Question

Background Information

How can we predict where a coding gene will be in bacteria? And can we then predict what protein will be produced?

Take the DNA sequence below, for example.

tcaggctttaattcatccgtgatctttgacgacggtaaatacgatgcagatataatacgatgaccgatgccaatcgaccgatcaaggaggcaccgaatggcgatgatggcgatgattgcgattaacgaagtggaacgcattatggcgggcattaacgaagatacccatgcgaccggcgaaaacgaaaccatttgcagctgcgcgaactttgaagaactgacccatgcgaccggccgcgaagcgacctaaaagtcgtaattacgtatcaagtcatgggccgcgggcgcccggcccactgactagactagggccgggcgcccgcggcccaccatataaataaaaaaaaaaaaaacgaggctatagctcatcaatgacct

If you were a bacterial RNA polymerase, what sequence(s) should there be in this DNA for you to bind and begin transcribing? And if you found such sequence(s), where would you begin transcription? As a human being looking at this fragment of DNA, what type of consensus sequence(s) would you look for, and where would you place the TSS (or +1)?

Let's then assume that transcription begins...
... where will it end? Remember that these are bacteria and that they will have a termination sequence. Can you see it?

As a researcher, if you found the sequence(s) that you would normally find in a bacterial core promoter and a strong termination signal, then there would be a good chance that you are indeed in front of a functional gene that will be transcribed into RNA. How would you now determine if the bacteria will try to translate this RNA? In other words, how would you determine if the transcribed RNA is actually a messenger RNA (mRNA)? What kind of sequence does a bacterial mRNA need to be bound and translated by ribosomes?

Finally, if you determine that the above DNA indeed coded for a functional mRNA, what would be the protein produced from it? What would you (or a ribosome) look for to determine where to begin and proceed with translation? Where will translation stop? And what would be the polypeptide produced?

Instructions

Your job now is to copy the above DNA sequence and highlight each of the different sequence elements that are relevant to this particular gene (I suggest that you use different font backgrounds for each sequence element) and briefly explain what each of them do . Then, write the sequence of the mRNA that would be transcribed from this DNA sequence, identifying the AUG and STOP codon (I suggest that you bold and underline text this time).

Once you've established the protein coding sequence in your mRNA, use any of the gazillion free online protein translators to upload the sequence of nucleotides between the AUG and the STOP codons to translate the nucleotide sequence into amino acid sequence (Note: I do not mean genetic code tables that you may find online - I literally mean online translators in which you can upload a sequence of nucleotides starting with AUG, and obtain the predicted sequence of amino acids that would be translated from them). Finally, write the expected polypeptide sequence using one letter amino acid notation (A for alanine, W for tryptophan, etc).

Answer 1

The first step is to find closely-related genomes to a given bacterial genome. The second step is to extract intergenic regions among the selected genomes and to apply the BLAST program to compare intergenic regions pair wisely.Once you have the software, one of the commands is to make your own BLAST database - you can use either the genome sequence of quail (in a FASTA file) or a file of all the CDS from quail, to make your database.
Once you have the database made you can use the local BLAST command to search for the chicken protein sequence in the quail genome, using the tBLASTn function.
RNA polymerase binds to a sequence of DNA called the promoter, found near the beginning of a gene. Each gene (or group of co-transcribed genes, in bacteria) has its own promoter. Once bound, RNA polymerase separates the DNA strands, providing the single-stranded template needed for transcription.