Bioinformatic analysis of beta carbonic anhydrase sequences from protozoans and metazoans

Abstract

BackgroundDespite the high prevalence of parasitic infections, and their impact on global health and economy, the number of drugs available to treat them is extremely limited. As a result, the potential consequences of large-scale resistance to any existing drugs are a major concern. A number of recent investigations have focused on the effects of potential chemical inhibitors on bacterial and fungal carbonic anhydrases. Among the five classes of carbonic anhydrases (alpha, beta, gamma, delta and zeta), beta carbonic anhydrases have been reported in most species of bacteria, yeasts, algae, plants, and particular invertebrates (nematodes and insects). To date, there has been a lack of knowledge on the expression and molecular structure of beta carbonic anhydrases in metazoan (nematodes and arthropods) and protozoan species.MethodsHere, the identification of novel beta carbonic anhydrases was based on the presence of the highly-conserved amino acid sequence patterns of the active site. A phylogenetic tree was constructed based on codon-aligned DNA sequences. Subcellular localization prediction for each identified invertebrate beta carbonic anhydrase was performed using the TargetP webserver.ResultsWe verified a total of 75 beta carbonic anhydrase sequences in metazoan and protozoan species by proteome-wide searches and multiple sequence alignment. Of these, 52 were novel, and contained highly conserved amino acid residues, which are inferred to form the active site in beta carbonic anhydrases. Mitochondrial targeting peptide analysis revealed that 31 enzymes are predicted with mitochondrial localization; one was predicted to be a secretory enzyme, and the other 43 were predicted to have other undefined cellular localizations.ConclusionsThese investigations identified 75 beta carbonic anhydrases in metazoan and protozoan species, and among them there were 52 novel sequences that were not previously annotated as beta carbonic anhydrases. Our results will not only change the current information in proteomics and genomics databases, but will also suggest novel targets for drugs against parasites.

Innovative molecular diagnosis of Trichinella species based on β‐carbonic anhydrase genomic sequence

“…One of them was β‐CA protein sequence from T. spiralis (UniProt ID: E5SH53). Our previous results also revealed that β‐CA proteins show high similarity among various Drosophila species and other species of dipteran flies (Zolfaghari Emameh et al ., ). This led us to hypothesize that the high similarity is extensible to other species of one defined genus, such as Trichinella spp.…”

“…Many protozoan, arthropod, and nematode species (invertebrate metazoans) contain β-CA gene and protein sequences in their genomes and proteomes respectively. BLAST homology analysis of predefined β-CA protein sequences from D. melanogaster (Uniprot ID: Q9VHJ5) and C. elegans (Uniprot ID: Q22460) resulted in identification of more than 75 β-CA protein sequences from protozoans and invertebrate metazoans (Zolfaghari Emameh et al, 2014). One of them was β-CA protein sequence from T. spiralis (UniProt ID: E5SH53).…”

“…Moreover, they participate in some biosynthetic reactions, such as gluconeogenesis, lipogenesis and ureagenesis in animals (Vullo et al ., 2004; 2005; Alterio et al ., ; Nishimori et al ., ; Supuran, ), growth of some bacterial species (Merlin et al ., ; Mitsuhashi et al ., ) and photosynthesis in plants and algae (Fawcett et al ., ; Funke et al ., ). The previous investigations have confirmed that β‐CA gene sequences are completely absent in vertebrate genomes, whereas they can be found in plants, algae, yeasts, bacteria, archaea, protozoa and invertebrate metazoans (Fawcett et al ., ; Funke et al ., ; Smith et al ., ; Merlin et al ., ; Mitsuhashi et al ., ; Aguilera et al ., ; Fasseas et al ., ; Syrjanen et al ., ; Zolfaghari Emameh et al ., ). By this background, we hypothesized that genomic β‐CA sequences from prokaryotic pathogens and eukaryotic parasites would be an ideal host‐specific determinant for molecular diagnostics, with minimal interfering effects from mammalian genomes.…”

“…One effective strategy for specific detection of Trichinella infection is identification of a genomic or proteomic determinant, which is absent in host genomes or proteomes (Duplessis and Moineau, ). Beta carbonic anhydrase (β‐CA) could be one of such host‐specific markers (Fasseas et al ., ; Syrjanen et al ., ; Zolfaghari Emameh et al ., 2014; 2015). Six evolutionary divergent gene families encode for CAs (α, β, γ, δ, ζ and η) (Lane et al ., ; Xu et al ., ; Ferry, ; Del Prete et al ., ; Zolfaghari Emameh et al ., ).…”

“…Beta carbonic anhydrase (β‐CA) could be one of such host‐specific markers (Fasseas et al ., ; Syrjanen et al ., ; Zolfaghari Emameh et al ., 2014; 2015). Six evolutionary divergent gene families encode for CAs (α, β, γ, δ, ζ and η) (Lane et al ., ; Xu et al ., ; Ferry, ; Del Prete et al ., ; Zolfaghari Emameh et al ., ). Different CA isozymes are involved in many biological processes, such as respiration involving transport of CO 2 and bicarbonate between metabolizing tissues, pH homeostasis, electrolyte transfer, bone resorption, and calcification.…”