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CysQ of Cryptosporidium parvum, a Protozoa, May Have Been Acquired from Bacteria by Horizontal Gene Transfer.

Lee JY, Kim S - Genomics Inform (2012)

Bottom Line: Analysis with NCBI's Conserved Domain Tree showed phylogenetic incongruence, in that C. parvum CysQ protein was located within a branch of proteobacteria in the cd01638 domain, a bacterial member of the inositol monophosphatase family.According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes.Therefore, we conclude that C. parvum regained cysQ from proteobacteria by HGT, although its functional role is elusive.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics & Life Sciences, Soongsil University, Seoul 156-743, Korea.

ABSTRACT
Horizontal gene transfer (HGT) is the movement of genetic material between kingdoms and is considered to play a positive role in adaptation. Cryptosporidium parvum is a parasitic protozoan that causes an infectious disease. Its genome sequencing reported 14 bacteria-like proteins in the nuclear genome. Among them, cgd2_1810, which has been annotated as CysQ, a sulfite synthesis pathway protein, is listed as one of the candidates of genes horizontally transferred from bacterial origin. In this report, we examined this issue using phylogenetic analysis. Our BLAST search showed that C. parvum CysQ protein had the highest similarity with that of proteobacteria. Analysis with NCBI's Conserved Domain Tree showed phylogenetic incongruence, in that C. parvum CysQ protein was located within a branch of proteobacteria in the cd01638 domain, a bacterial member of the inositol monophosphatase family. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes. However, the Apicomplexa, including C. parvum, largely lack orthologous genes of the pathway, suggesting its loss in those protozoan lineages. Therefore, we conclude that C. parvum regained cysQ from proteobacteria by HGT, although its functional role is elusive.

No MeSH data available.


Related in: MedlinePlus

Conserved Domain Tree (CDTree) involving CysQ (cgd2_1810) protein. (A) Whole hierarchy of Fig superfamily. Branch colors indicate Eukaryota (pink), Bacteria (bright blue), and Archaea (orange) domains; Cryptosporidium parvum sequence is added (red branch and circle). On the right side, color bar marked with domain accession names displays subfamilies in Fig superfamily. All CDs except for cd01637 are well clustered. cd01637 is scattered around the tree and highlighted in black ticks. (B) CDTree of cd01638 domain. The cd01638 clade that includes only bacteria is classified by taxonomic lineage. Bacteria are subdivided into two distinct parts, gram-negative and gram-positive bacteria. Each bacterial phylum is colored as shown in legend. CysQ protein of C. parvum is shown in red dashed branch with a red circle near Proteobacteria.
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Figure 1: Conserved Domain Tree (CDTree) involving CysQ (cgd2_1810) protein. (A) Whole hierarchy of Fig superfamily. Branch colors indicate Eukaryota (pink), Bacteria (bright blue), and Archaea (orange) domains; Cryptosporidium parvum sequence is added (red branch and circle). On the right side, color bar marked with domain accession names displays subfamilies in Fig superfamily. All CDs except for cd01637 are well clustered. cd01637 is scattered around the tree and highlighted in black ticks. (B) CDTree of cd01638 domain. The cd01638 clade that includes only bacteria is classified by taxonomic lineage. Bacteria are subdivided into two distinct parts, gram-negative and gram-positive bacteria. Each bacterial phylum is colored as shown in legend. CysQ protein of C. parvum is shown in red dashed branch with a red circle near Proteobacteria.

Mentions: CysQ protein of C. parvum contains a CysQ domain (accession no. cd01638), which is one of the children of the Fig (FBPase/inositol monophosphatase [IMPase]/glpX-like domain) superfamily. The Fig superfamily is a metal-dependent phosphatase that organizes two subsets of direct children in the hierarchy of the superfamily: FBPase glpX domain (cd01516) and IMPase-like domain (cd01637). Cd01637 has 9 children domains: CysQ (cd01638), IMPase (cd01639), bacterial IMPaselike 1 (cd01641), bacterial IMPase-like 2 (cd01643), IPPase (cd10640), FBPase (cd00354), Arch FBPase 1 (cd 01515), Arch FBPase 2 (cd01642), and PAP phosphatase (cd10517). The whole hierarchy tree of the Fig superfamily comprises a total of 360 cellular organisms: 246 bacteria, 95 eukaryotes, and 19 Archaea (Fig. 1A). Some domains (cd01516, cd01637, cd01638, cd01641, and cd0643) comprise predominantly bacterial proteins in their CDTree, whereas the other domains have a combined composition (cd000354, cd0517, and cd01639) or a high level of Archaea (cd01642 and cd01515). Domains cd01638, cd01641, and cd01643 are bacterial members of the IMPase family. All of them show a high proportion of Proteobacteria, at about 65%, 50%, and 43% respectively. In cd01638, C. parvum CysQ protein is located within the monophyletic gram-negative subtree, ranging from Pseudomonas sringae, Gammaproteobacteria, to Campylobacter jejuni, Epsilonproteobacteria (Fig. 1B). On the other hand, the gram-negative subtree is paraphyletic, in that it has 27 branches of Proteobacteria and Aquificae, Cyanobacteria, and Bacteroidetes, respectively. Taken together, the phylogenetic analysis strongly supports the hypothesis that the cysQ gene of C. parvum may have been acquired from Proteobacteria by horizontal gene transfer.


CysQ of Cryptosporidium parvum, a Protozoa, May Have Been Acquired from Bacteria by Horizontal Gene Transfer.

Lee JY, Kim S - Genomics Inform (2012)

Conserved Domain Tree (CDTree) involving CysQ (cgd2_1810) protein. (A) Whole hierarchy of Fig superfamily. Branch colors indicate Eukaryota (pink), Bacteria (bright blue), and Archaea (orange) domains; Cryptosporidium parvum sequence is added (red branch and circle). On the right side, color bar marked with domain accession names displays subfamilies in Fig superfamily. All CDs except for cd01637 are well clustered. cd01637 is scattered around the tree and highlighted in black ticks. (B) CDTree of cd01638 domain. The cd01638 clade that includes only bacteria is classified by taxonomic lineage. Bacteria are subdivided into two distinct parts, gram-negative and gram-positive bacteria. Each bacterial phylum is colored as shown in legend. CysQ protein of C. parvum is shown in red dashed branch with a red circle near Proteobacteria.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
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Figure 1: Conserved Domain Tree (CDTree) involving CysQ (cgd2_1810) protein. (A) Whole hierarchy of Fig superfamily. Branch colors indicate Eukaryota (pink), Bacteria (bright blue), and Archaea (orange) domains; Cryptosporidium parvum sequence is added (red branch and circle). On the right side, color bar marked with domain accession names displays subfamilies in Fig superfamily. All CDs except for cd01637 are well clustered. cd01637 is scattered around the tree and highlighted in black ticks. (B) CDTree of cd01638 domain. The cd01638 clade that includes only bacteria is classified by taxonomic lineage. Bacteria are subdivided into two distinct parts, gram-negative and gram-positive bacteria. Each bacterial phylum is colored as shown in legend. CysQ protein of C. parvum is shown in red dashed branch with a red circle near Proteobacteria.
Mentions: CysQ protein of C. parvum contains a CysQ domain (accession no. cd01638), which is one of the children of the Fig (FBPase/inositol monophosphatase [IMPase]/glpX-like domain) superfamily. The Fig superfamily is a metal-dependent phosphatase that organizes two subsets of direct children in the hierarchy of the superfamily: FBPase glpX domain (cd01516) and IMPase-like domain (cd01637). Cd01637 has 9 children domains: CysQ (cd01638), IMPase (cd01639), bacterial IMPaselike 1 (cd01641), bacterial IMPase-like 2 (cd01643), IPPase (cd10640), FBPase (cd00354), Arch FBPase 1 (cd 01515), Arch FBPase 2 (cd01642), and PAP phosphatase (cd10517). The whole hierarchy tree of the Fig superfamily comprises a total of 360 cellular organisms: 246 bacteria, 95 eukaryotes, and 19 Archaea (Fig. 1A). Some domains (cd01516, cd01637, cd01638, cd01641, and cd0643) comprise predominantly bacterial proteins in their CDTree, whereas the other domains have a combined composition (cd000354, cd0517, and cd01639) or a high level of Archaea (cd01642 and cd01515). Domains cd01638, cd01641, and cd01643 are bacterial members of the IMPase family. All of them show a high proportion of Proteobacteria, at about 65%, 50%, and 43% respectively. In cd01638, C. parvum CysQ protein is located within the monophyletic gram-negative subtree, ranging from Pseudomonas sringae, Gammaproteobacteria, to Campylobacter jejuni, Epsilonproteobacteria (Fig. 1B). On the other hand, the gram-negative subtree is paraphyletic, in that it has 27 branches of Proteobacteria and Aquificae, Cyanobacteria, and Bacteroidetes, respectively. Taken together, the phylogenetic analysis strongly supports the hypothesis that the cysQ gene of C. parvum may have been acquired from Proteobacteria by horizontal gene transfer.

Bottom Line: Analysis with NCBI's Conserved Domain Tree showed phylogenetic incongruence, in that C. parvum CysQ protein was located within a branch of proteobacteria in the cd01638 domain, a bacterial member of the inositol monophosphatase family.According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes.Therefore, we conclude that C. parvum regained cysQ from proteobacteria by HGT, although its functional role is elusive.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics & Life Sciences, Soongsil University, Seoul 156-743, Korea.

ABSTRACT
Horizontal gene transfer (HGT) is the movement of genetic material between kingdoms and is considered to play a positive role in adaptation. Cryptosporidium parvum is a parasitic protozoan that causes an infectious disease. Its genome sequencing reported 14 bacteria-like proteins in the nuclear genome. Among them, cgd2_1810, which has been annotated as CysQ, a sulfite synthesis pathway protein, is listed as one of the candidates of genes horizontally transferred from bacterial origin. In this report, we examined this issue using phylogenetic analysis. Our BLAST search showed that C. parvum CysQ protein had the highest similarity with that of proteobacteria. Analysis with NCBI's Conserved Domain Tree showed phylogenetic incongruence, in that C. parvum CysQ protein was located within a branch of proteobacteria in the cd01638 domain, a bacterial member of the inositol monophosphatase family. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes. However, the Apicomplexa, including C. parvum, largely lack orthologous genes of the pathway, suggesting its loss in those protozoan lineages. Therefore, we conclude that C. parvum regained cysQ from proteobacteria by HGT, although its functional role is elusive.

No MeSH data available.


Related in: MedlinePlus