Other RNA Processing Events Chapter 16

Ribosomal RNA Processing rRNA genes of both eukaryotes and bacteria are transcribed as larger precursors must be processed to yield rRNAs of mature size - Several different rRNA molecules are embedded in a long precursor and each must be cut out

Eukaryotic rRNA processing The rRNA are separated by regions called nontranscribed spacers (NTSs). Transcribed spacers - regions of the gene that are transcribed as part of rRNA precursor - and then removed in processing of precursor to mature rRNA species. NTSs are distinguished from transcribed spacers

Eukaryotic rRNA Processing Ribosomal RNAs are made in eukaryotic nucleoli as precursors that must be processed to release mature rRNAs Order of RNAs in the precursor is (fig: 16.2) 18S 5.8S 28S in all eukaryotes Exact sizes of the mature rRNAs vary from one species to another The rRNA are separated by regions called nontranscribed spacers (NTSs). NTSs are distinguished from transcribed spacers, regions of the gene that are transcribed as part of rRNA precursor and then removed in processing of precursor to mature rRNA species.

Eukaryotic rRNA Processing rRNA processing – nucleolus – small nucleolar RNAs (snoRNAs) + proteins = Small nucleolar ribonucleoproteins (snoRNPs) E1, E2 and E3 – interact with distinct regions in pre-rRNA

Bacterial rRNA Processing Bacterial rRNA precursors contain tRNA and all 3 rRNA rRNA are released from their precursors by RNase III and RNase E RNase III is the enzyme that performs at least the initial cleavages that separate the individual large rRNAs RNase E is another ribonuclease that is responsible for removing the 5S rRNA from the precursor

Processing Bacterial rRNA

Transfer RNA Processing Transfer RNAs are made in all cells as overly long precursors These must be processed by removing RNA at both ends Nuclei of eukaryotes contain precursors of a single tRNA In bacteria - precursor may contain one or more tRNA - Sometimes a mixture of rRNAs and tRNAs

Cutting apart Polycistronic Precursors In processing bacterial RNA that contain more than one tRNA First step is to cut precursor up into fragments with just one tRNA each Cutting between tRNAs in precursors having 2 or more tRNA Cutting between tRNAs and rRNAs in precursors Enzyme that performs both chores is the RNase III

Forming Mature 5’-Ends of tRNA Extra nucleotides are removed from the 5’-ends of pre-tRNA in one step by an endonucleolytic cleavage catalyzed by RNase P RNase P from bacteria and eukaryotic nuclei have a catalytic RNA subunit called M1 RNA RNase P makes a cut at the site that becomes mature 5’-end of a tRNA

Processing 3’-Ends of tRNA RNase D, RNase BN, RNase T, RNase PH, RNase II and polynucleotide phosphorylase (PNPase)

Forming mature 3’-Ends of tRNA RNase II and polynucleotide phosphorylase cooperate To remove most of extra nucleotides at the end of a tRNA precursor RNases PH and T are most active in removing the last 2 nucleotides from RNA RNase T is the major participant in removing very last nucleotide

Trans-Splicing Splicing that occurs in all eukaryotic species is called cis-splicing because it involves 2 or more exons that exist together in the same gene trans-splicing has exons that are not part of the same gene at all - may not even be on the same chromosome

The Mechanism of Trans-Splicing Trans-splicing occurs in several organisms Parasitic and free-living worms First discovered in trypanosomes Trypanosome mRNA are formed by trans-splicing between a short leader exon and any one of many independent coding exons

Trans-Splicing

Trans-Splicing Scheme Branchpoint adenosine within the half-intron attached to the coding exon attacks the junction between the leader exon and its half-intron Creates a Y-shaped intron-exon intermediate analogous to the lariat intermediate

Mechanism of Editing Unedited transcripts can be found along with edited versions of the same mRNAs Editing occurs in the poly(A) tails of mRNAs that are added posttranscriptionally Partially edited transcripts have been isolated - always edited at their 3’-ends but not at their 5’-ends Trypanosomatid mitochondria encode incomplete mRNA that must be edited before being translated Editing occurs in the 3’5’ direction by successive action of one or more guide RNAs

Role of gRNA in Editing Guide RNAs (gRNA) could direct the insertion and deletion of UMPs over a stretch of nucleotides in the mRNA When editing is done, gRNA could hybridize near the 5’-end of newly edited region

Guide RNA Editing 5’-end of the first gRNA hybridizes to an unedited region at the 3’-border of editing I the pre-mRNA The 5’-ends of the rest of the gRNAs hybridize to edited regions progressively closer to the 5’-end of the region to be edited in the pre-mRNA All of these gRNAs provide A’s and G’s as templates for the incorporation of U’s missing from the mRNA

Mechanism of Removing U’s Sometimes the gRNA is missing an A or G to pair with a U in the mRNA In this case the U is removed Mechanism of removing U’s involves Cutting pre-mRNA just beyond U to be removed Removal of U by exonuclease Ligating the two pieces of pre-mRNA together Mechanism of adding U’s uses same first and last step Middle step involves addition of one or more U’s from UTP by TUTase

RNA Interference RNA interference occurs when a cell encounters dsRNA from: Virus Transposon Transgene Trigger dsRNA is degraded into 21-23 nt fragments (siRNAs) by an RNase III-like enzyme called Dicer Double-stranded siRNA, with Dicer and Dicer-associated protein R2D2 form a complex called complex B

Complex B Complex B delivers the siRNA to the RISC loading complex (RLC) Separates 2 strands of siRNA Transfers guide strand to RNA-induced silencing complex (RISC) that introduces a protein- Ago2

Complex B The guide strand of siRNA base-pairs with target mRNA in the active site of PIWI domain of Ago2 Ago2 is an RNase H-like enzyme known as a slicer Slicer cleaves the target mRNA in middle of the region of its base-pairing with the siRNA ATP-dependent step has cleaved RNA ejected from RISC which then accepts a new molecule of mRNA for degradation

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