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In silico ionomics segregates parasitic from free-living eukaryotes.

Greganova E, Steinmann M, Mäser P, Fankhauser N - Genome Biol Evol (2013)

Bottom Line: Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand.Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites.Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism.

View Article: PubMed Central - PubMed

Affiliation: Swiss Tropical and Public Health Institute, Basel, Switzerland.

ABSTRACT
Ion transporters are fundamental to life. Due to their ancient origin and conservation in sequence, ion transporters are also particularly well suited for comparative genomics of distantly related species. Here, we perform genome-wide ion transporter profiling as a basis for comparative genomics of eukaryotes. From a given predicted proteome, we identify all bona fide ion channels, ion porters, and ion pumps. Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand. This surprising finding indicates strong convergent evolution of the parasites regarding the acquisition and homeostasis of inorganic ions. Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites. Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism. This finding is in agreement with the phenomenon of iron withholding as a primordial antimicrobial strategy of infected mammals.

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Overview on the in silico approach for ionomics.
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evt134-F1: Overview on the in silico approach for ionomics.

Mentions: Before converting the redundancy-reduced sets of ion transporter reference sequences into profiles, predicted ankyrin repeats and cyclic nucleotide binding domains were removed from the sequences. These domains were identified with hmmsearch of the HMMer 3.0 package using the profiles Ank (PF00023) and cNMP_binding (PF00027) from Pfam (http://pfam.sanger.ac.uk/, last accessed October 1, 2013). The parts matching these profiles with E < 10−8 were replaced with letters X in each sequence. Then, a ClustalW multiple alignment (Thompson et al. 1994) was performed for each sequence set and converted into a position-dependent scoring matrix with hmmbuild. The resulting profiles were concatenated to a HMM library for ion transporters. Negative control libraries were constructed by randomly selecting sets of 61 entries from the Pfam-A database (version 26.0: 13,672 entries). All the steps as outlined in figure 1 were carried out with self-made Perl scripts.Fig. 1.—


In silico ionomics segregates parasitic from free-living eukaryotes.

Greganova E, Steinmann M, Mäser P, Fankhauser N - Genome Biol Evol (2013)

Overview on the in silico approach for ionomics.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814192&req=5

evt134-F1: Overview on the in silico approach for ionomics.
Mentions: Before converting the redundancy-reduced sets of ion transporter reference sequences into profiles, predicted ankyrin repeats and cyclic nucleotide binding domains were removed from the sequences. These domains were identified with hmmsearch of the HMMer 3.0 package using the profiles Ank (PF00023) and cNMP_binding (PF00027) from Pfam (http://pfam.sanger.ac.uk/, last accessed October 1, 2013). The parts matching these profiles with E < 10−8 were replaced with letters X in each sequence. Then, a ClustalW multiple alignment (Thompson et al. 1994) was performed for each sequence set and converted into a position-dependent scoring matrix with hmmbuild. The resulting profiles were concatenated to a HMM library for ion transporters. Negative control libraries were constructed by randomly selecting sets of 61 entries from the Pfam-A database (version 26.0: 13,672 entries). All the steps as outlined in figure 1 were carried out with self-made Perl scripts.Fig. 1.—

Bottom Line: Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand.Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites.Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism.

View Article: PubMed Central - PubMed

Affiliation: Swiss Tropical and Public Health Institute, Basel, Switzerland.

ABSTRACT
Ion transporters are fundamental to life. Due to their ancient origin and conservation in sequence, ion transporters are also particularly well suited for comparative genomics of distantly related species. Here, we perform genome-wide ion transporter profiling as a basis for comparative genomics of eukaryotes. From a given predicted proteome, we identify all bona fide ion channels, ion porters, and ion pumps. Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand. This surprising finding indicates strong convergent evolution of the parasites regarding the acquisition and homeostasis of inorganic ions. Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites. Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism. This finding is in agreement with the phenomenon of iron withholding as a primordial antimicrobial strategy of infected mammals.

Show MeSH
Related in: MedlinePlus