Review

Introduction

Uracil phosphoribosyltransferase is an enzyme which catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphat. Uracil phosphoribosyltransferase could be a target for drug design (Li et al., 2007). Saccharolobus solfataricus is a species of extremophilic archaeon. It grows best in temperatures around 70-75° Celsius, a pH level between 2 and 3. Being a facultative autotroph it receives energy from growing on sulfur (Brock et al., 1972).

About protein

There are six 3D structures, 5 of which were received by x-ray diffraction analysis and one was predicted, structure of A/B/C/D chains has maximum resolution 1.80 Å. Protein is part of clusters UniRef100 (3 protein size), UniRef90 (17 protein size), UniRef50 (34 protein size). History: protein first appeared in 2001 in TrEMBL database, in 2002 record was reviewed and transferred to Swiss-Prot database. Since 2001 has been changed ID, added alternative protein names, organism-source was transferred into another genus (from Sulfolobus to Saccharolobus), were discovered 3D structures, was extended information about protein functions, published new articles about, was added feature table. The last modification was done 23th of February 2022, link to another database was deleted. In field СС I noticed fact about enzyme optimum that concord with organism lifestyle feature — "Optimum pH is 5.0-5.6 at 60 degrees Celsius".

Choice and downloading proteomes

Using advanced search the Proteomes database I find reference proteome Sulfolobus solfataricus (ID: UP000001974, 2937 proteins). To choose control genome I searched by taxonomy among Sulfolobaceae familia, there were 16 reference proteomes in search results, I chose Metallosphaera sedula proteome (ID: UP000000242, 2256 proteins) due to bacteria's ability to oxidize pyrite (FeS2), it is significant metabolic difference. According to indicators proteomes are allright, BUSCO showed more than 95% single-copy orthologs, CPD are standart or close to standart (high value), genome representation in RefSeq is full. S. solfataricus proteome is more studied, it has 489 reviewed proteins out of 2980 (16.4%), and M. sedula proteome has 169 out of 2256 (7.5%). To download all proteins from proteomes to kodomo server I used next instructions in command line:

"wget 'https://www.uniprot.org/uniprot/?query=proteome:up000001974&format=txt&compress=yes' -O term2/pr8/UP000001974.swiss.gz" for S. solfataricus and "wget 'https://www.uniprot.org/uniprot/?query=proteome:up000000242&format=txt&compress=yes' -O term2/pr8/UP000000242.swiss.gz" for M. sedula

Comparison of proteomes according to the representation of certain groups of proteins

I used these python programs

Transmembrane proteins: As I read in UniProtKB user manual, KW field must contain "Transmembrane" (KW-0812) and FT field contain TRANSMEM type if protein is transmembrane. I found 592(19.7%) and 442(19.6%) transmembrane proteins for S. solfataricus and M. sedula respectively. Both organisms have a lot of transmembrane proteins, it is adaptation to high temprature, to do cellular membrane more thick and stable.

Enzymes: I searched "EC=" in DE line to find all enzymes among proteins. There were 695(23.3%) and 499(22.1%) enzymes for S. solfataricus and M. sedula respectively.

Oxidoreductases: Adding to previous request enzyme class I got 152(5.1%) and 110(4.9%) for S. solfataricus and M. sedula respectively.

Top 10 more frequently encountered keyword in these proteomes

*Keyword "ECO:0000256|SAM:Phobius}" not worth considering, because it is the transferred ending of different other keyword

I probably made mistake when I chose control genome, I can't find any essential distinctions. However I practiced english writing, programming on python, explored UniProtKB entries organization, knew how insignificant are differences between proteomes of organisms from the same family