scholarly journals Discovery proteomics in aging human skeletal muscle finds change in spliceosome, immunity, proteostasis and mitochondria

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Ceereena Ubaida-Mohien ◽  
Alexey Lyashkov ◽  
Marta Gonzalez-Freire ◽  
Ravi Tharakan ◽  
Michelle Shardell ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Alternative Splicing ◽  
Ribosomal Proteins ◽  
Older Persons ◽  
Molecular Mechanisms ◽  
Tca Cycle ◽  
Rna Seq ◽  
Energetic Metabolism ◽  
Innate And Adaptive Immunity ◽  
The Tca Cycle

A decline of skeletal muscle strength with aging is a primary cause of mobility loss and frailty in older persons, but the molecular mechanisms of such decline are not understood. Here, we performed quantitative proteomic analysis from skeletal muscle collected from 58 healthy persons aged 20 to 87 years. In muscle from older persons, ribosomal proteins and proteins related to energetic metabolism, including those related to the TCA cycle, mitochondria respiration, and glycolysis, were underrepresented, while proteins implicated in innate and adaptive immunity, proteostasis, and alternative splicing were overrepresented. Consistent with reports in animal models, older human muscle was characterized by deranged energetic metabolism, a pro-inflammatory environment and increased proteolysis. Changes in alternative splicing with aging were confirmed by RNA-seq analysis. We propose that changes in the splicing machinery enables muscle cells to respond to a rise in damage with aging.

scholarly journals Aging Skeletal Muscle Proteomics Finds Changes in Spliceosome, Immune factors, Proteostasis and Mitochondria

2019 ◽  
Author(s):  
Ceereena Ubaida-Mohien ◽  
Alexey Lyashkov ◽  
Marta Gonzalez-Freire ◽  
Ravi Tharakan ◽  
Michelle Shardell ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Alternative Splicing ◽  
Ribosomal Proteins ◽  
Older Persons ◽  
Molecular Mechanisms ◽  
Tca Cycle ◽  
Energetic Metabolism ◽  
Proteomic Data ◽  
The Tca Cycle ◽  
Muscle Proteomics

AbstractA progressive decline of skeletal muscle strength with aging is a primary cause of mobility loss and frailty in older persons, but the molecular mechanisms of such decline are not fully understood. Here, using quantitative discovery proteomic data from skeletal muscle specimens collected from 58 healthy persons aged 20 to 87 years show that ribosomal proteins and proteins related to energetic metabolism, including those related to the TCA cycle, mitochondria respiration, and glycolysis were underrepresented in older persons. Proteins with important roles in innate and adaptive immunity, involved in proteostasis and regulation of alternative splicing were all overrepresented in muscle from older persons. Changes with aging of alternative splicing were confirmed by RNA-seq. Overall, older muscle has a profound deficit of energetic metabolism, a pro-inflammatory environment and increased proteostasis. Upregulation of the splicing machinery maybe an attempt to compensate for these changes and this could be tested in future studies.

scholarly journals Mitochondrial Mistranslation in Brain Provokes a Metabolic Response Which Mitigates the Age-Associated Decline in Mitochondrial Gene Expression

2021 ◽  
Vol 22 (5) ◽  
pp. 2746
Author(s):  
Dimitri Shcherbakov ◽  
Reda Juskeviciene ◽  
Adrián Cortés Sanchón ◽  
Margarita Brilkova ◽  
Hubert Rehrauer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Response ◽  
Mitochondrial Gene ◽  
Tca Cycle ◽  
Brain Mitochondria ◽  
Mitochondrial Gene Expression ◽  
Rna Seq ◽  
The Tca Cycle ◽  
Neurological Phenotype

Mitochondrial misreading, conferred by mutation V338Y in mitoribosomal protein Mrps5, in-vivo is associated with a subtle neurological phenotype. Brain mitochondria of homozygous knock-in mutant Mrps5V338Y/V338Y mice show decreased oxygen consumption and reduced ATP levels. Using a combination of unbiased RNA-Seq with untargeted metabolomics, we here demonstrate a concerted response, which alleviates the impaired functionality of OXPHOS complexes in Mrps5 mutant mice. This concerted response mitigates the age-associated decline in mitochondrial gene expression and compensates for impaired respiration by transcriptional upregulation of OXPHOS components together with anaplerotic replenishment of the TCA cycle (pyruvate, 2-ketoglutarate).

scholarly journals Comparative Transcriptome Analysis Reveals Sex-Based Differences during the Development of the Adult Parasitic Wasp Cotesia vestalis (Hymenoptera: Braconidae)

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 896
Author(s):  
Yuenan Zhou ◽  
Pei Yang ◽  
Shuang Xie ◽  
Min Shi ◽  
Jianhua Huang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Adult Development ◽  
Sexual Development ◽  
Molecular Mechanisms ◽  
Parasitic Wasp ◽  
Differentially Expressed Gene ◽  
Regulation Mechanism ◽  
Rna Seq ◽  
Male And Female ◽  
Cotesia Vestalis

The endoparasitic wasp Cotesia vestalis is an important biological agent for controlling the population of Plutella xylostella, a major pest of cruciferous crops worldwide. Though the genome of C. vestalis has recently been reported, molecular mechanisms associated with sexual development have not been comprehensively studied. Here, we combined PacBio Iso-Seq and Illumina RNA-Seq to perform genome-wide profiling of pharate adult and adult development of male and female C. vestalis. Taking advantage of Iso-Seq full-length reads, we identified 14,466 novel transcripts as well as 8770 lncRNAs, with many lncRNAs showing a sex- and stage-specific expression pattern. The differentially expressed gene (DEG) analyses showed 2125 stage-specific and 326 sex-specific expressed genes. We also found that 4819 genes showed 11,856 alternative splicing events through combining the Iso-Seq and RNA-Seq data. The results of comparative analyses showed that most genes were alternatively spliced across developmental stages, and alternative splicing (AS) events were more prevalent in females than in males. Furthermore, we identified six sex-determining genes in this parasitic wasp and verified their sex-specific alternative splicing profiles. Specifically, the characterization of feminizer and doublesex splicing between male and female implies a conserved regulation mechanism of sexual development in parasitic wasps.

P207 Synergetic effect of amino acid and ketone metabolism underlies empagliflozin-mediated cardioprotection in the type 2 diabetic heart

2020 ◽  
Vol 41 (Supplement_1) ◽  
Author(s):  
H Kouzu ◽  
H Oshima ◽  
T Miki ◽  
A Kuno ◽  
T Sato ◽  
...  
Keyword(s):  
Amino Acid ◽  
Survival Rate ◽  
Molecular Mechanisms ◽  
Synergetic Effect ◽  
Tca Cycle ◽  
Oxidative Capacity ◽  
Metabolome Analysis ◽  
Coa Transferase ◽  
The Tca Cycle

Abstract Funding Acknowledgements Boehringer Ingelheim Background  Although emerging evidence has indicated that sodium glucose cotransporter 2 (SGLT2) inhibitors restore impaired cardiac energetics in type 2 diabetes mellitus (T2DM), the underlying molecular mechanisms have yet to be established.  Augmented utilization of ketone is one proposed hypothesis, but depletion of succinyl-CoA triggered by the conversion of ketone back to acetyl-CoA by SCOT (succinyl-CoA:3-oxoacid CoA transferase) may hamper oxidative capacity of the tricarboxylic acid (TCA) cycle, which also requires succinyl-CoA.  The recent finding that empagliflozin augments systemic amino acid metabolism in patients with T2DM led us to hypothesize that the anaplerotic effect of amino acid on the TCA cycle complements ketone oxidation. Methods and Results  Myocardial infarction (MI) was induced in T2DM rats (OLETF) and control rats (LETO).  Survival rate at 48 hours after MI was significantly lower in OLETF than in LETO (40% vs 84%), and empagliflozin treatment (10 mg/kg/day, 14 days) before MI improved the survival rate in OLETF to 70%.  Metabolome analysis was performed using heart tissues from the non-infarct region 12 hours after MI.  Using principal component analysis, data from 92 metabolites that were detected were compressed into 2 dimensions, and the first component (PC1) clearly separated empagliflozin-treated OLETF from non-treated LETO and OLETF.  Analysis of factor loading of each metabolite for PC1 revealed that branched chain amino acids leucine, isoleucine and valine, the latter two of which can be oxidized to succynyl-CoA, and β-hydroxybutyrate were the top four metabolites that characterized empagliflozin treatment.  Furthermore, in comparison to LETO, OLETF treated with empagliflozin showed 50% higher levels of glutamine and glutamate, both of which can replenish the TCA cycle at the level of α-ketoglutarate.  In OLETF, empagliflozin significantly increased the TCA cycle intermediates citrate, cis-aconitate and malate by 74%, 119% and 59%, respectively.  OLETF showed 86% higher lactate and 38% lower ATP than those in LETO, but levels of the metabolites were normalized by empagliflozin, suggesting improved glucose oxidation. Conclusions   The present analyses showed that amino acid and ketone metabolism are metabolic pathways that are most affected by empagliflozin.  Coordination of these "starvation-induced pathways" may underlie the favorable metabolic effect of empagliflozin in T2DM hearts.

scholarly journals The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers

BMC Genomics ◽  
2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Xiaohong Ou ◽  
Shipeng Li ◽  
Peiran Liao ◽  
Xiuming Cui ◽  
Binglian Zheng ◽  
...  
Keyword(s):  
Crop Production ◽  
Tca Cycle ◽  
Panax Notoginseng ◽  
Ammonium Nitrogen ◽  
Nitrogen Fertilizers ◽  
Rna Seq ◽  
Root Yield ◽  
Qrt Pcr ◽  
The Tca Cycle ◽  
Nitrate Fertilizer

Abstract Background The sensitivity of plants to ammonia is a worldwide problem that limits crop production. Excessive use of ammonium as the sole nitrogen source results in morphological and physiological disorders, and retarded plant growth. Results In this study we found that the root growth of Panax notoginseng was inhibited when only adding ammonium nitrogen fertilizer, but the supplement of nitrate fertilizer recovered the integrity, activity and growth of root. Twelve RNA-seq profiles in four sample groups were produced and analyzed to identify deregulated genes in samples with different treatments. In comparisons to NH${~}_{4}^{+}$ 4 + treated samples, ACLA-3 gene is up-regulated in samples treated with NO${~}_{3}^{-}$ 3 − and with both NH$_{4}^{+}$ 4 + and NO${~}_{3}^{-}$ 3 − , which is further validated by qRT-PCR in another set of samples. Subsequently, we show that the some key metabolites in the TCA cycle are also significantly enhanced when introducing NO${~}_{3}^{-}$ 3 − . These potentially enhance the integrity and recover the growth of Panax notoginseng roots. Conclusion These results suggest that the activated TCA cycle, as demonstrated by up-regulation of ACLA-3 and several key metabolites in this cycle, contributes to the increased Panax notoginseng root yield when applying both ammonium and nitrate fertilizer.

scholarly journals Transcriptome sequencing of Saccharina japonica sporophytes during whole developmental periods reveals regulatory networks underlying alginate and mannitol biosynthesis

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhanru Shao ◽  
Pengyan Zhang ◽  
Chang Lu ◽  
Shaoxuan Li ◽  
Zhihang Chen ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Ribosomal Proteins ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Brown Seaweed ◽  
Saccharina Japonica ◽  
Tca Cycle ◽  
New Genes ◽  
Mannitol Metabolism

Abstract Background Alginate is an important cell wall component and mannitol is a soluble storage carbon substance in the brown seaweed Saccharina japonica. Their contents vary with kelp developmental periods and harvesting time. Alginate and mannitol regulatory networks and molecular mechanisms are largely unknown. Results With WGCNA and trend analysis of 20,940 known genes and 4264 new genes produced from transcriptome sequencing of 30 kelp samples from different stages and tissues, we deduced that ribosomal proteins, light harvesting complex proteins and “imm upregulated 3” gene family are closely associated with the meristematic growth and kelp maturity. Moreover, 134 and 6 genes directly involved in the alginate and mannitol metabolism were identified, respectively. Mannose-6-phosphate isomerase (MPI2), phosphomannomutase (PMM1), GDP-mannose 6-dehydrogenase (GMD3) and mannuronate C5-epimerase (MC5E70 and MC5E122) are closely related with the high content of alginate in the distal blade. Mannitol accumulation in the basal blade might be ascribed to high expression of mannitol-1-phosphate dehydrogenase (M1PDH1) and mannitol-1-phosphatase (M1Pase) (in biosynthesis direction) and low expression of mannitol-2-dehydrogenase (M2DH) and Fructokinase (FK) (in degradation direction). Oxidative phosphorylation and photosynthesis provide ATP and NADH for mannitol metabolism whereas glycosylated cycle and tricarboxylic acid (TCA) cycle produce GTP for alginate biosynthesis. RNA/protein synthesis and transportation might affect alginate complex polymerization and secretion processes. Cryptochrome (CRY-DASH), xanthophyll cycle, photosynthesis and carbon fixation influence the production of intermediate metabolite of fructose-6-phosphate, contributing to high content of mannitol in the basal blade. Conclusions The network of co-responsive DNA synthesis, repair and proteolysis are presumed to be involved in alginate polymerization and secretion, while upstream light-responsive reactions are important for mannitol accumulation in meristem of kelp. Our transcriptome analysis provides new insights into the transcriptional regulatory networks underlying the biosynthesis of alginate and mannitol during S. japonica developments.

scholarly journals Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Anne-Laure Bougé ◽  
Eva Murauer ◽  
Emmanuelle Beyne ◽  
Julie Miro ◽  
Jessica Varilh ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Alternative Splicing ◽  
Cdna Sequence ◽  
454 Sequencing ◽  
Exon Skipping ◽  
Rna Seq ◽  
Splicing Pattern ◽  
Alternative Splicing Events ◽  
Diagnostic Research ◽  
Dmd Gene

Abstract We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript. In contrast to previous assumptions, we evidenced that most of the 79 DMD exons are constitutively spliced in skeletal muscle. Only a limited number of 12 alternative splicing events were identified, all present at a very low level. These include previously known exon skipping events but also newly described pseudoexon inclusions and alternative 3′ splice sites, of which one is the first functional NAGNAG splice site reported in the DMD gene. This study provides the first RNA-Seq-based reference of DMD splicing pattern in skeletal muscle and reports on an experimental procedure well suited to detect condition-specific differences in this low abundance transcript that may prove useful for diagnostic, research or RNA-based therapeutic applications.

scholarly journals Evidence for reverse flux through pyruvate kinase in skeletal muscle

2009 ◽  
Vol 296 (4) ◽  
pp. E748-E757 ◽  
Author(s):  
Eunsook S. Jin ◽  
A. Dean Sherry ◽  
Craig R. Malloy
Keyword(s):  
Skeletal Muscle ◽  
Glucose Production ◽  
Tca Cycle ◽  
Hepatic Glycogen ◽  
Direct Transfer ◽  
The Tca Cycle ◽  
Tca Cycle Intermediates ◽  
Minced Muscle ◽  
Labeling Pattern

Conversion of lactate to glucose was examined in myotubes, minced muscle tissue, and rats exposed to 2H2O or 13C-enriched substrates. Myotubes or minced skeletal muscle incubated with [U-13C3]lactate released small amounts of [1,2,3-13C3]- or [4,5,6-13C3]glucose. This labeling pattern is consistent with direct transfer from lactate to glucose without randomization in the tricarboxylic acid (TCA) cycle. After exposure of incubated muscle to 2H2O, [U-13C3]lactate, glucose, and glutamine, there was minimal release of synthesized glucose to the medium based on a low level of 2H enrichment in medium glucose but 50- to 100-fold greater 2H enrichment in glucosyl units from glycogen. The 13C enrichment pattern in glycogen from incubated skeletal muscle was consistent only with direct transfer of lactate to glucose without exchange in TCA cycle intermediates. 13C nuclear magnetic resonance (NMR) spectra of glutamate from the same tissue showed flux from lactate through pyruvate dehydrogenase but not flux through pyruvate carboxylase into the TCA cycle. Carbon from an alternative substrate for glucose production that requires metabolism through the TCA cycle, propionate, did not enter glycogen, suggesting that TCA cycle intermediates do not exchange with phospho enolpyruvate. In vivo, the 13C labeling patterns in hepatic glycogen and plasma glucose after administration of [U-13C3]lactate did not differ significantly. However, skeletal muscle glycogen was substantially enriched in [1,2,3-13C3]- and [4,5,6-13C3]glucose units that could only occur through skeletal muscle glyconeogenesis rather than glycogenesis. Lactate serves as a substrate for glyconeogenesis in vivo without exchange into symmetric intermediates of the TCA cycle.

scholarly journals Tricarboxylic Acid (TCA) Cycle Intermediates: Regulators of Immune Responses

2020 ◽  
Author(s):  
Inseok Choi ◽  
Hyewon Son ◽  
Jea-Hyun Baek
Keyword(s):  
Immune Responses ◽  
Molecular Mechanisms ◽  
Tricarboxylic Acid Cycle ◽  
Tca Cycle ◽  
Tricarboxylic Acid ◽  
Cell Stress ◽  
Danger Signals ◽  
Cellular Processes ◽  
The Tca Cycle ◽  
Tca Cycle Intermediates

Tricarboxylic acid cycle (TCA) is a series of chemical reactions in aerobic organisms used to generate energy via the oxidation of acetyl-CoA derived from carbohydrates, fatty acids, and proteins. In the eukaryotic system, the TCA cycle completely occurs in mitochondria, while the intermediates of the TCA cycle are retained in mitochondria due to their polarity and hydrophilicity. Under conditions of cell stress, mitochondria become disrupted and release their contents, which act as danger signals in the cytosol. Of note, the TCA cycle intermediates may also leak from dysfunctioning mitochondria and regulate cellular processes. Increasing evidence shows that the metabolites of the TCA cycle are substantially involved in the regulation of immune responses. In this review, we aimed to provide a comprehensive systematic overview of the molecular mechanisms of each TCA cycle intermediate that may play key roles in regulating cellular immunity in cell stress and discuss their implications for immune activation and suppression.

scholarly journals Transcriptome profiling reveals transcriptional and alternative splicing regulation in the early embryonic development of hair follicles in the cashmere goat

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yanjun Zhang ◽  
Lele Wang ◽  
Zhen Li ◽  
Dong Chen ◽  
Wenjing Han ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Molecular Mechanisms ◽  
Transcriptome Profiling ◽  
Hair Follicles ◽  
Splicing Regulation ◽  
Cashmere Goat ◽  
Rna Seq ◽  
Three Stages ◽  
Functional Pathways ◽  
First Time

AbstractThe undercoat fiber of the cashmere goat, from the secondary hair follicle (HF), possesses commercial value. However, very few studies have focused on the molecular details of primary and secondary HF initiation and development in goat embryos. In this study, skin samples at embryonic day 45, 55, and 65 (E45, E55, and E65) were collected and prepared for RNA sequencing (RNA-seq). We found that the HF probably initiated from E55 to E65 by analyzing the functional pathways of differentially expressed genes (DEGs). Most key genes in canonical signaling pathways, including WNT, TGF-β, FGF, Hedgehog, NOTCH, and other factors showed clear expression changes from E55 to E65. We, for the first time, explored alternative splicing (AS) alterations, which showed distinct patterns among these three stages. Functional pathways of AS-regulated genes showed connections to HF development. By comparing the published RNA-seq samples from the E60, E120, and newborn (NB) stages, we found the majority of WNT/β-catenin signaling genes were important in the initiation of HF development, while other factors including FOXN1, GATA3, and DLX3 may have a consistent influence on HF development. Our investigation supported the time points of embryonic HF initiation and identified genes that have potential functions of embryonic HF initiation and development. We further explored the potential regulatory roles of AS in HF initiation, which extended our knowledge about the molecular mechanisms of HF development.

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