1/ Yesterday, I wrote about how SARS-CoV2 makes our ribosome translate its first 11 proteins – today, I'll write about how it does the next 5 proteins. All this to prep for the Genetics class I am teaching at @SFSU @SFStateBIO
2/ These first 11 proteins take up a little over 13,000 nucleotides and end with a stop codon, but #SARSCoV2 has 30,000 so how does it read the other 17,000? It's first key trick to translate beyond the stop codon is to "shift frame".
3/ Remember that during translation, nucleotides are read in groups of three (triplets). Each triplet translates into an amino acid. This is the famous genetic code. For example, AAA translates to the amino acid Lysine. en.wikipedia.org/wiki/Genetic_c… 
4/ Here I drew a mini open reading frame, starting with the start codon AUG, then GAC, then CAU and then UAG (one of the stop codons). This translates to Methionine (M), Aspartic Acid (D), Histidine (H) – a string of only 3 amino acids – real proteins are much longer.
5/ Importantly, translation normally stops at the stop codon. But viruses have tricks to make our ribosome slip and miss a letter – and if you miss a letter, but keep reading in triplets, the stop codon is no longer there! Instead of UAG, there is AGA.
6/ In SARS-CoV2, this frame shift which leads to reading through the stop codon leads to a polyprotein of ~7000 amino acids (as compared to the original 4382) – and the additional part includes another 5 proteins.
7/ This trick of frame shifting to read through a stop codon is used by many viruses, including influenza (ncbi.nlm.nih.gov/pubmed/22745253)
and HIV (ncbi.nlm.nih.gov/pubmed/2447506) Reference for SARS CoV1: ncbi.nlm.nih.gov/pubmed/15506971
and HIV (ncbi.nlm.nih.gov/pubmed/2447506) Reference for SARS CoV1: ncbi.nlm.nih.gov/pubmed/15506971
8/ In this picture, you can see the organization of the first 21,000 nucleotides of the SARS-CoV2 genome, with ORF1a which stops at the stopcodon and ORF1b which continues after the stopcodon thanks the ribosomal frameshift. Image from @ViralZone viralzone.expasy.org/30?outline=all…
9/ Maybe the most important protein in the ORF1b is RdRp or RNA-dependent RNA polymerase – an enzyme that can make RNA from an RNA template.
In intro genetics, you'd normally learn about RNA polymerase that uses a DNA template to make RNA ( = transcription)
In intro genetics, you'd normally learn about RNA polymerase that uses a DNA template to make RNA ( = transcription)
10/ But many viruses don't ever use DNA. They use RNA to store their genetic material, and so they need a way to replicate the RNA. Therefore, in its genome it brings the information to create its own copying machine as it were. en.wikipedia.org/wiki/RNA-depen…
11/ note though that while some viruses are RNA only (like coronaviruses, polio), there are also viruses w DNA (like herpes) and viruses that use both (HIV and Hep B – though not in the same way). The "Baltimore classification" gives an overview. en.wikipedia.org/wiki/Baltimore…
12/ so to recap, #SARSCov2 uses our ribosome to translate its RNA. It stops at a stop codon OR does a virus trick called ribosomal frameshift which makes it read through the stop and translate another 5 proteins incl the key enzyme RNA-dependent RNA polymerase.
13/ about 2/3 of the genome now translated. ~9,000 nucleotides left and 13 proteins more to make. I'll tell you how that works tomorrow! It involves "leader" sequences which reminds me of @LondonBreed Dr Fauci Angela Merkel @NYGovCuomo and all those on the frontlines!
14/ P.S. I came across the name Naomi Kitamura who did a lot of early genome work on the polio virus at @stonybrooku but unlike the others involved she doesn't have a wikipedia page – and I can't find her on the web. Anyone knows where she is? @profvrr
en.wikipedia.org/wiki/Poliovirus
en.wikipedia.org/wiki/Poliovirus
