Browsing by Author "Karamyshev, Andrey L. (TTUHSC)"
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Item Aberrant protein targeting activates quality control on the ribosome(2023) Karamysheva, Zemfira N. (TTU); Karamyshev, Andrey L. (TTUHSC)Cells synthesize thousands of different proteins that should be delivered to different cellular compartments, integrated into membranes, or secreted outside of the cell to conduct their functions. Over 20 thousand genes are detected in a human genome including about 3,000 genes encoding secreted proteins and 5,500 genes encoding membrane proteins (Uhlen et al., 2015). Thus, about 40% of all proteins are transported through or integrated into cellular membranes. What happens to secretory/membrane proteins that are not able to be targeted to the endoplasmic reticulum (ER) because of the mutations in the signal peptides or defects in the protein transport machinery? These proteins are potentially harmful to cells if they are mislocalized. In this article we discuss secretory protein targeting, signal peptides interactions with transport machinery of the cells, defects in these processes, their possible implications in human diseases, and cellular mechanisms preventing synthesis of defective secretory proteins.Item Drug‐induced lipid remodeling in leishmania parasites(2021) Gutierrez Guarnizo, Sneider Alexander (TTUHSC); Tikhonova, Elena B. (TTUHSC); Zabet‐moghaddam, Masoud (TTU); Zhang, Kai (TTU); Muskus, Carlos; Karamyshev, Andrey L. (TTUHSC); Karamysheva, Zemfira N. (TTU)Leishmania parasites efficiently develop resistance against several types of drugs including antimonials, the primary antileishmanial drug historically implemented. The resistance to antimo-nials is considered to be a major risk factor for effective leishmaniasis treatment. To detect bi-omarkers/biopatterns for the differentiation of antimony‐resistant Leishmania strains, we employed untargeted global mass spectrometry to identify intracellular lipids present in antimony sensitive and resistant parasites before and after antimony exposure. The lipidomic profiles effectively dif-ferentiated the sensitive and resistant phenotypes growing with and without antimony pressure. Resistant phenotypes were characterized by significant downregulation of phosphatidylcholines, sphingolipid decrease, and lysophosphatidylcholine increase, while sensitive phenotypes were characterized by the upregulation of triglycerides with long‐chain fatty acids and a tendency to-ward the phosphatidylethanolamine decrease. Our findings suggest that the changes in lipid composition in antimony‐resistant parasites contribute to the physiological response conducted to com-bat the oxidative stress unbalance caused by the drug. We have identified several lipids as potential biomarkers associated with the drug resistance.Item Pathogenic signal peptide variants in the human genome(2023) Guarnizo, Sneider Alexander Gutierrez (TTUHSC); Kellogg, Morgana K. (TTUHSC); Miller, Sarah C. (TTUHSC); Tikhonova, Elena B. (TTUHSC); Karamysheva, Zemfira N. (TTU); Karamyshev, Andrey L. (TTUHSC)Secreted and membrane proteins represent a third of all cellular proteins and contain N-terminal signal peptides that are required for protein targeting to endoplasmic reticulum (ER). Mutations in signal peptides affect protein targeting, translocation, processing, and stability, and are associated with human diseases. However, only a few of them have been identified or characterized. In this report, we identified pathogenic signal peptide variants across the human genome using bioinformatic analyses and predicted the molecular mechanisms of their pathology. We recovered more than 65 thousand signal peptide mutations, over 11 thousand we classified as pathogenic, and proposed framework for distinction of their molecular mechanisms. The pathogenic mutations affect over 3.3 thousand genes coding for secreted and membrane proteins. Most pathogenic mutations alter the signal peptide hydrophobic core, a critical recognition region for the signal recognition particle, potentially activating the Regulation of Aberrant Protein Production (RAPP) quality control and specific mRNA degradation. The remaining pathogenic variants (about 25%) alter either the N-terminal region or signal peptidase processing site that can result in translocation deficiencies at the ER membrane or inhibit protein processing. This work provides a conceptual framework for the identification of mutations across the genome and their connection with human disease.Item Ribosome Specialization in Protozoa Parasites(2023) Rodríguez-Almonacid, Cristian Camilo (TTU); Kellogg, Morgana K. (TTUHSC); Karamyshev, Andrey L. (TTUHSC); Karamysheva, Zemfira N. (TTU)Ribosomes, in general, are viewed as constitutive macromolecular machines where protein synthesis takes place; however, this view has been recently challenged, supporting the hypothesis of ribosome specialization and opening a completely new field of research. Recent studies have demonstrated that ribosomes are heterogenous in their nature and can provide another layer of gene expression control by regulating translation. Heterogeneities in ribosomal RNA and ribosomal proteins that compose them favor the selective translation of different sub-pools of mRNAs and functional specialization. In recent years, the heterogeneity and specialization of ribosomes have been widely reported in different eukaryotic study models; however, few reports on this topic have been made on protozoa and even less on protozoa parasites of medical importance. This review analyzes heterogeneities of ribosomes in protozoa parasites highlighting the specialization in their functions and their importance in parasitism, in the transition between stages in their life cycle, in the change of host and in response to environmental conditions.Item Specialized Ribosomes in Health and Disease(2023) Miller, Sarah C. (TTUHSC); MacDonald, Clinton C. (TTUHSC); Kellogg, Morgana K. (TTUHSC); Karamysheva, Zemfira N. (TTU); Karamyshev, Andrey L. (TTUHSC)Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.Item The Enrichment of miRNA-Targeted mRNAs in Translationally Less Active over More Active Polysomes(2023) Wang, Tingzeng (TTU); Tian, Shuangmei (TTU); Tikhonova, Elena B. (TTUHSC); Karamyshev, Andrey L. (TTUHSC); Wang, Jing J.; Zhang, Fangyuan (TTU); Wang, Degeng (TTU)miRNAs moderately inhibit the translation and enhance the degradation of their target mRNAs via cognate binding sites located predominantly in the 3′-untranslated regions (UTR). Paradoxically, miRNA targets are also polysome-associated. We studied the polysome association by the comparative translationally less-active light- and more-active heavy-polysome profiling of a wild type (WT) human cell line and its isogenic mutant (MT) with a disrupted DICER1 gene and, thus, mature miRNA production. As expected, the open reading frame (ORF) length is a major determinant of light- to heavy-polysome mRNA abundance ratios, but is rendered less powerful in WT than in MT cells by miRNA-regulatory activities. We also observed that miRNAs tend to target mRNAs with longer ORFs, and that adjusting the mRNA abundance ratio with the ORF length improves its correlation with the 3′-UTR miRNA-binding-site count. In WT cells, miRNA-targeted mRNAs exhibit higher abundance in light relative to heavy polysomes, i.e., light-polysome enrichment. In MT cells, the DICER1 disruption not only significantly abrogated the light-polysome enrichment, but also narrowed the mRNA abundance ratio value range. Additionally, the abrogation of the enrichment due to the DICER1 gene disruption, i.e., the decreases of the ORF-length-adjusted mRNA abundance ratio from WT to MT cells, exhibits a nearly perfect linear correlation with the 3′-UTR binding-site count. Transcription factors and protein kinases are the top two most enriched mRNA groups. Taken together, the results provide evidence for the light-polysome enrichment of miRNA-targeted mRNAs to reconcile polysome association and moderate translation inhibition, and that ORF length is an important, though currently under-appreciated, transcriptome regulation parameter.Item Uncovering the cellular capacity for intensive and specific feedback self-control of the argonautes and MicroRNA targeting activity(2020) Wang, Degeng; Wang, Tingzeng; Gill, Audrey (TTU); Hilliard, Terrell; Chen, Fengqian; Karamyshev, Andrey L. (TTUHSC); Zhang, Fangyuan (TTU)The miRNA pathway has three segments - biogenesis, targeting and downstream regulatory effectors. We aimed to better understand their cellular control by exploring the miRNA-mRNA-targeting relationships. We first used human evolutionarily conserved sites. Strikingly, AGOs 1-3 are all among the top 14 mRNAs with the highest miRNA site counts, along with ANKRD52, the phosphatase regulatory subunit of the recently identified AGO phosphorylation cycle; and the AGO phosphorylation cycle mRNAs share much more than expected miRNA sites. The mRNAs for TNRC6, which acts with AGOs to channel miRNA-mediated regulatory actions onto specific mRNAs, are also heavily miRNA-targeted. In contrast, upstream miRNA biogenesis mRNAs are not, and neither are downstream regulatory effectors. In short, binding site enrichment in miRNA targeting machinery mRNAs, but neither upstream biogenesis nor downstream effector mRNAs, was observed, endowing a cellular capacity for intensive and specific feedback control of the targeting activity. The pattern was confirmed with experimentally determined miRNA-mRNA target relationships. Moreover, genetic experiments demonstrated cellular utilization of this capacity. Thus, we uncovered a capacity for intensive, and specific, feedback-regulation of miRNA targeting activity directly by miRNAs themselves, i.e. segment-specific feedback auto-regulation of miRNA pathway, complementing miRNAs pairing with transcription factors to form hybrid feedback-loop.Item Unexpected Role of Sterol Synthesis in RNA Stability and Translation in Leishmania(2021) Karamysheva, Zemfira N. (TTU); Moitra, Samrat (TTU); Perez, Andrea (TTU); Mukherjee, Sumit (TTU); Tikhonova, Elena B. (TTUHSC); Karamyshev, Andrey L. (TTUHSC); Zhang, Kai (TTU)Leishmania parasites are trypanosomatid protozoans that cause leishmaniasis affecting millions of people worldwide. Sterols are important components of the plasma and organellar membranes. They also serve as precursors for the synthesis of signaling molecules. Unlike animals, Leishmania does not synthesize cholesterol but makes ergostane-based sterols instead. C-14-demethylase is a key enzyme involved in the biosynthesis of sterols and an important drug target. In Leishmania parasites, the inactivation of C-14-demethylase leads to multiple defects, including increased plasma membrane fluidity, mitochondrion dysfunction, hypersensitivity to stress and reduced virulence. In this study, we revealed a novel role for sterol synthesis in the maintenance of RNA stability and translation. Sterol alteration in C-14-demethylase knockout mutant leads to increased RNA degradation, reduced translation and impaired heat shock response. Thus, sterol biosynthesis in Leishmania plays an unexpected role in global gene regulation.