Ciro Santilli @cirosantilli 34

Database of promoter.

E.g. for E. Coli K-12 MG1655: biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI For some context see e. Coli K-12 MG1655 gene thrL + e. Coli K-12 MG1655 gene thrA + thrB + thrC all of which are in the same transcription unit.

UniProt entry: www.uniprot.org/uniprot/P00561.

NCBI entry: www.ncbi.nlm.nih.gov/gene/945803.

The second gene in the E. Coli K-12 MG1655 genome. Part of the E. Coli K-12 MG1655 operon thrLABC.

Part of a reaction that produces threonine.

This protein is an enzyme. The UniProt entry clearly shows the chemical reactions that it catalyses. In this case, there are actually two! It can either transforming the metabolite:Also interestingly, we see that both of those reaction require some extra energy to catalyse, one needing adenosine triphosphate and the other nADP+.

TODO: any mention of how much faster it makes the reaction, numerically?

Since this is an enzyme, it would also be interesting to have a quick search for it in the KEGG entry starting from the organism: www.genome.jp/pathway/eco01100+M00022 We type in the search bar "thrA", it gives a long list, but the last entry is our "thrA". Selecting it highlights two pathways in the large graph, so we understand that it catalyzes two different reactions, as suggested by the protein name itself (fused blah blah). We can now hover over:Note that common cofactor are omitted, since we've learnt from the UniProt entry that this reaction uses ATP.

If we can now click on the L-Homoserine edge, it takes us to: www.genome.jp/entry/eco:b0002+eco:b3940. Under "Pathway" we see an interesting looking pathway "Glycine, serine and threonine metabolism": www.genome.jp/pathway/eco00260+b0002 which contains a small manually selected and extremely clearly named subset of the larger graph!

But looking at the bottom of this subgraph (the UI is not great, can't Ctrl+F and enzyme names not shown, but the selected enzyme is slightly highlighted in red because it is in the URL www.genome.jp/pathway/eco00260+b0002 vs www.genome.jp/pathway/eco00260) we clearly see that thrA, thrB and thrC for a sequence that directly transforms "L-aspartate 4-semialdehyde" into "Homoserine" to "O-Phospho-L-homoserine" and finally tothreonine. This makes it crystal clear that they are not just located adjacently in the genome by chance: they are actually functionally related, and likely controlled by the same transcription factor: when you want one of them, you basically always want the three, because you must be are lacking threonine. TODO find transcription factor!

The UniProt entry also shows an interactive browser of the tertiary structure of the protein. We note that there are currently two sources available: X-ray crystallography and AlphaFold. To be honest, the AlphaFold one looks quite off!!!

By inspecting the FASTA for the entire genome, or by using the NCBI open reading frame tool, we see that this gene lies entirely in its own open reading frame, so it is quite boring

From the FASTA we see that the very first three Codons at position 337 arewhere ATG is the start codon, and CGA GTG should be the first two that actually go into the protein:

ecocyc.org/gene?orgid=ECOLI&id=ASPKINIHOMOSERDEHYDROGI-MONOMER mentions that the enzime is most active as protein complex with four copies of the same protein:TODO image?

UniProt entry: www.uniprot.org/uniprot/P0AD86.

NCBI gene entry: www.ncbi.nlm.nih.gov/gene/944742.

The first gene in the E. Coli K-12 MG1655 genome. Remember however that bacterial chromosome is circular, so being the first doesn't mean much, how the choice was made: Section "E. Coli genome starting point".

Part of E. Coli K-12 MG1655 operon thrLABC.

At only 65 bp, this gene is quite small and boring. For a more interesting gene, have a look at the next gene, e. Coli K-12 MG1655 gene thrA.

Does something to do with threonine.

This is the first in the sequence thrL, thrA, thrB, thrC. This type of naming convention is quite common on related adjacent proteins, all of which must be getting transcribed into a single RNA by the same promoter. As mentioned in the analysis of the KEGG entry for e. Coli K-12 MG1655 gene thrA, those A, B and C are actually directly functionally linked in a direct metabolic pathway.

We can see that thrL, A, B, and C are in the same transcription unit by browsing the list of promoter at: biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI. By finding the first one by position we reach; biocyc.org/ECOLI/NEW-IMAGE?object=TU0-42486.

Reference strain: E. Coli K-12 MG1655.

Size: 1-2 micrometers long and about 0.25 micrometer in diameter, so: 2 * 0.5 * 0.5 * 10e-18 and thus 0.5 micrometer square.

Reference strain: E. Coli K-12 MG1655.

Genome:

Synthesis project: www.sciencemag.org/news/2016/08/biologists-are-close-reinventing-genetic-code-life

Omics modeling: www.ncbi.nlm.nih.gov/pmc/articles/PMC5611438/ Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level Zixi Chen, Lei Chen, Weiwen Zhang.

Bibliography:

The bioinformatics database: www.ncbi.nlm.nih.gov/

Here's a good example of what you can get out of it: E. Coli K-12 MG1655

For an example with context, have a look at E. Coli K-12 MG1655 and the second protein of the genome, e. Coli K-12 MG1655 gene thrA.