Translation (biology)

Translation is the third stage of protein biosynthesis (part of the overall process of gene expression). In translation, messenger RNA (mRNA) produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. In Bacteria, translation occurs in the cell's cytoplasm, where the large and small subunits of the ribosome are located, and bind to the mRNA. In Eukaryotes, translation occurs across the membrane of the endoplasmic reticulum. The ribosome facilitates decoding by inducing the binding of tRNAs with complementary anticodon sequences to that of the mRNA. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is "read" by the ribosome in a fashion reminiscent to that of a stock ticker and ticker tape.

In many instances, the entire ribosome/mRNA complex will bind to the outer membrane of the rough endoplasmic reticulum and release the nascent protein polypeptide inside for later vesicle transport and secretion outside of the cell. Many types of transcribed RNA, such as transfer RNA, ribosomal RNA, and small nuclear RNA, do not undergo translation into proteins.

Translation proceeds in four phases: activation, initiation, elongation and termination (all describing the growth of the amino acid chain, or polypeptide that is the product of translation). Amino acids are brought to ribosomes and assembled into proteins.

In activation, the correct amino acid is covalently bonded to the correct transfer RNA (tRNA). The amino acid is joined by its carboxyl group to the 3' OH of the tRNA by a ester bond. When the tRNA has an amino acid linked to it, it is termed "charged". Initiation involves the small subunit of the ribosome binding to 5' end of mRNA with the help of initiation factors (IF). Termination of the polypeptide happens when the A site of the ribosome faces a stop codon (UAA, UAG, or UGA). No tRNA can recognize or bind to this codon. Instead, the stop codon induces the binding of a release factor protein that prompts the disassembly of the entire ribosome/mRNA complex.

A number of antibiotics act by inhibiting translation; these include anisomycin, cycloheximide, chloramphenicol, tetracycline, streptomycin, erythromycin, and puromycin, among others. Prokaryotic ribosomes have a different structure from that of eukaryotic ribosomes, and thus antibiotics can specifically target bacterial infections without any detriment to a eukaryotic host's cells.

Contents


Basic mechanisms

The mRNA carries genetic information encoded as a ribonucleotide sequence from the chromosomes to the ribosomes. The ribonucleotides are "read" by translational machinery in a sequence of nucleotide triplets called codons. Each of those triplets codes for a specific amino acid.

The ribosome molecules translate this code to a specific sequence of amino acids. The ribosome is a multisubunit structure containing rRNA and proteins. It is the "factory" where amino acids are assembled into proteins. tRNAs are small noncoding RNA chains (74-93 nucleotides) that transport amino acids to the ribosome. tRNAs have a site for amino acid attachment, and a site called an anticodon. The anticodon is an RNA triplet complementary to the mRNA triplet that codes for their cargo amino acid.

Aminoacyl tRNA synthetase (an enzyme) catalyzes the bonding between specific tRNAs and the amino acids that their anticodons sequences call for. The product of this reaction is an aminoacyl-tRNA molecule. This aminoacyl-tRNA travels inside the ribosome, where mRNA codons are matched through complementary base pairing to specific tRNA anticodons. The amino acids that the tRNAs carry are then used to assemble a protein. After the new amino acid is added to the chain, the energy provided by the hydrolysis of a GTP bound to the translocase EF-G (in prokaryotes) and eEF-2 (in eukaryotes) moves the ribosome down one codon towards the 3'end. The energy required for translation of proteins is significant. For a protein containing n amino acids, the number of high-energy Phosphate bonds required to translate it is 4n+1 . The rate of translation varies; it is significantly higher in prokaryotic cells (up to 17-21 amino acid residues per second) than in eukaryotic cells (up to 6-9 amino acid residues per second). [1]

Genetic code

Whereas other aspects such as the 3D structure, called tertiary structure, of protein can only be predicted using sophisticated algorithms, the amino acid sequence, called primary structure, can be determined solely from the nucleic acid sequence with the aid of a translation table.

This approach may not give the correct amino acid composition of the protein, in particular if unconventional amino acids such as selenocysteine are incorporated into the protein, which is coded for by a conventional stop codon in combination with a downstream hairpin (SElenoCysteine Insertion Sequence, or SECIS).

There are many computer programs capable of translating a DNA/RNA sequence into a protein sequence. Normally this is performed using the Standard Genetic Code; many bioinformaticians have written at least one such program at some point in their education. However, few programs can handle all the "special" cases, such as the use of the alternative initiation codons. For instance, the rare alternative start codon CTG codes for Methionine when used as a start codon, and for Leucine in all other positions.

Example: Condensed translation table for the Standard Genetic Code (from the NCBI Taxonomy webpage).

   AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
 Starts = ---M---------------M---------------M----------------------------
 Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG


Translation tables

Even when working with ordinary Eukaryotic sequences such as the Yeast genome, it is often desired to be able to use alternative translation tables—namely for translation of the mitochondrial genes. Currently the following translation tables are defined by the NCBI Taxonomy Group for the translation of the sequences in GenBank:

 1: The Standard
 2: The Vertebrate Mitochondrial Code
 3: The Yeast Mitochondrial Code
 4: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the
Mycoplasma/Spiroplasma Code 5: The Invertebrate Mitochondrial Code 6: The Ciliate, Dasycladacean and Hexamita Nuclear Code 9: The Echinoderm and Flatworm Mitochondrial Code 10: The Euplotid Nuclear Codecbn dxh 11: The Bacterial and Plant Plastid Code 12: The Alternative Yeast Nuclear Code 13: The Ascidian Mitochondrial Code 14: The Alternative Flatworm Mitochondrial Code 15: Blepharisma Nuclear Code 16: Chlorophycean Mitochondrial Code 21: Trematode Mitochondrial Code 22: Scenedesmus obliquus mitochondrial Code 23: Thraustochytrium Mitochondrial Code

Software examples

Example of computational translation - notice the indication of (alternative) start-codons:

VIRTUAL RIBOSOME
----
Translation table: Standard SGC0

>Seq1
Reading frame: 1

    M  V  L  S  A  A  D  K  G  N  V  K  A  A  W  G  K  V  G  G  H  A  A  E  Y  G  A  E  A  L
5' ATGGTGCTGTCTGCCGCCGACAAGGGCAATGTCAAGGCCGCCTGGGGCAAGGTTGGCGGCCACGCTGCAGAGTATGGCGCAGAGGCCCTG 90
   >>>...)))..............................................................................)))

    E  R  M  F  L  S  F  P  T  T  K  T  Y  F  P  H  F  D  L  S  H  G  S  A  Q  V  K  G  H  G
5' GAGAGGATGTTCCTGAGCTTCCCCACCACCAAGACCTACTTCCCCCACTTCGACCTGAGCCACGGCTCCGCGCAGGTCAAGGGCCACGGC 180
   ......>>>...))).......................................))).................................

    A  K  V  A  A  A  L  T  K  A  V  E  H  L  D  D  L  P  G  A  L  S  E  L  S  D  L  H  A  H
5' GCGAAGGTGGCCGCCGCGCTGACCAAAGCGGTGGAACACCTGGACGACCTGCCCGGTGCCCTGTCTGAACTGAGTGACCTGCACGCTCAC 270
   ..................)))..................)))......))).........)))......)))......))).........

    K  L  R  V  D  P  V  N  F  K  L  L  S  H  S  L  L  V  T  L  A  S  H  L  P  S  D  F  T  P
5' AAGCTGCGTGTGGACCCGGTCAACTTCAAGCTTCTGAGCCACTCCCTGCTGGTGACCCTGGCCTCCCACCTCCCCAGTGATTTCACCCCC 360
   ...)))...........................))).........))))))......)))..............................

    A  V  H  A  S  L  D  K  F  L  A  N  V  S  T  V  L  T  S  K  Y  R  *
5' GCGGTCCACGCCTCCCTGGACAAGTTCTTGGCCAACGTGAGCACCGTGCTGACCTCCAAATACCGTTAA 429
   ...............))).........)))..................)))...............***

Annotation key:
>>> : START codon (strict)
))) : START codon (alternative)
*** : STOP

See also

References

  1. Ross JF, Orlowski M (February 1982). . J. Bacteriol. 149 (2): 650–3. . 
  • Champe, Pamela C; Harvey, Richard A; Ferrier, Denise R (2004). (3rd ed.). Hagerstwon, MD: Lippincott Williams & Wilkins. . 
  • Cox, Michael; Nelson, David R.; Lehninger, Albert L (2005). (4th ed.). San Francisco...: W.H. Freeman. . 
  • Malys N, McCarthy JEG (2010). . Cellular and Molecular Life Sciences. .