Limits...
The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer.

van der Giezen M, Cox S, Tovar J - BMC Evol. Biol. (2004)

Bottom Line: E. histolytica IscU and IscS were found to contain all features considered essential for their biological activity, including amino acid residues involved in substrate and/or co-factor binding.The bacterial-type FeS cluster assembly genes of E. histolytica suggest their lateral acquisition from epsilon proteobacteria.This is a clear example of horizontal gene transfer (HGT) from eubacteria to unicellular eukaryotic organisms, a phenomenon known to contribute significantly to the evolution of eukaryotic genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK. mark.vandergiezen@rhul.ac.uk

ABSTRACT

Background: Iron-sulfur (FeS) proteins are present in all living organisms and play important roles in electron transport and metalloenzyme catalysis. The maturation of FeS proteins in eukaryotes is an essential function of mitochondria, but little is known about this process in amitochondriate eukaryotes. Here we report on the identification and analysis of two genes encoding critical FeS cluster (Isc) biosynthetic proteins from the amitochondriate human pathogen Entamoeba histolytica.

Results: E. histolytica IscU and IscS were found to contain all features considered essential for their biological activity, including amino acid residues involved in substrate and/or co-factor binding. The IscU protein differs significantly from other eukaryotic homologs and resembles the long type isoforms encountered in some bacteria. Phylogenetic analyses of E. histolytica IscS and IscU showed a close relationship with homologs from Helicobacter pylori and Campylobacter jejuni, to the exclusion of mitochondrial isoforms.

Conclusions: The bacterial-type FeS cluster assembly genes of E. histolytica suggest their lateral acquisition from epsilon proteobacteria. This is a clear example of horizontal gene transfer (HGT) from eubacteria to unicellular eukaryotic organisms, a phenomenon known to contribute significantly to the evolution of eukaryotic genomes.

Show MeSH
Alignment of the putative E. histolytica IscU and IscS with homologs from C. jejuni, A. vinelandii, R. prowazekii, S. cerevisiae, and H. sapiens. A. Alignment of the E. histolytica long-form IscU with similar isoforms from C. jejuni and A. vinelandii. In addition, short-form IscU homologs from R. prowazekii, S. cerevisiae, and H. sapiens are aligned concatenated with their Nfu1 homologs (arrow indicates start of Nfu1 homologs) which resemble the C-terminal extension found on the long-form IscU. The conserved cysteine residues which provide a scaffold for the IscS-directed sequential assembly of labile FeS-clusters [14] are boxed. The cysteine residue that forms a disulfide bridge with a conserved cysteine residue on IscS (see B) is indicated by a closed square (■). The yeast Nfu1 mitochondrial transit peptide has been deleted. B. Alignment of the E. histolytica IscS with homologs from the above mentioned organisms. Important residues for function are as described by Tachezy, Sánchez and Müller [20]; the conserved lysine involved in co-factor binding (pyridoxal-5'-phosphate, PLP) is indicated by a closed circle (●), other residues involved in PLP interaction are indicated by open circles (○), the cysteine residue that forms a disulfide bridge with a cysteine residue on IscU (see A) is indicated by a closed box (■), residues involved in substrate binding (L-cysteine) are indicated by open squares (□), the conserved histidine involved in substrate deprotonation is indicated by an arrow. Typical eukaryotic/eubacterial conserved cysteine and C-terminal residues are boxed. Note that organisms that contain a long-form IscU (see Fig. 2B and 3A) do not have these conserved residues suggesting that the C-terminal IscU extension might take over the role of these residues. Part of the mitochondrial transit peptides from the yeast and human IscS homologs have been omitted (~) for reasons of clarity. Amino acids were shaded according to similarity/identity scores: dark grey indicates fully conserved residues while light grey indicates similar residues according to the PAM250 matrix [59].
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC373444&req=5

Figure 3: Alignment of the putative E. histolytica IscU and IscS with homologs from C. jejuni, A. vinelandii, R. prowazekii, S. cerevisiae, and H. sapiens. A. Alignment of the E. histolytica long-form IscU with similar isoforms from C. jejuni and A. vinelandii. In addition, short-form IscU homologs from R. prowazekii, S. cerevisiae, and H. sapiens are aligned concatenated with their Nfu1 homologs (arrow indicates start of Nfu1 homologs) which resemble the C-terminal extension found on the long-form IscU. The conserved cysteine residues which provide a scaffold for the IscS-directed sequential assembly of labile FeS-clusters [14] are boxed. The cysteine residue that forms a disulfide bridge with a conserved cysteine residue on IscS (see B) is indicated by a closed square (■). The yeast Nfu1 mitochondrial transit peptide has been deleted. B. Alignment of the E. histolytica IscS with homologs from the above mentioned organisms. Important residues for function are as described by Tachezy, Sánchez and Müller [20]; the conserved lysine involved in co-factor binding (pyridoxal-5'-phosphate, PLP) is indicated by a closed circle (●), other residues involved in PLP interaction are indicated by open circles (○), the cysteine residue that forms a disulfide bridge with a cysteine residue on IscU (see A) is indicated by a closed box (■), residues involved in substrate binding (L-cysteine) are indicated by open squares (□), the conserved histidine involved in substrate deprotonation is indicated by an arrow. Typical eukaryotic/eubacterial conserved cysteine and C-terminal residues are boxed. Note that organisms that contain a long-form IscU (see Fig. 2B and 3A) do not have these conserved residues suggesting that the C-terminal IscU extension might take over the role of these residues. Part of the mitochondrial transit peptides from the yeast and human IscS homologs have been omitted (~) for reasons of clarity. Amino acids were shaded according to similarity/identity scores: dark grey indicates fully conserved residues while light grey indicates similar residues according to the PAM250 matrix [59].

Mentions: Both proteins align along their whole length to homologous proteins from other organisms (Fig. 3). Residues implicated in function are conserved in both IscU and IscS proteins. The three cysteine residues that are conserved in Escherichia coli IscU which provide a scaffold for the assembly of iron-sulfur clusters [14] are conserved in the E. histolytica protein (Fig. 3A). In addition, in E. coli one of these IscU cysteines interacts with a conserved cysteine from IscS which is also present in the E. histolytica IscS (Figs. 3A and 3B). Most residues considered to be important for IscS function are also present on the E. histolytica protein (Fig. 3B). To test whether the E. histolytica IscS protein assumes a normal three-dimensional conformation, this protein was modeled on the solved NifS protein structure from Thermotoga maritima. The overall topology of both proteins is quite similar and the force field energy of the computed E. histolytica IscS model is -13,800 kJ/mol, indicating an energetically plausible model [31]. The putative active site architecture of E. histolytica IscS and the solved active site of T. maritima NifS show similar structures (Fig. 4). The ring of the cofactor vitamin B6 (or pyridoxal-5'-phosphate; PLP) is sandwiched between EhHis106/TmHis99 and EhThr184/TmVal179 and further fixed by residues EhAsp182/TmAsp177 and EhGln185/TmGln180. The phosphate-group is anchored by six hydrogen bonds from EhThr76/TmThr71, EhHis207/TmHis202, EhThr198/TmSer200, and EhThr243/TmThr238 [32]. The presence of all residues considered to be important for IscU and IscS activity on the E. histolytica proteins suggest that these proteins are indeed involved in FeS cluster assembly.


The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer.

van der Giezen M, Cox S, Tovar J - BMC Evol. Biol. (2004)

Alignment of the putative E. histolytica IscU and IscS with homologs from C. jejuni, A. vinelandii, R. prowazekii, S. cerevisiae, and H. sapiens. A. Alignment of the E. histolytica long-form IscU with similar isoforms from C. jejuni and A. vinelandii. In addition, short-form IscU homologs from R. prowazekii, S. cerevisiae, and H. sapiens are aligned concatenated with their Nfu1 homologs (arrow indicates start of Nfu1 homologs) which resemble the C-terminal extension found on the long-form IscU. The conserved cysteine residues which provide a scaffold for the IscS-directed sequential assembly of labile FeS-clusters [14] are boxed. The cysteine residue that forms a disulfide bridge with a conserved cysteine residue on IscS (see B) is indicated by a closed square (■). The yeast Nfu1 mitochondrial transit peptide has been deleted. B. Alignment of the E. histolytica IscS with homologs from the above mentioned organisms. Important residues for function are as described by Tachezy, Sánchez and Müller [20]; the conserved lysine involved in co-factor binding (pyridoxal-5'-phosphate, PLP) is indicated by a closed circle (●), other residues involved in PLP interaction are indicated by open circles (○), the cysteine residue that forms a disulfide bridge with a cysteine residue on IscU (see A) is indicated by a closed box (■), residues involved in substrate binding (L-cysteine) are indicated by open squares (□), the conserved histidine involved in substrate deprotonation is indicated by an arrow. Typical eukaryotic/eubacterial conserved cysteine and C-terminal residues are boxed. Note that organisms that contain a long-form IscU (see Fig. 2B and 3A) do not have these conserved residues suggesting that the C-terminal IscU extension might take over the role of these residues. Part of the mitochondrial transit peptides from the yeast and human IscS homologs have been omitted (~) for reasons of clarity. Amino acids were shaded according to similarity/identity scores: dark grey indicates fully conserved residues while light grey indicates similar residues according to the PAM250 matrix [59].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC373444&req=5

Figure 3: Alignment of the putative E. histolytica IscU and IscS with homologs from C. jejuni, A. vinelandii, R. prowazekii, S. cerevisiae, and H. sapiens. A. Alignment of the E. histolytica long-form IscU with similar isoforms from C. jejuni and A. vinelandii. In addition, short-form IscU homologs from R. prowazekii, S. cerevisiae, and H. sapiens are aligned concatenated with their Nfu1 homologs (arrow indicates start of Nfu1 homologs) which resemble the C-terminal extension found on the long-form IscU. The conserved cysteine residues which provide a scaffold for the IscS-directed sequential assembly of labile FeS-clusters [14] are boxed. The cysteine residue that forms a disulfide bridge with a conserved cysteine residue on IscS (see B) is indicated by a closed square (■). The yeast Nfu1 mitochondrial transit peptide has been deleted. B. Alignment of the E. histolytica IscS with homologs from the above mentioned organisms. Important residues for function are as described by Tachezy, Sánchez and Müller [20]; the conserved lysine involved in co-factor binding (pyridoxal-5'-phosphate, PLP) is indicated by a closed circle (●), other residues involved in PLP interaction are indicated by open circles (○), the cysteine residue that forms a disulfide bridge with a cysteine residue on IscU (see A) is indicated by a closed box (■), residues involved in substrate binding (L-cysteine) are indicated by open squares (□), the conserved histidine involved in substrate deprotonation is indicated by an arrow. Typical eukaryotic/eubacterial conserved cysteine and C-terminal residues are boxed. Note that organisms that contain a long-form IscU (see Fig. 2B and 3A) do not have these conserved residues suggesting that the C-terminal IscU extension might take over the role of these residues. Part of the mitochondrial transit peptides from the yeast and human IscS homologs have been omitted (~) for reasons of clarity. Amino acids were shaded according to similarity/identity scores: dark grey indicates fully conserved residues while light grey indicates similar residues according to the PAM250 matrix [59].
Mentions: Both proteins align along their whole length to homologous proteins from other organisms (Fig. 3). Residues implicated in function are conserved in both IscU and IscS proteins. The three cysteine residues that are conserved in Escherichia coli IscU which provide a scaffold for the assembly of iron-sulfur clusters [14] are conserved in the E. histolytica protein (Fig. 3A). In addition, in E. coli one of these IscU cysteines interacts with a conserved cysteine from IscS which is also present in the E. histolytica IscS (Figs. 3A and 3B). Most residues considered to be important for IscS function are also present on the E. histolytica protein (Fig. 3B). To test whether the E. histolytica IscS protein assumes a normal three-dimensional conformation, this protein was modeled on the solved NifS protein structure from Thermotoga maritima. The overall topology of both proteins is quite similar and the force field energy of the computed E. histolytica IscS model is -13,800 kJ/mol, indicating an energetically plausible model [31]. The putative active site architecture of E. histolytica IscS and the solved active site of T. maritima NifS show similar structures (Fig. 4). The ring of the cofactor vitamin B6 (or pyridoxal-5'-phosphate; PLP) is sandwiched between EhHis106/TmHis99 and EhThr184/TmVal179 and further fixed by residues EhAsp182/TmAsp177 and EhGln185/TmGln180. The phosphate-group is anchored by six hydrogen bonds from EhThr76/TmThr71, EhHis207/TmHis202, EhThr198/TmSer200, and EhThr243/TmThr238 [32]. The presence of all residues considered to be important for IscU and IscS activity on the E. histolytica proteins suggest that these proteins are indeed involved in FeS cluster assembly.

Bottom Line: E. histolytica IscU and IscS were found to contain all features considered essential for their biological activity, including amino acid residues involved in substrate and/or co-factor binding.The bacterial-type FeS cluster assembly genes of E. histolytica suggest their lateral acquisition from epsilon proteobacteria.This is a clear example of horizontal gene transfer (HGT) from eubacteria to unicellular eukaryotic organisms, a phenomenon known to contribute significantly to the evolution of eukaryotic genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK. mark.vandergiezen@rhul.ac.uk

ABSTRACT

Background: Iron-sulfur (FeS) proteins are present in all living organisms and play important roles in electron transport and metalloenzyme catalysis. The maturation of FeS proteins in eukaryotes is an essential function of mitochondria, but little is known about this process in amitochondriate eukaryotes. Here we report on the identification and analysis of two genes encoding critical FeS cluster (Isc) biosynthetic proteins from the amitochondriate human pathogen Entamoeba histolytica.

Results: E. histolytica IscU and IscS were found to contain all features considered essential for their biological activity, including amino acid residues involved in substrate and/or co-factor binding. The IscU protein differs significantly from other eukaryotic homologs and resembles the long type isoforms encountered in some bacteria. Phylogenetic analyses of E. histolytica IscS and IscU showed a close relationship with homologs from Helicobacter pylori and Campylobacter jejuni, to the exclusion of mitochondrial isoforms.

Conclusions: The bacterial-type FeS cluster assembly genes of E. histolytica suggest their lateral acquisition from epsilon proteobacteria. This is a clear example of horizontal gene transfer (HGT) from eubacteria to unicellular eukaryotic organisms, a phenomenon known to contribute significantly to the evolution of eukaryotic genomes.

Show MeSH