Bacterial translation
Bacterial translation is the process by which messenger RNA is translated into proteins in bacteria.
Initiation
Initiation of translation in bacteria involves the assembly of the components of the translation system, which are: the two ribosomal subunits (
The ribosome has three active sites: the A site, the P site, and the E site. The A site is the point of entry for the aminoacyl tRNA (except for the first aminoacyl tRNA, which enters at the P site). The P site is where the peptidyl tRNA is formed in the ribosome. And the E site which is the exit site of the now uncharged tRNA after it gives its amino acid to the growing peptide chain.[1]
Canonical initiation: Shine-Dalgarno sequence
The majority of mRNAs in E. coli are prefaced with a
There are a lot of uncertainties even in the canonical model. The initiation site has been shown to be not strictly limited to AUG. Well-known coding regions that do not have AUG initiation codons are those of lacI (GUG)
The SD sequence also does not appear strictly necessary, as a wide range of mRNAs lack them and are still translated, with an entire phylum of bacteria (
70S scanning model
When translating a
Leaderless initiation
A number of bacterial mRNAs have no 5'UTR whatsoever, or a very short one. The complete 70S ribosome, with the help of IF2 (recruiting fMet-tRNA),[8] can simply start translating such a "leaderless" mRNA.[1]
A number of factors modify the efficiency of leaderless initiation. A 5' phosphate group attached to the start codon seems near-essential.[1] AUG is strongly preferred in E. coli, but not necessarily in other species. IF3 inhibits leaderless initiation.[1] A longer 5'UTR or one with significant secondary structure also inhibits leaderless initiation.[9]
Elongation
Elongation of the
Elongation starts when the fMet-tRNA enters the P site, causing a
The ribosome continues to translate the remaining codons on the mRNA as more aminoacyl-tRNA bind to the A site, until the ribosome reaches a stop codon on mRNA(UAA, UGA, or UAG).
The translation machinery works relatively slowly compared to the enzyme systems that catalyze DNA replication. Proteins in bacteria are synthesized at a rate of only 18 amino acid residues per second, whereas bacterial replisomes synthesize DNA at a rate of 1000 nucleotides per second. This difference in rate reflects, in part, the difference between polymerizing four types of nucleotides to make nucleic acids and polymerizing 20 types of amino acids to make proteins. Testing and rejecting incorrect aminoacyl-tRNA molecules takes time and slows protein synthesis. In bacteria, translation initiation occurs as soon as the 5' end of an mRNA is synthesized, and translation and transcription are coupled. This is not possible in eukaryotes because transcription and translation are carried out in separate compartments of the cell (the nucleus and cytoplasm).
Termination
Termination occurs when one of the three
Recycling
The post-termination complex formed by the end of the termination step consists of mRNA with the termination codon at the A-site, an uncharged tRNA in the P site, and the intact 70S ribosome. Ribosome recycling step is responsible for the disassembly of the post-termination ribosomal complex.
Depending on the tRNA,
Polysomes
Translation is carried out by more than one ribosome simultaneously. Because of the relatively large size of ribosomes, they can only attach to sites on mRNA 35 nucleotides apart. The complex of one mRNA and a number of ribosomes is called a polysome or polyribosome.[16]
Regulation of translation
When bacterial cells run out of nutrients, they enter stationary phase and downregulate protein synthesis. Several processes mediate this transition.[17] For instance, in E. coli, 70S ribosomes form 90S dimers upon binding with a small 6.5 kDa protein, ribosome modulation factor RMF.[18][19] These intermediate ribosome dimers can subsequently bind a hibernation promotion factor (the 10.8 kDa protein, HPF) molecule to form a mature 100S ribosomal particle, in which the dimerization interface is made by the two 30S subunits of the two participating ribosomes.[20] The ribosome dimers represent a hibernation state and are translationally inactive.[21] A third protein that can bind to ribosomes when E. coli cells enter the stationary phase is YfiA (previously known as RaiA).[22] HPF and YfiA are structurally similar, and both proteins can bind to the catalytic A- and P-sites of the ribosome.[23][24] RMF blocks ribosome binding to mRNA by preventing interaction of the messenger with 16S rRNA.[25] When bound to the ribosomes the C-terminal tail of E. coli YfiA interferes with the binding of RMF, thus preventing dimerization and resulting in the formation of translationally inactive monomeric 70S ribosomes.[25][26]
In addition to ribosome dimerization, the joining of the two ribosomal subunits can be blocked by RsfS (formerly called RsfA or YbeB).
Another ribosome-dissociation factor in Escherichia coli is HflX, previously a GTPase of unknown function. Zhang et al. (2015) showed that HflX is a heat shock–induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes. The N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock and possibly other stress conditions.[28]
Effect of antibiotics
Several
See also
- Prokaryotic initiation factors
- Prokaryotic elongation factors
References
- ^ PMID 26259514.
- S2CID 4208767.
- ^ "E.coli lactose operon with lacI, lacZ, lacY and lacA genes". Nucleotide Database. National Library of Medicine. 1993-05-05. Retrieved 2017-03-01.
- PMID 28334756.
- PMID 26912810.
- PMID 26888283.
- PMC 7518266.
- PMID 14670970.
- PMID 35456773.
- ^ Structure of the E. coli protein-conducting channel bound to at translating ribosome, K. Mitra, et al. Nature (2005), vol 438, p 318
- PMID 23582332.
- PMID 34756086.
- PMID 16166657.
- PMID 16487710.
- PMID 18497739.
- ^ Alberts B, et al. (2017). Molecular Biology of the Cell (6th ed.). Garland Science. pp. 301–303.
- PMID 24279750.
- PMID 8440252.
- PMID 11292794.
- PMID 20541509.
- PMID 7677746.
- PMID 10535924.
- S2CID 35493538.
- PMID 20733057.
- ^ PMID 22605777.
- S2CID 25255882.
- ^ PMID 22829778.
- S2CID 9228012.