Translation Conceptofcolinearity: a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a

Para além do fenómeno do wobble,… … há que considerar

• Desvios ao código genético – Excepções ao código genético universal (constituitivos)- desvios muito observados em genomas mitocondriais – Pontuais (site-specific variations)- geralmente envolvem o codão stop. • Ex. inserção da selenocisteína no codão UGA

• Ambiguidades no código genético – Codão de iniciação: AUG, GUG, UUG, CUG – fMet-tRNAfMet

Incorporation of selenocysteine into a growing polypeptide chain

A specialized tRNA is charged with serine by the normal seryl-tRNA synthetase, and the serine is subsequently converted enzymatically to selenocysteine

A specific RNA structure in the mRNA (a stem and loop structure with a particular nucleotide sequence) signals that selenocysteine is to be inserted at the neighboring UGA codon. This event requires the participation of a selenocysteine-specific factor containing selenocystein

Protein Organism

Prokaryotic enzymes Formate Clostridium thermoaceticum, Clostridium thermoautotrophicum, Enterobacter dehydrogenase aerogenes, Escherichia coli, Methanococcus vaniellii Glycine reductase Clostridium purinolyticum, Clostridium sticklandii NiFeSe hydrogenase Desulfomicrobium baculatum, Methanococcus voltae

Eukaryotic enzymes Glutathione Human, cow, rat, mouse peroxidase Selenoprotein P Human, cow, rat Selenoprotein W Rat Type 1 deiodinase Human, rat, mouse, dog Type 2 deiodinase Frog Type 3 deiodinase Human, rat, frog Unusual types of aminoacylation

In some bacteria, tRNAGln is aminoacylated with glutamic acid, which is then converted to glutamine by transamidation The special tRNA used in initiation of translation in bacteria is aminoacylated with , which is then converted to N-formylmethionine (transformilase)

tRNASeCys in various organisms is initially aminoacylated with serine

Selenocysteine is the same as cysteine but with the sulfur replaced with a selenium atom in the R group

Genomes 11.5 Translation in prokaryotes Procaryotic initiate transcription at -binding sites Structure of a typical bacterial mRNA molecule

Shine-Dalgarno sequences can be located anywhere (but specifically) along an mRNA molecule.

This permits bacteria to synthesize more than one type of protein from a single mRNA molecule Shine-Dalgarno consensus sequence vs Ribosome binding site

* rRNArRNA 16S16S bacteriannobacterianno

Emparelhamento de bases que Posições dentro do rRNA 16S de E. coli que confere estrutura a rRNA 16S interagem com a proteína ribossomal 5S Prokaryotic ribosome (functional sites)

Peptidyl Transferase (rRNA 23S) 3’ end 16S rRNA

f-MetentersattheP site In prokaryotic cells, transcription and translation take place simultaneously An mRNA molecule may be transcribed simultaneously by several ribosomes

Ribossomes organized in polissomes

The mRNA is translated in the 5 -to-3 direction, and the N-terminal end of a protein is made first, with each cycle adding one to the C-terminus of the polypeptide chain Four steps involved in translation INITIATION of translation in bacterial cells requires several initiation factors and GTP

Dynamic equilibrium

IF3 binds to the small unit of ribosome preventing large subunit from binding F-Met-tRNA forms a complex with IF-2 and GTP. IF-2 directs initiator tRNAMet

EF-1, blocks A site and is responsible for conformational modification of small subunit IF-1, IF-2 and IF-3 dissociate from the complex, GTP is hydrolyzed to GDP and the large subunit joins to create the 70S initiation complex The ELONGATION of translation comprises three steps

Charged tRNA is placed into the A site, GTP is cleaved and EF-Tu-GDP complex is released

Complex EF-Tu, EF-Ts, GTP and charged tRNA EF-Tu, directs the next tRNA

EF-G, mediates translocation

The peptide bond formation releasestheaaintheP site from its tRNA

The position at which the growing peptide chain is attached to a tRNA does not change during the elongation cycle: it is always linked to the tRNA present in the P site of the large subunit TERMINATION of translation

Translation ends when a stop codon is encountered; there is no tRNA with an anticodon that can pair with the codon in the site A

Peptide release from the tRNA in the P site

RF-1 UAA UAG RF-2 UAA UGA RF-3 stimulates dissociation of RF-1 and RF-2

RRF- ribosome recycling factor

Translation in Translation in eukaryotes

• Efficient translation initiation also requires the poly-A tail of the mRNA bound by poly-A- binding proteins which, in turn, interact with eIF4G. In this way, the translation apparatus ascertains that both ends of the mRNA are intact before initiating translation An eukaryotic polyribosome

Schematic drawing showing how a series of ribosomes can simultaneously translate the same eucaryotic mRNA molecule

Electron micrograph of a polyribosome from a eucaryotic cell The competition between mRNA translation and mRNA decay

The same two features of mRNA the 5’ cap and the 3’ poly-A site are used in both translation initiation and deadenylation-dependent mRNA decay

The enzyme (called DAN) that shortens the poly-A tail in the 3’ to 5’ direction associates with the 5’ cap Two mechanisms of translation initiation

Internal ribosome entry sites

The cap-dependent mechanism requires a set of The IRES-dependent mechanism requires only a initiation factors whose assembly on the mRNA is subset of the normal translation initiating factors, stimulated by the presence of a 5’ cap and a poly-A tail and these assemble directly on the folded IRES The initiation phase of protein synthesis in eucaryotes

eIF4E

eIF2 binds to tRNAMet eIF4A and eIF4B have activity eEF-1, , similar to EF-Tu

eEF-2, translocation factor, similar to EF-G eRF-1 similar to tRNA and recognizes termination codon eRF-3 similar to bacteria RF-3 Regulation of at translational level – Translation initiation efficiency (includes RBS affinity in prokaryotes)

– Polarity (in prokaryotes)

– Codon usage (codon preference or codon bias)

– mRNA degradation Production of distinct amylase mRNA molecules by different splicing events in cells of the salivary gland and liver of the mouse affects the translation efficiency and though the level of amylase synthesis

Transcripts with different 5’-UTR Negative translational control

• This form of control is mediated by a sequence-specific RNA-binding protein that acts as a translation repressor. Binding of the protein to an mRNA molecule decreases the translation of the mRNA

• The illustration is modeled on the mechanism that causes more ferritin (an iron storage protein) to be synthesized when the free iron concentration in the cytosol rises; the iron-sensitive translation repressor protein is called aconitase Two posttranscriptional controls mediated by iron

Both responses are mediated by the same iron-responsive regulatory protein, aconitase, which recognizes common features in a stem-and-loop structure in the mRNAs encoding ferritin and transferrin receptor

IRE- iron response element

Transferrin receptor and ferritin are regulated by different types of mechanisms, their levels respond oppositely to iron concentrations even though they are regulated by the same iron-responsive regulatory protein

In response to an increase in iron … and decreases synthesis of concentration in the cytosol, a cell transferrin receptors in order to increases its synthesis of ferritin import less iron across the in order to bind the extra iron… plasma membrane Steps at which eucaryotic gene expression can be controlled

1- transcriptional activators methylation chromatin remodelation … 4- polyadenylation/deanylation 5’-UTR binding proteins RNAi 2- altenative splicing … RNA editing RNAi …