Protein analysis by SDS-PAGE and detection by Coomassie blue or silver staining

Expression of Untagged Arrestins in E. coli and Their Purification

Purified arrestin proteins are necessary for biochemical, biophysical, and structural studies of these versatile regulators of cell signaling. Described herein is a basic protocol for arrestin expression in Escherichia coli and purification of tag-free wild-type and mutant arrestins. The method includes ammonium sulfate precipitation of arrestins from cell lysates, followed by Heparin-Sepharose chromatography. Depending on the arrestin type and/or mutations, the next step is Q-Sepharose or SP-Sepharose chromatography. In many cases, the nonbinding column is used as a filter to bind contaminants without retaining arrestin. In some cases, both chromatographic steps must be performed sequentially to achieve high purity. Purified arrestins can be concentrated up to 10 mg/ml, remain fully functional, and withstand several cycles of freezing and thawing, provided that the overall salt concentration is maintained at or above physiological levels. © 2023 Wiley Periodicals LLC. Basic Protocol: Large-scale expression and purification of arrestins Alternate Protocol: Purification of arrestin-3 and truncated form of arrestin-1-(1-378) Support Protocol: Small-scale test expression of wild-type and mutant arrestins in E. coli.

Arrestin-3-Dependent Activation of c-Jun N-Terminal Kinases (JNKs)

Only 1 out of 4 mammalian arrestin subtypes, arrestin-3, facilitates the activation of c-Jun N-terminal kinase (JNK) family kinases. Here, we describe two different sets of protocols used for elucidating the mechanisms involved. One is based on reconstitution of signaling modules from the following purified proteins: arrestin-3, MKK4, MKK7, JNK1, JNK2, and JNK3. The main advantage of this method is that it unambiguously establishes which effects are direct because only intended purified proteins are present in these assays. The key drawback is that the upstream-most kinases of these cascades, ASK1 or other MAP3Ks, are not available in purified form, limiting reconstitution to incomplete two-kinase modules. The other approach is used for analyzing the effects of arrestin-3 on JNK activation in intact cells. In this case, signaling modules include ASK1 and/or other MAP3Ks. However, as every cell expresses thousands of different proteins, their possible effects on the readout cannot be excluded. Nonetheless, the combination of in vitro reconstitution from purified proteins and cell-based assays makes it possible to elucidate the mechanisms of arrestin-3-dependent activation of JNK family kinases. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Construction of arrestin-3-scaffolded MKK4/7-JNK1/2/3 signaling modules in vitro using purified proteins Alternate Protocol 1: Characterization of arrestin-3-mediated JNK1/2 activation by MKK4/7 by measurement of JNK1/2 phosphorylation using immunoblotting with anti-phospho-JNK antibody Support Protocol 1: Expression, purification, and activation of GST-MKK4 Support Protocol 2: Expression, purification, and activation of GST-MKK7-His6 Support Protocol 3: Expression, purification, and activation of tagless JNK1Α1 Support Protocol 4: Expression, purification, and activation of tagless JNK2Α2 Basic Protocol 2: Analysis of the role of arrestin-3 in ASK1/MKK4/MKK7-induced JNK activation in intact cells Alternate Protocol 2: Analysis of the role of arrestin-3 in MKK4-induced JNK activation in intact cells Basic Protocol 3: Characterization of the biphasic effect of arrestin-3 on ASK1/MKK7-stimulated JNK phosphorylation in cells.

Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates (K-BILDS)

Protein phosphorylation is catalyzed by kinases to regulate a large variety of cellular activities, including growth and signal transduction. Methods to identify kinase substrates are crucial to fully understand phosphorylation-mediated cellular events and disease states. Here, we report a set of protocols to identify substrates of a target kinase using Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates (K-BILDS). As described in these protocols, K-BILDS involves inactivation of endogenous kinases in lysates, followed by addition of an active exogenous kinase and the γ-phosphate-modified ATP analog ATP-biotin for kinase-catalyzed biotinylation of cellular substrates. Avidin enrichment isolates biotinylated substrates of the active kinase, which can be monitored by western blot. Substrates of the target kinase can also be discovered using mass spectrometry analysis. Key advantages of K-BILDS include compatibility with any lysate, tissue homogenate, or complex mixture of biological relevance and any active kinase of interest. K-BILDS is a versatile method for studying or discovering substrates of a kinase of interest to characterize biological pathways thoroughly. © 2023 Wiley Periodicals LLC. Basic Protocol 1: FSBA treatment of lysates to inactivate kinases Basic Protocol 2: Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates (K-BILDS).

Recombinant expression and characterization of a new laccase, bioinformatically identified, from the Antarctic thermophilic bacterium Geobacillus sp. ID17

Geobacillus sp. ID17 is a gram-positive thermophilic bacterium isolated from Deception Island, Antarctica, which has shown to exhibit remarkable laccase activity in crude extract at high temperatures. A bioinformatic search using local databases led to the identification of three putative multicopper oxidase sequences in the genome of this microorganism. Sequence analysis revealed that one of those sequences contains the four-essential copper-binding sites present in other well characterized laccases. The gene encoding this sequence was cloned and overexpressed in Escherichia coli, partially purified and preliminary biochemically characterized. The resulting recombinant enzyme was recovered in active and soluble form, exhibiting optimum copper-dependent laccase activity at 55 °C, pH 6.5 with syringaldazine substrate, retaining over 60% of its activity after 1 h at 55 and 60 °C. In addition, this thermophilic enzyme is not affected by common inhibitors SDS, NaCl and L-cysteine. Furthermore, biodecolorization assays revealed that this laccase is capable of degrading 60% of malachite green, 54% of Congo red, and 52% of Remazol Brilliant Blue R, after 6 h at 55 °C with aid of ABTS as redox mediator. The observed properties of this enzyme and the relatively straightforward overexpression and partial purification of it could be of great interest for future biotechnology applications.

Cloning and characterization of nitrate reductase gene in kelp Saccharina japonica (Laminariales, Phaeophyta)

BACKGROUND

Brown macroalgae dominate temperate coastal ecosystems, and their productivity is typically limited by nitrate availability. As an economically important kelp, Saccharina japonica is the most productive farmed seaweed and needs to be supplemented with sufficient nitrate throughout the cultivation process. However, molecular characterization of genes involved in nitrogen assimilation has not been conducted in brown macroalgae.

RESULTS

Here, we described the identification of the nitrate reductase (NR) gene from S. japonica (SjNR). Using two different cloning methods for SjNR, i.e. rapid amplification of cDNA ends (RACE) and cDNA cloning alone, a single fragment was obtained respectively. According to results of sequence analysis between these two fragments, the tentative coding sequence in two clones, SjNR-L and SjNR-S, were suggested to represent two transcripts of the single copy SjNR, and the ATG of SjNR-S was located inside the third exon of SjNR-L. In the 5' upstream sequence of each transcript, promoter core elements, response elements, especially multiple N response elements which occurred in microalgal NR, were all predicted. Further sequence analysis revealed that both transcripts encoded all five domains conserved in eukaryotic plant NRs. RT-qPCR results showed that the transcription level of SjNR in juvenile sporophytes could be significantly induced by nitrate and inhibited by ammonium, which was in line with plant NRs. The recombinant SjNR-L and SjNR-S were all proved to have NR activity, suggesting that the single-copy gene SjNR might be regulated on transcription level based on alternative promoters and multiple transcriptional start sites. Moreover, both NADH and NADPH were found to be able to act as electron donors for SjNR alone, which is the first confirmation that brown algal NR has a NAD(P)H-bispecific form.

CONCLUSION

These results will provide a scientific basis for understanding the N demand of kelp in various stages of cultivation and evaluating the environmental remediation potential of kelp in eutrophic sea areas.

Histone Acid Extraction and High Throughput Mass Spectrometry to Profile Histone Modifications in Arabidopsis thaliana

Histone post-translational modifications (PTMs) play important roles in many biological processes, including gene regulation and chromatin dynamics, and are thus of high interest across many fields of biological research. Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is a powerful tool to profile histone PTMs in vivo. This method, however, is largely dependent on the specificity and availability of suitable commercial antibodies. While mass spectrometry (MS)-based proteomic approaches to quantitatively measure histone PTMs have been developed in mammals and several other model organisms, such methods are currently not readily available in plants. One major challenge for the implementation of such methods in plants has been the difficulty in isolating sufficient amounts of pure, high-quality histones, a step rendered difficult by the presence of the cell wall. Here, we developed a high-yielding histone extraction and purification method optimized for Arabidopsis thaliana that can be used to obtain high-quality histones for MS. In contrast to other methods used in plants, this approach is relatively simple, and does not require membranes or additional specialized steps, such as gel excision or chromatography, to extract highly purified histones. We also describe methods for producing MS-ready histone peptides through chemical labeling and digestion. Finally, we describe an optimized method to quantify and analyze the resulting histone PTM data using a modified version of EpiProfile 2.0 for Arabidopsis. In all, the workflow described here can be used to measure changes to histone PTMs resulting from various treatments, stresses, and time courses, as well as in different mutant lines. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Nuclear isolation and histone acid extraction Basic Protocol 2: Peptide labeling, digestion, and desalting Basic Protocol 3: Histone HPLC-MS/MS and data analysis.

From the Discovery of Extremozymes to an Enzymatic Product: Roadmap Based on Their Applications

With the advent of the industrial revolution, the use of toxic compounds has grown exponentially, leading to a considerable pollution of the environment. Consequently, the development of more environmentally conscious technologies is an urgent need. Industrial biocatalysis appears as one potential solution, where a higher demand for more robust enzymes aims to replace toxic chemical catalysts. To date, most of the commercially available enzymes are of mesophilic origin, displaying optimal activity in narrow ranges of temperature and pH (i.e., between 20°C and 45°C, neutral pH), limiting their actual application under industrial reaction settings, where they usually underperform, requiring larger quantities to compensate loss of activity. In order to obtain novel biocatalysts better suited for industrial conditions, an efficient solution is to take advantage of nature by searching and discovering enzymes from extremophiles. These microorganisms and their macromolecules have already adapted to thrive in environments that present extreme physicochemical conditions. Hence, extremophilic enzymes stand out for showing higher activity, stability, and robustness than their mesophilic counterparts, being able to carry out reactions at nonstandard conditions. In this brief research report we describe three examples to illustrate a stepwise strategy for the development and production of commercial extremozymes, including a catalase from an Antarctic psychrotolerant microorganism, a laccase from a thermoalkaliphilic bacterium isolated from a hot spring and an amine-transaminase from a thermophilic bacterium isolated from a geothermal site in Antarctica. We will also explore some of their interesting biotechnological applications and comparisons with commercial enzymes.

Native Isolation of 3×HA-Tagged Protein Complexes to Characterize Protein-Protein Interactions

Co-immunoprecipitation (Co-IP) is a straightforward method that is widely used in studying direct protein-protein interactions in physiological environments. This technique is based on the antigen-antibody interaction: the protein of interest (bait) is captured by a specific antibody, followed by antibody-bait precipitation. The proteins interacting with the bait protein (prey) co-precipitate with the antibody-bait complex from a cell lysate as an antibody-bait/prey complex. Nowadays, a variety of surface-functionalized materials with antibodies immobilized on agarose or magnetic beads are available, replacing the precipitation of antibodies and simplifying the application. However, unspecific binding of cellular proteins to matrix surfaces and/or antibodies has become a common issue. Unspecific binding that leads to false-positive signals and a high background can hamper further analysis. Our protocol describes a strategy to tremendously reduce unspecific background when isolating native proteins and protein complexes. Instead of eluting our samples under denaturing conditions, we elute triple hemagglutinin (3×HA)-tagged bait/prey complexes in their native form with a competitive peptide simulating the 3×HA tag of the bait protein. Matrix-unspecific interacting proteins and Co-IP antibodies remain on the matrix instead of being eluted under conventionally applied denaturing conditions. We optimized the elution by altering incubation time, eluent concentration, and temperature. These improvements result in more pure proteins. This strategy not only reduces background in SDS-PAGE and western blot but also allows complex characterization in vitro. © 2021 Wiley Periodicals LLC.

At-Line Reversed Phase Liquid Chromatography for In-Process Monitoring of Inclusion Body Solubilization

Refolding is known as the bottleneck in inclusion body (IB) downstream processing in the pharmaceutical industry: high dilutions leading to large operating volumes, slow refolding kinetics and low refolding yields are only a few of the problems that impede industrial application. Solubilization prior to refolding is often carried out empirically and the effects of the solubilizate on the subsequent refolding step are rarely investigated. The results obtained in this study, however, indicate that the quality of the IB solubilizate has a severe effect on subsequent refolding. As the solubilizate contains chaotropic reagents in high molarities, it is commonly analyzed with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). SDS-PAGE, however, suffers from a long analysis time, making at-line analytical implementation difficult. In this study, we established an at-line reversed phase liquid chromatography method to investigate the time-dependent quality of the solubilizate. To verify the necessity of at-line solubilization monitoring, we varied the essential solubilization conditions for horseradish peroxidase IBs. The solubilization time was found to have a major influence on subsequent refolding, underlining the high need for an at-line analysis of solubilization. Furthermore, we used the developed reversed phase liquid chromatography method for an in-process control (IPC). In conclusion, the presented reversed phase liquid chromatography method allows a proper control of IB solubilization applicable for tailored refolding.

Mapping Interactions between Glycans and Glycan-Binding Proteins by Live Cell Proximity Tagging

Interactions between glycans and glycan-binding proteins (GBPs) consist of weak, noncovalent, and transient binding events, making them difficult to study in live cells void of a static, isolated system. Furthermore, the glycans are often presented as protein glycoconjugates, but there are limited efforts to identify these proteins. Proximity labeling permits covalent tagging of the glycoprotein interactors to query GBP in live cells. Coupled with high-resolution mass spectrometry, it facilitates determination of the proteins bearing the interacting glycans. In this method, fusion protein constructs of a GBP of interest with a peroxidase enzyme allows for in situ spatiotemporal radical-mediated tagging of interacting glycoproteins in living cells that can be enriched for identification. Using this method, the capture and study of glycan-GBP interactions no longer relies on weak, transient interactions, and results in robust capture and identification of the interactome of a GBP while preserving the native cellular environment. This protocol focuses on (1) expression and characterization of a recombinant fusion protein consisting of a peroxidase and the GBP galectin-3, (2) corresponding in situ labeling and visualization of interactors, (3) and proteomic workflow and analysis of captured proteins for robust identification using mass spectrometry. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Expression, purification, and characterization of recombinant fusion protein Alternate Protocol 1: Manual Ni-NTA purification of recombinant fusion protein Basic Protocol 2: In situ proximity labeling and evaluation by fluorescence microscopy Alternate Protocol 2: Western blot analysis of in situ proximity labeling Basic Protocol 3: Proximity labeling of cells for quantitative MS-based proteomics with tandem mass tags.

Methods for Rapid Protein Depletion in C. elegans using Auxin-Inducible Degradation

Numerous methods have been developed in model systems to deplete or inactivate proteins to elucidate their functional roles. In Caenorhabditis elegans, a common method for protein depletion is RNA interference (RNAi), in which mRNA is targeted for degradation. C. elegans is also a powerful genetic organism, amenable to large-scale genetic screens and CRISPR-mediated genome editing. However, these approaches largely lead to constitutive inhibition, which can make it difficult to study proteins essential for development or to dissect dynamic cellular processes. Thus, there have been recent efforts to develop methods to rapidly inactivate or deplete proteins to overcome these barriers. One such method that is proving to be exceptionally powerful is auxin-inducible degradation. In order to apply this approach in C. elegans, a 44-amino acid degron tag is added to the protein of interest, and the Arabidopsis ubiquitin ligase TIR1 is expressed in target tissues. When the plant hormone auxin is added, it mediates an interaction between TIR1 and the degron-tagged protein of interest, which triggers ubiquitination of the protein and its rapid degradation via the proteasome. Here, we have outlined multiple methods for inducing auxin-mediated depletion of target proteins in C. elegans, highlighting the versatility and power of this method. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Long-term auxin-mediated depletion on plates Support Protocol: Preparation of NGM and NGM-auxin plates Basic Protocol 2: Rapid auxin-mediated depletion via soaking Basic Protocol 3: Acute auxin-mediated depletion in isolated embryos Basic Protocol 4: Assessing auxin-mediated depletion.