protein isoforms
Recently Published Documents





eLife ◽  
2022 ◽  
Vol 11 ◽  
Ananya Chakravarti ◽  
Heshani N Thirimanne ◽  
Savanna Brown ◽  
Brian R Calvi

p53 gene family members in humans and other organisms encode a large number of protein isoforms whose functions are largely undefined. Using Drosophila as a model, we find that a p53B isoform is expressed predominantly in the germline where it colocalizes with p53A into subnuclear bodies. It is only p53A, however, that mediates the apoptotic response to ionizing radiation in the germline and soma. In contrast, p53A and p53B are both required for the normal repair of meiotic DNA breaks, an activity that is more crucial when meiotic recombination is defective. We find that in oocytes with persistent DNA breaks p53A is also required to activate a meiotic pachytene checkpoint. Our findings indicate that Drosophila p53 isoforms have DNA lesion and cell type-specific functions, with parallels to the functions of mammalian p53 family members in the genotoxic stress response and oocyte quality control.

2022 ◽  
Margaret K.R. Donovan ◽  
Yingxiang Huang ◽  
John E. Blume ◽  
Jian Wang ◽  
Daniel Hornberg ◽  

Comprehensive assessment of the human proteome remains challenging due to multiple forms of a protein, or proteoforms, arising from alternative splicing, allelic variation, and protein modifications. As proteoforms can serve distinct functions and act as functional link between genotype and phenotype, proteoform-level knowledge is critical in understanding the molecular mechanisms underlying health and disease. However, identification of proteoforms requires unbiased protein coverage at amino acid resolution. Scalable, deep, and unbiased proteomics studies have been impractical due to cumbersome and lengthy workflows required for complex samples, like blood plasma. Here, we demonstrate the power of the Proteograph™ Product Suite in enabling unbiased, deep, and rapid proteomics at scale in a proof-of-concept proteoform analysis to dissect differences between protein isoforms in plasma samples from 80 healthy controls and 61 patients with early-stage non-small-cell lung cancer (NSCLC). Processing the 141 plasma samples with Proteograph yielded 22,993 peptides corresponding to 2,569 protein groups at a confidence of 1% false discovery rate. We extracted four proteins with peptides with significant abundance differences (p < 0.05; Benjamini-Hochberg corrected) in healthy control and cancer plasma samples. For one, the abundance variation can be explained by underlying annotated protein isoforms. For a second, we find evidence for differentially transcribed isoforms in the broader sequence data, but not in the known annotated protein isoforms. The others may be explained by novel isoforms or post-translational modifications. In addition, we sought to identify protein variants arising from allelic variation. To this end, we first performed whole exome sequencing on buffy coat samples from 29 individuals in the NSCLC study. Then, we created personalized mass spectrometry search databases for each individual subject from the exome sequences. From these libraries, we identified 422 protein variants, one of which has previously been shown to relate to lung cancer. In conclusion, our results demonstrate that Proteograph can generate unbiased and deep plasma proteome profiles that enable identification of proteoforms present in plasma at a scale sufficient to enable population-scale proteomic studies powered to reveal novel mechanistic and biomedical insights.

2022 ◽  
Vol 12 (1) ◽  
Arkadiusz Kajdasz ◽  
Daria Niewiadomska ◽  
Michal Sekrecki ◽  
Krzysztof Sobczak

AbstractCUG-binding protein, ELAV-like Family Member 1 (CELF1) plays an important role during the development of different tissues, such as striated muscle and brain tissue. CELF1 is an RNA-binding protein that regulates RNA metabolism processes, e.g., alternative splicing, and antagonizes other RNA-binding proteins, such as Muscleblind-like proteins (MBNLs). Abnormal activity of both classes of proteins plays a crucial role in the pathogenesis of myotonic dystrophy type 1 (DM1), the most common form of muscular dystrophy in adults. In this work, we show that alternative splicing of exons forming both the 5′ and 3′ untranslated regions (UTRs) of CELF1 mRNA is efficiently regulated during development and tissue differentiation and is disrupted in skeletal muscles in the context of DM1. Alternative splicing of the CELF1 5′UTR leads to translation of two potential protein isoforms that differ in the lengths of their N-terminal domains. We also show that the MBNL and CELF proteins regulate the distribution of mRNA splicing isoforms with different 5′UTRs and 3′UTRs and affect the CELF1 expression by changing its sensitivity to specific microRNAs or RNA-binding proteins. Together, our findings show the existence of different mechanisms of regulation of CELF1 expression through the distribution of various 5′ and 3′ UTR isoforms within CELF1 mRNA.

2022 ◽  
Vol 22 (1) ◽  
Dulce Rosario Alberto-Aguilar ◽  
Verónica Ivonne Hernández-Ramírez ◽  
Juan Carlos Osorio-Trujillo ◽  
Dolores Gallardo-Rincón ◽  
Alfredo Toledo-Leyva ◽  

Abstract Background Ovarian cancer is the most aggressive gynecological malignancy. Transcriptional regulators impact the tumor phenotype and, consequently, clinical progression and response to therapy. PHD finger protein 20-like protein 1 (PHF20L1) is a transcriptional regulator with several isoforms, and studies on its role in ovarian cancer are limited. We previously reported that PHF20L1 is expressed as a fucosylated protein in SKOV-3 cells stimulated with ascites from patients with ovarian cancer. Methods We decided to analyze the expression of PHF20L1 in ovarian cancer tissues, determine whether a correlation exists between PHF20L1 expression and patient clinical data, and analyze whether ascites can modulate the different isoforms of this protein. Ovarian cancer biopsies from 29 different patients were analyzed by immunohistochemistry, and the expression of the isoforms in ovarian cancer cells with or without exposure to the tumor microenvironment, i.e., the ascitic fluid, was determined by western blotting assays. Results Immunohistochemical results suggest that PHF20L1 exhibits increased expression in sections of tumor tissues from patients with ovarian cancer and that higher PHF20L1 expression correlates with shorter progression-free survival and shorter overall survival. Furthermore, western blotting assays determined that protein isoforms are differentially regulated in SKOV-3 cells in response to stimulation with ascites from patients with epithelial ovarian cancer. Conclusion The results suggest that PHF20L1 could play a relevant role in ovarian cancer given that higher PHF20L1 protein expression is associated with lower overall patient survival.

2022 ◽  
Vol 51 (1) ◽  
Brendan M. Floyd ◽  
Edward M. Marcotte

Despite tremendous gains over the past decade, methods for characterizing proteins have generally lagged behind those for nucleic acids, which are characterized by extremely high sensitivity, dynamic range, and throughput. However, the ability to directly characterize proteins at nucleic acid levels would address critical biological challenges such as more sensitive medical diagnostics, deeper protein quantification, large-scale measurement, and discovery of alternate protein isoforms and modifications and would open new paths to single-cell proteomics. In response to this need, there has been a push to radically improve protein sequencing technologies by taking inspiration from high-throughput nucleic acid sequencing, with a particular focus on developing practical methods for single-molecule protein sequencing (SMPS). SMPS technologies fall generally into three categories: sequencing by degradation (e.g., mass spectrometry or fluorosequencing), sequencing by transit (e.g., nanopores or quantum tunneling), and sequencing by affinity (as in DNA hybridization–based approaches). We describe these diverse approaches, which range from those that are already experimentally well-supported to the merely speculative, in this nascent field striving to reformulate proteomics. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see for revised estimates.

2022 ◽  
Vol 15 (1) ◽  
Sebastian Öther-Gee Pohl ◽  
Kevin B. Myant

ABSTRACT Alternative splicing is a process by which a single gene is able to encode multiple different protein isoforms. It is regulated by the inclusion or exclusion of introns and exons that are joined in different patterns prior to protein translation, thus enabling transcriptomic and proteomic diversity. It is now widely accepted that alternative splicing is dysregulated across nearly all cancer types. This widespread dysregulation means that nearly all cellular processes are affected – these include processes synonymous with the hallmarks of cancer – evasion of apoptosis, tissue invasion and metastasis, altered cellular metabolism, genome instability and drug resistance. Emerging evidence indicates that the dysregulation of alternative splicing also promotes a permissive environment for increased tumour heterogeneity and cellular plasticity. These are fundamental regulators of a patient's response to therapy. In this Review, we introduce the mechanisms of alternative splicing and the role of aberrant splicing in cancer, with particular focus on newfound evidence of alternative splicing promoting tumour heterogeneity, cellular plasticity and altered metabolism. We discuss recent in vivo models generated to study alternative splicing and the importance of these for understanding complex tumourigenic processes. Finally, we review the effects of alternative splicing on immune evasion, cell death and genome instability, and how targeting these might enhance therapeutic efficacy.

2021 ◽  
Muneesh Pal ◽  
Divya Chaubey ◽  
Mohit Tanwar ◽  
Beena Pillai

Abstract The Kalrn gene encodes several multi-domain protein isoforms that localise to neuronal synapses, and play dynamic roles in shaping axonal outgrowth, dendrite morphology and dendritic spine re-modelling. The genomic locus is implicated in several neurodevelopmental and neuropsychiatric diseases including autism, schizophrenia and bipolar disease. Mutations in the coding regions, inherited in a classical Mendelian manner, have also been implicated in certain forms of autism and intellectual disability. At the molecular level, the protein isoforms, encoded by reported transcript isoforms, share some core domains arising from the central exons, while other domains, especially towards the C terminal may be selectively incorporated. This heterogeneity seems to confer the ability to grow and retract dendritic spines, thus making Kalirin a critical and dynamic player in dendritogenesis. We have previously shown that in the zebrafish genome, a novel brain specific non-coding RNA arising from the 5’ end of the Kalirin gene, durga regulates neuronal morphology. In search of the mammalian equivalent, we characterized the mammalian Kalrn loci in detail, annotating multiple novel non-coding RNAs, including linear and circular variants, through analysis of transcriptomics data and experimental approaches. By comparing the mouse and human loci and studying the expression of the novel lncRNAs arising from the locus during differentiation of primary cortical neurons in culture, we show that certain non-coding RNAs arising from the locus show a temporal expression profile that coincides with a subset of Kalirin protein coding isoforms. In humans, mouse and zebrafish the 5’end of the Kalrn locus gives rise to a chromatin associated lncRNA that is present in adult ovaries besides being expressed during brain development and in certain regions of the adult brain. Besides correcting some of the annotations available in public databases, we propose that this lncRNA arising from the 5’end of the Kalrn locus is the mammalian ortholog of zebrafish lncRNA durga.

2021 ◽  
Vol 3 (12) ◽  
Suraya Muzafar ◽  
Neeraj Chauhan ◽  
Ravi Datta Sharma ◽  
Rajendra Prasad

Alternative gene splicing (AS) is a process by which a single gene can give rise to different protein isoforms, generating proteome diversity. Despite recent advances in our understanding of AS in basic cellular processes, the role of AS in drug resistance and fungal pathogenesis is poorly understood. In Candida albicans, approximately 6% of the genes contain introns. Considering this low and random distribution of introns, we focused our study on alternative splicing (AS) and its impact on the development of drug resistance, an area largely unexplored in this yeast. We performed comparative RNA sequencing of sequential isogenic azole sensitive and resistant isolates of C. albicans. The analysis revealed differential expression of splice junctions/isoforms in 14 genes, between the drug sensitive and resistant isolates. Furthermore, C. albicans WT cells exposed to antifungal drugs, heat stress or metal deficiency also showed differential expression of isoforms for the genes undergoing AS. In this study we present data on the effect of AS on the function of SOD3. The C. albicans SOD3 has a single intron and is important for the removal of superoxide radicals. The overexpression of the two isoforms of SOD3 in its null background highlighted importance of spliced isoform in complementing the susceptibility to menadione. However, the two isoforms did not differ in rescuing the susceptibility of sod3Δ/Δto Amphotericin B. Collectively, these data suggest that AS may be a novel mechanism in C. albicans for stress adaptation and overcoming drug resistance.

2021 ◽  
Anjani Kumari ◽  
Saam Sedehizadeh ◽  
John David Brook ◽  
Piotr Kozlowski ◽  
Marzena Wojciechowska

AbstractThe discovery of introns over four decades ago revealed a new vision of genes and their interrupted arrangement. Throughout the years, it has appeared that introns play essential roles in the regulation of gene expression. Unique processing of excised introns through the formation of lariats suggests a widespread role for these molecules in the structure and function of cells. In addition to rapid destruction, these lariats may linger on in the nucleus or may even be exported to the cytoplasm, where they remain stable circular RNAs (circRNAs). Alternative splicing (AS) is a source of diversity in mature transcripts harboring retained introns (RI-mRNAs). Such RNAs may contain one or more entire retained intron(s) (RIs), but they may also have intron fragments resulting from sequential excision of smaller subfragments via recursive splicing (RS), which is characteristic of long introns. There are many potential fates of RI-mRNAs, including their downregulation via nuclear and cytoplasmic surveillance systems and the generation of new protein isoforms with potentially different functions. Various reports have linked the presence of such unprocessed transcripts in mammals to important roles in normal development and in disease-related conditions. In certain human neurological-neuromuscular disorders, including myotonic dystrophy type 2 (DM2), frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS) and Duchenne muscular dystrophy (DMD), peculiar processing of long introns has been identified and is associated with their pathogenic effects. In this review, we discuss different mechanisms involved in the processing of introns during AS and the functions of these large sections of the genome in our biology.

2021 ◽  
Vol 12 ◽  
Klára Kosová ◽  
Pavel Vítámvás ◽  
Ilja Tom Prášil ◽  
Miroslav Klíma ◽  
Jenny Renaut

Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.

Sign in / Sign up

Export Citation Format

Share Document