Lecture 12 rRNA-tRNA processing-Protein Synthesis (2023)

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Lecture 12 tRNA/rRNA processing & Protein Synthesis Using Chapter 5 and 9 from Lodish et al., Molecular Biology; 9 th edition
Transport of mRNA Across the Nuclear Envelope • An mRNP exporter ensures directional export by binding mRNPs in the nucleus , facilitating transport across the NPC , and releasing the mRNPs when mRNP adapter proteins are phosphorylated in the cytoplasm . • The mRNP exporter binds most mRNAs cooperatively with SR proteins bound to exonic splicing enhancers and with REF associated with exon-junction complexes as well as with additional mRNP proteins. • Pre-mRNAs still bound to spliceosomes are not exported, ensuring only mature mRNAs reach the cytoplasm .
Remodeling of mRNPs during nuclear export (Fig. 9-26) • mRNP exporter: • Transports mRNPs through the Nuclear Pore Complex (NPC) • Heterodimer – large NXF1 (nuclear export factor) subunit and a small NXT1 (nuclear export transporter) • NXF1 – binds RNA and proteins in the mRNP complex proteins including REF (RNA export factor) , a component of the exon-junction complexes • Associates with SR proteins bound to exonic splicing enhancers
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Remodeling of mRNPs during nuclear export (Fig. 9-26) • mRNP export – mRNP remodeling: • Some mRNP proteins dissociate from nuclear mRNP complexes before export through an NPC. • Some mRNPs remain associated – CBC (cap binding complex), NXF1/NXT1, and PABPN1 (nuclear poly(A)- binding protein) bound to the poly(A) tail • exported with the mRNP • dissociate from the mRNP in the cytoplasm and are shuttled back into the nucleus through an NPC
Remodeling of mRNPs during nuclear export (Fig. 9-26) • mRNP in cytoplasm: • Translation initiation factor eIF4E replaces CBC bound to the 5ʹ cap. • PABPC1 (cytoplasmic poly(A)-binding protein) replaces PABPN1.
Cytoplasmic Mechanisms of Post-transcriptional Control • Stability of most mRNAs is controlled by poly(A) tail length and binding of various proteins to 3’ UTR sequences. • mRNA translation can be regulated by micro-RNAs and RNA interference by siRNAs and various degradation , cytoplasmic splicing, and polyadenylation mechanisms. • Many mRNAs are transported to specific subcellular locations by sequence- specific RNA-binding proteins that bind 3ʹ UTR localization sequences.
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Pathways for degradation of eukaryotic mRNAs (Fig. 9-30) • Cytoplasmic control of gene expression – mechanisms control the stability and localization of mRNA and translation into protein. • mRNA cytoplasmic degradation – several mechanisms (most eukaryote mRNAs have half-lives of many hours; some are much less stable).
Pathways for degradation of eukaryotic mRNAs (Fig. 9-30) • (a) Deadenylation-dependent mRNA degradation (most common pathway): • Deadenylase complex shortens poly(A) tail to ≤ 20 A residues. • Destabilizes cytoplasmic poly(A)-binding proteins PABPC1 (PABPC1) binding • PABC1 loss weakens interactions between the 5ʹ cap and translation initiation factors. • Deadenylated mRNA: • (1) decapped by the DCP1/DCP2 (Decapping enzymes) deadenylation complex and degraded by XRN1 (Exoribonuclease 1) , a 5ʹ→3ʹ exonuclease • (2) degraded by 3ʹ→5ʹ exonucleases in cytoplasmic exosomes Exosome: the multiprotein complex that degrades unprotected RNAs in the nucleus and cytoplasm
Pathways for degradation of eukaryotic mRNAs (Fig. 9-30) • (b) Deadenylation-independent mRNA degradation : • mRNAs decapped before deadenylation. • Degraded by XRN1 5ʹ→3ʹ exonuclease
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Pathways for degradation of eukaryotic mRNAs (Fig. 9-30) • (c) Endonuclease-mediated mRNA decay : • mRNAs – cleaved internally by an endonuclease • Fragments degraded by a cytoplasmic exosome and XRN1 exonuclease
Three roles of RNA in protein synthesis (Fig. 5-29) Three RNAs involved in protein synthesis: mRNA, tRNA, and rRNA.
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mRNA: nucleotide sequence encodes the order of amino acids a ribosome assembles into polypeptide chain Three roles of RNA in protein synthesis (Fig. 5-29)
tRNAs: • Each amino acid type is covalently bound to a subset of tRNAs containing a specific three-nucleotide anticodon sequence. • Each anticodon base-pairs with its complementary mRNA codon to position the encoded amino acid in the ribosome A site where it is covalently linked to the C-terminus of the growing peptide Three roles of RNA in protein synthesis (Fig. 5-29)
rRNA: • Ribosomes are composed of numerous proteins and three (bacterial) or four (eukaryotic) ribosomal RNA (rRNA) molecules (not shown). • One of the rRNAs catalyzes peptide bond formation between incoming aa- tRNA amino-group and the carboxy-terminus of the growing protein chain Three roles of RNA in protein synthesis (Fig. 5-29)
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How tRNAs are processed (Fig. 9-48) • Pre-tRNAs (synthesized by RNA Pol3) undergo extensive cleavage and base modification in the nucleus. • Cleavages: • 14-nucleotide intron (blue) in the anticodon loop – removed by splicing • 16-nucleotide 5ʹ end sequence (green) – cleaved by RNase P
How tRNAs are processed (Fig. 9-48) • Base modifications: ~10% of bases modified • (1) 3ʹ end U residues replaced with a CCA sequence. • CCA sequence – required for tRNA charging with amino acid by aminoacyl-tRNA synthetase • Only properly folded tRNAs are recognized by aminoacyl-tRNA synthetase – may function as a tRNA quality-control point • (2) Specific uridines are converted to dihydrouridine, pseudouridine , or ribothymidine residues. (D = dihydrouridine; Ψ = pseudouridine ) adding structural stability as well as stability during ribosomal interactions.
Translating nucleic acid sequence into amino acid sequence (Fig. 5-31) The L-shaped folded structure of tRNA (70–80 nucleotides long), with the anticodon and amino acid acceptor stem on the ends of the two arms, promotes its decoding functions. Molecular model of the human mitochondrial aminoacyl-tRNA synthetase for Phe in complex with tRNA Phe
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Translating nucleic acid sequence into amino acid sequence (Fig. 5-31) Aminoacyl-tRNA synthetase coupling amino acid to tRNA . • Step 1: An aminoacyl-tRNA synthetase couples a specific amino acid via a high-energy ester bond (making the amino acid activated ) to either the 2ʹ or 3ʹ hydroxyl of the terminal adenosine in the tRNA that has the proper anticodon (cognate tRNA). • The energy of the ester bond subsequently drives the formation of the peptide bonds linking adjacent amino acids in a growing polypeptide chain in the ribosome.
Translating nucleic acid sequence into amino acid sequence (Fig. 5-31) Aminoacyl-tRNA synthetase coupling amino acid to tRNA. • Step 2: The anticodon three-base sequence in the tRNA base-pairs with a complementary codon in the mRNA specifying the attached amino acid. • The anticodon three nucleotides are located in a loop where they are accessible for codon-anticodon base pairing.
Structure of tRNAs (Fig. 5-32) (a) All tRNA structures: • Fold into four base-paired stems and four loops. • Have a CCA sequence at the 3ʹ end (acceptor stem), to which an amino acid is attached by an aminoacyl tRNA synthetase. • Have an anticodon triplet at the tip of the anticodon loop. • Have post-transcriptionally modified A, C, G, and U residues. (b) Three-dimensional model of the generalized L-shaped backbone of all tRNAs.
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• Ribosome structure and function • Translation mechanism — protein synthesis Stepwise Synthesis of Proteins on Ribosomes
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Structure of the bacterial ribosome (Fig. 5-34) • Ribosome: protein synthesis organelle • rRNA in ribosome: third RNA required for protein synthesis (in addition to mRNA and tRNA). • Ribosomes differ in bacteria, archaea, and eukaryotes, but share structural and functional similarities. • Ribosome ( Thermus thermophilus) structure: • Small (30S) subunit — 16S rRNA and proteins. • Large (50S) subunit — 23S and 5S rRNAs and proteins. • Internal positions of tRNAs in the A, P, and E sites and elongating peptide attached to the tRNA in the P site. exit site (E) peptidyl site (P) aminoacyl site (A)
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How rRNAs are processed (Fig. 9-43) • Three coding regions – encode 18S, 5.8S, and 28S rRNAs (in ribosomes of eukaryotes) • Variations in the lengths of the transcribed spacer regions (blue) – account for most of the difference in the lengths of pre-rRNA transcription units in different organisms
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How rRNAs are processed (Fig. 9-44) • Nascent pre-rRNA transcripts (synthesized by RNA Pol1) – bound immediately by proteins into pre-ribosomal ribonucleoprotein particles (pre- rRNPs) • Yeast ~6.6 kb primary rRNA transcript: • Cut in a series of cleavage and exonucleolytic steps to generate the mature rRNAs found in ribosomes (Endoribonucleases – internal cleavages [scissors]; Exoribonucleases – digest from either 5ʹ or 3ʹ end [Pac-Men]) • Processing cleavages – begin when transcription is nearly complete
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Eukaryotic Ribosomal subunit assembly (Fig. 9-46) • 40S subunit: • Ribosomal proteins associate with the nascent pre-rRNA during transcription . • 90S rRNP precursor cleavage – releases a pre-40S particle – requires only a few more remodeling steps before transport to the cytoplasm
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• 60s subunit: • Considerable remodeling through many more transient interactions with nonribosomal proteins before export to the cytoplasm – • GTPases – involved in quality control checkpoints • ATPases – large molecular movements required to fold the large, complex rRNA into the proper conformation • Cytoplasmic maturation – includes removal of export factors Eukaryotic Ribosomal subunit assembly (Fig. 9-46)
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Comparison of the common core structure at the center of ribosomes from all domains of life and bacterial, yeast, and human ribosomes (Fig. 5-35) (a) RNA in the common core structure (light blue) and protein domains common to all ribosomes (pink). (b, c) Additions to the common core structure: RNA (dark blue) and proteins (red). (d) Human ribosome with tRNA in the E site (green). • RNA constitutes about 60 percent of the mass of a bacterial ribosome and 50 percent of the mass of a human ribosome. • Many antibiotics exploit ribosome differences and inhibit bacterial protein synthesis without affecting the function of mammalian ribosomes.
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Initiation of Translation in Eukaryotes (Fig. 5-36) Eight initiation steps involving eukaryotic translation initiation factors (eIFs) and GTP hydrolysis, which stabilizes some complexes:
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Initiation of Translation in Eukaryotes (Fig. 5-36) • Step 1: eIF2·GTP (eukaryotic initiation factor 2) binds a tRNAi Met to form eIF2 ternary complex. • Step 2: eIF2 ternary complex and eIF5 bind ribosome 40S subunit already bound by eIF1, eIF1A, and eIF3 (added at the termination of the previous round of protein synthesis) to form 43S preinitiation complex.
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Initiation of Translation in Eukaryotes (Fig. 5-36) • Step 3: Multisubunit eIF4 complex binds to mRNA ; subunit eIF4E binds to the mRNA 5ʹ cap , and subunit eIF4G binds multiple copies of cytoplasmic poly(A)-binding protein (PABPC) bound to the mRNA poly(A) tail (only one PABPC-eIF4G binding is shown). This circularizes mRNA by forming a bridge between the 5ʹ (cap) and 3ʹ (poly(A)) ends of the mRNA.
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Initiation of Translation in Eukaryotes (Fig. 5-36) • Step 4: The 43S preinitiation complex binds an eIF4-mRNA complex.
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Initiation of Translation in Eukaryotes (Fig. 5-36) • Step 5: eIF4B-stimulated eIF4A RNA helicase activity unwinds any RNA secondary structure at the 5ʹ end of the mRNA as the 40S subunit scans in the 5ʹ→ 3ʹ direction until it recognizes the AUG initiation codon (in a conserved Kozak sequence ). Kozak sequence GCC R CCAUG G (R=purine; A of AUG= +1) Position -3 and +4 have strong effect on translation efficiency
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Initiation of Translation in Eukaryotes (Fig. 5-36) • Step 6: Initiation codon recognition causes eIF5 to stimulate hydrolysis of eIF2-bound GTP (2-GTP to 2-GDP), which switches the conformation of the scanning complex to a 48S initiation complex with the tRNAiMet anticodon base-paired to the initiator AUG in the P site .
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Initiation of Translation in Eukaryotes (Fig. 5-36) • Step 7: The 60S subunit joins the 40S subunit , causing binding of eIF5B-GTP to eIF1A in the ribosomal A site and release of most of the earlier-acting eIFs. (The released eIF4 complex and eIF4B reassociate with the 5ʹ cap and PABPC [step 3] to initiate synthesis by another ribosome on the same mRNA [not shown]).
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Initiation of Translation in Eukaryotes (Fig. 5-36) • Step 8: Association of the 40S and 60S subunits causes eIF5B-GTP hydrolysis, release of eIF5B-GDP and eIF1A, forming the 80S initiation complex with tRNAi Met base-paired to the initiation codon in the ribosomal P site .
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Chain elongation in eukaryotes (Fig. 5-37) • During chain elongation, each incoming tRNA moves through three sites: A, P, and E. • Key steps in elongation: (1) Entry of each succeeding aminoacyl- tRNA with an anticodon complementary to the next codon into the A site (2) Formation of a peptide bond catalyzed by large rRNA (3) Translocation of the ribosome one codon at a time along the mRNA.
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Chain elongation in eukaryotes (Fig. 5-37) • Step 1: tRNA-aa2 ternary complex binds to the A site by mRNA codon-tRNA anticodon base pairing. Starting with 80S ribosome with Met-tRNAi Met in the ribosome P site
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Chain elongation in eukaryotes (Fig. 5-37) • Step 2: EF1α·GTP hydrolysis causes EF1α conformational change, releasing the EF1α·GDP and positioning the aminoacylated 3ʹ end of the tRNA in the A site close to the 3ʹ end of the Met-tRNA i Met in the P site.
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Chain elongation in eukaryotes (Fig. 5-37) • Step 3: The large rRNA catalyzes peptide bond formation (peptidyl transferase reaction ) between Met i and aa2.
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Chain elongation in eukaryotes (Fig. 5-37) • Step 4: EF2·GTP hydrolysis causes ribosome conformational change that translocates the ribosome one codon along the mRNA and shifts the unacylated tRNAi Met to the E site and the tRNA with the bound peptide to the P site.
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Chain elongation in eukaryotes (Fig. 5-37) • Cycle begins again with the binding of a ternary complex bearing aa3 to the open A site. • In the second and subsequent elongation cycles, conformational change induced by hydrolysis of GTP in EF1α·GTP (step 2 ) ejects the tRNA in the E site. • Energy released by GTP hydrolysis at several steps drives reactions in one direction. • Ribosomes add three to five amino acids per second.
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Termination of translation in eukaryotes. (Fig. 5-38) • Translation is terminated by release factors when a stop codon ( UAA, UGA, UAG ) is in the A site.
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Termination of translation in eukaryotes. (Fig. 5-38) • eRF3·GTP hydrolysis causes cleavage of the peptide chain from the tRNA in the P site and ejection of the tRNA in the E site, forming a post-termination complex.
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Termination of translation in eukaryotes. (Fig. 5-38) • Ribosomal subunits are separated by the action of the ABCE1 ATPase together with eIF1, eIF1A, and eIF3 binding to the 40S subunit.
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Circular structure of mRNA increases translation efficiency (Fig. 5-39) • Circular mRNA, polysomes, and rapid ribosome recycling increase the efficiency of translation. • Polysome: structure with multiple individual ribosomes simultaneously translating a eukaryotic mRNA.
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