BMSC 320 Nucleic Acids - Lecture 28

BMSC 320 Nucleic Acids - Lecture 28

• Lecture date: November 27, 2024
• Instructor: Kyle Anderson
• Topic: Nucleic Acids (specifically, review of miRNAs, eukaryotic translation, and ribosomes)

Review of microRNAs (miRNAs)

• Typical miRNAs have 7 or 8 bases of complementarity
• Atypical miRNAs may have 6 bases or require looping to function
• miRNAs are highly conserved across eukaryotes
• miRNAs in worms can control similar processes to humans
• miRNA dysregulation can cause or signal disease or tissue damage
• Some miRNAs enhance translation
• Circular RNAs (circRNAs) and long noncoding RNAs (lncRNAs) can act as miRNA sponges, preventing them from regulating their targets

Eukaryotic Translation: A Reminder of the Basic Process

• This module reviews the basics of eukaryotic translation from prior courses to focus on problems of efficiency and defective mRNA

Prokaryotic vs. Eukaryotic Translation

• Prokaryotic:
  • Translation is coupled to transcription
  • No nucleus
  • 70S ribosomes (50S and 30S subunits)
  • Small subunit recognizes Shine-Dalgarno sequence
  • N-formyl-methionine is the first amino acid
  • mRNA is linear
  • Polycistronic messages (common)
• Eukaryotic:
  • Translation occurs in the cytoplasm
  • Nucleus for pre-mRNA processing
  • 80S ribosomes (60S and 40S subunits)
  • tRNA and small subunit scan from 5’ cap to Kozak sequence
  • Regular methionine is the first amino acid
  • mRNA is held in a loop
  • Polycistronic messages are rare

Ribosome Differences and Similarities

• Prokaryotes have ~55 ribosomal proteins, eukaryotes have ~80
• Different proteins alter target sites, thus many antibiotics that block prokaryotic protein synthesis don't affect eukaryotes
• E.g., cycloheximide blocks eukaryotic ribosomes but not prokaryotic ones
• The human 5.8S and 28S rRNA are equivalent to the prokaryotic 23S rRNA
• Main rRNA is catalytic; locates mRNA start site, and checks tRNAs

Export of All Nuclear RNA is Controlled

• Small RNAs (like tRNA and miRNA) associate with export factors to pass through the nuclear pore
• snRNAs (components of spliceosome) are exported, associate with spliceosomal proteins, and are reimported into the nucleus
• Several factors associate with mRNAs and rRNAs to allow export from nucleus

mRNA Export is Tightly Regulated

• mRNA binds to CBC through capping and PABP through tailing
• Splicing creates complexes with SR proteins
• TREX complex associates with RNA polymerase II (RNA pol II) during synthesis and processing
• Nuclear export proteins (Mex67 and Mtr2) are recruited by TREX, pass through the nuclear pore complex (NPC), and are released back into cytoplasm
• Proteins facilitate interactions with other components

mRNA/mRNP Export is Rate-Limiting

• RNA labeling assays show mRNA persists longer in the nucleus than the cytoplasm
• Export is an active, rate-limiting process
• mRNA is in the nucleus ~5 times longer than in the cytoplasm
• Export may regulate/buffer mRNA levels in the cytoplasm
• Only fully capped, tailed, and spliced mRNAs leave the nucleus

Translation Cycle

• 40S (small subunit) and initiation factors bind methionine-tRNA to create 43S complex
• 43S associates with mRNA via cap-binding complex (CBC) and eIF4
• Helicase unwinds mRNA’s 5'UTR to scan for Kozak sequence in vertebrates
• Large subunit binds, tRNAs, elongation factors allow protein synthesis
• Stop codons are detected which trigger release factors and ribosome disassembly

Alternative Initiation: The IRES

• 99% of human genes translate via 5' cap and CBC via eIF4
• Some human genes have internal ribosome entry sites (IRES) within 5' UTR
• mRNA with IRES can be translated without a 5' cap or 5' end in circRNAs
• This is more common in eukaryotic viruses but ~100 human genes use IRES (including polycistronic mRNAs)

Translation and Proofreading

• All mRNA is degraded; problematic mRNA is degraded faster
• Methods to prevent translation of "bad" mRNA
• Truncated proteins that result from improperly spliced or prematurely terminated mRNAs can create dominant negative proteins (enzymes, proteins that bind to DNA, RNA, or other proteins, or proteins creating non-functional dimers).
• Cells have four methods of proofreading:
  • Nonsense-mediated decay
  • Non-sense associated alternative splicing (less understood/less used)
  • Non-stop mediated decay
  • No-go decay

This quiz covers the critical concepts discussed in Lecture 28 of BMSC 320, focusing on nucleic acids, particular microRNAs, and the mechanisms of eukaryotic translation. Review the roles of miRNAs in genetic control and their implications in health and disease. It also contrasts prokaryotic and eukaryotic translation processes.