RNA World Hypothesis

RNA World

• Gilbert W. officially named the RNA world in a 1986 Nature publication.
• The concept was originally proposed by C. Woese.
• Carl Woese, Francis Crick, and Leslie Orgel had previously postulated the idea that RNA could be the original information molecule in the 1960s.
• The RNA World hypothesis postulates that life began on Earth with RNA and catalytic RNA (ribozymes).

RNA as Ancestral Nucleic Acid

• RNA genes in hypothetical RNA World Organisms used RNA for replication catalyzed by RNAs.
• Modern organisms utilize DNA genes for transcription catalyzed by proteins into mRNAs, which then undergo translation catalyzed by the ribosome (RNA) into proteins; DNA replicates via catalysis by proteins.
• In an RNA-first process, life likely emerged on Earth ~4.2 bya.

Evidence for Catalytic RNA

• Ribonucleoprotein particles (RNPs) contain both proteins and RNA.
• Examples of catalytic RNA include:
  • Telomerase (derived RT plus guide RNA).
  • snRNPs (small nuclear ribonucleoprotein particles involved in spliceosomal intron splicing).
  • RNase P (modifies 5' ends of tRNA).
  • Ribosomes (5S, 18S, 5.8S, 26S RNA molecules plus ribosomal proteins).

RNA Structure

• The presence of a 2' OH group in ribose allows RNA can fold, due to extra H2 bonding capacity.
• RNA can form G-U, A-U and G-C base pairs, and form RNA zippers.

Ribozymes Discovery

• T. Cech discovered ribozymes in 1981.
• Cech's group focused on a "genetic element" present in the nuclear large ribosomal subunit gene.
• About 90% of RNA is ribosomes.
• Cech received the Nobel Prize in Chemistry in 1989 for work on catalytic RNA, particularly group I introns.
• Cech shared Nobel Prize in Chemistry in 1989 with Sidney Altman who also identified ribozymes.

rDNA and Introns

• In eukaryotes, rRNA genes are grouped together into rDNA repeat units.
• Eukaryotes usually have many copies of the rDNA repeat unit.
• The order of ribosomal RNA genes in Eukaryotes is typically, promoter, 18s, 5.8S and 24-28S.
  • ITS = internal transcribed spacer
  • NTS = non-transcribed spacer
  • ETS = external transcribed spacer
• The rDNA-repeat is larger in the nuclear genome.

Spliceosomal Introns

• Eukaryotes have many genes with spliceosomal introns (split genes with exons and introns).
• Introns are removed during RNA processing in the nucleus.
• Mature mRNAs are composed of exons.
• Intron removal is complex and requires snRNPs and many other factors = spliceosome (a giant ribozyme).
• Internal A 2'OH group initiates transesterification reactions.
• The first transesterification reaction is initiated by an internal A 2'OH group.
• Lariat formation is stabilized by a 5'2' bond.
• 3'OH of an upstream exon will initiate the next transesterification reaction resulting in a free intron lariat and spliced exons.
• An intron starts with GU and ends with AG.

Group I Introns

• Self-splicing introns.
• Reactions have Mg+2. Products of self-splicing reactions:
  • pre-rRNA.
  • Nuclear extract.
  • GTP.
  • Spliced exon.
• Additional proteins are NOT needed for splicing of this pre-rRNA
• GTP and Mg++ is required for products to appear.
• A segment of RNA "self-spliced" ~ 400 bp resulting in linear and circular forms.
• Labelled GTP is incorporated into a linear 400 bp segment.
• Self-splicing occurs in rDNA via the rLSU gene.
• Linear and circular forms can be detected.
• A key part of these is that they must be close to happen properly; includes paired region or a helix.
• Requires 3’OH and O -> "nucleophile.
• P1 includes IGS – internal guide sequence.

Splicing Reactions

• Two transesterification reactions result in creation of a 3' exon starting with external GTP.
• ExoG (exogenous G) is on the Omega G (3' end of intron).
• Linear (core L19IVS) product will be ~4 nts after cleaving off Radioactive OCTP.
• Lost 19 inter-vening sequence" prevents "reverse splicing.
• A final "stable product" has several activities including an intron core -> L19IVS.
  • Can "grab and donate" NTPs, P groups, and Ligate RNA segments

Introns

• 2 major types: Based on 2nd RNA structure and splicing mechanism.
• The two types include group I and group II which are self-splicing.
• Group I introns
  • Do not require proteins.
• Group II introns
• Do not require protein.
• Introns are mobile elements.

Reverse Splicing

• RNA inserts into RNA or single-stranded DNA (for group II).
• Mediated by protein mobility.
• Homing (group I) and retro-homing (group II) requires an RNA intermediate.
• Group I introns are found in Eubacteria, Archaea, bacteriophages and in the organelles of fungi, plants, protists; and in ribosomal nuclear genes (rDNA) of some fungi and protists and in the mtDNA's of sea anemones and soft corals.
• Mobile introns are widespread and are not present in nuclear genomes of metazoans and plants
• Organellar genomes of some protozoans, fungi, algae, plants, and early branching metazoans.

Group II Introns

• The Secondary Structure is "wheel with six fingers".
• Some group II elements encode reverse transcriptase in the domain 4 region.
• Is important to note in domain 6 the A* → "A-2'ОН .
• D1 is the Scaffold domain and it allows the intron to have base pair complementary.
• ORFs equal open reading frame.

Transesterification and Splicing

• Group II introns are often mobile and they are reverse spliced.
• They commonly have " Intron RNA" inserting into RNA or singled-stranded DNA (for group II)
• Group II is retro to mobility as it always requires an RNA intermediate.

Evolutionary significance

• Group II introns are ancestors to "modern introns" or snRNP RNAs.
• Reverse transcriptase (RT) is a large family of proteins that includes: telomerases, RNA dependent polymerases, components of CRISPR/cas (RTs), and Reverse transcriptases found in retroviruses.
• Reverse transcriptase was originally used by more primitive systems like in bacteria.
• Relics from the RNA world is seen with the help of ribozymes to cut RNA, DNA, and ligate.

Gene Regulation

• Gene regulation can also be affected by RNA, specifically with riboswitch binding.
• Riboswitches make cells metabolite and genetic regulators.

Riboswitches

• RNA folds at the 5' UTR can that hide or expose RBS (ribosome binding site).
• Group I intron can control translation at the RNA level.

Three-dimensional Structure

• There may be other types, such as Hairpin, Delta hepatitis, Varkud (pl), glmS ribozyme, P1-twister, twister-sister, hatchet, and pistol but the hammerheads are especially well-known.

Viroids and Satellite RNAs

• Viroids and virusoids are satellite RNAs.
  • Cause diseases in plants
  • Do not have any Capsids
  • Naked Viruses
    • They west RNA polymerase
• Tertiary structure and Mg2+ is needed
• These Can fold on their own.

Ribosome

• A peptidyl transferase activity catalyzed by RNA
• Can "gene operate with RNA, DNA
• Mobile through (~recombination).
• Phosphatase.
• Ligases.
• RNA polymerase.
• Ribosomes (peptidyl transferase).

Replicators

• Can depend on environmental conditions.
• Can build or contain information
• Be catalytic

Ultimately

• Limited by the catalytic abilities
• DNA is far more stable.