PMC:3475487 / 10424-14072 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3475487","sourcedb":"PMC","sourceid":"3475487","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3475487","text":"Orthologs on sulfate assimilation pathway\nCysQ protein participates in sulfate assimilation on sulfur metabolism. In Fig. 2, we show a simplified version of the KEGG pathway, classifying the enzymes into three groups, according to their direction and steps: Class I for EC 2.7.7.4 (CysN) and EC 2.7.7.5 (CysD); Class II for EC 2.7.1.25 (CysC); and Class III for EC 3.1.3.7 (CysQ). If CysQ of C. parvum is a true CysQ enzyme, playing a role in sulfate assimilation in the parasite, the other components of the pathway should be present in it. On the contrary, we could not identify such genes in the annotated gene list.\nThe KEGG pathway did not list C. parvum proteins in the sulfate assimilation pathway. We looked for the C. parvum proteins by searching the genome sequence using TBLASTN with M. tuberculosis CysN (Rv1286) and CysD (Rv1285) and E. coli CysN (b2751), CysD (b2752), and CysC (b2750) proteins as queries.\nAmong class I and II proteins, only CysN showed marginal matches to cgd6_3990 (29% and 33% identities, respectively) to M. tuberculosis and E. coli sequences. Interestingly, this C. parvum protein was reported as elongation factor 1 alpha, not a sulfate adenylyltransferase. This protein had high similarities to other protozoan or fungal elongation factor 1 alpha proteins. Thus, we consider this as a false hit. The class III protein, CysQ, matched to cgd2_1810 (24% and 36% identities, respectively, for M. tuberculosis and E. coli proteins). This C. parvum gene was annotated \"CysQ, sulfite synthesis pathway protein.\" As no other components of the sulfate assimilation pathway, except for CysQ, are found in C. parvum, we may conclude that the pathway does not function in this organism. We compiled the orthologs of the genes in this pathway using the KO database (Table 1).\nEukaryotic kingdoms, except for protists harbored full ranges of orthologs in all three classes. Animals and plants showed similar trends in Class I and II, because two classes shared two orthologs (K13811: 3'-phosphoadenosine 5'-phosphosulfate synthase [PAPSS], K00955: bifunctional enzyme CysN/CysC [CysNC]), and even K13811 is specialized in animals and plants. Fungi also have many orthologs, like animals and plants, in Class I and II, but they have different orthologs (Class I, K00958, sulfate adenylyltransferase [E2.7.7.4C, met3]; Class II, K00860, adenylylsulfatekinase [CysC]).\nIn prokaryotes, the proportion of Class I genes is higher than Class II. All Cyanobacteria, two-thirds of Proteobacteria, and Actinobacteria contained one of the orthologs in Class I, whereas Firmicutes, other bacteria, and the Archaea group have a few orthologs in Class I, II, and III.\nOn the other hand, there were very few orthologs of the sulfate assimilation pathway in protists. We expanded the protist lineage, cataloging the proteins at the class or species level (Table 2).\nSome protists (Choanoflagellates, Entamoeba of Amoebozoa, and Diatoms) had at least one orthologous gene in each of three classes, while most Alveolates, Amoeboflagellate, Euglenozoa, and Diplomonads did not have any orthologs in three classes, many of which are known as parasites causing infectious diseases.\nWhile the sulfate assimilation pathway is generally well conserved in both prokaryotes and eukaryotes, in some protist lineages, the pathway is missing. Thus, we hypothesize that the pathway may have been lost during the evolution of the lineages. C. parvum, like other Aveolates, also may have lost it, and cge2_1810 can not function as CysQ properly. Its function remains elusive, as the sequence similarity to CysQ of M. tuberculosis or E. coli is rather low.","divisions":[{"label":"Title","span":{"begin":0,"end":41}}],"tracks":[]}