Prokaryotic Translation and Transcription

Transcription
Transcription is the process of transcribing one strand of DNA into a complementary strand of RNA. It is catalyzed by the enzyme RNA polymerase. It takes place in the direction from the 5' end of the new RNA molecule to its 3' end.

Transcription in prokaryotes follows a similar basic mechanism to that of eukaryotes. For more information with an explanation, see the article Transcription in Prokaryotes and the Operon Model.

RNA polymerase
Transcription in bacteria is ensured by a single RNA polymerase:


 * 5 protein subunits α, β, β', ω and σ; α in two copies
 * The σ subunit is used to bind n DNA, it dissociates after the start of synthesis

Initiation
Initiation of RNA synthesis occurs in bacteria as follows:


 * promoter recognition using the sigma factor (multiple promoter variants + σ)
 * σ recognizes −35 and −10 (TATA box/Pribnow box) of the consensus sequence
 * opening of the transcription bubble
 * synthesis of a short chain around 9 nt, dissociation of the σ factor
 * energetically, transcription is driven by hydrolysis of the macroergic bond of the incoming ribonucleoside triphosphate

Termination
Transcription termination of prokaryotes can be Rho (ρ) independent or ρ dependent:

– Rho independent termination:


 * a termination sequence containing inverted repeats separated by a non-repetitive stretch rich in GC pairs
 * forming a transcription-stopping loop structure
 * the following stretch of polyA (in DNA) allows easy dissociation

– Rho dependent


 * The Rho factor recognizes a sequence in RNA
 * it moves towards the polymerase and causes dissociation

Translation
Translation is the process of synthesizing a polypeptide chain based on the information contained in mRNA. Triplets of nucleotides in RNA are translated into the form of individual amino acids of a polypeptide according to the rules of the genetic code. Translation in prokaryotes follows a similar basic mechanism to that of eukaryotes. Further information with an explanation can be found in the article Translation in prokaryotes, Translation and the question Translation in eukaryotes , the basic features and specificities of prokaryotic translation are presented here.

Aminoacyl-tRNA synthesis
The tRNA molecule brings the amino acid residue to the ribosome. Bacterial tRNAs are characterized by:


 * roughly 60 types of tRNA (versus 100–110 in a mammalian cell)
 * 73–93 nucleotides in length
 * secondary structure of the shape of a four-leaf clover, tertiary structure of the letter L
 * acceptor arm terminated by a CCA triplet
 * dihydrouridine arm (D or DHU), pseudouridine arm (T or TΨC), variable arm
 * anticodon arm

Activation of tRNA by binding to an amino acid residue occurs through the enzyme aminoacyl-tRNA-synthetase with the consumption of ATP:


 * amino acid + ATP ↔ aminoacyl-AMP + pyrophosphate
 * aminoacyl-AMP + tRNA ↔ aminoacyl-tRNA + AMP

The reaction is thermodynamically driven by pyrophosphate decomposition.

Prokaryotic ribosome
The bacterial ribosome, like the eukaryotic ribosome, consists of two subunits:

– 30S subunit


 * 16S rRNA (with 3' end complementary to Shine-Delgarno sequence)
 * 21 proteins

– 50S subunit


 * 5S rRNA, 23S rRNA (with peptidyltransferase activity – catalyzes peptide chain elongation)
 * 31 proteins

Translation initiation
Proteosynthesis itself can be divided into initiation, elongation and termination. Bacterial initiation proceeds as follows:


 * the first amino acid of most bacteria is N-formylmethionine attached to the special tRNA fMet . Usually 1–3 N-terminal amino acids are cleaved post-translationally.
 * N-formylmethionyl-tRNA fMet binds to the free 30S subunit of the ribosome
 * The mRNA is bound by the interaction of the 3' end of the 16S rRNA with a Shine-Delgarno sequence near the 5' end (RBS - ribosome-binding site), usually 8 nucleotides from the initiation codon AUG
 * fMet-tRNA interacts by anticodon with initiation codon AUG (sometimes GUG)
 * The 50S subunit of the ribosome binds so that the fMet-tRNA is in the P site of the ribosome
 * initiation of translation requires initiation factors IF1, IF2 and IF3 and consumes energy in the form of GTP

Elongation
During elongation, amino acid residues are added to the C-terminus of the polypeptide through a repeating sequence of events:


 * The P site of the ribosome (see translation ) is occupied by N-formylmethionyl-tRNAfMet or peptidyl tRNA, and the A site is empty
 * aminoacyl-tRNA corresponding to the following codon binds to the A site with the help of EF-Tu factor and GTP consumption
 * a transpeptidase reaction catalyzed by 23S rRNA takes place – the α-amino group of the amino acid residue in the A site nucleophilically attacks the α-carboxyl group of the C-terminal amino acid in the P site. The peptide thereby moves to the tRNA in the A site. The reaction does not consume any energy-rich molecules.
 * translocation occurs: the peptidyl-tRNA moves from the A site to the P site, the ribosome moves one codon to the mRNA, and the previous tRNA moves to the E site. The process requires the EF-G factor and the hydrolysis of a GTP molecule
 * The tRNA at the E site leaves the ribosome and the cycle repeats

Termination
Termination of translation in a prokaryotic cell occurs as follows:


 * one of the three (usually) termination (nonsense) codons – UAA, UAG or UGA – gets to A instead of the ribosome
 * is recognized by one of three termination factors (RF-1, RF-2 or RF-3)
 * the peptide is hydrolytically released by peptidyl transferase activity
 * dissociation of ribosome subunits and translation proteins occurs.
 * IF-3 remains bound to the 30S subunit, preventing reassociation with the 50S subunit

Related articles

 * Transcription
 * Transcription in Prokaryotes
 * Translation in Prokaryotes
 * Translation in Eukaryotes
 * Translation
 * Regulation of gene expresion in Prokaryotes
 * RNA
 * mRNA