Showing papers in "Methods in Enzymology in 2017"

WGCNA Application to Proteomic and Metabolomic Data Analysis.

Abstract: Progresses in mass spectrometric instrumentation and bioinformatics identification algorithms made over the past decades allow quantitative measurements of relative or absolute protein/metabolite amounts in cells in a high-throughput manner, which has significantly expedited the exploration into functions and dynamics of complex biological systems. However, interpretation of high-throughput data is often restricted by the limited availability of suitable computational methods and enough statistical power. While many computational methodologies have been developed in the past decades to address the issue, it becomes clear that network-focused rather than individual gene/protein-focused strategies would be more appropriate to obtain a complete picture of cellular responses. Recently, an R analytical package named as weighted gene coexpression network analysis (WGCNA) was developed and applied to high-throughput microarray or RNA-seq datasets since it provides a systems-level insights, high sensitivity to low abundance, or small fold changes genes without any information loss. The approach was also recently applied to proteomic and metabolomic data analysis. However, due to the fact that low coverage of the current proteomic and metabolomic analytical technologies, causing the format of datasets are often incomplete, the method needs to be modified so that it can be properly utilized for meaningful biologically interpretation. In this chapter, we provide a detailed introduction of the modified protocol and its tutorials for applying the WGCNA approach in analyzing proteomic and metabolomic datasets.

DNA Fiber Analysis: Mind the Gap!

Abstract: Understanding the mechanisms of replication stress response following genotoxic stress induction is rapidly emerging as a central theme in cell survival and human disease. The DNA fiber assay is one of the most powerful tools to study alterations in replication fork dynamics genome-wide at single-molecule resolution. This approach relies on the ability of many organisms to incorporate thymidine analogs into replicating DNA and is widely used to study how genotoxic agents perturb DNA replication. Here, we review different approaches available to prepare DNA fibers and discuss important limitations of each approach. We also review how DNA fiber analysis can be used to shed light upon several replication parameters including fork progression, restart, termination, and new origin firing. Next, we discuss a modified DNA fiber protocol to monitor the presence of single-stranded DNA (ssDNA) gaps on ongoing replication forks. ssDNA gaps are very common intermediates of several replication stress response mechanisms, but they cannot be detected by standard DNA fiber approaches due to the resolution limits of this technique. We discuss a novel strategy that relies on the use of an ssDNA-specific endonuclease to nick the ssDNA gaps and generate shorter DNA fibers that can be used as readout for the presence of ssDNA gaps. Finally, we describe a follow-up DNA fiber approach that can be used to study how ssDNA gaps are repaired postreplicatively.

Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry.

Abstract: Mass spectrometry-based proteomics has experienced an unprecedented advance in comprehensive analysis of proteins and posttranslational modifications, with particular technical progress in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an optimized LC-MS/MS platform to quantitate whole proteome and phosphoproteome. The major steps include protein extraction and digestion, TMT labeling, two-dimensional liquid chromatography, TiO2-mediated phosphopeptide enrichment, high-resolution mass spectrometry, and computational data processing. This protocol routinely leads to confident quantification of more than 10,000 proteins and approximately 30,000 phosphosites in mammalian samples. Quality control steps are implemented for troubleshooting and evaluating experimental variation. Such a multiplexed robust method provides a powerful tool for dissecting proteomic signatures at the systems level in a variety of complex samples, ranging from cell culture, animal tissues to human clinical specimens.

Filter-Aided Sample Preparation: The Versatile and Efficient Method for Proteomic Analysis.

Abstract: Filter-aided sample preparation (FASP) is a versatile and efficient way of processing protein extracts for bottom-up proteomic analysis. The method repurposes centrifugal ultrafiltration concentrators for removal of detergents, protein cleavage, and isolation of pure peptide fractions. FASP can be used for protein cleavage with different proteinases either with single enzymes or in a mode of successive multienzyme digestion (MED)-FASP. The FASP methods are useful for processing of samples ranging in their sizes from submicrogram to several milligram amounts of total protein. They also allow peptide fractionation, and isolation and quantitation of total RNA and DNA acid contents. This chapter describes principles, limitations, and applications of FASP. Additionally detailed FASP and MED-FASP protocols are provided.

Recent Advances in Development of Genetically Encoded Fluorescent Sensors.

Abstract: Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Forster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications.

Recent Advances in Biological Single-Molecule Applications of Optical Tweezers and Fluorescence Microscopy

Abstract: Over the past two decades, single-molecule techniques have evolved into robust tools to study many fundamental biological processes. The combination of optical tweezers with fluorescence microscopy and microfluidics provides a powerful single-molecule manipulation and visualization technique that has found widespread application in biology. In this combined approach, the spatial (~nm) and temporal (~ms) resolution, as well as the force scale (~pN) accessible to optical tweezers is complemented with the power of fluorescence microscopy. Thereby, it provides information on the local presence, identity, spatial dynamics, and conformational dynamics of single biomolecules. Together, these techniques allow comprehensive studies of, among others, molecular motors, protein-protein and protein-DNA interactions, biomolecular conformational changes, and mechanotransduction pathways. In this chapter, recent applications of fluorescence microscopy in combination with optical trapping are discussed. After an introductory section, we provide a description of instrumentation together with the current capabilities and limitations of the approaches. Next we summarize recent studies that applied this combination of techniques in biological systems and highlight some representative biological assays to mark the exquisite opportunities that optical tweezers combined with fluorescence microscopy provide.

MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes.

Abstract: Recombinant expression of large, multiprotein complexes is essential and often rate limiting for determining structural, biophysical, and biochemical properties of DNA repair, replication, transcription, and other key cellular processes Baculovirus-infected insect cell expression systems are especially well suited for producing large, human proteins recombinantly, and multigene baculovirus systems have facilitated studies of multiprotein complexes In this chapter, we describe a multigene baculovirus system called MacroBac that uses a Biobricks-type assembly method based on restriction and ligation (Series 11) or ligation-independent cloning (Series 438) MacroBac cloning and assembly is efficient and equally well suited for either single subcloning reactions or high-throughput cloning using 96-well plates and liquid handling robotics MacroBac vectors are polypromoter with each gene flanked by a strong polyhedrin promoter and an SV40 poly(A) termination signal that minimize gene order expression level effects seen in many polycistronic assemblies Large assemblies are robustly achievable, and we have successfully assembled as many as 10 genes into a single MacroBac vector Importantly, we have observed significant increases in expression levels and quality of large, multiprotein complexes using a single, multigene, polypromoter virus rather than coinfection with multiple, single-gene viruses Given the importance of characterizing functional complexes, we believe that MacroBac provides a critical enabling technology that may change the way that structural, biophysical, and biochemical research is done

Glycoprotein Enrichment Analytical Techniques: Advantages and Disadvantages.

Abstract: Protein glycosylation is one of the most important posttranslational modifications. Numerous biological functions are related to protein glycosylation. However, analytical challenges remain in the glycoprotein analysis. To overcome the challenges associated with glycoprotein analysis, many analytical techniques were developed in recent years. Enrichment methods were used to improve the sensitivity of detection, while HPLC and mass spectrometry methods were developed to facilitate the separation of glycopeptides/proteins and enhance detection, respectively. Fragmentation techniques applied in modern mass spectrometers allow the structural interpretation of glycopeptides/proteins, while automated software tools started replacing manual processing to improve the reliability and throughput of the analysis. In this chapter, the current methodologies of glycoprotein analysis were discussed. Multiple analytical techniques are compared, and advantages and disadvantages of each technique are highlighted.

Using Hydrogen–Deuterium Exchange Mass Spectrometry to Examine Protein–Membrane Interactions

Abstract: Many fundamental cellular processes are controlled via assembly of a network of proteins at membrane surfaces. The proper recruitment of proteins to membranes can be controlled by a wide variety of mechanisms, including protein lipidation, protein-protein interactions, posttranslational modifications, and binding to specific lipid species present in membranes. There are, however, only a limited number of analytical techniques that can study the assembly of protein-membrane complexes at the molecular level. A relatively new addition to the set of techniques available to study these protein-membrane systems is the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS experiments measure protein conformational dynamics in their native state, based on the rate of exchange of amide hydrogens with solvent. This review discusses the use of HDX-MS as a tool to identify the interfaces of proteins with membranes and membrane-associated proteins, as well as define conformational changes elicited by membrane recruitment. Specific examples will focus on the use of HDX-MS to examine how large macromolecular protein complexes are recruited and activated on membranes, and how both posttranslational modifications and cancer-linked oncogenic mutations affect these processes.

Lipid Nanodiscs as a Tool for High-Resolution Structure Determination of Membrane Proteins by Single-Particle Cryo-EM.

Abstract: The "resolution revolution" in electron cryomicroscopy (cryo-EM) profoundly changed structural biology of membrane proteins. Near-atomic structures of medium size to large membrane protein complexes can now be determined without crystallization. This significantly accelerates structure determination and also the visualization of small bound ligands. There is an additional advantage: the structure of membrane proteins can now be studied in their native or nearly native lipid bilayer environment. A popular lipid bilayer mimetic are lipid nanodiscs, which have been thoroughly characterized and successfully utilized in multiple applications. Here, we provide a guide for using lipid nanodiscs as a tool for single-particle cryo-EM of membrane proteins. We discuss general methodological aspects and specific challenges of protein reconstitution into lipid nanodiscs and high-resolution structure determination of the nanodisc-embedded complexes. Furthermore, we describe in detail case studies of two successful applications of nanodiscs in cryo-EM, namely, the structure determination of the rabbit ryanodine receptor, RyR1, and the pore-forming TcdA1 toxin subunit from Photorhabdus luminescens. We discuss cryo-EM-specific hurdles concerning sample homogeneity, distribution of reconstituted particles in vitreous ice, and solutions to overcome them.

SSM-Based Electrophysiology for Transporter Research.

Abstract: Functional characterization of transport proteins using conventional electrophysiology can be challenging, especially for low turnover transporters or transporters from bacteria and intracellular compartments. Solid-supported membrane (SSM)-based electrophysiology is a sensitive and cell-free assay technique for the characterization of electrogenic membrane proteins. Purified proteins reconstituted into proteoliposomes or membrane vesicles from cell culture or native tissues are adsorbed to the sensor holding an SSM. A substrate or a ligand is applied via rapid solution exchange. The electrogenic transporter activity charges the sensor, which is recorded as a transient current. The high stability of the SSM allows cumulative measurements on the same sensor using different experimental conditions. This allows the determination of kinetic properties including EC50, IC50, Km, KD, and rate constants of electrogenic reactions. About 100 different transporters have been measured so far using this technique, among them symporters, exchangers, uniporters, ATP-, redox-, and light-driven ion pumps, as well as receptors and ion channels. Different instruments apply this technique: the laboratory setups use a closed flow-through arrangement, while the commercially available SURFE2R N1 resembles a pipetting robot. For drug screening purposes high-throughput systems, such as the SURFE2R 96SE enable the simultaneous measurement of up to 96 sensors.

Label-Free and Standard-Free Absolute Quantitative Proteomics Using the "Total Protein" and "Proteomic Ruler" Approaches.

Abstract: Understanding biological systems and their variation upon stimuli requires knowledge on their composition, primarily including information on organization and dynamics of proteomes. The total protein approach (TPA) is a label- and standard-free method for absolute protein quantitation of proteins using large-scale proteomic data. The method relies on the assumption that the total MS signal from all identified proteins in the dataset reflects-in a biochemical sense-the total protein and the MS signal from a single protein corresponds its abundance in the studied sample. The method offers an easy way to quantify thousands of protein per sample. A related method, the "Proteomic Ruler," enables conversion of the protein abundance data calculated by TPA to compute numbers of protein copies per cell. TPA and the Proteomic Ruler are powerful tools for studying dynamics of cell architecture.

Methods to Study Chaperone-Mediated Autophagy.

Abstract: Chaperone-mediated autophagy (CMA), a selective form of degradation of cytosolic proteins in lysosomes, contributes to maintenance of proteostasis and to the cellular adaptation to stress. CMA substrates are selectively recognized and delivered by a cytosolic chaperone to the lysosomal surface, where, upon unfolding, they are internalized through a membrane translocation complex. Defective or dysfunctional CMA has been associated with human pathologies such as neurodegeneration, cancer, immunodeficiency, or diabetes, increasing the overall interest in methods to monitor this selective autophagic pathway. In this chapter, we review the different experimental approaches used to evaluate CMA activity in different organs from animals or in cell cultures in vitro.

Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology

Abstract: Functional epigenetic regulation occurs by dynamic modification of chromatin, including genetic material (i.e., DNA methylation), histone proteins, and other nuclear proteins. Due to the highly complex nature of the histone code, mass spectrometry (MS) has become the leading technique in identification of single and combinatorial histone modifications. MS has now overcome antibody-based strategies due to its automation, high resolution, and accurate quantitation. Moreover, multiple approaches to analysis have been developed for global quantitation of posttranslational modifications (PTMs), including large-scale characterization of modification coexistence (middle-down and top-down proteomics), which is not currently possible with any other biochemical strategy. Recently, our group and others have simplified and increased the effectiveness of analyzing histone PTMs by improving multiple MS methods and data analysis tools. This review provides an overview of the major achievements in the analysis of histone PTMs using MS with a focus on the most recent improvements. We speculate that the workflow for histone analysis at its state of the art is highly reliable in terms of identification and quantitation accuracy, and it has the potential to become a routine method for systems biology thanks to the possibility of integrating histone MS results with genomics and proteomics datasets.

Glycoengineered Outer Membrane Vesicles as a Platform for Vaccine Development.

Abstract: As we enter into the postantibiotic era, vaccines to prevent bacterial infections previously treatable with antibiotics are urgently needed. Most successful antibacterial vaccines are glycoconjugates, composed of cell surface carbohydrates chemically attached to a carrier protein. Glycoconjugate vaccines provide a safe and consistent strategy against polysaccharide-encapsulated pathogens. The best examples are the conjugate vaccines against Haemophilus influenzae type b, Streptococcus pneumoniae, and Neisseria meningitidis, all based on capsular polysaccharides. Although these types of vaccines are effective, their current manufacturing process presents multiple drawbacks, such as biosafety risks and batch-to-batch variability. Furthermore, inclusion of additional serotypes is extremely slow, mainly due to the intricate chemical methods of conjugation. Thus, novel platforms for antibacterial vaccines are required. Gram-negative bacteria are able to produce outer membrane vesicles (OMVs). OMVs are mainly composed of lipopolysaccharide (LPS), outer membrane and periplasmic proteins, and phospholipids. Although their biogenesis is poorly understood, it is known that OMVs are formed by blebbing of the outer membrane. OMVs are attractive candidates for novel vaccine delivery platforms due to their immunogenic properties, self-adjuvanticity, and capacity for enhancement by recombinant engineering. We have shown that OMVs can be engineered to display surface glycans from different bacteria and that these glycoengineered OMVs (geOMVs) are effective in diverse animal models of infection. Here we provide a detailed method for the design and preparation of geOMV displaying the O-antigen from a prominent uropathogenic Escherichia coli (UPEC) serotype, O25b, as a proof of concept for the use of geOMVs as vaccine candidates.

A comparison of two hybrid approaches for detecting protein-protein interactions

Abstract: Two-hybrid systems are one of the most popular, preferred, cost effective, and scalable in vivo genetic approaches for screening protein-protein interactions. A number of variants of yeast and bacterial two-hybrid systems exist, rendering them ideal for modern, flexible proteomics-driven studies. For mapping protein interactions at genome scales (that is, constructing an interactome), the yeast two-hybrid system has been extensively tested and is preferred over bacterial two-hybrid systems, given that users have created more resources such as a variety of vectors and other modifications. Each system has its own advantages and limitations and thus needs to be compared directly. For instance, the bacterial two-hybrid method seems a better fit than the yeast two-hybrid system to screen membrane-associated proteins. In this chapter, we provide detailed protocols for yeast and bacterial two-hybrid systems as well as a comparison of outcomes for each approach using our own and published data.

The Use of DQ-BSA to Monitor the Turnover of Autophagy-Associated Cargo

Abstract: There is increasing evidence documenting the critical role played by autophagic and autophagy-associated processes in maintaining cell homeostasis and overall systemic health. Autophagy is considered a degradative as well as a recycling pathway that relies on encapsulated intracellular components trafficking to and fusing with degradative compartments, including lysosomes. In this chapter, we describe the use of DQ™-BSA to study autophagosome–lysosome fusion as well as a means by which to analyze hybrid autophagic pathways. Such noncanonical pathways include LC3-associated phagocytosis, better known as LAP. Both autophagosomes and LAPosomes (LC3-associated phagosomes) deliver cargo for degradation. The use of fluorescent DQ™-BSA in conjugation with autophagic makers and biomarkers of hybrid autophagy offers a reliable technique to monitor the formation of autolysosomes and LAPo-lysosomes in both fixed- and live-cell studies. This technique relies on cleavage of the self-quenched DQ™ Green- or DQ™ Red BSA protease substrates in an acidic compartment to generate a highly fluorescent product.

Comparative Analysis and Validation of Different Steps in Glycomics Studies.

Abstract: Large-scale glycomics studies enable identification of aberrant glycosylation patterns in disease and provide information about functional relevance of individual glycans through genome-wide association studies. Developed high-throughput methodologies have to be sensitive, robust, and stable during long periods of time (few months) to be able to reliably detect small biological variations in glycosylation. Here, we describe a simple, robust, and affordable protocol for immunoglobulin G N-glycan analysis by hydrophilic interaction liquid chromatography–ultra-performance liquid chromatography (HILIC-UPLC), as well as useful strategies for method optimization: Plackett–Burman screening design and analysis of source of variation. We put our focus on experimental design for high-throughput glycan analysis, critical steps in sample preparation procedure for obtaining high-quality data, and propose a validation protocol relevant for high-throughput methods in terms of their long-term robustness and ability to detect biologically relevant changes in glycosylation. The quality of the procedure was assessed by employing appropriate experimental designs and subsequent statistical techniques.

Kinetic Deuterium Isotope Effects in Cytochrome P450 Reactions.

Abstract: Cytochrome P450 (P450, CYP) research provides many opportunities for the application of kinetic isotope effect (KIE) strategies. P450s collectively catalyze oxidations of more substrates than any other group of enzymes, and CH bond cleavage is a major feature in a large fraction of these reactions. The presence of a significant primary deuterium KIE is evidence that hydrogen abstraction is at least partially rate-limiting in the reactions, and this appears to be the case in many P450 reactions. The first report of a KIE in (P450-linked) drug metabolism appeared in 1961 (for morphine N-demethylation), and in a number of cases, it has been possible to modulate the in vivo metabolism or toxicity of chemicals by deuterium substitution. A number of efforts are in progress to utilize deuterium substitution to alter the metabolism of drugs in an advantageous manner.

Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination.

Abstract: Homologous recombination (HR) is a universally conserved DNA double-strand break repair pathway. Single-molecule fluorescence imaging approaches have revealed new mechanistic insights into nearly all aspects of HR. These methods are especially suited for studying protein complexes because multicolor fluorescent imaging can parse out subassemblies and transient intermediates that associate with the DNA substrates on the millisecond to hour timescales. However, acquiring single-molecule datasets remains challenging because most of these approaches are designed to measure one molecular reaction at a time. The DNA curtains platform facilitates high-throughput single-molecule imaging by organizing arrays of DNA molecules on the surface of a microfluidic flowcell. Here, we describe a second-generation UV lithography-based protocol for fabricating flowcells for DNA curtains. This protocol greatly reduces the challenges associated with assembling DNA curtains and paves the way for the rapid acquisition of large datasets from individual single-molecule experiments. Drawing on our recent studies of human HR, we also provide an overview of how DNA curtains can be used for observing facilitated protein diffusion, processive enzyme translocation, and nucleoprotein filament dynamics on single-stranded DNA. Together, these protocols and case studies form a comprehensive introduction for other researchers that may want to adapt DNA curtains for high-throughput single-molecule studies of DNA replication, transcription, and repair.

Single-Stranded DNA Curtains for Studying Homologous Recombination.

Abstract: Homologous recombination is an important pathway involved in the repair of double-stranded DNA breaks. Genetic studies form the foundation of our knowledge on homologous recombination. Significant progress has also been made toward understanding the biochemical and biophysical properties of the proteins, complexes, and reaction intermediates involved in this essential DNA repair pathway. However, heterogeneous or transient recombination intermediates remain extremely difficult to assess through traditional ensemble methods, leaving an incomplete mechanistic picture of many steps that take place during homologous recombination. To help overcome some of these limitations, we have established DNA curtain methodologies as an experimental platform for studying homologous DNA recombination in real-time at the single-molecule level. Here, we present a detailed overview describing the preparation and use of single-stranded DNA curtains in applications related to the study of homologous DNA recombination with emphasis on recent work related to the study of the eukaryotic recombinase Rad51.

Guide to the Preparation of Molecularly Imprinted Polymer Nanoparticles for Protein Recognition by Solid-Phase Synthesis.

Abstract: Molecularly imprinted polymers (MIPs) are synthetic antibody mimics possessing specific cavities designed for a target molecule. Nowadays, molecular imprinting of proteins still remains a challenge as the generation of selective imprinted cavities is extremely difficult, due to their flexible structure and the presence of a multitude of functional sites. To overcome this difficulty, we propose a solid-phase synthesis strategy to prepare MIPs specific for any protein that can be immobilized in an oriented way on a solid support. Trypsin and kallikrein were used as model proteins. The solid-phase support consists of glass beads functionalized with two affinity ligands of the enzymes, the competitive inhibitor p-aminobenzamidine to orient the enzymes via their active site, or a Cu2+chelate to orient via the surface histidine residues of the enzyme. Thermoresponsive molecularly imprinted polymer nanoparticles (MIP-NPs) are then synthesized around the immobilized enzyme. The MIP-NPs are released by a simple temperature change, resulting in protein-free polymers endowed with improved binding site homogeneity since all binding sites have the same orientation. The MIP-NPs exhibit apparent dissociation constants between 0.02 and 2nM toward their target proteins, which is comparable to those of natural antibodies. Moreover, these water-compatible polymers, targeting different domains of the enzyme, can also function as protective agents (armor), hence preventing the target proteins from denaturation by heat or pH.

Saposin-Lipoprotein Scaffolds for Structure Determination of Membrane Transporters.

Abstract: Membrane proteins depend on their natural lipid environment for function, which makes them more difficult to study in isolation. A number of approaches that mimic the lipid bilayer of biological membranes have been described (nanodiscs, SMALPs), enabling novel ways to assay activity and elucidate structures of this important class of proteins. More recently, the use of saposin A, a protein that is involved in lipid transport, to form Salipro (saposin-lipid-protein) complexes was demonstrated for a range of membrane protein targets (Frauenfeld et al., 2016). The method is fast and requires few resources. The saposin-lipid-scaffold adapts to various sizes of transmembrane regions during self-assembly, forming a minimal lipid nanoparticle. This results in the formation of a well-defined membrane protein-lipid complex, which is desirable for structural characterization. Here, we describe a protocol to reconstitute the sarco-endoplasmic reticulum calcium ATPase (SERCA) into Salipro nanoparticles. The complex formation is analyzed using negative stain electron microscopy (EM), allowing to quickly determine an initial structure of the membrane protein and to evaluate sample conditions for structural studies using single-particle cryo-EM in a detergent-free environment.

Posttranslational Modifications and Plant–Environment Interaction

Abstract: Posttranslational modifications (PTMs) of proteins such as phosphorylation and ubiquitination are crucial for controlling protein stability, localization, and conformation. Genetic information encoded in DNA is transcribed, translated, and increases its complexity by multiple PTMs. Conformational change introduced by PTMs affects interacting partners of each proteins and their downstream signaling; therefore, PTMs are the major level of modulations of total outcome of living cells. Plants are living in harsh environment that requires unremitting physiological modulation to survive, and the plant response to various environment stresses is regulated by PTMs of proteins. This review deals with the novel knowledge of PTM-focused proteomic studies on various life conditions. PTMs are focused that mediate plant-environment interaction such as stress perception, protein homeostasis, control of energy shift, and defense by immune system. Integration of diverse signals on a protein via multiple PTMs is discussed as well, considering current situation where signal integration became an emerging area approached by systems biology into account.

Secreted Phospholipase A2 Specificity on Natural Membrane Phospholipids

Abstract: The secreted phospholipase A2 (sPLA2) family contains 10 catalytically active isoforms. Current in vitro biochemical studies have shown that individual sPLA2s have distinct substrate selectivity in terms of the polar head groups or sn-2 fatty acids of their substrate phospholipids. Importantly, transgenic or knockout mice for distinct sPLA2s display nonoverlapping phenotypes, arguing that they do act on different phospholipid substrates and mobilize unique lipid metabolites in vivo. In an effort to comprehensively understand lipid metabolism driven by individual sPLA2s under pathophysiological conditions, we took advantages of mass spectrometric lipidomics technology to monitor the spatiotemporal changes in phospholipids (substrates) and products (fatty acids, lysophospholipids, and their metabolites) in tissues or cells of sPLA2-transgenic or knockout mice. The in vivo lipidomic data were compared with the in vitro activity of recombinant sPLA2s toward phospholipid mixtures extracted from the target tissues, cells, or extracellular membrane components on which sPLA2s may intrinsically act. These approaches reveal that the overall tendency in in vitro assays using natural membranes is recapitulated in several in vivo systems, often with even more selective patterns of hydrolysis. In this chapter, we will summarize current understanding of the in vivo substrate specificity of sPLA2s toward natural membrane phospholipids.

High-Resolution Optical Tweezers Combined With Single-Molecule Confocal Microscopy

Abstract: We describe the design, construction, and application of an instrument combining dual-trap, high-resolution optical tweezers and a confocal microscope. This hybrid instrument allows nanomechanical manipulation and measurement simultaneously with single-molecule fluorescence detection. We present the general design principles that overcome the challenges of maximizing optical trap resolution while maintaining single-molecule fluorescence sensitivity, and provide details on the construction and alignment of the instrument. This powerful new tool is just beginning to be applied to biological problems. We present step-by-step instructions on an application of this technique that highlights the instrument's capabilities, detecting conformational dynamics in a nucleic acid-processing enzyme.

Microneedle Enzyme Sensor Arrays for Continuous In Vivo Monitoring.

Abstract: Microneedle enzyme sensors by virtue of their minimally invasive and hence pain-free penetration of skin allow for the measurement of metabolites, biomarkers, and drugs in the interstitial fluid that bathes the dermal tissue. Such devices if they are to be adopted widely into clinical practice need to be capable of delivering reliable measurements over extended periods of time (days) and to be fabricated by low-cost, scalable methods. Using injection molding of the base structures in polycarbonate, metal film deposition by sputtering and enzyme immobilization by electrodeposition can meet these requirements. The workflow to produce devices for clinical evaluation is then completed by sterilization and packaging. In vitro evaluation of the sensors' response to varying analyte concentrations and their mechanical testing establish performance and safety characteristics. While most of the work is focused on glucose sensing, reflecting the significance of the global diabetes "epidemic," the microneedles can also be used to measure lactate (another metabolite) and theophylline (a therapeutic drug).

Application of CRISPR/Cas9 to Autophagy Research.

Abstract: The ability to efficiently modulate autophagy activity is paramount in the study of the field. Conventional broad-range autophagy inhibitors and genetic manipulation using RNA interference (RNAi), although widely used in autophagy research, are often limited in specificity or efficacy. In this chapter, we address the problems of conventional autophagy-modulating tools by exploring the use of three different CRISPR/Cas9 systems to abrogate autophagy in numerous human and mouse cell lines. The first system generates cell lines constitutively deleted of ATG5 or ATG7 whereas the second and third systems express a Tet-On inducible-Cas9 that enables regulated deletion of ATG5 or ATG7. We observed the efficiency of autophagy inhibition using the CRISPR/Cas9 strategy to surpass that of RNAi, and successfully generated cells with complete and sustained autophagy disruption through the CRISPR/Cas9 technology.

Dynamics of Atg5-Atg12-Atg16L1 Aggregation and Deaggregation.

Abstract: Macroautophagy is a physiological process that is implicated in various pathological conditions, including neurodegenerative diseases and cancer. The execution of canonical autophagy is regulated by a core signaling cascade and it involves two well-characterized, ubiquitin-like conjugation systems-the Atg5/Atg12/Atg16L1 and the Atg8-phosphatidyl ethanolamine (PE), which are both catalyzed by Atg7. The conjugation of Atg5-Atg12 and the subsequent interaction with the positive regulator Atg16L1 are essential for the conjugation of Atg8 to PE and the subsequent formation of autophagosomes. The interaction between Atg5-Atg12 complex and Atg16L1 is highly dynamic, induced upon activation of the autophagic process, and required for the recruitment of the At5-Atg12 complex to sites of autophagosome formation. Monitoring the Atg5-Atg12-Atg16L1 aggregation and deaggregation may be used not only as means to study the dynamics of autophagy, but in another important point, it may provide important insights on the basic molecular mechanisms of autophagy in physiological and pathological settings. In this chapter, we describe methods of monitoring the Atg5-Atg12-Atg16L1 aggregation and deaggregation, with emphasis on prostate cancer.

Functional Analysis of Mitochondrial CB1 Cannabinoid Receptors (mtCB1) in the Brain.

Abstract: Recent evidence indicates that, besides its canonical localization at cell plasma membranes, the type-1 cannabinoid receptor, CB1 is functionally present at brain and muscle mitochondrial membranes (mtCB1). Through mtCB1 receptors, cannabinoids can directly regulate intramitochondrial signaling and respiration. This new and surprising discovery paves the way to new potential fields of research, dealing with the direct impact of G protein-coupled receptors on bioenergetic processes and its functional implications. In this chapter, we summarize some key experimental approaches established in our laboratories to identify anatomical, biochemical, and functional features of mtCB1 receptors in the brain. In particular, we describe the procedures to obtain reliable and controlled detection of mtCB1 receptors by immunogold electromicroscopy and by immunoblotting methods. Then, we address the study of direct cannabinoid effects on the electron transport system and oxidative phosphorylation. Finally, we present a functional example of the impact of mtCB1 receptors on mitochondrial mobility in cultured neurons. Considering the youth of the field, these methodological approaches will very likely be improved and refined in the future, but this chapter aims at presenting the methods that are currently used and, in particular, at underlining the need of rigorous controls to obtain reliable results. We hope that this chapter might help scientists becoming interested in this new and exciting field of research.