Achieving the promise and avoiding the peril of chemical probes using genetics

Chemical probes can be valuable tools for studying protein targets, but addressing concerns about a probe's cellular target or its specificity can be challenging. A reliable strategy is to use a mutation that does not alter a target's function but confers resistance (or sensitizes) to the inhibitor in both cellular and biochemical assays. However, challenges remain in finding such mutations. Here, we discuss structure- and cell-based approaches to identify resistance- and sensitivity-conferring mutations. Further, we describe how resistance-conferring mutations can help with compound design, and the use of saturation mutagenesis to characterize a compound binding site. We highlight how genetic approaches can ensure the proper use of chemical inhibitors to pursue mechanistic studies and test therapeutic hypotheses.     

High-throughput analysis of the protein sequence-stability landscape using a quantitative yeast surface two-hybrid system and fragment reconstitution

Stability evaluation of many mutants can lead to a better understanding of the sequence determinants of a structural motif and of factors governing protein stability and protein evolution. The traditional biophysical analysis of protein stability is low throughput, limiting our ability to widely explore sequence space in a quantitative manner. In this study, we have developed a high-throughput library screening method for quantifying stability changes, which is based on protein fragment reconstitution and yeast surface display. Our method exploits the thermodynamic linkage between protein stability and fragment reconstitution and the ability of the yeast surface display technique to quantitatively evaluate protein-protein interactions. The method was applied to a fibronectin type III (FN3) domain. Characterization of fragment reconstitution was facilitated by the co-expression of two FN3 fragments, thus establishing a yeast surface two-hybrid method. Importantly, our method does not rely on competition between clones and thus eliminates a common limitation of high-throughput selection methods in which the most stable variants are recovered predominantly. Thus, it allows for the isolation of sequences that exhibit a desired level of stability. We identified more than 100 unique sequences for a β-bulge motif, which was significantly more informative than natural sequences of the FN3 family in revealing the sequence determinants for the β-bulge. Our method provides a powerful means for the rapid assessment of the stability of many variants, for the systematic assessment of the contribution of different factors to protein stability, and for enhancement of the protein stability.     

High-throughput yeast two-hybrid assays for large-scale protein interaction mapping

Protein-protein interactions play fundamental roles in many biological processes. Hence, protein interaction mapping is becoming a well-established functional genomics approach to generate functional annotations for predicted proteins that so far have remained uncharacterized. The yeast two-hybrid system is currently one of the most standardized protein interaction mapping techniques. Here, we describe the protocols for a semiautomated, high-throughput, Gal4-based yeast two-hybrid system.     

High-throughput screening for improved microbial cell factories,perspective and promise

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The peril of the plankton

The pelagic environment is characterized by unevenly distributed resources and risks. Such unpredictability presents adaptive challenges to diverse planktonic organisms including the larvae of benthic marine invertebrates. Estimates of mortality during planktonic development are highly variable, ranging from 0% to 100% per day. Predation is considered a significant source of this mortality, but what explains the variability in estimates of the mortality of marine invertebrate larvae? While differential exposure of larval prey to predators may explain these widely variable estimates, adaptations that reduce vulnerability of marine larvae to predators may also be important. Although there are excellent reviews of predation upon larvae and of larval mortality and defenses, nearly 15 years have elapsed since these topics were formally reviewed. Here, we highlight recent advances in understanding the behavioral, chemical, and morphological defenses that larvae possess and assess their effectiveness in reducing the risk of predation. While recent work confirms that larval mortality is generally high, it also demonstrates that larvae can reduce their risk of predation in several ways, including: (1) temporarily escaping the benthos during vulnerable early stages, (2) producing chemical compounds that reduce palatability, (3) possessing morphological defenses such as spines and shells, and (4) exhibiting induced defensive responses whereby larvae can alter their behavior, morphology, and life histories in the presence of predators. Taken together, these studies indicate that marine invertebrate larvae possess a sophisticated suite of defensive phenotypes that have allowed them to persist in the life cycle of benthic invertebrates for eons.     

High-throughput behavioral analysis in C. elegans

We designed a real-time computer vision system, the Multi-Worm Tracker (MWT), which can simultaneously quantify the behavior of dozens of Caenorhabditis elegans on a Petri plate at video rates. We examined three traditional behavioral paradigms using this system: spontaneous movement on food, where the behavior changes over tens of minutes; chemotaxis, where turning events must be detected accurately to determine strategy; and habituation of response to tap, where the response is stochastic and changes over time. In each case, manual analysis or automated single-worm tracking would be tedious and time-consuming, but the MWT system allowed rapid quantification of behavior with minimal human effort. Thus, this system will enable large-scale forward and reverse genetic screens for complex behaviors.     

Linkage analysis of schizophrenia: challenges and promise.

Schizophrenia is a serious mental illness affecting nearly 1 per cent of the general population. Family, twin, and adoption studies suggest that genetics plays a major role in the etiology of schizophrenia. The inheritance pattern appears complex, similar to that of other common conditions like heart disease. To uncover a causal genetic factor, researchers have recently begun to apply a linkage analysis strategy to schizophrenia. Early results suggest that there are many challenges facing scientists who undertake schizophrenia genetics research. While one study has shown significant linkage of schizophrenia to a region on chromosome 5, several other studies have not found linkage to this area. The likelihood that there are several major genes predisposing to the illness and uncertainties about inheritance patterns and diagnostic boundaries are potential difficulties to overcome. Many more families need to be studied, and creative complementary research strategies pursued, to achieve the potential success offered by a genetic linkage approach.     

High-throughput human metabolism and toxicity analysis

Poor drug candidate safety profiles are often identified late in the drug development process, manifesting themselves in the preclinical and clinical phases and significantly contributing to the high cost and low yield of drug discovery. As a result, new tools are needed to accelerate the assessment of drug candidate toxicity and human metabolism earlier in the drug development process, from primary drug candidate screening to lead optimization. Although high-throughput screens exist for much of the discovery phase of drug development, translating such screening techniques into platforms that can accurately mimic the human in vivo response and predict the impact of drug candidates on human toxicology has proven difficult. Nevertheless, some success has been achieved in recent years, which may ultimately yield widespread acceptance in the pharmaceutical industry.     

Applications of the yeast two-hybrid system.

In recent years, the yeast two-hybrid system has become the method of choice for detection and analysis of protein-protein interactions in an in vivo context. This system, which capitalizes on the significant genetic history and ease of protocols for manipulation of Saccharomyces cerevisiae, is accessible to most laboratories and is applicable to the pursuit of a large variety of experimental goals. To date, the two-hybrid system has seen widespread application for identification of interaction partners by screening methods using a particular protein of interest as a "bait." Large-scale ventures are also in progress, for example, a cataloging of interactions among the cellular proteins in yeast. However, this method also has tremendous potential for more focused analyses of specific proteins and should become more routine as an alternative or adjunct approach for many structure-function investigations.