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Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor.

DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT - Mol. Cell Proteomics (2009)

Bottom Line: Thus, to gain a broad perspective on the origins and evolution of the NPC, we performed proteomics analyses of NPC-containing fractions from a divergent eukaryote (Trypanosoma brucei) and obtained a comprehensive inventory of its nucleoporins.Strikingly trypanosome nucleoporins clearly share with metazoa and yeast their fold type, domain organization, composition, and modularity.Overall these data provide conclusive evidence that the majority of NPC architecture is indeed conserved throughout the Eukaryota and was already established in the last common eukaryotic ancestor.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA.

ABSTRACT
The nuclear pore complex (NPC) is a macromolecular assembly embedded within the nuclear envelope that mediates bidirectional exchange of material between the nucleus and cytoplasm. Our recent work on the yeast NPC has revealed a simple modularity in its architecture and suggested a common evolutionary origin of the NPC and vesicle coating complexes in a progenitor protocoatomer. However, detailed compositional and structural information is currently only available for vertebrate and yeast NPCs, which are evolutionarily closely related. Hence our understanding of NPC composition in a full evolutionary context is sparse. Moreover despite the ubiquitous nature of the NPC, sequence searches in distant taxa have identified surprisingly few NPC components, suggesting that much of the NPC may not be conserved. Thus, to gain a broad perspective on the origins and evolution of the NPC, we performed proteomics analyses of NPC-containing fractions from a divergent eukaryote (Trypanosoma brucei) and obtained a comprehensive inventory of its nucleoporins. Strikingly trypanosome nucleoporins clearly share with metazoa and yeast their fold type, domain organization, composition, and modularity. Overall these data provide conclusive evidence that the majority of NPC architecture is indeed conserved throughout the Eukaryota and was already established in the last common eukaryotic ancestor. These findings strongly support the hypothesis that NPCs share a common ancestry with vesicle coating complexes and that both were established very early in eukaryotic evolution.

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Correlation between the frequency of glycine and charged residues in trypanosome, yeast, and human FG repeat Nups. The percent composition of Gly is plotted against Asp, Glu, Arg, and Lys (DERK) residue frequency. Each data point represents an FG Nup from either S. cerevisiae (blue) or H. sapiens (red) or a candidate FG Nup from T. brucei (green). The diameter of each data point is directly proportional to the phenylalanine concentration within the respective Nup. FG Nups tend to cluster into two groups: high Gly, low DERK (Group I) and low Gly, high DERK (Group II). The average natural occurrence (in vertebrates) for Phe is ∼4% and for Gly is ∼7%, and the sum natural occurrence for the charged residues is ∼23%.
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Figure 5: Correlation between the frequency of glycine and charged residues in trypanosome, yeast, and human FG repeat Nups. The percent composition of Gly is plotted against Asp, Glu, Arg, and Lys (DERK) residue frequency. Each data point represents an FG Nup from either S. cerevisiae (blue) or H. sapiens (red) or a candidate FG Nup from T. brucei (green). The diameter of each data point is directly proportional to the phenylalanine concentration within the respective Nup. FG Nups tend to cluster into two groups: high Gly, low DERK (Group I) and low Gly, high DERK (Group II). The average natural occurrence (in vertebrates) for Phe is ∼4% and for Gly is ∼7%, and the sum natural occurrence for the charged residues is ∼23%.

Mentions: Like their opisthokont counterparts, the FG regions of trypanosome FG Nups are predicted to be natively unfolded. An extraordinarily high rate of amino acid substitution within FG Nups (60, 61) results in huge sequence divergence (supplemental Table S2A), confounding in silico identification of homology. A high level of genomic plasticity may be a common feature among FG Nups. An example of such plasticity may be TbNup140 and TbNup149, which are encoded by adjacent genes with an abnormally small intergenic region; whereas Northern and Western blotting suggests two separately transcribed messages (supplemental Figs. S1 and S9), in the related kinetoplastid Leishmania major, the ortholog LmjF28.3030 is apparently expressed as a single polypeptide. The vertebrate, S. cerevisiae, and trypanosome FG repeat domains generally have a similar frequency of Phe residues approximately ∼3-fold higher than the mean occurrence in their respective proteomes. Additionally these domains are generally depleted in large side chain amino acids and enriched in small side chain residues. This compositional bias is likely a general feature for natively unfolded regions (60, 62). The abundance of Gly varies considerably between FG repeat domains and displays a clear inverse correlation to the acidic and basic residues Asp, Glu, Arg, and Lys (Fig. 5 and supplemental Fig. S4). Thus, Nup FG repeat domains generally fall into two groups: group I contains Gly-enriched, DERK-deficient sequences, and group II contains significantly less Gly than group A and substantially more DERK residues (Fig. 5). Among the FG Nups, the homologs of TbNup158 can be uniquely identified because of the characteristic nature of their characteristic domains (see above). It is noteworthy that the FG regions of all the homologs of TbNup158 fall into group I, suggesting that the function of a given FG domain is conserved even if its sequence is not. In yeast and vertebrates, FG Nups that are symmetrically localized tend to fall into group I, whereas Nups with an asymmetric localization fall into group II albeit with some exceptions. Although the locations of these trypanosome Nups are currently not known, it will be of significant interest to ascertain whether this compositional feature is a potential predictor for FG Nup location. There is also some conservation in the structured domains of the FG Nups; TbNup53a, TbNup53b, TbNup59, and TbNup62 all possess a putative coiled coil domain, which as it does in their yeast and vertebrate counterparts likely serves to anchor these Nups to the NPC (Fig. 4) (12).


Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor.

DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT - Mol. Cell Proteomics (2009)

Correlation between the frequency of glycine and charged residues in trypanosome, yeast, and human FG repeat Nups. The percent composition of Gly is plotted against Asp, Glu, Arg, and Lys (DERK) residue frequency. Each data point represents an FG Nup from either S. cerevisiae (blue) or H. sapiens (red) or a candidate FG Nup from T. brucei (green). The diameter of each data point is directly proportional to the phenylalanine concentration within the respective Nup. FG Nups tend to cluster into two groups: high Gly, low DERK (Group I) and low Gly, high DERK (Group II). The average natural occurrence (in vertebrates) for Phe is ∼4% and for Gly is ∼7%, and the sum natural occurrence for the charged residues is ∼23%.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC2742445&req=5

Figure 5: Correlation between the frequency of glycine and charged residues in trypanosome, yeast, and human FG repeat Nups. The percent composition of Gly is plotted against Asp, Glu, Arg, and Lys (DERK) residue frequency. Each data point represents an FG Nup from either S. cerevisiae (blue) or H. sapiens (red) or a candidate FG Nup from T. brucei (green). The diameter of each data point is directly proportional to the phenylalanine concentration within the respective Nup. FG Nups tend to cluster into two groups: high Gly, low DERK (Group I) and low Gly, high DERK (Group II). The average natural occurrence (in vertebrates) for Phe is ∼4% and for Gly is ∼7%, and the sum natural occurrence for the charged residues is ∼23%.
Mentions: Like their opisthokont counterparts, the FG regions of trypanosome FG Nups are predicted to be natively unfolded. An extraordinarily high rate of amino acid substitution within FG Nups (60, 61) results in huge sequence divergence (supplemental Table S2A), confounding in silico identification of homology. A high level of genomic plasticity may be a common feature among FG Nups. An example of such plasticity may be TbNup140 and TbNup149, which are encoded by adjacent genes with an abnormally small intergenic region; whereas Northern and Western blotting suggests two separately transcribed messages (supplemental Figs. S1 and S9), in the related kinetoplastid Leishmania major, the ortholog LmjF28.3030 is apparently expressed as a single polypeptide. The vertebrate, S. cerevisiae, and trypanosome FG repeat domains generally have a similar frequency of Phe residues approximately ∼3-fold higher than the mean occurrence in their respective proteomes. Additionally these domains are generally depleted in large side chain amino acids and enriched in small side chain residues. This compositional bias is likely a general feature for natively unfolded regions (60, 62). The abundance of Gly varies considerably between FG repeat domains and displays a clear inverse correlation to the acidic and basic residues Asp, Glu, Arg, and Lys (Fig. 5 and supplemental Fig. S4). Thus, Nup FG repeat domains generally fall into two groups: group I contains Gly-enriched, DERK-deficient sequences, and group II contains significantly less Gly than group A and substantially more DERK residues (Fig. 5). Among the FG Nups, the homologs of TbNup158 can be uniquely identified because of the characteristic nature of their characteristic domains (see above). It is noteworthy that the FG regions of all the homologs of TbNup158 fall into group I, suggesting that the function of a given FG domain is conserved even if its sequence is not. In yeast and vertebrates, FG Nups that are symmetrically localized tend to fall into group I, whereas Nups with an asymmetric localization fall into group II albeit with some exceptions. Although the locations of these trypanosome Nups are currently not known, it will be of significant interest to ascertain whether this compositional feature is a potential predictor for FG Nup location. There is also some conservation in the structured domains of the FG Nups; TbNup53a, TbNup53b, TbNup59, and TbNup62 all possess a putative coiled coil domain, which as it does in their yeast and vertebrate counterparts likely serves to anchor these Nups to the NPC (Fig. 4) (12).

Bottom Line: Thus, to gain a broad perspective on the origins and evolution of the NPC, we performed proteomics analyses of NPC-containing fractions from a divergent eukaryote (Trypanosoma brucei) and obtained a comprehensive inventory of its nucleoporins.Strikingly trypanosome nucleoporins clearly share with metazoa and yeast their fold type, domain organization, composition, and modularity.Overall these data provide conclusive evidence that the majority of NPC architecture is indeed conserved throughout the Eukaryota and was already established in the last common eukaryotic ancestor.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA.

ABSTRACT
The nuclear pore complex (NPC) is a macromolecular assembly embedded within the nuclear envelope that mediates bidirectional exchange of material between the nucleus and cytoplasm. Our recent work on the yeast NPC has revealed a simple modularity in its architecture and suggested a common evolutionary origin of the NPC and vesicle coating complexes in a progenitor protocoatomer. However, detailed compositional and structural information is currently only available for vertebrate and yeast NPCs, which are evolutionarily closely related. Hence our understanding of NPC composition in a full evolutionary context is sparse. Moreover despite the ubiquitous nature of the NPC, sequence searches in distant taxa have identified surprisingly few NPC components, suggesting that much of the NPC may not be conserved. Thus, to gain a broad perspective on the origins and evolution of the NPC, we performed proteomics analyses of NPC-containing fractions from a divergent eukaryote (Trypanosoma brucei) and obtained a comprehensive inventory of its nucleoporins. Strikingly trypanosome nucleoporins clearly share with metazoa and yeast their fold type, domain organization, composition, and modularity. Overall these data provide conclusive evidence that the majority of NPC architecture is indeed conserved throughout the Eukaryota and was already established in the last common eukaryotic ancestor. These findings strongly support the hypothesis that NPCs share a common ancestry with vesicle coating complexes and that both were established very early in eukaryotic evolution.

Show MeSH
Related in: MedlinePlus