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What Are Ribosomes?

Ribosomes are one of the essential cell organelles, which play a critical part in the course of translating the genetic information reserved in the genome into protein products. Ribosomes are found in both prokaryotes and eukaryotes. They float freely in the cytosol of prokaryotic/eukaryotic cells or on the endoplasmic reticulum of eukaryotic cells. The ribosome is a complex made of protein and ribonucleic acid (RNA). Around 37%- 62% of ribosomes is comprised of RNA and the rest is proteins, specifically ribosomal RNA (rRNA) and transfer RNA (tRNA). The ribosome consists of two subunits. The small subunit is where message RNAs (mRNAs) bind and decode, whereas the large subunit is where the amino acids are synthesized. Prokaryotes have 70S ribosomes comprised of the small subunit of 30S and the large subunit of 50S, while eukaryotes have 80S ribosomes comprised of the small subunit of 40S and the large subunit of 60S.

Ribosomes are comprised of a large subunit (top) and a small subunit (bottom).

Figure 1. Ribosomes are comprised of a large subunit (top) and a small subunit (bottom).

Functions of Ribosomes

As mentioned above, ribosomes are where the mRNAs are translated into protein molecules. During cellular translation, which is the second major step of gene expression, mRNAs relates the DNA sequences to the amino acid sequences. The mRNA sequences thus serve as a template to assemble the chain of amino acids orderly. The tRNA molecules are responsible for reading the triplet code in the mRNA through complementary base-pairing and attaching to a specific amino acid. Within the ribosome, the mRNA and aminoacyl-tRNA complexes are held together closely, which facilitates base-pairing. The rRNAs are in charge of catalyzing the attachment of each new amino acid to the extended amino acid chain. The ribosome moves along the mRNA until it reaches one of the “stop” codes. The ribosome subsequently releases both the polypeptide and the mRNA. The polypeptide will fold into its native conformation and act as a protein in the metabolism of the cells.

Ribosome Profiling

Ribosome profiling, also known as ribo-seq, is a next-generation sequencing (NGS)-based technique that produces a global snapshot of the ribosomes active in a cell at the particular conditions, known as a translatome. Genome-wide analyses of gene expression have focused on the abundance of mRNA molecules as measured either by RNA sequencing (RNA-seq) or microarray. Ribosome profiling targets only mRNA molecules protected by ribosomes, which is different from RNA-seq. It is a powerful tool for revealing the location of translation initiation sites, the complement of translated ORFs, the distribution of ribosomes on an mRNA, and the efficiency of translating ribosomes. Ribosome profiling uses deep sequencing to monitor in vivo translation. Studies using this method have provided new insights into the identity and the amount of proteins that are created by cells, as well as detailed views into the mechanism of protein synthesis.

 Workflow for ribosome profiling

Figure 2. Workflow for ribosome profiling (Brar and Weissman 2015).

References:

  1. Ingolia N T. Ribosome profiling: new views of translation, from single codons to genome scale. Nature Reviews Genetics, 2014, 15(3): 205-213.
  2. Brar G A, Weissman J S. Ribosome profiling reveals the what, when, where and how of protein synthesis. Nature reviews Molecular cell biology, 2015, 16(11): 651-664.

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