- Email: [email protected]
Quality, Quantity and Function on the Web
Comment different oligonucleotides allowing the simultaneous evaluation of many thousands of genes/transcripts. The prediction that 500000 to a million gene sequences will be identified in the next few years is daunting, but even the complete human genome will not occupy more than 4 Gigabites, not much more than the average size of a hard disc for a top-of-the-line personal computer. More of a problem for the future is our mindset; parasitologists will have to work with bioinformatics scientists to exploit this information. A different problem is the threat that access to databases will cease to be free. The complex projects of genome sequencing and database curation are transcending organizational
and even national structures. They are far too expensive to be funded by a single group or company. Who will pay? References 1 Wellcome Trust Malaria Genome Collaboration (1995) Parasitol. Today 11, 1–4 2 Ivens, A.C. and Smith, D.F. (1997) Trans. R. Soc. Trop. Med. Hyg. 91, 111–115 3 Blackwell, J.M. (1997) Trans. R. Soc. Trop. Med. Hyg. 91, 107–110 4 Walliker, D. et al. (1987) Science 236, 1661–1666 5 Foote, S.J. and Cowman, A.F. (1994) Acta Trop. 56, 157–171 6 Hood, L. et al. (1993) Cold Spring Harbor Symp. Quant. Biol. 58, 339–348 7 Koop, B.F. and Hood, L. (1994) Nat. Genet. 7, 48–53 8 Kuwabara, P.E. and Shah, S. (1994) Nucleic Acids Res. 22, 4414–4418
9 Kilian, A. et al. (1997) Plant Mol. Biol. 35, 187–195 10 Fichera, M.E. and Roos, D.S. (1997) Nature 390, 407–409 11 Burge, C. and Karlin, S. (1997) J. Mol. Biol. 268, 78–94 12 Snyder, E.E. and Stormo, G.D. (1995) J. Mol. Biol. 248, 1–18 13 DeRisi, J.L. et al. (1997) Science 278, 680–686 14 Friedrich, G.A. (1996) Nat. Biotechnol. 14, 1234–1237 15 Oliver, S.G. (1997) Curr. Opin. Genet. Dev. 7, 405–409 16 Hacia, J.G. et al. (1996) Nat. Genet. 14, 441–447
Simon J. Foote, Terry Speed and Emanuela Handman are at The Walter and Eliza Hall Institute of Medical Research, Victoria 3050, Australia. Tel: +613 9345 2555, Fax: +613 9347 0852, e-mail: handman@ wehi.edu.au
ParaSite
Quality, Quantity and Function on the Web Malaria discussion group ([email protected]) Pf155/RESA: amount and function? Nathalie Soutthiphong (Imperial College School of Medicine, London, UK) asked how much Pf155/RESA [ring erythrocyte surface antigen] is in a ring stage P. falciparum (in pmole or µg)? Ross Coppel (Monash University, Australia) said little was known about the absolute amounts of any parasite protein, even LDH [lactate dehydrogenase] and the heat-shock protein hsp70, which he believed to be the most abundant. He also thought it extremely difficult to quantitate RESA using current methods of detection as they employ ‘antisera directed against repetitive epitopes, giving a great amplification of signal. Thus there appears to be much more RESA than is there … Further, RESA is poorly stained by Coomassie relative to other proteins because of its highly charged nature.’ David Bzik (Dartmouth College, NH, USA) agreed about ‘absolute’ figures but said various enzymes, including LDH, can be quantitated in terms of specific activity (D.L. Vander Jagt et al., Partial purification and characterization of lactate dehydrogenase from Plasmodium falciparum. Mol. Biochem. Parasitol. 4, 255–264, 1981). But ‘regarding the “most abundant malaria protein”, I have to vote for the serine repeat antigen (SERA) … In SDS-PAGE, SERA appears to be more abundant than LDH … in cDNA libraries, SERA message (~2% of cDNA!) is more abundant than LDH (~0.1 %).’ However, Mark Wiser (Tulane University, New Orleans, USA) wondered if that was true of P. falciparum specifically, as it appeared not to apply to P. vinckei, P. berghei or P. chabaudi. He had no comparisons with LDH or hsp70, but there seemed to be more MSP-1 [merozoite surface protein 1] than SERA homologues. As to function, Leann Tilley (La Trobe University, Victoria, Australia) said RESA protected spectrin from heat-induced denaturation (E. Da Silva et al., The Plasmodium falciparum protein RESA interacts with the erythrocyte cytoskeleton and modifies erythrocyte thermal stability. Mol. Biochem. Parasitol. 66, 59–69, 1994). She thought its role in protein trafficking had not been studied but ‘it is the only parasite protein known to be at the RBC membrane in Parasitology Today, vol. 14, no. 9, 1998
the ring-stage of infection and it disappears later in the life cycle when the bulk of trafficking occurs.’ Mark Wiser reacted: ‘highly antigenic acidic phosphoproteins are associated with the red cell membrane at the ring stage of P. chabaudi, unlike RESA, they remain associated with the membrane throughout the blood stage cycle, and analogous proteins seem to exist in P. falciparum’ (M.F. Wiser et al., Plasmodium chabaudi: immunogenicity of a highly antigenic glutamate-rich protein. Exp. Parasitol. 85, 43–54, 1997). RESA is synthesized during the schizont stage and is localized to dense granules of merozoites, especially to finger-like projections of the parasitophorous vacuolar membrane (M. Aikawa and C.T. Atkinson, Immunoelectron-microscopy of parasites. Adv. Parasitol. 29, 151–214, 1990; J.G. Culvenor et al., Plasmodium falciparum ring-infected erythrocyte surface antigen is released from merozoite dense granules after erythrocyte invasion. Infect. Immun. 59, 1183– 1187, 1991). ‘Although the bulk of trafficking might occur later in schizogony, there is substantial trafficking during the early ring stage and throughout the blood stage cycle’ (M.F. Wiser et al., A novel alternate secretory pathway for the export of Plasmodium proteins into the host erythrocyte. Proc. Natl. Acad. Sci. U. S. A. 94, 9108–9113, 1997). Leann Tilley apologized for forgetting rodent parasites [often done!] but wondered if ‘protein trafficking to the RBC membrane in say P. chabaudi occurs by the same mechanism as in P. falciparum?’ Mark Wiser accepted the apology; his bias is that all ‘the Plasmodium species will export proteins into the host erythrocyte by the same mechanism.’ Finally Jerry McLaughlin (University of Indiana, USA) recommended caution about conclusions from partiallength homologies: ‘a prediction of function … may not follow even from a real homology … Are there hints by location on chromosome(s) as to function, eg. is RESA near virulence genes, etc.?’
ParaSite was compiled, from the Internet, by Janice Taverne ( [email protected])
Copyright © 1998, Elsevier Science Ltd All rights reserved 0169–4758/98/$19.00 PII: S0169-4758(98)01308-8
347
and even national structures. They are far too expensive to be funded by a single group or company. Who will pay? References 1 Wellcome Trust Malaria Genome Collaboration (1995) Parasitol. Today 11, 1–4 2 Ivens, A.C. and Smith, D.F. (1997) Trans. R. Soc. Trop. Med. Hyg. 91, 111–115 3 Blackwell, J.M. (1997) Trans. R. Soc. Trop. Med. Hyg. 91, 107–110 4 Walliker, D. et al. (1987) Science 236, 1661–1666 5 Foote, S.J. and Cowman, A.F. (1994) Acta Trop. 56, 157–171 6 Hood, L. et al. (1993) Cold Spring Harbor Symp. Quant. Biol. 58, 339–348 7 Koop, B.F. and Hood, L. (1994) Nat. Genet. 7, 48–53 8 Kuwabara, P.E. and Shah, S. (1994) Nucleic Acids Res. 22, 4414–4418
9 Kilian, A. et al. (1997) Plant Mol. Biol. 35, 187–195 10 Fichera, M.E. and Roos, D.S. (1997) Nature 390, 407–409 11 Burge, C. and Karlin, S. (1997) J. Mol. Biol. 268, 78–94 12 Snyder, E.E. and Stormo, G.D. (1995) J. Mol. Biol. 248, 1–18 13 DeRisi, J.L. et al. (1997) Science 278, 680–686 14 Friedrich, G.A. (1996) Nat. Biotechnol. 14, 1234–1237 15 Oliver, S.G. (1997) Curr. Opin. Genet. Dev. 7, 405–409 16 Hacia, J.G. et al. (1996) Nat. Genet. 14, 441–447
Simon J. Foote, Terry Speed and Emanuela Handman are at The Walter and Eliza Hall Institute of Medical Research, Victoria 3050, Australia. Tel: +613 9345 2555, Fax: +613 9347 0852, e-mail: handman@ wehi.edu.au
ParaSite
Quality, Quantity and Function on the Web Malaria discussion group ([email protected]) Pf155/RESA: amount and function? Nathalie Soutthiphong (Imperial College School of Medicine, London, UK) asked how much Pf155/RESA [ring erythrocyte surface antigen] is in a ring stage P. falciparum (in pmole or µg)? Ross Coppel (Monash University, Australia) said little was known about the absolute amounts of any parasite protein, even LDH [lactate dehydrogenase] and the heat-shock protein hsp70, which he believed to be the most abundant. He also thought it extremely difficult to quantitate RESA using current methods of detection as they employ ‘antisera directed against repetitive epitopes, giving a great amplification of signal. Thus there appears to be much more RESA than is there … Further, RESA is poorly stained by Coomassie relative to other proteins because of its highly charged nature.’ David Bzik (Dartmouth College, NH, USA) agreed about ‘absolute’ figures but said various enzymes, including LDH, can be quantitated in terms of specific activity (D.L. Vander Jagt et al., Partial purification and characterization of lactate dehydrogenase from Plasmodium falciparum. Mol. Biochem. Parasitol. 4, 255–264, 1981). But ‘regarding the “most abundant malaria protein”, I have to vote for the serine repeat antigen (SERA) … In SDS-PAGE, SERA appears to be more abundant than LDH … in cDNA libraries, SERA message (~2% of cDNA!) is more abundant than LDH (~0.1 %).’ However, Mark Wiser (Tulane University, New Orleans, USA) wondered if that was true of P. falciparum specifically, as it appeared not to apply to P. vinckei, P. berghei or P. chabaudi. He had no comparisons with LDH or hsp70, but there seemed to be more MSP-1 [merozoite surface protein 1] than SERA homologues. As to function, Leann Tilley (La Trobe University, Victoria, Australia) said RESA protected spectrin from heat-induced denaturation (E. Da Silva et al., The Plasmodium falciparum protein RESA interacts with the erythrocyte cytoskeleton and modifies erythrocyte thermal stability. Mol. Biochem. Parasitol. 66, 59–69, 1994). She thought its role in protein trafficking had not been studied but ‘it is the only parasite protein known to be at the RBC membrane in Parasitology Today, vol. 14, no. 9, 1998
the ring-stage of infection and it disappears later in the life cycle when the bulk of trafficking occurs.’ Mark Wiser reacted: ‘highly antigenic acidic phosphoproteins are associated with the red cell membrane at the ring stage of P. chabaudi, unlike RESA, they remain associated with the membrane throughout the blood stage cycle, and analogous proteins seem to exist in P. falciparum’ (M.F. Wiser et al., Plasmodium chabaudi: immunogenicity of a highly antigenic glutamate-rich protein. Exp. Parasitol. 85, 43–54, 1997). RESA is synthesized during the schizont stage and is localized to dense granules of merozoites, especially to finger-like projections of the parasitophorous vacuolar membrane (M. Aikawa and C.T. Atkinson, Immunoelectron-microscopy of parasites. Adv. Parasitol. 29, 151–214, 1990; J.G. Culvenor et al., Plasmodium falciparum ring-infected erythrocyte surface antigen is released from merozoite dense granules after erythrocyte invasion. Infect. Immun. 59, 1183– 1187, 1991). ‘Although the bulk of trafficking might occur later in schizogony, there is substantial trafficking during the early ring stage and throughout the blood stage cycle’ (M.F. Wiser et al., A novel alternate secretory pathway for the export of Plasmodium proteins into the host erythrocyte. Proc. Natl. Acad. Sci. U. S. A. 94, 9108–9113, 1997). Leann Tilley apologized for forgetting rodent parasites [often done!] but wondered if ‘protein trafficking to the RBC membrane in say P. chabaudi occurs by the same mechanism as in P. falciparum?’ Mark Wiser accepted the apology; his bias is that all ‘the Plasmodium species will export proteins into the host erythrocyte by the same mechanism.’ Finally Jerry McLaughlin (University of Indiana, USA) recommended caution about conclusions from partiallength homologies: ‘a prediction of function … may not follow even from a real homology … Are there hints by location on chromosome(s) as to function, eg. is RESA near virulence genes, etc.?’
ParaSite was compiled, from the Internet, by Janice Taverne ( [email protected])
Copyright © 1998, Elsevier Science Ltd All rights reserved 0169–4758/98/$19.00 PII: S0169-4758(98)01308-8
347