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Current Opinion in Biotechnology Apr 2016Environmental biotechnology relies on the exploration of novel biological systems and a thorough understanding of the underlying molecular mechanisms. Next-generation... (Review)
Review
Environmental biotechnology relies on the exploration of novel biological systems and a thorough understanding of the underlying molecular mechanisms. Next-generation proteomics based on the latest generation of mass analyzers currently allows the recording of complete proteomes from any microorganism. Interpreting these data can be straightforward if the genome of the organism is established, or relatively easy to perform through proteogenomics approaches if a draft sequence can be obtained. However, next-generation proteomics faces new, interesting challenges when the organism is distantly related to previously characterized organisms or when mixtures of organisms have to be analyzed. New mass spectrometers and innovative bioinformatics tools are reshaping the possibilities of homology-based proteomics, proteogenomics, and metaproteomics for the characterization of biological systems. Novel time- and cost-effective screening strategies are also possible with this methodology, as exemplified by whole proteome thermal profiling and subpopulation proteomics. The complexity of environmental samples allows for unique developments of approaches and concepts.
Topics: Animals; Biotechnology; Genome; Proteome; Proteomics
PubMed: 26950175
DOI: 10.1016/j.copbio.2016.02.025 -
Journal of Biochemistry Dec 2021Recent advances in biotinylation-based proximity labelling (PL) have opened up new avenues for mapping the protein composition of cellular compartments and protein... (Review)
Review
Recent advances in biotinylation-based proximity labelling (PL) have opened up new avenues for mapping the protein composition of cellular compartments and protein complexes in living cells at high spatiotemporal resolution. In particular, PL combined with mass spectrometry-based proteomics has been successfully applied to defining protein-protein interactions, protein-nucleic acid interactions, (membraneless) organelle proteomes and secretomes in various systems ranging from cultured cells to whole animals. In this review, we first summarize the basics and recent biological applications of PL proteomics and then highlight recent developments in enrichment techniques for biotinylated proteins and peptides, focusing on the advantages of PL and technical considerations.
Topics: Animals; Biotinylation; Humans; Mass Spectrometry; Organelles; Protein Binding; Protein Interaction Maps; Proteome; Proteomics; Secretome
PubMed: 34752609
DOI: 10.1093/jb/mvab123 -
Chembiochem : a European Journal of... May 2022The mitochondrion is the core site of cell signaling, energy metabolism and biosynthesis. Here, taking advantage of activity-based probes, we synthesized two...
The mitochondrion is the core site of cell signaling, energy metabolism and biosynthesis. Here, taking advantage of activity-based probes, we synthesized two photocontrollable probes (YGH-1 and YGH-2), composed of a mitochondrial localization moiety "triphenylphosphonium", a photo-triggered group to achieve spatially and temporally controlled protein capture, and an alkyne group to enrich the labeled protein. Proteomic validation was further carried out to facilitate identification of the mitochondrial proteome in HeLa cells. The results show that half of the identified protein hits (∼300) labeled by YGH-1 and YGH-2 belong to mitochondria, and are mostly localized in the mitochondrial matrix and inner mitochondrial membrane. Our results provide a new tool for spatial and temporal analysis of subcellular proteomes.
Topics: HeLa Cells; Humans; Mitochondria; Mitochondrial Proteins; Proteome; Proteomics
PubMed: 35344259
DOI: 10.1002/cbic.202200066 -
Nature Communications Aug 2022Enzymatic-based proximity labeling approaches based on activated esters or phenoxy radicals have been widely used for mapping subcellular proteome and protein...
Enzymatic-based proximity labeling approaches based on activated esters or phenoxy radicals have been widely used for mapping subcellular proteome and protein interactors in living cells. However, activated esters are poorly reactive which leads to a wide labeling radius and phenoxy radicals generated by peroxide treatment may disturb redox-sensitive pathways. Herein, we report a photoactivation-dependent proximity labeling (PDPL) method designed by genetically attaching photosensitizer protein miniSOG to a protein of interest. Triggered by blue light and tunned by irradiation time, singlet oxygen is generated, thereafter enabling spatiotemporally-resolved aniline probe labeling of histidine residues. We demonstrate its high-fidelity through mapping of organelle-specific proteomes. Side-by-side comparison of PDPL with TurboID reveals more specific and deeper proteomic coverage by PDPL. We further apply PDPL to the disease-related transcriptional coactivator BRD4 and E3 ligase Parkin, and discover previously unknown interactors. Through over-expression screening, two unreported substrates Ssu72 and SNW1 are identified for Parkin, whose degradation processes are mediated by the ubiquitination-proteosome pathway.
Topics: Esters; Nuclear Proteins; Proteome; Proteomics; Transcription Factors; Ubiquitin-Protein Ligases
PubMed: 35987950
DOI: 10.1038/s41467-022-32689-z -
Proteomics. Clinical Applications Feb 2015Owing to recent advances in proteomics analytical methods and bioinformatics capabilities there is a growing trend toward using these capabilities for the development of... (Review)
Review
Owing to recent advances in proteomics analytical methods and bioinformatics capabilities there is a growing trend toward using these capabilities for the development of drugs to treat human disease, including target and drug evaluation, understanding mechanisms of drug action, and biomarker discovery. Currently, the genetic sequences of many major organisms are available, which have helped greatly in characterizing proteomes in model animal systems and humans. Through proteomics, global profiles of different disease states can be characterized (e.g. changes in types and relative levels as well as changes in PTMs such as glycosylation or phosphorylation). Although intracellular proteomics can provide a broad overview of physiology of cells and tissues, it has been difficult to quantify the low abundance proteins which can be important for understanding the diseased states and treatment progression. For this reason, there is increasing interest in coupling comparative proteomics methods with subcellular fractionation and enrichment techniques for membranes, nucleus, phosphoproteome, glycoproteome as well as low abundance serum proteins. In this review, we will provide examples of where the utilization of different proteomics-coupled enrichment techniques has aided target and biomarker discovery, understanding the drug targeting mechanism, and mAb discovery. Taken together, these improvements will help to provide a better understanding of the pathophysiology of various diseases including cancer, autoimmunity, inflammation, cardiovascular disease, and neurological conditions, and in the design and development of better medicines for treating these afflictions.
Topics: Animals; Chromatography, Affinity; Disease; Humans; Proteins; Proteome; Proteomics
PubMed: 25523641
DOI: 10.1002/prca.201400097 -
International Journal of Molecular... Feb 2024The liver is the central metabolic organ and produces 85-90% of the proteins found in plasma. Accordingly, the plasma proteome is an attractive source of liver disease... (Review)
Review
The liver is the central metabolic organ and produces 85-90% of the proteins found in plasma. Accordingly, the plasma proteome is an attractive source of liver disease biomarkers that reflects the different cell types present in this organ, as well as the processes such as responses to acute and chronic injury or the formation of an extracellular matrix. In the first part, we summarize the biomarkers routinely used in clinical evaluations and their biological relevance in the different stages of non-malignant liver disease. Later, we describe the current proteomic approaches, including mass spectrometry and affinity-based techniques, that allow a more comprehensive assessment of the liver function but also require complex data processing. The many approaches of analysis and interpretation and their potential caveats are delineated. While these advances hold the promise to transform our understanding of liver diseases and support the development and validation of new liver-related drugs, an interdisciplinary collaboration is needed.
Topics: Humans; Proteome; Proteomics; Biomarkers; Liver Diseases
PubMed: 38396688
DOI: 10.3390/ijms25042008 -
Proteomics Feb 2015There is increasing realisation that human health status in adulthood depends critically upon environmental conditions pertaining around the time of conception and... (Review)
Review
There is increasing realisation that human health status in adulthood depends critically upon environmental conditions pertaining around the time of conception and during pregnancy. Poor maternal diet or adverse environmental conditions around the periconception period somehow induces the resultant embryo to adapt predictively in order to survive this level of stress for the whole of its life. However, if there is a mismatch between expectation and reality, where the conditions during later life are better than expected, things go wrong and the adult suffers a range of illnesses, including diabetes, heart disease, hypertension and stroke. Understanding the molecular signals that direct the early embryo to adopt appropriate adaptations to suit its future life would be extremely valuable. However, although it appears to be an ideal task for proteomic applications, there are technical, ethical and practical limitations to what can be achieved with the current framework of proteomic technology. Here, we review what has been achieved to date, explain some of the experimental problems and suggest some strategies for taking this field forward.
Topics: Animals; Female; Fertilization; Humans; Mice; Pregnancy; Proteome; Proteomics
PubMed: 25404351
DOI: 10.1002/pmic.201400362 -
Current Opinion in Chemical Biology Feb 2017Cells alter the proteome to respond to environmental and developmental cues. Global analysis of proteomic responses is of limited value in heterogeneous environments,... (Review)
Review
Cells alter the proteome to respond to environmental and developmental cues. Global analysis of proteomic responses is of limited value in heterogeneous environments, where there is no 'average' cell. Advances in sequencing, protein labeling, mass spectrometry, and data analysis have fueled recent progress in the investigation of specific subpopulations of cells in complex systems. Here we highlight recently developed chemical tools that enable cell-selective proteomic analysis of complex biological systems, from bacterial pathogens to whole animals.
Topics: Animals; Bacteria; Cell Line; Humans; Mass Spectrometry; Protein Biosynthesis; Proteins; Proteome; Proteomics
PubMed: 28088696
DOI: 10.1016/j.cbpa.2016.12.026 -
Proteomics Mar 2023In mass spectrometry (MS)-based bottom-up proteomics, protease digestion plays an essential role in profiling both proteome sequences and post-translational... (Review)
Review
In mass spectrometry (MS)-based bottom-up proteomics, protease digestion plays an essential role in profiling both proteome sequences and post-translational modifications (PTMs). Trypsin is the gold standard in digesting intact proteins into small-size peptides, which are more suitable for high-performance liquid chromatography (HPLC) separation and tandem MS (MS/MS) characterization. However, protein sequences lacking Lys and Arg cannot be cleaved by trypsin and may be missed in conventional proteomic analysis. Proteases with cleavage sites complementary to trypsin are widely applied in proteomic analysis to greatly improve the coverage of proteome sequences and PTM sites. In this review, we survey the common and newly emerging proteases used in proteomics analysis mainly in the last 5 years, focusing on their unique cleavage features and specific proteomics applications such as missing protein characterization, new PTM discovery, and de novo sequencing. In addition, we summarize the applications of proteases in structural proteomics and protein function analysis in recent years. Finally, we discuss the future development directions of new proteases and applications in proteomics.
Topics: Peptide Hydrolases; Proteomics; Amino Acid Sequence; Structure-Activity Relationship; Proteome; Humans; Sequence Analysis, Protein; Protein Conformation
PubMed: 36382392
DOI: 10.1002/pmic.202200132 -
Proteomics Sep 2020Animal venoms are renowned for their toxicity, biochemical complexity, and as a source of compounds with potential applications in medicine, agriculture, and industry.... (Review)
Review
Animal venoms are renowned for their toxicity, biochemical complexity, and as a source of compounds with potential applications in medicine, agriculture, and industry. Polypeptides underlie much of the pharmacology of animal venoms, and elucidating these arsenals of polypeptide toxins-known as the venom proteome or venome-is an important step in venom research. Proteomics is used for the identification of venom toxins, determination of their primary structure including post-translational modifications, as well as investigations into the physiology underlying their production and delivery. Advances in proteomics and adjacent technologies has led to a recent upsurge in publications reporting venom proteomes. Improved mass spectrometers, better proteomic workflows, and the integration of next-generation sequencing of venom-gland transcriptomes and venomous animal genomes allow quicker and more accurate profiling of venom proteomes with greatly reduced starting material. Technologies such as imaging mass spectrometry are revealing additional insights into the mechanism, location, and kinetics of venom toxin production. However, these numerous new developments may be overwhelming for researchers designing venom proteome studies. Here, the field of venom proteomics is reviewed and some practical solutions for simplifying mass spectrometry workflows to study animal venoms are offered.
Topics: Animals; Mass Spectrometry; Proteome; Proteomics; Transcriptome; Venoms
PubMed: 32820606
DOI: 10.1002/pmic.201900324