scholarly journals Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles

Animals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1130
Author(s):  
Rui-Yi Chen ◽  
Bui Thi Ngoc Hieu ◽  
Gilbert Audira ◽  
Bao Lou ◽  
Ming-Der Lin ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Protein Expression ◽  
Fish Species ◽  
Binding Proteins ◽  
Binding Protein ◽  
Transcriptomic Analysis ◽  
Oxygen Binding ◽  
Putative Gene ◽  
Expression Levels ◽  
Rnaseq Data

Oxygen-binding proteins, such as myoglobin, hemoglobin, neuroglobin, and cytoglobin, play a role in oxygen binding and delivery to tissues. In icefish, the loss of myoglobin and hemoglobin genes has been reported to be an adaptive evolution event. This interesting finding prompted us to exam oxygen-binding protein expression in diverse fish species. Taking advantage of substantial RNAseq data deposited in the NCBI (National Center for Biotechnology Information) database, we adopted a meta-transcriptomic approach to explore and compare four oxygen-binding protein gene expression levels in the skeletal muscle of 25 diverse fish species for the first time. RNAseq data were downloaded from the NCBI Sequence Read Archive (SRA) database, and de novo assembly was performed to generate transcript contigs. The genes encoding oxygen-binding proteins were then identified by the BLAST search, and the relative expression level of oxygen-binding protein genes was normalized by the RPKM (Reads per Kilobase Million) method. By performing expression profiling, hierarchy clustering, and principal component analysis, pacu and loach fish were noticed by their high myoglobin expression levels in skeletal muscle tissues among 25 diverse fish species. In conclusion, we demonstrated that meta-transcriptomic analysis of RNAseq data is an informative approach to compare the oxygen-binding protein expression and putative gene expansion event in fish.

Abstract 20140: Minibrain Relate Kinase / Dyrk1B Links Skeletal Muscle Glycolytic Metabolism with Insulin Resistance and Causes Metabolic Syndrome

Circulation ◽  
2014 ◽  
Vol 130 (suppl_2) ◽  
Author(s):  
Mohsen Fathzadeh ◽  
Ali Reza Keramati ◽  
Gwang Go ◽  
Rajvir Singh ◽  
Kazem Sarajzadeh ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
Skeletal Muscle ◽  
Metabolic Syndrome ◽  
Protein Expression ◽  
Ppar Gamma ◽  
Glycolytic Metabolism ◽  
Expression Levels ◽  
Fiber Composition ◽  
Mutation Carriers ◽  
Fast Twitch

We have identified a novel nonconservative mutation in Minibrain related serine/threonine kinase (Mirk/ Dyrk1B) in outlier kindreds with metabolic syndrome. The mutation substitutes cysteine for arginine (R102C) and segregates with most traits of metabolic syndrome, including central obesity, diabetes and hypertension. Oral glucose tolerance test (OGTT) in young nondiabetic mutation carriers revealed insulin resistance compared to noncarrier family members. Since skeletal muscle (SM) is the largest organ for glucose uptake and metabolism, we obtained Vastus Lateralis biopsies of mutation carriers and their unaffected relatives and examined them for gene/protein expression by deep RNA sequencing (RNA-Seq) and Western blot analysis and for fiber composition by immunostaining. The fiber composition data demonstrated fewer slow-twitch fibers (35% vs. 75%) and more fast -twitch fibers (65% vs. 25%) in SM of mutation carriers vs. controls. Interestingly, there were increased protein expression levels of fast-twitch fiber type proteins (MYH11, MYLPF), pyruvate dehydrogenase kinase, pyruvate kinase, and neuronal nitric oxide synthase in SM of mutation carriers vs. noncarriers. Consistent with these findings, the protein expression levels of the master regulator of cellular energy metabolism mitochondrial biogenesis, PPAR-gamma coactivator (PGC-1a), were reduced and the nuclear expression levels of FOXO1 and NFAT were increased. Similar findings were observed when wildtype and mutant (R102C) Dyrk1B were overexpressed in C2C12 cells. The overexpression of the kinase deficient Dyrk1B (Y271/273F) similarly resulted in reduced expression of PGC-1a and increased expression of nuclear FOXO1, suggesting kinase independent effects. Taken together, these findings suggest that enhanced kinase-independent activities of Dyrk1B, either through increased expression or by its gain of function mutation R102C induce insulin resistance by promoting glycolytic metabolism and reducing oxidative phosphorylation. In conclusion, Dyrk1B is a potential target for development of novel drugs that aim to enhance skeletal muscle insulin sensitivity.

scholarly journals Transcriptome Analysis and Molecular Characterization of Olfactory Binding Protein genes in Parasitoid wasp Anagrus nilaparvatae（Hymenoptera: Mymaridae）

2021 ◽  
Author(s):  
Yin Ma ◽  
Tingfa Huang ◽  
Binjie Tang ◽  
Bingyang Wang ◽  
Jianbai Liu ◽  
...  
Keyword(s):  
Olfactory System ◽  
Binding Proteins ◽  
Binding Protein ◽  
Full Length ◽  
Chemical Information ◽  
Parasitoid Wasps ◽  
Transcriptome Data ◽  
Phylogenetic Tree Analysis ◽  
Expression Levels ◽  
Relative Expression

Anagrus nilaparvatae is an important egg parasitoid wasps of rice pests rice planthopper. Based on the powerful olfactory system of sensing chemical information in nature, A. nilaparvatae shows complicated life activities and behaviors, such as feeding, mating and hosting. In this study, we constructed a full-length transcriptome library and further to identify the characteristics of olfactory binding proteins, the first participant in the olfactory system. Through full-length transcriptome sequencing, splicing, assembly, and data correction by Illumina, we obtained 163.59Mb of transcriptome data and 501,179 items of annotation information, and performed GO functional classification of unigenes of the transcriptome. We analyzed the sequence characteristics of olfactory binding protein genes, and 8 genes (AnilOBP2, AnilOBP9 AnilOBP23, AnilOBP56, AnilOBP83, AnilCSP5, AnilCSP6 and AnilNPC2) were identified. After sequence alignment and conserved domain prediction, the 8 proteins were consistent with the typical characteristics of OBPs, CSPs and NPC2s in insects. The phylogenetic tree analysis showed that the 8 genes share low homology relationship with other species in Hymenopteran. Finally, RT-qPCR was used to analyze the expression responses of the 8 genes in different genders and stimulated by volatiles. The relative expression levels of AnilOBP9, AnilOBP26, AnilOBP83, AnilCSP5 and AnilNPC2 in males were significantly higher than those in female, while the relative expression levels of AnilCSP6 were opposite. The expression levels of AnilOBP9 and AnilCSP6 were significantly altered by the stimulation of β-caryophylene, suggesting the two genes may be related to host searching. In this study, the transcriptome data of parasitoid wasps A. nilaparvatae could provide a reference for the molecular biology research of the parasitoids, and the identification and analysis of olfactory binding proteins not only help us further clarify the physiological characteristics and parasitic mechanism of the parasitoids, but also promote the utilization of natural enemy resources.

scholarly journals The Effects of Exogenous Lactate Administration on the IGF1/Akt/mTOR Pathway in Rat Skeletal Muscle

2020 ◽  
Vol 17 (21) ◽  
pp. 7805
Author(s):  
Sunghwan Kyun ◽  
Choongsung Yoo ◽  
Hun-Young Park ◽  
Jisu Kim ◽  
Kiwon Lim
Keyword(s):  
Skeletal Muscle ◽  
Protein Synthesis ◽  
Protein Expression ◽  
Lactate Concentration ◽  
Ring Finger ◽  
Receptor Protein ◽  
Mrna Levels ◽  
Sprague Dawley ◽  
Expression Levels ◽  
Igf Receptor

We investigated the effects of oral lactate administration on protein synthesis and degradation factors in rats over 2 h after intake. Seven-week-old male Sprague–Dawley rats were randomly divided into four groups (n = 8/group); their blood plasma levels of lactate, glucose, insulin, and insulin-like growth factor 1 (IGF1) were examined following sacrifice at 0, 30, 60, or 120 min after sodium lactate (2 g/kg) administration. We measured the mRNA expression levels of protein synthesis-related genes (IGF receptor, protein kinase B (Akt), mammalian target of rapamycin (mTOR)) or degradation-related genes (muscle RING-finger protein-1 (MuRF1), atrogin-1) and analyzed the protein expression and phosphorylation (activation) of Akt and mTOR. Post-administration, the plasma lactate concentration increased to 3.2 mmol/L after 60 min. Plasma glucose remained unchanged throughout, while insulin and IGF1 levels decreased after 30 min. The mRNA levels of IGF receptor and mTOR peaked after 60 min, and Akt expression was significantly upregulated from 30 to 120 min. However, MuRF1 and atrogin-1 expression levels were unaffected. Akt protein phosphorylation did not change significantly, whereas mTOR phosphorylation significantly increased after 30 min. Thus, lactate administration increased the mRNA and protein expression of protein-synthesis factors, suggesting that it can potentially promote skeletal muscle synthesis.

Developmental regulation of a secreted gelatin-binding protein during myogenesis in vitro

1987 ◽  
Vol 65 (12) ◽  
pp. 1031-1038 ◽  
Author(s):  
Anat Lev ◽  
Paul C. Holland
Keyword(s):  
Skeletal Muscle ◽  
Molecular Weight ◽  
Binding Proteins ◽  
Type I Collagen ◽  
De Novo ◽  
Binding Protein ◽  
Apparent Molecular Weight ◽  
Muscle Cells ◽  
Type I ◽  
Collagen Binding

Collagen has a stimulatory effect on the differentiation of skeletal muscle cells in culture. Putative collagen-binding proteins were isolated from detergent-solubilized cultures of the L6 rat muscle cell line and primary clonal cultures of human skeletal muscle satellite cells, using gelatin–Sepharose affinity chromatography. In addition to fibronectin, which has been reported by others to be synthesized by cultured muscle cells, we found that muscle cultures synthesized gelatin-binding proteins of lower apparent molecular weight. Only one of these proteins was secreted into the growth medium and bound to type I collagen. Binding of this protein to gelatin and collagen–Sepharose was resistant to repeated washing with 1 M NaCl and nonionic detergent. The secreted gelatin-binding protein had an apparent molecular weight of 63 000 – 72 000, depending upon the conditions of electrophoresis. The lack of reactivity of the secreted protein with polyclonal antisera against fibronectin, the lack of effect of protease inhibitors on its appearance in the medium, and the rapid de novo production of the protein during pulse labeling with radioactive methionine indicated that it was not a fibronectin fragment. The rate of synthesis of the secreted gelatin-binding protein increased markedly during the myogenesis of rat and human cultures.

scholarly journals Activated protein kinase C α associates with annexin VI from skeletal muscle

1998 ◽  
Vol 330 (2) ◽  
pp. 675-681 ◽  
Author(s):  
Carsten SCHMITZ-PEIFFER ◽  
L. Carol BROWNE ◽  
H. John WALKER ◽  
J. Trevor BIDEN
Keyword(s):  
Skeletal Muscle ◽  
Protein Kinase C ◽  
Protein Kinase ◽  
Binding Proteins ◽  
Muscle Protein ◽  
Binding Protein ◽  
Calcium Dependent ◽  
Kinase C ◽  
Annexin Vi ◽  
Overlay Assay

We have previously detected a number of protein kinase C (PKC) α-binding proteins in skeletal muscle cytosol by blot overlay assay, and now identify the major, 69 kDa binding protein as annexin VI by immunoblotting and overlay assay of hydroxyapatite chromatography fractions. Annexin VI was also detected in immunoprecipitates of PKC α. Annexin VI and PKC α are both calcium-dependent phospholipid-binding proteins, and detection of the interaction was dependent on the presence of calcium and phosphatidylserine (PS). The association probably involves specific protein-protein interactions rather than mere bridging by lipid molecules: firstly, detection of PKC α-annexin VI complexes by overlay assay was not diminished when PS concentrations were increased over a 10-fold range, while that of other PKC α-binding protein complexes was reduced or abolished; secondly, the presence in the overlay assay of a PKC pseudosubstrate peptide, analogous to a PKC sequence previously found to be involved in PKC binding activity, reduced complex formation; thirdly, we were also able to detect annexin VI interaction with PKC β by overlay of skeletal muscle cytosol, but not with PKC ϴ, the major novel PKC in this tissue, suggesting sequences specific to calcium-dependent PKC isoenzymes are involved. While other annexin isoforms may be PKC substrates or inhibitors, annexin VI phosphorylation by PKC α could not be detected after co-purification, while phosphorylation of subsequently-added histone IIIS was readily observed. Annexin VI is a major skeletal muscle protein and our data are consistent with a role for this isoform in the control of calcium-dependent PKC.

Expression of calcium-binding proteins in pathways from the nucleus of the basal optic root to the cerebellum in pigeons

2008 ◽  
Vol 25 (5-6) ◽  
pp. 701-707 ◽  
Author(s):  
DOUGLAS R.W. WYLIE ◽  
JANELLE M.P. PAKAN ◽  
CRISTIÁN GUTIÉRREZ-IBÁÑEZ ◽  
ANDREW N. IWANIUK
Keyword(s):  
Protein Expression ◽  
Calcium Binding ◽  
Binding Proteins ◽  
Binding Protein ◽  
Calcium Binding Proteins ◽  
Calcium Binding Protein ◽  
Neural Pathways ◽  
Optokinetic Response ◽  
Neuronal Tracing ◽  
Fluorescent Immunohistochemistry

AbstractCalcium-binding protein expression has proven useful in delineating neural pathways. For example, in birds, calbindin is strongly expressed in the tectofugal pathway, whereas parvalbumin (PV) is strongly expressed in the thalamofugal pathway. Whether neurons within other visual regions also differentially express calcium-binding proteins, however, has not been extensively studied. The nucleus of the basal optic root (nBOR) is a retinal-recipient nucleus that is critical for the generation of the optokinetic response. The nBOR projects to the cerebellum both directly and indirectly via the inferior olive (IO). The cerebellar and IO projections originate from different neurons within the nBOR, but whether they can also be differentiated based on calcium-binding protein expression is unknown. In this study, we combined retrograde neuronal tracing from the cerebellum and IO with fluorescent immunohistochemistry for PV and calretinin (CR) in the nBOR of pigeons. We found that about half (52.3%) of the cerebellar-projecting neurons were CR+ve, and about one-third (33.6%) were PV+ve. Most (90%) of these PV+ve cells were also labeled for CR. In contrast, very few of the IO-projecting neurons expressed CR or PV (≤2%). Thus, the direct nBOR–cerebellar and indirect nBOR–olivocerebellar pathways to the cerebellum can be distinguished based on the differential expression of CR and PV.

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