日本：疟疾抗原基因的SNP在封闭群中表现稳定
生物谷讯：本周出版的Science刊登一则快报，日本科学家研究表明疟疾在一个相对封闭群中，其抗原的SNP表现很稳定，这项研究给疟疾的防治，尤其是疟疾的疫苗的研究带来新的曙光!这项研究的思路和方法是值得中国科学家学习和研究
Stable SNPs in Malaria Antigen Genes in Isolated Populations
K. Tanabe,1* N. Sakihama,1 A. Kaneko2,3
1 Osaka Institute of Technology, Osaka 535-8585, Japan.
2 Tokyo Women's Medical University, Tokyo 162-8666, Japan.
, http://www.100md.com
3 Karolinska Hospital, Stockholm 172-76, Sweden.
* To whom correspondence should be addressed. E-mail: kztanabe@ge.oit.ac.jp
Surface antigens of the human malaria parasite Plasmodium falciparum are under intense immune pressure, and their loci are subject to positive selection (1, 2). P. falciparum shows substantial genetic variability, as seen in rapid emergence of drug resistance [e.g., 10 mutations in pfcrt, the chloroquine (CQ) resistance transporter gene over 20 years (3)]. Hence, selection of parasite populations resistant to naturally acquired immunity or vaccine-induced immunity is of potential concern. Here we present evidence of stable single-nucleotide polymorphisms (SNPs) but rapid repeat length changes in P. falciparum antigen loci in Vanuatu, in the southwestern Pacific.
, 百拇医药
The epidemiological settings for malaria in Vanuatu are suitable to test whether antigen polymorphisms evolve rapidly because limited human movement among the islands and low transmission levels limit the diversity of parasite populations (4). We analyzed three vaccine candidate antigen loci, msp1, msp2, and csp of P. falciparum populations from four islands (Malakula, Gaua, Santo, and Pentecost) from 1996 to 1998 (4). We obtained 90 complete msp1 sequences (six alleles). The aligned region contained 48 SNPs, including seven synonymous substitutions (Fig. 1). The number of nucleotide substitutions between pairs of alleles varied from 4 to 37. Notably, there was no stepwise progression of SNPs between alleles. In 136 complete csp sequences, we identified six alleles, five of which differed in the number and pattern of central 12–base pair repeats (Fig. 1). In the nonrepeat region, two SNPs occurred in Th3R, the T cell epitope region, resulting in substitutions N
D and E Q (5). There was no intermediate allele; i.e., neither NQ nor DE. Partial msp2 sequences (n = 142) were either of the FC27 or 3D7 allelic type (fig. S1). Outside the repeat regions, unique sequences contained six and three nonsynonymous SNPs in FC27 type and 3D7 type, respectively. In both types, substitutions were not stepwise progressions. Thus, SNPs did not show any stepwise changes among alleles at the three loci. Importantly, some alleles were found on more than one island. These findings suggest that the observed SNPs originated outside Vanuatu, and that novel SNPs have not evolved within Vanuatu, indicating stable SNPs on islands. 
Fig. 1. Variation and distribution of P. falciparum antigen alleles in Vanuatu (5). (A) msp1 alleles with synonymous (small letters) and nonsynonymous (capital letters) substitutions. M96, Malakula 1996; M98, Malakula 1998; Pen, Pentecost; San, Santo; Gau, Gaua. (B) csp alleles with two substitutions at positions 1054 and 1069 and varying number of NANP (red) and NVDP (blue) repeats. [View Larger Version of this Image (36K GIF file)]
, 百拇医药
In contrast to SNPs, the number of tandem repeats varied stepwise. The number of NANP repeats in csp alleles was 39 to 43 in Malakula (1996) and 39 to 41 in Gaua (Fig. 1). In msp2 alleles the number of 96–base pair repeats was two and three in Malakula (1996), and the number of GGSA repeats in 3D7 allelic type was 10 to 13 in Gaua (fig. S1). The observed repeat length varied in an identical haplotype background. The repeat variations found in the two loci in Malakula in 1996 had disappeared by 1998. Also, comparison of the present results for msp1 and msp2 from samples obtained in 1997 in Santo with previous results for these alleles in 1992 to 1994 in Santo (6) indicates reduction in repeat length variation. These findings suggest rapid evolution of repeat length polymorphism within a relatively short time span.
, 百拇医药
To infer the age of the observed SNPs in the three loci, we monitored polymorphism in pfcrt. All of the isolates studied had the Papua New Guinean CQ-resistant haplotype, SVMNT, at residues 72 to 76 (7). Although the first report of CQ resistance in Vanuatu was published in 1980, a high prevalence of CQ resistance in Vanuatu had been noticed as early as 1967 (8). Therefore, we presume that the observed SNPs are at least 30 years old in Vanuatu. There is limited human movement between Papua New Guinea and Vanuatu. Human movement–mediated interisland parasite gene flow is expected under CQ pressure. Some antigen alleles present before the appearance of CQ-resistant pfcrt should have survived as the result of recombination events between antigen loci and the pfcrt locus, suggesting that the SNPs are older than 30 years. Consistent with this, in linkage disequilibrium analysis we obtained evidence for substantial recombination events among loci on different chromosomes (table S1). These results indicate rapid evolution of repeat length polymorphism and stable SNPs in P. falciparum antigen loci. The presence of these stable SNPs implies that malaria vaccines will be more effective where there is a limited gene pool, as in isolated populations.
, http://www.100md.com
References and Notes
1.
M. K. Hughes, A. L. Hughes, Mol. Biochem. Parasitol. 71, 99 (1995).[CrossRef][ISI][Medline]
2.
A. A. Escalante, A. A. Lal, F. J. Ayala, Genetics 149, 189 (1998).[Abstract/Free Full Text]
3.
T. E. Wellems, C. V. Plowe, J. Infect. Dis. 184, 770 (2001).[CrossRef][ISI][Medline]
, http://www.100md.com
4.
Materials and Methods are available as supporting online material on Science Online.
5.
Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
6.
, 百拇医药
K. Maitland et al., Parasitology 120, 335 (2000).[CrossRef][ISI][Medline]
7.
J. C. Wootton et al., Nature 418, 320 (2002).[CrossRef][ISI][Medline]
8.
D. K. Bowden et al., Med. J. Aust. 2, 561 (1982).[Medline]
9.
We thank D. Conway, L. Ranford-Cartwright, and T. Horii for their comments. Supported by MEXT (14021125) and JSPS (B13576030, C14570224, and C15590377).
, http://www.100md.com
Supporting Online Material
www.sciencemag.org/cgi/content/full/303/5657/493/DC1
10.1126/science.1092077
Include this information when citing this paper.
PDF Version of this Article
Supporting Online Material, http://www.100md.com
Stable SNPs in Malaria Antigen Genes in Isolated Populations
K. Tanabe,1* N. Sakihama,1 A. Kaneko2,3
1 Osaka Institute of Technology, Osaka 535-8585, Japan.
2 Tokyo Women's Medical University, Tokyo 162-8666, Japan.
, http://www.100md.com
3 Karolinska Hospital, Stockholm 172-76, Sweden.
* To whom correspondence should be addressed. E-mail: kztanabe@ge.oit.ac.jp
Surface antigens of the human malaria parasite Plasmodium falciparum are under intense immune pressure, and their loci are subject to positive selection (1, 2). P. falciparum shows substantial genetic variability, as seen in rapid emergence of drug resistance [e.g., 10 mutations in pfcrt, the chloroquine (CQ) resistance transporter gene over 20 years (3)]. Hence, selection of parasite populations resistant to naturally acquired immunity or vaccine-induced immunity is of potential concern. Here we present evidence of stable single-nucleotide polymorphisms (SNPs) but rapid repeat length changes in P. falciparum antigen loci in Vanuatu, in the southwestern Pacific.
, 百拇医药
The epidemiological settings for malaria in Vanuatu are suitable to test whether antigen polymorphisms evolve rapidly because limited human movement among the islands and low transmission levels limit the diversity of parasite populations (4). We analyzed three vaccine candidate antigen loci, msp1, msp2, and csp of P. falciparum populations from four islands (Malakula, Gaua, Santo, and Pentecost) from 1996 to 1998 (4). We obtained 90 complete msp1 sequences (six alleles). The aligned region contained 48 SNPs, including seven synonymous substitutions (Fig. 1). The number of nucleotide substitutions between pairs of alleles varied from 4 to 37. Notably, there was no stepwise progression of SNPs between alleles. In 136 complete csp sequences, we identified six alleles, five of which differed in the number and pattern of central 12–base pair repeats (Fig. 1). In the nonrepeat region, two SNPs occurred in Th3R, the T cell epitope region, resulting in substitutions N
D and E Q (5). There was no intermediate allele; i.e., neither NQ nor DE. Partial msp2 sequences (n = 142) were either of the FC27 or 3D7 allelic type (fig. S1). Outside the repeat regions, unique sequences contained six and three nonsynonymous SNPs in FC27 type and 3D7 type, respectively. In both types, substitutions were not stepwise progressions. Thus, SNPs did not show any stepwise changes among alleles at the three loci. Importantly, some alleles were found on more than one island. These findings suggest that the observed SNPs originated outside Vanuatu, and that novel SNPs have not evolved within Vanuatu, indicating stable SNPs on islands. Fig. 1. Variation and distribution of P. falciparum antigen alleles in Vanuatu (5). (A) msp1 alleles with synonymous (small letters) and nonsynonymous (capital letters) substitutions. M96, Malakula 1996; M98, Malakula 1998; Pen, Pentecost; San, Santo; Gau, Gaua. (B) csp alleles with two substitutions at positions 1054 and 1069 and varying number of NANP (red) and NVDP (blue) repeats. [View Larger Version of this Image (36K GIF file)], 百拇医药
In contrast to SNPs, the number of tandem repeats varied stepwise. The number of NANP repeats in csp alleles was 39 to 43 in Malakula (1996) and 39 to 41 in Gaua (Fig. 1). In msp2 alleles the number of 96–base pair repeats was two and three in Malakula (1996), and the number of GGSA repeats in 3D7 allelic type was 10 to 13 in Gaua (fig. S1). The observed repeat length varied in an identical haplotype background. The repeat variations found in the two loci in Malakula in 1996 had disappeared by 1998. Also, comparison of the present results for msp1 and msp2 from samples obtained in 1997 in Santo with previous results for these alleles in 1992 to 1994 in Santo (6) indicates reduction in repeat length variation. These findings suggest rapid evolution of repeat length polymorphism within a relatively short time span.
, 百拇医药
To infer the age of the observed SNPs in the three loci, we monitored polymorphism in pfcrt. All of the isolates studied had the Papua New Guinean CQ-resistant haplotype, SVMNT, at residues 72 to 76 (7). Although the first report of CQ resistance in Vanuatu was published in 1980, a high prevalence of CQ resistance in Vanuatu had been noticed as early as 1967 (8). Therefore, we presume that the observed SNPs are at least 30 years old in Vanuatu. There is limited human movement between Papua New Guinea and Vanuatu. Human movement–mediated interisland parasite gene flow is expected under CQ pressure. Some antigen alleles present before the appearance of CQ-resistant pfcrt should have survived as the result of recombination events between antigen loci and the pfcrt locus, suggesting that the SNPs are older than 30 years. Consistent with this, in linkage disequilibrium analysis we obtained evidence for substantial recombination events among loci on different chromosomes (table S1). These results indicate rapid evolution of repeat length polymorphism and stable SNPs in P. falciparum antigen loci. The presence of these stable SNPs implies that malaria vaccines will be more effective where there is a limited gene pool, as in isolated populations.
, http://www.100md.com
References and Notes
1.
M. K. Hughes, A. L. Hughes, Mol. Biochem. Parasitol. 71, 99 (1995).[CrossRef][ISI][Medline]
2.
A. A. Escalante, A. A. Lal, F. J. Ayala, Genetics 149, 189 (1998).[Abstract/Free Full Text]
3.
T. E. Wellems, C. V. Plowe, J. Infect. Dis. 184, 770 (2001).[CrossRef][ISI][Medline]
, http://www.100md.com
4.
Materials and Methods are available as supporting online material on Science Online.
5.
Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
6.
, 百拇医药
K. Maitland et al., Parasitology 120, 335 (2000).[CrossRef][ISI][Medline]
7.
J. C. Wootton et al., Nature 418, 320 (2002).[CrossRef][ISI][Medline]
8.
D. K. Bowden et al., Med. J. Aust. 2, 561 (1982).[Medline]
9.
We thank D. Conway, L. Ranford-Cartwright, and T. Horii for their comments. Supported by MEXT (14021125) and JSPS (B13576030, C14570224, and C15590377).
, http://www.100md.com
Supporting Online Material
www.sciencemag.org/cgi/content/full/303/5657/493/DC1
10.1126/science.1092077
Include this information when citing this paper.
PDF Version of this Article
Supporting Online Material, http://www.100md.com