems. These new systems allow control over protein function with unprecedented precision and spatiotemporal resolution. While the primary application of CID has been on dissecting signal transductions, new emerging approaches have extended the ...
Source: Current Opinion in Chemical Biology - September 29, 2015 Category: Biochemistry Authors: Voß S, Klewer L, Wu YW Tags: Curr Opin Chem Biol Source Type: research

Combining C6 and C5 sugar metabolism for enhancing microbial bioconversion.
Abstract Mixed sugars, which are often obtained from renewable biomass, can be converted into biofuels and chemicals by microbial conversion. This sustainable production process can also mitigate man-made climate change when used to petroleum-based fuel and chemical production. In contrast to single sugar fermentations, such as corn-based or sugarcane-based ethanol fermentations, mixed sugar fermentations present significant challenges for cost-effective production of the target products. In particular, inefficient and slow microbial fermentation of non-glucose sugars, such as galactose and xylose from the depolym...
Source: Current Opinion in Chemical Biology - September 29, 2015 Category: Biochemistry Authors: Zhang GC, Liu JJ, Kong II, Kwak S, Jin YS Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Synthetic biomolecules: Synthetic protein modifications-a giant leap towards understanding and generating biological functions.
PMID: 26403808 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - September 21, 2015 Category: Biochemistry Authors: Hackenberger CP, Chen PR Tags: Curr Opin Chem Biol Source Type: research

Alkane production from biomass: chemo-, bio- and integrated catalytic approaches.
BF Abstract Linear, branched and cyclic alkanes are important intermediates and end products of the chemical industry and are nowadays mainly obtained from fossil resources. In search for alternatives, biomass feedstocks are often presented as a renewable carbon source for the production of fuels, chemicals and materials. However, providing a complete market for all these applications seems unrealistic due to both financial and logistic issues. Despite the very large scale of current alkane-based fuel applications, biomass definitely has the potential to offer a partial solution to the fuel business. For the smal...
Source: Current Opinion in Chemical Biology - September 8, 2015 Category: Biochemistry Authors: Deneyer A, Renders T, Van Aelst J, Van den Bosch S, Gabriëls D, Sels BF Tags: Curr Opin Chem Biol Source Type: research

Protein-polymer conjugation-moving beyond PEGylation.
Abstract In this review, we summarize-from a materials science perspective-the current state of the field of polymer conjugates of peptide and protein drugs, with a focus on polymers that have been developed as alternatives to the current gold standard, poly(ethylene glycol) (PEG). PEGylation, or the covalent conjugation of PEG to biological therapeutics to improve their therapeutic efficacy by increasing their circulation half-lives and stability, has been the gold standard in the pharmaceutical industry for several decades. After years of research and development, the limitations of PEG, specifically its non-deg...
Source: Current Opinion in Chemical Biology - September 7, 2015 Category: Biochemistry Authors: Qi Y, Chilkoti A Tags: Curr Opin Chem Biol Source Type: research

Genetic manipulation of lignocellulosic biomass for bioenergy.
Abstract Lignocellulosic biomass represents an abundant and sustainable raw material for biofuel production. The recalcitrance of biomass to degradation increases the estimated cost of biofuel production and limits its competitiveness in the market. Genetic engineering of lignin, a major recalcitrance factor, improves saccharification and thus the potential yield of biofuels. Recently, our understanding of lignification and its regulation has been advanced by new studies in various systems, all of which further enhances our ability to manipulate the biosynthesis and deposition of lignin in energy crops for produci...
Source: Current Opinion in Chemical Biology - September 3, 2015 Category: Biochemistry Authors: Wang P, Dudareva N, Morgan JA, Chapple C Tags: Curr Opin Chem Biol Source Type: research

An emerging playbook for antibody-drug conjugates: lessons from the laboratory and clinic suggest a strategy for improving efficacy and safety.
Abstract Antibody-drug conjugates (ADCs) have become de rigueur for pharmaceutical oncology drug development pipelines. There are more than 40 ADCs undergoing clinical trials and many more in preclinical development. The field has rushed to follow the initial successes of Kadcyla™ and Adcetris™, and moved forward with new targets without much pause for optimization. In some respects, the ADC space has become divided into the clinical realm-where the proven technologies continue to represent the bulk of clinical candidates with a few exceptions-and the research realm-where innovations in conjugation che...
Source: Current Opinion in Chemical Biology - August 21, 2015 Category: Biochemistry Authors: Drake PM, Rabuka D Tags: Curr Opin Chem Biol Source Type: research

Genetic code expansion enabled site-specific dual-color protein labeling: superresolution microscopy and beyond.
Abstract Genetic code expansion is emerging as an important tool for manipulation and labeling of proteins in vitro and in vivo. In combination with click-chemistry it allows site-specific labeling of target proteins with small organic fluorophores. This is achieved by cotranslational incorporation of noncanonical amino acids (ncAAs) in target proteins via orthogonal tRNA/amino-acyl tRNA synthetase pairs. In a subsequent step, ncAAs are labeled with small dyes via click-chemistry. Small labeling tags and free choice of which fluorophore to use and where to put it into the protein are of particular importance for s...
Source: Current Opinion in Chemical Biology - August 21, 2015 Category: Biochemistry Authors: Nikić I, Lemke EA Tags: Curr Opin Chem Biol Source Type: research

The emergence of commodity-scale genetic manipulation.
Abstract Since the 1970s technological advancements in the fields of synthetic biology and metabolic engineering have led to a dramatic reduction in both time and cost required for generating genomic mutations in a variety of organisms. The union of genomic editing machinery, DNA inkjet printers, and bioinformatics algorithms allows engineers to design a library of thousands of unique oligos as well as build and test these designs on a ∼2 months time-scale and at a cost of roughly ∼0.3 cents per base pair. The implications of these capabilities for a variety of fields are far-reaching, with potential impac...
Source: Current Opinion in Chemical Biology - August 18, 2015 Category: Biochemistry Authors: Halweg-Edwards AL, Grau WC, Winkler JD, Garst AD, Gill RT Tags: Curr Opin Chem Biol Source Type: research

Protein-specific imaging of posttranslational modifications.
Abstract Protein posttranslational modifications (PTMs) modulate protein function, trafficking, and interactions. Many PTMs ubiquitously occurs on hundreds and thousands of proteins, which makes cellular imaging of the PTM state of a specific protein like looking for a needle in a haystack. A proximity-enabled strategy, which exploits the spatial proximity between the PTM and the modified protein, has emerged as a valuable tool for protein-specific imaging of PTMs in single cells and tissue sections. The protein and the PTM are dually labeled with two distinct tags, which enable the generation of the nanometer pro...
Source: Current Opinion in Chemical Biology - August 17, 2015 Category: Biochemistry Authors: Lin W, Gao L, Chen X Tags: Curr Opin Chem Biol Source Type: research

Orthogonal bioorthogonal chemistries.
This article highlights the development of orthogonal bioorthogonal reactions and their application in multi-target imaging and macromolecule assembly. Methods to tune and control orthogonal reactivity are also discussed, along with prospects for identifying new classes of compatible reactions. PMID: 26276062 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - August 10, 2015 Category: Biochemistry Authors: Patterson DM, Prescher JA Tags: Curr Opin Chem Biol Source Type: research

Synthetic histone code.
Abstract Chromatin is the universal template of genetic information in all eukaryotic cells. This complex of DNA and histone proteins not only packages and organizes genomes but also regulates gene expression. A multitude of posttranslational histone modifications and their combinations are thought to constitute a code for directing distinct structural and functional states of chromatin. Methods of protein chemistry, including protein semisynthesis, amber suppression technology, and cysteine bioconjugation, have enabled the generation of so-called designer chromatin containing histones in defined and homogeneous m...
Source: Current Opinion in Chemical Biology - August 5, 2015 Category: Biochemistry Authors: Fischle W, Mootz HD, Schwarzer D Tags: Curr Opin Chem Biol Source Type: research

Sustainability of biofuels and renewable chemicals production from biomass.
Abstract In the sectors of biofuel and renewable chemicals the big feedstock demand asks, first, to expand the spectrum of carbon sources beyond primary biomass, second, to establish circular processing chains and, third, to prioritize product sectors exclusively depending on carbon: chemicals and heavy-duty fuels. Large-volume production lines will reduce greenhouse gas (GHG) emission significantly but also low-volume chemicals are indispensable in building 'low-carbon' industries. The foreseeable feedstock change initiates innovation, securing societal wealth in the industrialized world and creating employment i...
Source: Current Opinion in Chemical Biology - August 5, 2015 Category: Biochemistry Authors: Kircher M Tags: Curr Opin Chem Biol Source Type: research

Multiply labeling proteins for studies of folding and stability.
Abstract Fluorescence spectroscopy is a powerful method for monitoring protein folding in real-time with high resolution and sensitivity, but requires the site-specific introduction of labels into the protein. The ability to genetically incorporate unnatural amino acids (Uaas) allows for the efficient synthesis of fluorescently labeled proteins with minimally perturbing fluorophores. Here, we describe recent uses of labeled proteins in dynamic structure determination experiments and advances in unnatural amino acid incorporation for dual site-specific fluorescent labeling. The advent of increasingly sophisticated ...
Source: Current Opinion in Chemical Biology - August 4, 2015 Category: Biochemistry Authors: Haney CM, Wissner RF, Petersson EJ Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Molecular imaging: Cellular imaging approaches.
PMID: 26238588 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - July 31, 2015 Category: Biochemistry Authors: Miyawaki A, Jaffrey SR Tags: Curr Opin Chem Biol Source Type: research

Biocatalysts for biomass deconstruction from environmental genomics.
Abstract Plant biomass offers a sustainable alternative to the energy and materials produced from fossil fuels. The industrial scale production or biorefining of fermentable sugars and aromatics from plant biomass is currently limited by the lack of cost effective and efficient biocatalysts. One potential solution to this problem is the discovery of biomass deconstructing biocatalysts from uncultivated microbial communities. Here we review recent progress in recovering such biological devices from environmental genomes and consider how this information can be used to build better biorefining ecosystems. PMID:...
Source: Current Opinion in Chemical Biology - July 28, 2015 Category: Biochemistry Authors: Armstrong Z, Mewis K, Strachan C, Hallam SJ Tags: Curr Opin Chem Biol Source Type: research

Synthetic approaches to protein phosphorylation.
Abstract Reversible protein phosphorylation is critically important in biology and medicine. Hundreds of thousands of sites of protein phosphorylation have been discovered but our understanding of the functions of the vast majority of these post-translational modifications is lacking. This review describes several chemical and biochemical methods that are under development and in current use to install phospho-amino acids and their mimics site-specifically into proteins. The relative merits of total chemical synthesis, semisynthesis, and nonsense suppression strategies for studying protein phosphorylation are disc...
Source: Current Opinion in Chemical Biology - July 17, 2015 Category: Biochemistry Authors: Chen Z, Cole PA Tags: Curr Opin Chem Biol Source Type: research

Repurposing the translation apparatus for synthetic biology.
Abstract The translation system (the ribosome and associated factors) is the cell's factory for protein synthesis. The extraordinary catalytic capacity of the protein synthesis machinery has driven extensive efforts to harness it for novel functions. For example, pioneering efforts have demonstrated that it is possible to genetically encode more than the 20 natural amino acids and that this encoding can be a powerful tool to expand the chemical diversity of proteins. Here, we discuss recent advances in efforts to expand the chemistry of living systems, highlighting improvements to the molecular machinery and genom...
Source: Current Opinion in Chemical Biology - July 14, 2015 Category: Biochemistry Authors: Des Soye BJ, Patel JR, Isaacs FJ, Jewett MC Tags: Curr Opin Chem Biol Source Type: research

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways.
Abstract Designing putative metabolic pathways is of great interest in synthetic biology. Retrobiosynthesis is a discipline that involves the design, evaluation, and optimization of de novo biosynthetic pathways for the production of high-value compounds and drugs from renewable resources and natural or engineered enzymes. The best candidate pathways are then engineered within a metabolic network of microorganisms that serve as synthetic platforms for synthetic biology. The complexity of biological chemistry and metabolism requires computational approaches to explore the full possibilities of engineering synthetic...
Source: Current Opinion in Chemical Biology - July 10, 2015 Category: Biochemistry Authors: Hadadi N, Hatzimanikatis V Tags: Curr Opin Chem Biol Source Type: research

Advances in de novo strain design using integrated systems and synthetic biology tools.
Abstract Recent efforts in expanding the range of biofuel and biorenewable molecules using microbial production hosts have focused on the introduction of non-native pathways in model organisms and the bio-prospecting of non-model organisms with desirable features. Current challenges lie in the assembly and coordinated expression of the (non-)native pathways and the elimination of competing pathways and undesirable regulation. Several systems and synthetic biology approaches providing contrasting top-down and bottom-up strategies, respectively, have been developed. In this review, we discuss recent advances in both...
Source: Current Opinion in Chemical Biology - July 9, 2015 Category: Biochemistry Authors: Ng CY, Khodayari A, Chowdhury A, Maranas CD Tags: Curr Opin Chem Biol Source Type: research

Butyrolactone signalling circuits for synthetic biology.
Abstract Signalling circuits based on quorum sensing mechanisms have been popular tools for synthetic biology. Recent advances in our understanding of the analogous systems regulating antibiotics production in soil bacteria suggest that these might provide useful complementary tools to increase the complexity of possible circuit designs. Here we discuss the diversity of these natural circuits, which use γ-butyrolactones (GBLs) as their main inter-cellular signal, highlighting the range of new building blocks they could provide, as well as a number of exciting recent applications of GBL-based circuits in hete...
Source: Current Opinion in Chemical Biology - July 8, 2015 Category: Biochemistry Authors: Biarnes-Carrera M, Breitling R, Takano E Tags: Curr Opin Chem Biol Source Type: research

Fast kinetics of calcium signaling and sensor design.
Abstract Fast calcium signaling is regulated by numerous calcium channels exhibiting high spatiotemporal profiles which are currently measured by fluorescent calcium sensors. There is still a strong need to improve the kinetics of genetically encoded calcium indicators (sensors) to capture calcium dynamics in the millisecond time frame. In this review, we summarize several major fast calcium signaling pathways and discuss the recent developments and application of genetically encoded calcium indicators to detect these pathways. A new class of genetically encoded calcium indicators designed with site-directed mutag...
Source: Current Opinion in Chemical Biology - July 4, 2015 Category: Biochemistry Authors: Tang S, Reddish F, Zhuo Y, Yang JJ Tags: Curr Opin Chem Biol Source Type: research

The evolving capabilities of rhodopsin-based genetically encoded voltage indicators.
Abstract Protein engineering over the past four years has made rhodopsin-based genetically encoded voltage indicators a leading candidate to achieve the task of reporting action potentials from a population of genetically targeted neurons in vivo. Rational design and large-scale screening efforts have steadily improved the dynamic range and kinetics of the rhodopsin voltage-sensing domain, and coupling these rhodopsins to bright fluorescent proteins has supported bright fluorescence readout of the large and rapid rhodopsin voltage response. The rhodopsin-fluorescent protein fusions have the highest achieved signal...
Source: Current Opinion in Chemical Biology - July 1, 2015 Category: Biochemistry Authors: Gong Y Tags: Curr Opin Chem Biol Source Type: research

Folding and function in α/β-peptides: targets and therapeutic applications.
Folding and function in α/β-peptides: targets and therapeutic applications. Curr Opin Chem Biol. 2015 Jun 29;28:75-82 Authors: Werner HM, Horne WS Abstract Combining natural α-amino acid residues and unnatural β-amino acid residues in a single chain leads to heterogeneous-backbone oligomers called α/β-peptides. Despite their unnatural backbones, α/β-peptides can manifest a variety of folding patterns and biological functions reminiscent of natural peptides and proteins. Moreover, incorporation of β-residues can impart useful properties to the oligomer s...
Source: Current Opinion in Chemical Biology - June 29, 2015 Category: Biochemistry Authors: Werner HM, Horne WS Tags: Curr Opin Chem Biol Source Type: research

Enzymatic conversion of lignin into renewable chemicals.
Abstract The aromatic heteropolymer lignin is a major component of plant cell walls, and is produced industrially from paper/pulp manufacture and cellulosic bioethanol production. Conversion of lignin into renewable chemicals is a major unsolved problem in the development of a biomass-based biorefinery. The review describes recent developments in the understanding of bacterial enzymes for lignin breakdown, such as DyP peroxidases, bacterial laccases, and beta-etherase enzymes. The use of pathway engineering methods to construct genetically modified microbes to convert lignin to renewable chemicals (e.g. vanillin, ...
Source: Current Opinion in Chemical Biology - June 25, 2015 Category: Biochemistry Authors: Bugg TD, Rahmanpour R Tags: Curr Opin Chem Biol Source Type: research

Homogeneously modified immunoglobulin domains for therapeutic application.
Abstract The field of therapeutic antibodies has been revolutionized over the past decade, led by the development of novel antibody-modification technologies. Besides the huge success achieved by therapeutic monoclonal antibodies, a diversity of antibody derivatives have emerged with hope to outperform their parental antibodies. Here we review the recent development of methodologies to modify immunoglobulin domains and their therapeutic applications. The innovative genetic and chemical approaches enable novel and controllable modifications on immunoglobulin domains, producing homogeneous therapeutics with new func...
Source: Current Opinion in Chemical Biology - June 25, 2015 Category: Biochemistry Authors: Liu T, Du J, Luo X, Schultz PG, Wang F Tags: Curr Opin Chem Biol Source Type: research

Fluorescence imaging using synthetic GFP chromophores.
Abstract Green fluorescent protein and related proteins carry chromophores formed within the protein from their own amino acids. Corresponding synthetic compounds are non-fluorescent in solution due to photoinduced isomerization of the benzylideneimidiazolidinone core. Restriction of this internal rotation by binding to host molecules leads to pronounced, up to three orders of magnitude, increase of fluorescence intensity. This property allows using GFP chromophore analogs as fluorogenic dyes to detect metal ions, proteins, nucleic acids, and other hosts. For example, RNA aptamer named Spinach, which binds to and ...
Source: Current Opinion in Chemical Biology - June 24, 2015 Category: Biochemistry Authors: Walker CL, Lukyanov KA, Yampolsky IV, Mishin AS, Bommarius AS, Duraj-Thatte AM, Azizi B, Tolbert LM, Solntsev KM Tags: Curr Opin Chem Biol Source Type: research

Near-infrared fluorescent proteins engineered from bacterial phytochromes.
We describe phenotypes of NIR FPs and their photochemical and intracellular properties. We discuss NIR FP applications for imaging of various cell types, tissues and animal models in basic and translational research. In this discussion, we focus on NIR FPs that efficiently incorporate endogenous biliverdin chromophore and therefore can be used as straightforward as GFP-like proteins. We also overview a usage of NIR FPs in different imaging platforms, from planar epifluorescence to tomographic and photoacoustic technologies. PMID: 26115447 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - June 23, 2015 Category: Biochemistry Authors: Shcherbakova DM, Baloban M, Verkhusha VV Tags: Curr Opin Chem Biol Source Type: research

Genetically encoded voltage indicators for large scale cortical imaging come of age.
g C Abstract Electrical signals are fundamental to cellular sensing, communication and motility. In the nervous system, information is represented as receptor, synaptic and action potentials. Understanding how brain functions emerge from these electrical signals is one of the ultimate challenges in neuroscience and requires a methodology to monitor membrane voltage transients from large numbers of cells at high spatio-temporal resolution. Optical voltage imaging holds longstanding promises to achieve this, and has gained a fresh powerful momentum with the development of genetically encoded voltage indicators (GEVI...
Source: Current Opinion in Chemical Biology - June 23, 2015 Category: Biochemistry Authors: Knöpfel T, Gallero-Salas Y, Song C Tags: Curr Opin Chem Biol Source Type: research

Rational design and evolutional fine tuning of Saccharomyces cerevisiae for biomass breakdown.
Abstract Conferring biomass hydrolysis activity on yeast through genetic engineering has paved the way for the development of groundbreaking processes for producing liquid fuels and commodity chemicals from lignocellulosic biomass. However, the overproduction and misfolding of heterologous and endogenous proteins can trigger cellular stress, increasing the metabolic burden and retarding growth. Improving the efficiency of lignocellulosic breakdown requires engineering of yeast secretory pathway based on system-wide metabolic analysis as well as DNA constructs for enhanced cellulase gene expression with advanced mo...
Source: Current Opinion in Chemical Biology - June 22, 2015 Category: Biochemistry Authors: Hasunuma T, Ishii J, Kondo A Tags: Curr Opin Chem Biol Source Type: research

A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future.
Abstract Since our ability to engineer biological systems is directly related to our ability to control gene expression, a central focus of synthetic biology has been to develop programmable genetic regulatory systems. Researchers are increasingly turning to RNA regulators for this task because of their versatility, and the emergence of new powerful RNA design principles. Here we review advances that are transforming the way we use RNAs to engineer biological systems. First, we examine new designable RNA mechanisms that are enabling large libraries of regulators with protein-like dynamic ranges. Next, we review em...
Source: Current Opinion in Chemical Biology - June 18, 2015 Category: Biochemistry Authors: Chappell J, Watters KE, Takahashi MK, Lucks JB Tags: Curr Opin Chem Biol Source Type: research

Recent progress in luminescent proteins development.
Abstract Bioimaging requires not only high sensitivity but also minimal invasiveness. Bioimaging using luminescent proteins is potentially free from problems such as photo-induced damage or an undesirable physical reaction to the sample, which are often caused by illumination with an external light required in fluorescence imaging. The recent development of several luminescent proteins and substrates have greatly improved the brightness of luminescence imaging, facilitating its application by many researchers. In this short review, we summarize recent advances in development of luminescent proteins, substrates, an...
Source: Current Opinion in Chemical Biology - June 18, 2015 Category: Biochemistry Authors: Saito K, Nagai T Tags: Curr Opin Chem Biol Source Type: research

Peeling away the layers of ubiquitin signaling complexities with synthetic ubiquitin-protein conjugates.
Abstract Covalent attachment of ubiquitin, a process termed ubiquitination, affects the location, function, and stability of modified proteins. Significant advances have been made in building synthetic ubiquitin-protein conjugates that can be used to investigate how ubiquitin regulates diverse biological processes. Herein we describe recent advances and discuss how chemical methods have been implemented to address the molecular underpinnings of ubiquitin-dependent cellular signaling. PMID: 26093241 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - June 17, 2015 Category: Biochemistry Authors: Pham GH, Strieter ER Tags: Curr Opin Chem Biol Source Type: research

LOV-based reporters for fluorescence imaging.
Abstract Chromophore-binding domains from plant and bacterial photoreceptor proteins have recently gathered increasing attention as new sources of genetically encoded fluorescent proteins (FPs). In particular, FPs based on the flavin-binding LOV (light, oxygen, or voltage sensing) domain offer advantages over green fluorescent protein (GFP) owing to their smaller size, pH and thermal stability, utility under anaerobic conditions and their ability to generate reactive oxygen species. This review focuses on the potential applications of this emerging class of fluorescent reporters, discusses the advantages and limit...
Source: Current Opinion in Chemical Biology - June 15, 2015 Category: Biochemistry Authors: Buckley AM, Petersen J, Roe AJ, Douce GR, Christie JM Tags: Curr Opin Chem Biol Source Type: research

Quantitative two-photon imaging of fluorescent biosensors.
Abstract Fluorescent biosensors are now routinely imaged using two-photon microscopy in intact tissue, for instance, in brain slices and brains in living animals. But most studies measure temporal variation-for example, calcium transients in response to neuronal activity-rather than calibrated levels of biosensor occupancy (and thus levels of the sensed analyte). True quantitative measurements are challenging, since it is difficult or impossible to calibrate a sensor's dose-response in situ, and difficult to compare the optical signals from tissue to those during in vitro calibration. Ratiometric measurements (at ...
Source: Current Opinion in Chemical Biology - June 12, 2015 Category: Biochemistry Authors: Yellen G, Mongeon R Tags: Curr Opin Chem Biol Source Type: research

Synthetic protein lipidation.
Abstract Fatty acylation of proteins is a versatile co-translational or post-translational modification that plays a key role in human physiology and disease. It is tightly controlled by a set of enzymes which catalyze the covalent attachment of fatty acids onto protein substrates, resulting in regulation of protein function, stability and interaction with other proteins or membranes. Some fatty acyltransferases have emerged to function as tumor suppressors or oncogenes, while others contribute to pathogenesis and neurodegenerative disorders. Yet our understanding of the molecular mechanism of action of these enzy...
Source: Current Opinion in Chemical Biology - June 12, 2015 Category: Biochemistry Authors: Hannoush RN Tags: Curr Opin Chem Biol Source Type: research

Designs and sensing mechanisms of genetically encoded fluorescent voltage indicators.
Abstract Neurons tightly regulate the electrical potential difference across the plasma membrane with millivolt accuracy and millisecond resolution. Membrane voltage dynamics underlie the generation of an impulse, the transduction of impulses from one end of the neuron to the other, and the release of neurotransmitters. Imaging these voltage dynamics in multiple neurons simultaneously is therefore crucial for understanding how neurons function together within circuits in intact brains. Genetically encoded fluorescent voltage sensors have long been desired to report voltage in defined subsets of neurons with optica...
Source: Current Opinion in Chemical Biology - June 11, 2015 Category: Biochemistry Authors: St-Pierre F, Chavarha M, Lin MZ Tags: Curr Opin Chem Biol Source Type: research

Dark dyes-bright complexes: fluorogenic protein labeling.
Abstract Complexes formed between organic dyes and genetically encoded proteins combine the advantages of stable and tunable fluorescent molecules and targetable, biologically integrated labels. To overcome the challenges imposed by labeling with bright fluorescent dyes, a number of approaches now exploit chemical or environmental changes to control the properties of a bound dye, converting dyes from a weakly fluorescent state to a bright, easily detectable complex. Optimized, such approaches avoid the need for removal of unbound dyes, facilitate rapid and simple assays in cultured cells and enable hybrid labeling...
Source: Current Opinion in Chemical Biology - June 5, 2015 Category: Biochemistry Authors: Bruchez MP Tags: Curr Opin Chem Biol Source Type: research

DNA nanotechnology: new adventures for an old warhorse.
Abstract As the blueprint of life, the natural exploits of DNA are admirable. However, DNA should not only be viewed within a biological context. It is an elegantly simple yet functionally complex chemical polymer with properties that make it an ideal platform for engineering new nanotechnologies. Rapidly advancing synthesis and sequencing technologies are enabling novel unnatural applications for DNA beyond the realm of genetics. Here we explore the chemical biology of DNA nanotechnology for emerging applications in communication and digital data storage. Early studies of DNA as an alternative to magnetic and opt...
Source: Current Opinion in Chemical Biology - June 5, 2015 Category: Biochemistry Authors: Zakeri B, Lu TK Tags: Curr Opin Chem Biol Source Type: research

Synthetic biology expands chemical control of microorganisms.
Abstract The tools of synthetic biology allow researchers to change the ways engineered organisms respond to chemical stimuli. Decades of basic biology research and new efforts in computational protein and RNA design have led to the development of small molecule sensors that can be used to alter organism function. These new functions leap beyond the natural propensities of the engineered organisms. They can range from simple fluorescence or growth reporting to pathogen killing, and can involve metabolic coordination among multiple cells or organisms. Herein, we discuss how synthetic biology alters microorganisms' ...
Source: Current Opinion in Chemical Biology - June 5, 2015 Category: Biochemistry Authors: Ford TJ, Silver PA Tags: Curr Opin Chem Biol Source Type: research

Novel theranostic agents for next-generation personalized medicine: small molecules, nanoparticles, and engineered mammalian cells.
Abstract Modern medicine is currently undergoing a paradigm shift from conventional disease treatments based on the diagnosis of a generalized disease state to a more personalized, customized treatment model based on molecular-level diagnosis. This uses novel biosensors that can precisely extract disease-related information from complex biological systems. Moreover, with the recent progress in chemical biology, materials science, and synthetic biology, it has become possible to simultaneously conduct diagnosis and targeted therapy (theranostics/theragnosis) by directly connecting the readout of a biosensor to a th...
Source: Current Opinion in Chemical Biology - June 5, 2015 Category: Biochemistry Authors: Kojima R, Aubel D, Fussenegger M Tags: Curr Opin Chem Biol Source Type: research

Development of biosensors and their application in metabolic engineering.
Abstract In a sustainable bioeconomy, many commodities and high value chemicals, including pharmaceuticals, will be manufactured using microbial cell factories from renewable feedstocks. These cell factories can be efficiently generated by constructing libraries of diversified genomes followed by screening for the desired phenotypes. However, methods available for microbial genome diversification far exceed our ability to screen and select for those variants with optimal performance. Genetically encoded biosensors have shown the potential to address this gap, given their ability to respond to small molecule bindin...
Source: Current Opinion in Chemical Biology - June 4, 2015 Category: Biochemistry Authors: Zhang J, Jensen MK, Keasling JD Tags: Curr Opin Chem Biol Source Type: research

Getting pumped: membrane efflux transporters for enhanced biomolecule production.
Abstract Small molecule production in microbial hosts is limited by the accumulation of the product inside the cell. Efflux transporters show promise as a solution to removal of the often-toxic products. Recent advances in transporter identification through expression profiling, heterologous expression, and knockout studies have identified transporters capable of secreting compounds of biotechnological interest. In addition, engineering of well-studied transporters has shown that substrate specificity in these transporters is malleable. Future work in identification, engineering, and expression of small molecule e...
Source: Current Opinion in Chemical Biology - June 4, 2015 Category: Biochemistry Authors: Boyarskiy S, Tullman-Ercek D Tags: Curr Opin Chem Biol Source Type: research

Emerging fluorescent protein technologies.
Abstract Fluorescent proteins (FPs), such as the Aequorea jellyfish green FP (GFP), are firmly established as fundamental tools that enable a wide variety of biological studies. Specifically, FPs can serve as versatile genetically encoded markers for tracking proteins, organelles, or whole cells, and as the basis for construction of biosensors that can be used to visualize a growing array of biochemical events in cells and tissues. In this review we will focus on emerging applications of FPs that represent unprecedented new directions for the field. These emerging applications include new strategies for using FPs ...
Source: Current Opinion in Chemical Biology - May 28, 2015 Category: Biochemistry Authors: Enterina JR, Wu L, Campbell RE Tags: Curr Opin Chem Biol Source Type: research