Regulators of Signal Transduction: Families of GTP-Binding Proteins
Robert I. Glazer in Developments in Cancer Chemotherapy, 2019
Each α subunit contains a single high-affinity binding site for guanine nucleotides. They also have an intrinsic ability to catalyze the hydrolysis of GTP and when purified contain tightly bound GDP. Each α subunit is a substrate for at least one of the bacterial toxins, cholera, or pertussis toxin. cDNA cloning and sequencing of these four α subunits has been performed in several laboratories.12-19 When the amino acid sequences are aligned a high degree of homology is apparent. The results strongly suggest the presence of additional G-protein a subunits beyond the four listed previously. Whether these represent multiple genes of a single G-protein (isoforms) or additional structurally related but distinct G-proteins remains to be detemined. The extent to which these structurally related proteins can cross-react functionally is an important question which needs to be addressed in greater detail experimentally.
Molecular Biology of the Amelogenin Gene
Colin Robinson, Jennifer Kirkham, Roger Shore in Dental Enamel, 2017
The significance of alternative processing of mRNA transcripts in general has been reviewed by a number of workers.62-70 A general feature of alternative splicing is that it produces protein isoforms that share extensive regions of structural identity but differ in specific domains. Seven modes of alternative splicing have been described.66 Only two of these appear to be used in the splicing of amelogenin transcripts: alternative 3′-splice sites and exon skipping. Regulated alternative splicing is now known to be a common mechanism for adjusting gene expression and complements effectors of promoter activity. The amelogenin gene is tightly regulated and displays a highly restricted pattern of expression. Although the gene is present in all tissues it is transcribed only by cells derived from the enamel organ epithelia.6,7 Promoter activation is synchronized with the initial secretion of predentine.71 Although the mechanism of transcriptional regulation of the amelogenin gene is unknown it is likely to involve a complex of upstream regulatory elements and their corresponding DNA-binding proteins. Regulated alternative splicing of amelogenin transcripts may offer a posttranscriptional mechanism to increase the synthesis of certain amelogenin isoforms, while simultaneously reducing the production of others. Such a system is potentially more responsive to changes in the composition of the enamel matrix and diminishes the regulatory burden of the promoter region.
Changes in Gene Expression During Aging of Mammals
Alvaro Macieira-Coelho in Molecular Basis of Aging, 2017
Alternative splicing of pre-mRNA is known to produce different mRNAs that are translated into different isoforms of a protein. Most pre-mRNAs transcribed from split genes are spliced in such a way that the original order of arrangement of the exons are maintained in the mature mRNAs. This is constitutive splicing. Some pre-mRNAs, however, are spliced in more than one way, thereby yielding a family of structurally related mRNAs that are translated into a family of protein isoforms. This is alternative splicing. Such splicing is seen in all organisms including humans, and occurs in several types of transcripts that encode varieties of proteins. This is a means of diversifying the output from a single gene without altering its genomic organization. In some cases, alternatively spliced mRNAs are produced concurrently in the same tissue, and several protein isoforms may perform the same or different functions. For example, four myelin basic protein isoforms derived from a single gene are all components of the myelin sheath. Some gene transcripts are spliced differently in different tissues. For example, the single mammalian calcitonin gene expresses calcitonin in the thyroid, but in the brain a different isoform is produced by a separate splicing pattern.
Chaperonomics in leptospirosis
Published in Expert Review of Proteomics, 2018
Arada Vinaiphat, Visith Thongboonkerd
Based on the availability of complete genome databases of several organisms, general strategy for chaperonomics frequently starts from identification and characterizations of the entire conserved sequences of chaperones, followed by investigations of spatial/temporal changes in their gene/transcript/protein expression profiles under interventions as well as their interactions. Further elucidation of gene products (RNA or proteins), such as alternative splicing that give rise to protein isoforms and/or post-translational modifications, can be also conducted [67]. Functional investigations, e.g., by knockdown, overexpression, chemical inhibition, etc., are finally required to obtain more complete information of the functional roles of chaperones. This implementation of analysis at the gene, transcript, or protein level, and on interactions among these components, is essential, considering functional complexity that will be generated from this large pool of the chaperone genome, transcriptome, proteome, and interactome datasets.
Proteomics for cancer drug design
Published in Expert Review of Proteomics, 2019
Amanda Haymond, Justin B. Davis, Virginia Espina
A mindset transformation needs to occur in drug discovery for drug developers, scientists, investors, and clinicians. We need to discard the concepts of ‘one hit wonder drugs’ and ‘one drug/one target’. These concepts are naïve assumptions and fail to account for biological variability between individuals as well as similarities between protein motifs and ligand binding domains. Alternative splicing of mRNA creates various protein isoforms, which are not routinely profiled in clinical specimens. The biological redundancy in protein motifs and ligand binding domains potentially creates specificity issues for drugs and small peptides. Characterizing functional phenotypes of individual cancer specimens, utilizing the full spectrum of proteomics technologies, will eventually permit true designer drug for individualized cancer treatments.
Targeted therapy in acute myeloid leukemia: current status and new insights from a proteomic perspective
Published in Expert Review of Proteomics, 2020
Anneke D. van Dijk, Eveline S. J. M. de Bont, Steven M. Kornblau
based proteomics is a well-established technique and commonly used for identification and quantitative assessment of proteins within complex samples. MS is based on the measurement of charged ions from a protein analyte. To increase the sensitivity of the measurement, different compounds in very complex samples can be separated by gel electrophoresis, liquid chromatography (LC-MS), gas chromatography (GC-MS), or another mass spectrometer (MS-MS) prior to analysis. Historically, there are two ways to detect proteins by MS including using a ‘top-down’ or ‘bottom-up’ approach [43,44]. After protein extraction, the top-down approach separates and quantitates purified intact proteins (ions) using 2D gel electrophoresis or MS-MS and enables the characterization of unique proteoforms including degradation products, protein isoforms, post-translational modifications (PTMs), as well as low-mass proteins. The usage of the top-down approach is however often limited to low-throughput individual protein studies. In contrast, the bottom-up approach is more broadly used for analyzing more complex protein mixtures. Bottom-up proteomics using LC-MS is also known as ‘shotgun proteomics’ [45]. With this technique, the proteins are digested into peptides by enzymes (e.g. trypsin) before analysis by MS. Since only one fraction of all produced peptides (ions) is restored into a protein, PTMs and alternative isoform information will not be recovered in bottom-up proteomics. Both approaches are thus associated with advantages and disadvantages and choice of technique depends on the research aim of the study.
Related Knowledge Centers
- Alternative Splicing
- Exon
- Protein
- Rna Splicing
- Messenger Rna
- Gene
- Promoter
- Post-Transcriptional Modification
- Post-Translational Modification
- Proteoform