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Lecture 18

Biology 2581B Lecture 18: Lec 18 – Modifications and Bioinformatics
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Department
Biology
Course Code
Biology 2581B
Professor
David R Smith

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Lecture 18 – Modifications and Bioinformatics What are genetic modifications? - Significant genetic alterations that are often not apparent or obvious given the primary DNA sequence alone o Impact genetic information but may not know about them if just looking at the sequence - Nonstandard codes o If know the sequence for a gene and but don’t know what code is used, could incorrectly interpret how the information is expressed - Knowing the code is crucial Cox 1 amino acid sequence (vertebrate mitochondrial code vs. standard genetic code) - Cox1 gene in mitochondrial genome - AA sequence for the gene: translate the gene using the nonstandard vertebrate mitochondrial code - If you didn’t know about the nonstandard codes and were asked to translate the gene for the amino acid sequence, would’ve had a different amino acid sequence o A sequence with many stop codons inserted throughout - Genetic modifications are crucial and if you don’t know about them, they can push you down another road RNA editing - Genetic modification - Modification that changes the underlying sequencing information - Thinking of genetics and central dogma, expect gene sequence to get transcribed to get an mRNA - mRNA should reflect perfectly the DNA sequence from which it was derived o Only difference we expect is T become Us o Usually holds true but it is not ALWAYS true Spikemoss Selaginella mitochondrial genome - Plant (gene within an intron within a gene) – resurrection plant “Rose de Jericho” (stays dry) - Peculiar editing in mitochondrial compartment + genome - Looking at the DNA sequence of a gene and the corresponding transcript (mRNA sequence) for the coding sequence o Everything looks right except the Ts have become Us o This is what we expect - In this organism in this genome, after the transcript is generated, a lot of the Cs get turned post transcriptionally to Us (not all) - RNA editing/post-transcriptional editing: tweaking the RNA sequence and changing it from what it was - Like the nonstandard code, if didn’t know about editing sites that are introduced, can get the wrong amino acid sequence o AUG is different than ACG, giving a different amino acid - 1000s of C-to-Us editing sites in the mitochondrial genome o Found in chloroplast genome too Selaginella - Cox 1 – DNA and RNA sequence - Cox1 gene in the plant - RNA sequence is derived from the DNA sequence o Ts became Us – the only different o Some Cs get post-transcriptionally edited to Us ▪ Not all of them get turned to U - DNA gets turned to RNA, then something changes all C to U o Substitutional RNA editing - > 200 C-to-U editing sites in a single gene - In mitochondrial genome, the RNA does not reflect the DNA o Impacts the products that get made from the genes o DNA  RNA  AA sequence ▪ AA sequence for cox1 based on DNA: would’ve gotten a different sequence than the one with the edited sites - Deduced amino acid sequence (using standard code) o After taking into account the editing sites, the sequence is different - For every site that gets edited, need proteins to bind to the RNA and the complex is called an edidosome o Protein complex with the purpose to edit sites o Edits and changes to U - Don’t use the same complex to edit all of the sites - Every Us that gets edited, needs a SEPARATE PROTEIN COMPLEX o Complexes are similar o Each site has its own complex that gets encoded and edits the site - For every site edited, need a unique protein complex - Dozens to hundreds of proteins to make 1 protein - Take the gene and want to turn it into cytochrome C oxidase subunit I o Making 1 protein requires 100s of other proteins to bind to the RNA to fix it Tree of land plants & green algae - Changing RNA sequence through editing is found in all land plants and their chloroplast and mitochondrial genomes o Evolved in one group and don’t see it in others o Occurred independently in trypanosomes too - Various degrees of RNA editing in mitochondrial and chloroplast genomes RNA editing - RNA editing has evolved many times independently throughout the tree of life Trypanosomes - mtDNA (kinetoplast DNA) o Polycistornic nuclear transcription o Weird DNA in chain mail structure - Mitochondrial genome: o Maxi circles encode the genes o Mini circles without genes - Mini circles serve to edit the genes o Us are inserted or deleted from the transcript - Uracil insertion/deletion RNA editing - DNA  RNA: Ts changed to Us o Editing occurs after transcription o Editing mechanism inserts and deletes Us ▪ Occurs repeatedly - In a single gene, can have hundreds of U’s can be inserted and deleted from a transcript - Selaginella: if had DNA sequence of cox 1 gene, could figure out its cox 1 even though it doesn’t look right o Can identify it from DNA o Editing was substantial but not enough to dissolve the information at the DNA level - Trypanosome: so many Us inserted and deleted that if you were given DNA, would never know what we were looking at o Wouldn’t know it was a gene sequence until RNA was present - Deletions, insertion sand editing is done by transcripts of the mini circles - Transcripts: o mRNA from maxi circle genes: long o Mini circles give little mRNAs that guide the editing - Long mRNA from maxi circles
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