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Crystal structure of malaria parasite nucleosome assembly protein: distinct modes of protein localization and histone recognition.

Gill J, Yogavel M, Kumar A, Belrhali H, Jain SK, Rug M, Brown M, Maier AG, Sharma A - J. Biol. Chem. (2009)

Bottom Line: Expression of green fluorescent protein-tagged PfNapL confirmed its exclusive localization to the parasite cytoplasm.A detailed analysis of PfNapL structure suggests unique histone binding properties.The crucial structural differences observed between parasite and yeast NAPs shed light on possible new modes of histone recognition by nucleosome assembly proteins.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi 110067, India.

ABSTRACT
Nucleosome assembly proteins (NAPs) are histone chaperones that are essential for the transfer and incorporation of histones into nucleosomes. NAPs participate in assembly and disassembly of nucleosomes and in chromatin structure organization. Human malaria parasite Plasmodium falciparum contains two nucleosome assembly proteins termed PfNapL and PfNapS. To gain structural insights into the mechanism of NAPs, we have determined and analyzed the crystal structure of PfNapL at 2.3 A resolution. PfNapL, an ortholog of eukaryotic NAPs, is dimeric in nature and adopts a characteristic fold seen previously for yeast NAP-1 and Vps75 and for human SET/TAF-1b (beta)/INHAT. The PfNapL monomer is comprised of domain I, containing a dimerization alpha-helix, and a domain II, composed of alpha-helices and a beta-subdomain. Structural comparisons reveal that the "accessory domain," which is inserted between the domain I and domain II in yeast NAP-1 and other eukaryotic NAPs, is surprisingly absent in PfNapL. Expression of green fluorescent protein-tagged PfNapL confirmed its exclusive localization to the parasite cytoplasm. Attempts to disrupt the PfNapL gene were not successful, indicating its essential role for the malaria parasite. A detailed analysis of PfNapL structure suggests unique histone binding properties. The crucial structural differences observed between parasite and yeast NAPs shed light on possible new modes of histone recognition by nucleosome assembly proteins.

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NES and NLS motifs in yNAP-1 and PfNapL. a, surface representation of yNAP-1. NES, accessory domain, and NLS are colored red, yellow, and magenta, respectively. b, surface representation of PfNapL. Predicted NES is colored red. The predicted NLS is indicated. c, sequence alignment of NES and NLS in yNAP-1 and PfNapL. The key residues are colored green. Superimposition of NES in yNAP-1 and PfNapL is shown with key residues shown in green as ball-and-stick representations.
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fig3: NES and NLS motifs in yNAP-1 and PfNapL. a, surface representation of yNAP-1. NES, accessory domain, and NLS are colored red, yellow, and magenta, respectively. b, surface representation of PfNapL. Predicted NES is colored red. The predicted NLS is indicated. c, sequence alignment of NES and NLS in yNAP-1 and PfNapL. The key residues are colored green. Superimposition of NES in yNAP-1 and PfNapL is shown with key residues shown in green as ball-and-stick representations.

Mentions: PfNapL Localization in Parasite Cytoplasm Using Transfection Studies—We have earlier shown that PfNapL is expressed during all of the blood stages and is localized to the parasite cytoplasm (13, 14). PfNapL also contains conserved NLS and NES motifs (Figs. 1c and 3, b and c) like the yNAP-1 (which is observed in both the cytoplasm and the nucleus). Corresponding to the presence of NES in yNAP1 (residues 88-103) (Fig. 3a), residues 35-50 of PfNapL have been predicted as an NES (Fig. 3, b and c). It has been suggested in yNAP-1 that this NES is masked by the accessory domain, which is thought to play an important role in the import and export of yNAP-1 into and from the nucleus (15) (Fig. 3a). As mentioned earlier, this accessory domain in yNAP-1 (residues 141-180) is the inserted α-helix, which is absent in PfNapL (Figs. 1c and 2a). Interestingly, hSET also lacks this accessory domain yet contains both NES and NLS motifs (16). Further, hSET is localized both in the cell cytoplasm and the nucleus, similar to yNAP-1 (36) and like other histone shuttling proteins. In this respect, PfNapL clearly stands as an exception despite its structural and sequence similarities with yeast NAP and human SET proteins.


Crystal structure of malaria parasite nucleosome assembly protein: distinct modes of protein localization and histone recognition.

Gill J, Yogavel M, Kumar A, Belrhali H, Jain SK, Rug M, Brown M, Maier AG, Sharma A - J. Biol. Chem. (2009)

NES and NLS motifs in yNAP-1 and PfNapL. a, surface representation of yNAP-1. NES, accessory domain, and NLS are colored red, yellow, and magenta, respectively. b, surface representation of PfNapL. Predicted NES is colored red. The predicted NLS is indicated. c, sequence alignment of NES and NLS in yNAP-1 and PfNapL. The key residues are colored green. Superimposition of NES in yNAP-1 and PfNapL is shown with key residues shown in green as ball-and-stick representations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2665062&req=5

fig3: NES and NLS motifs in yNAP-1 and PfNapL. a, surface representation of yNAP-1. NES, accessory domain, and NLS are colored red, yellow, and magenta, respectively. b, surface representation of PfNapL. Predicted NES is colored red. The predicted NLS is indicated. c, sequence alignment of NES and NLS in yNAP-1 and PfNapL. The key residues are colored green. Superimposition of NES in yNAP-1 and PfNapL is shown with key residues shown in green as ball-and-stick representations.
Mentions: PfNapL Localization in Parasite Cytoplasm Using Transfection Studies—We have earlier shown that PfNapL is expressed during all of the blood stages and is localized to the parasite cytoplasm (13, 14). PfNapL also contains conserved NLS and NES motifs (Figs. 1c and 3, b and c) like the yNAP-1 (which is observed in both the cytoplasm and the nucleus). Corresponding to the presence of NES in yNAP1 (residues 88-103) (Fig. 3a), residues 35-50 of PfNapL have been predicted as an NES (Fig. 3, b and c). It has been suggested in yNAP-1 that this NES is masked by the accessory domain, which is thought to play an important role in the import and export of yNAP-1 into and from the nucleus (15) (Fig. 3a). As mentioned earlier, this accessory domain in yNAP-1 (residues 141-180) is the inserted α-helix, which is absent in PfNapL (Figs. 1c and 2a). Interestingly, hSET also lacks this accessory domain yet contains both NES and NLS motifs (16). Further, hSET is localized both in the cell cytoplasm and the nucleus, similar to yNAP-1 (36) and like other histone shuttling proteins. In this respect, PfNapL clearly stands as an exception despite its structural and sequence similarities with yeast NAP and human SET proteins.

Bottom Line: Expression of green fluorescent protein-tagged PfNapL confirmed its exclusive localization to the parasite cytoplasm.A detailed analysis of PfNapL structure suggests unique histone binding properties.The crucial structural differences observed between parasite and yeast NAPs shed light on possible new modes of histone recognition by nucleosome assembly proteins.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi 110067, India.

ABSTRACT
Nucleosome assembly proteins (NAPs) are histone chaperones that are essential for the transfer and incorporation of histones into nucleosomes. NAPs participate in assembly and disassembly of nucleosomes and in chromatin structure organization. Human malaria parasite Plasmodium falciparum contains two nucleosome assembly proteins termed PfNapL and PfNapS. To gain structural insights into the mechanism of NAPs, we have determined and analyzed the crystal structure of PfNapL at 2.3 A resolution. PfNapL, an ortholog of eukaryotic NAPs, is dimeric in nature and adopts a characteristic fold seen previously for yeast NAP-1 and Vps75 and for human SET/TAF-1b (beta)/INHAT. The PfNapL monomer is comprised of domain I, containing a dimerization alpha-helix, and a domain II, composed of alpha-helices and a beta-subdomain. Structural comparisons reveal that the "accessory domain," which is inserted between the domain I and domain II in yeast NAP-1 and other eukaryotic NAPs, is surprisingly absent in PfNapL. Expression of green fluorescent protein-tagged PfNapL confirmed its exclusive localization to the parasite cytoplasm. Attempts to disrupt the PfNapL gene were not successful, indicating its essential role for the malaria parasite. A detailed analysis of PfNapL structure suggests unique histone binding properties. The crucial structural differences observed between parasite and yeast NAPs shed light on possible new modes of histone recognition by nucleosome assembly proteins.

Show MeSH
Related in: MedlinePlus