Description of Thermococcus kodakarensis proteome

Proteome selection

As the main proteorem I chose the Thermococcus kodakarensis proteome, not T. eurythermalis (my archaea) because its proteome wasn't reference, which is why I started looking for proteomes of close relatives.

This proteome is reference and has 2301 protein 429 of which are added from the Swiss-Prot database. As a contol proteome I chose the reference proteome of the archaea Metallosphaera sedula, which like mine is hyperthermophilic but unlike can survive at low pH.

Main proteome

• Organism: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)).
• Proteome ID: UP000000536, link to the UniProt.
• Protein count: 2301, 429 from the Swiss-Prot.
• BUSCO: 100% full proteins, CPD: Close to standard (high value).

Control proteome

• Organism: Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2).
• Proteome ID: UP000000242, link to the UniProt.
• Protein count: 2256, 169 from the Swiss-Prot.
• BUSCO: 98.5% full proteins, CPD: Standard.

Comparison of proteomes

All tasks were completed using Python code, which can be found at the link. There are 485 (21.07%) transmembrane proteins in Thermococcus kodakarensis proteome, 448 (19.85%) in Metallosphaera sedula and these numbers nearly don't differ because the attitude to oxygen and the habitat of organisms are similar.

There are 378 (16.42%) enzymes proteins in Thermococcus kodakarensis proteome and 502 (22.24%) in Metallosphaera sedula. In a subsequent code I analysed this issue in more detail so the possible reasons will be written below.

Also representatives of the genus Thermococcus are characterized by the possibility of sulfur metabolism, including the release of hydrogen sulfide. Since the control organism also has the ability to metabolize sulfur (FeS₂), it would be interesting to see the ratio of sulfur-related proteins. There are 11 (0.49%) sulfur-related proteins in T. kodakarensis and M. sedula — identical numbers what can say about approximately the same ability to live and work with sulfur-containing substrates.

I decided to compare the number of different classes of proteins. Two numbers will be presented below: left for T. kodakarensis proteome and right for M. sedula.

• Oxidoreductases: 31 (1.35%) and 111 (4.92%).
• Transferases: 137 (5.95%) and 152 (6.73%).
• Hydrolases: 96 (4.17%) and 89 (3.94%).
• Lyases: 43 (1.87%) and 69 (3.06%).
• Isomerases: 25 (1.09%) and 28 (1.24%).
• Ligases: 55 (2.39%) and 65 (2.88%).
• Translocases: 3 (0.13%) and 1 (0.04%).

The sum of enzymes by class exceeds the number of enzymes calculated in the previous task. Most likely, this is due to the fact that for some proteins the function was either intermediate or they have several functional sites at once. Also there are around three-fore times more oxidoreductases in M. sedula proteome that in T. kodakarensis proteome. Most likely this is due to M. sedula live in low pH values.