Resistance Exercise Training and The Regulation of Muscle Protein Synthesis
Peter M. Tiidus, Rebecca E. K. MacPherson, Paul J. LeBlanc, Andrea R. Josse in The Routledge Handbook on Biochemistry of Exercise, 2020
Ribosomes are organelles which act to produce peptide chains corresponding to an mRNA strand, and therefore an increase in their content or capacity would elevate the rates at which new muscle proteins could be produced. The two predominant ways this may occur are through (1) an increase in the number of ribosomes bound to a single mRNA strand, that is, upon full activation the distance between ribosomes on an mRNA strand can shorten from ∼90 to ∼30 nucleotides (106) and (2) an elevated total content of ribosomes, both of which increase the protein yield per strand of mRNA. Mechanistically, ribosomal biogenesis is regulated by a series of transcription factors which act to elevate the rates at which ribosomal RNA (rRNA) and mRNA corresponding to ribosomal proteins are transcribed (106). One such transcription factor is c-myc which regulates both rRNA and ribosomal protein mRNA expression (33, 92). Overexpression of this transcription factor elevates rRNA levels and ribosomal protein content (92), whereas its inhibition elicits reductions in such parameters (33). Research regarding the upstream regulation of this transcription factor is slightly contentious, with data suggesting both mTORC1-dependent (53) and -independent (5) post-translational modifications. Nevertheless, this mechanism is implicated in the regulation of ribosomal biogenesis and is reported to be sensitive to contraction, albeit in rodent skeletal muscle (111).
The Injured Cell
Jeremy R. Jass in Understanding Pathology, 2020
The nucleus is enclosed by a nuclear membrane and comprises chromosomes and a nucleolus. The material forming the chromosomes is called chromatin and consists of DNA and protein. The chromosomes only assume their characteristic condensed form during mitosis (cell division) (Fig. 5). During the remainder of the cell cycle (interphase), chromosomes are highly dispersed and cannot be seen individually. Chromatin exists either in a densely packed form (heterochromatin) or a more dispersed form (euchromatin). Euchromatin is the form that is being genetically expressed (transcribed). Chromatin has a very complicated structure. Short lengths of DNA (about 200 base pairs) are packaged up with proteins (histones) to form complexes known as nucleosomes. These are assembled as repeating units into higher order chromatin structures. The nucleolus is the site of ribosomal RNA synthesis and ribosome assembly.
Diamond–Blackfan Anemia
Dongyou Liu in Handbook of Tumor Syndromes, 2020
Ribosome is a cellular structure involved in the translation of messenger RNA (mRNA) to an amino acid sequence (protein). In eukaryotes, ribosome (measuring 80S in size) is separated into the small (40S) and the large (60S) subunit, each of which consists of ribosomal RNA (rRNA) and RP. The large 60S subunit comprises a 5S rRNA, a 28S rRNA, a 5.8S subunit, and ∼46 RP (or RPL, i.e., RP associated with large ribosomal subunit); whereas the small 40S subunit contains 18S rRNA and ∼33 RP (or RPS, i.e., RP associated with small ribosomal subunit). During ribosome biogenesis, RP are synthesized by RP genes in pre-existing ribosomes in the cytoplasm and transferred into the nucleus to assemble with rRNA for new ribosomes. In addition, some RP take part in signaling pathways within the cell that regulate cell division and control apoptosis [9–13].
Identification of circRNAs and circRNA-miRNA-mRNA regulatory network in radiation-induced heart disease
Published in International Journal of Radiation Biology, 2023
Shutong Shen, Ping Lyu, Baixia Yang, Xi Yang, Yida Li, Zhengfei Zhu, Li Shen
In mRNA and circRNA, ribosomal RNA is depleted, and the remaining RNA is divided into many small fragments, which are reverse transcribed to generate cDNA. The total amount of ribosomal RNA was 5 ug according to the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, CA, USA). After purifying, a portion of the poly(A)- or poly(A)+ RNA was minced into fragments using divalent cations at high temperature. Next, reverse transcription was performed using the cleaved RNA fragments to generate cDNA using the method of the mRNA-Seq sample preparation kit (Illumina, San Diego, CA, USA). Attach a single or dual indexed adapter to a fragment, then use AMPureXP beads for size selection. The double-stranded DNAs which were U-labeled was amplified by PCR using the UDG heat-labile enzyme method as following: 95 °C initial denaturation for 3 min; eight times of 98 °C denaturation for 15 s, 60 °C annealing for 15 s, and 72 °C extension for 30 s; and finally, 72 °C extension for 5 min. In the final cDNA library, the average length of the inserts was 300 bp (±50 bp). Ultimately, the paired-end sequencing was performed on the Illumina Hiseq 4000 (LC Bio, China).
Dysbiotic but nonpathogenic shift in the fecal mycobiota of patients with rheumatoid arthritis
Published in Gut Microbes, 2022
Eun Ha Lee, Hyun Kim, Jung Hee Koh, Kwang Hyun Cha, Kiseok Keith Lee, Wan-Uk Kim, Cheol-Ho Pan, Yong-Hwan Lee
The V3–V4 regions of 16S ribosomal RNA (rRNA) genes were amplified using the Illumina-adapted universal primers 314F/805R. Each PCR reaction contained 12.5 ng of genomic DNA, 2.5 μL of Ex Taq 10× PCR buffer (Takara, Japan), 2.5 μL of dNTP mixture (Takara), 0.125 μL of Takara Ex Taq (Takara), 5 μL of each primer (200 nM final concentration), and distilled water to a total volume of 25 μL. The following thermocycler protocol was used: initial denaturing at 95°C for 3 min; 25 cycles of denaturing at 95°C for 30s, primer annealing at 55°C for 30s, and extension at 72°C for 30s; and final extension at 72°C for 5 min. PCR products were purified using AMPure XP beads (Beckman Coulter, USA), then quantified using a KAPA Library Quantification kit (KAPA Biosystems, USA). Sequencing was conducted on the MiSeq platform using a paired-end 2 ×300 base pairs reagent kit (Illumina, USA).
Ribosomopathies and cancer: pharmacological implications
Published in Expert Review of Clinical Pharmacology, 2022
Gazmend Temaj, Sarmistha Saha, Shpend Dragusha, Valon Ejupi, Brigitta Buttari, Elisabetta Profumo, Lule Beqa, Luciano Saso
Ribosomes are ribonucleoprotein complexes discovered by Palade and Porter in 1954 as small round bodies associated with the endoplasmic reticulum (ER), as observed using an electronic microscope [1]. It is well known that genetic information is stored in deoxyribonucleic acid (DNA) molecules, and by the highly regulated mechanism of transcription, genes, as particular segments of DNA, are copied into mRNA (ribonucleic acid) by the RNA polymerase enzyme. Ribosome macromolecules catalyze the translation of information from mRNAs into functional polypeptide chains. Ribosomes consist of large and small subunits. Eukaryotic ribosome consists of a smaller 40S subunit and a large 60S subunit. The smaller 40S subunit consists of 18S ribosomal RNA (rRNA) and 33 ribosomal protein small (RPS) subunits, whereas the 60S subunit contains 28S, 5S, and 5.8S rRNA and 47 ribosomal protein large (RPL) [2,3].
Related Knowledge Centers
- Ribosomal DNA
- Ribosomal Protein
- Ribosome
- Ribozyme
- Transfer Rna
- Messenger Rna
- NON-Coding Rna
- Protein Biosynthesis
- Ribosomal DNA
- Ssu Rrna
- Lsu Rrna
- Transfer Rna
- Messenger Rna