New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum - PubMed (original) (raw)

Comparative Study

doi: 10.1371/journal.ppat.0020029. Epub 2006 Apr 14.

Jiong Lu, Wei Hu, Sheng-Yue Wang, Shu-Jian Cui, Ming Chi, Qing Yan, Xin-Rong Wang, Huai-Dong Song, Xue-Nian Xu, Ju-Jun Wang, Xiang-Lin Zhang, Xin Zhang, Zhi-Qin Wang, Chun-Liang Xue, Paul J Brindley, Donald P McManus, Peng-Yuan Yang, Zheng Feng, Zhu Chen, Ze-Guang Han

Affiliations

Comparative Study

New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum

Feng Liu et al. PLoS Pathog. 2006 Apr.

Abstract

Schistosomiasis remains a serious public health problem with an estimated 200 million people infected in 76 countries. Here we isolated ~ 8,400 potential protein-encoding cDNA contigs from Schistosoma japonicum after sequencing circa 84,000 expressed sequence tags. In tandem, we undertook a high-throughput proteomics approach to characterize the protein expression profiles of a number of developmental stages (cercariae, hepatic schistosomula, female and male adults, eggs, and miracidia) and tissues at the host-parasite interface (eggshell and tegument) by interrogating the protein database deduced from the contigs. Comparative analysis of these transcriptomic and proteomic data, the latter including 3,260 proteins with putative identities, revealed differential expression of genes among the various developmental stages and sexes of S. japonicum and localization of putative secretory and membrane antigens, enzymes, and other gene products on the adult tegument and eggshell, many of which displayed genetic polymorphisms. Numerous S. japonicum genes exhibited high levels of identity with those of their mammalian hosts, whereas many others appeared to be conserved only across the genus Schistosoma or Phylum Platyhelminthes. These findings are expected to provide new insights into the pathophysiology of schistosomiasis and for the development of improved interventions for disease control and will facilitate a more fundamental understanding of schistosome biology, evolution, and the host-parasite interplay.

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Conflict of interest statement

Competing interests. The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Characteristics of S. japonicum Clusters with Potential CDSs

(A) A comparison of GC content among all clusters, clusters with protein-coding genes, non-coding clusters, protein-coding regions, and 5′ and 3′ UTRs. (B) The subcellular localization of putative proteins deduced from complete CDSs and hypothetical genes predicted with the bioinformatics tools SignalP, TMHMM, and PSORT II.

Figure 2

Figure 2. A Comprehensive Proteomic Survey of S. japonicum

(A) Protein expression profiling across the life cycle, including C, cercariae; S, hepatic schistosomula; A, adults; E, eggs; and Mi, miracidia. The numbers on the right side represent the number of proteins observed at the developmental stages indicated to the left. The icon at the bottom indicates the expression pattern during the life cycle, and the numbers indicate the amount of stages in which protein is observed. PC, protein count. (B) Venn diagram of the distribution of observed proteins among E, eggs; Mi, miracidia; and ES, eggshell-containing samples. (C) Comparison of transcriptomic and proteomic data of the developmental stages. (D) Protein expression profiling of tegumental proteins across the life cycles, including S_t , hepatic schistosomula; F_t, female; M_t, male; and Mix_t, mixed-sex adults. (E) The tegumental localization of SjFKBP50 (immunophilin) by immunofluorescence microscopy. T, tegument; ST, subtegument; G, gut.

Figure 3

Figure 3. Correlation between Transcriptomic and Proteomic Data of Selected Schistosome Proteins among Developmental Stages and Sexes

(A) Some developmental stage-enriched proteins were consistent with the transcriptomic data indicated. C, cercariae; S, hepatic schistosomula; A, adults; E, eggs; and Mi, miracidia. Those significant proteins with more than a 3-fold difference were consistent with the differential display (p < 0.05) based on EST copy numbers throughout hepatic schistosomula, adults and eggs, or between female and male worms. For cercariae and miracidia, we only showed some proteins with more than 3-fold differences throughout the life cycle based on quantitative proteomics since both stages are devoid of ESTs. However, the selected proteins have low EST copy numbers in other developmental stages. (B) Gender-enriched proteins are also shown as colored boxes: F, females; M, males. Protein abundance and EST frequencies are shown in different colored boxes, as the icons indicate where the EST frequency represents the ratio of EST copy numbers of a given gene to the total number of all ESTs derived from the corresponding cDNA library and then multiplied by 10,000. The full datasets of stage-enriched and gender-enriched proteins with consistency between transcriptomic and proteomic data were given in Figure S4.

Figure 4

Figure 4. Genetic Polymorphisms in S. japonicum Genes

(A) The distribution of nucleotide transition and transversion due to SNPs. The bars between single-letter nucleotides indicate the substitution of the latter base for the former. (B) Summary of the dN/dS analysis. The average dN/dS ratios and identities of coding regions are shown for all orthologous genes between S. japonicum and S. mansoni. Av, average. (C) The pattern distributions of the repeated amino acid residues deduced from microsatellite repeats within protein-encoding regions.

Figure 5

Figure 5. Validation of Potential SNPs by RT-PCR and MS/MS Spectra

(A) The SNPs of the putative SM22.6 antigen (A12) were checked by re-sequencing of PCR products amplified from genomic DNA samples of field-collected isolates of S. japonicum obtained from five Chinese provinces, as indicated at the right. The SNPs indicated by the red arrows were identical to the findings based on EST data in this study, and the SNP sites indicated by black arrows were not identified by us, according to the stringent criteria employed. Substitutions of amino acid residues due to the missense mutations are illustrated based on the DNA sequences. (B) An example for the verification of the translated peptide variants due to nonsynonymous SNPs by MS/MS spectra. The amino acid S (serine) of SJCHGC01743 protein was replaced here by a smaller amino acid G (glycine), where the b3 ion was shifted to the lower mass range as indicated by arrows. Both peptides were detected in the same protein extracts from female schistosomes by the mass spectrometry data. The position of the peptide within the protein sequence is highlighted with red color.

Figure 6

Figure 6. Comparative Genomic Analysis of S. japonicum Genes with CDSs from Representative Sequenced Genomes

(A) The deduced S. japonicum proteins were compared with public protein datasets from mammalian hosts (Homo sapiens, R. norvegicus, and M. musculus), fish (T. nigroviridis and T. rubripes), insects (A. gambiae and D. melanogaster), nematodes (C. briggsae and C. elegans), protozoans (P. yoelii nigeriensis [17XNL], P. falciparum [3D7]), (Cryptosporidium parvum and C. hominis), and fungi (S. cerevisiae) at a cutoff of different BLASTP E values indicated by icons. The black bars indicated that the numbers of the deduced protein were identified by this proteomic analyses. (B) Potential Phylum Platyhelminthes- and _Schistosoma_-specific genes were predicted through interrogating the platyhelminth and Schistosoma ESTs in GenBank. The numbers within the largest (orange) circle indicate S. japonicum CDSs that were not similar to any known protein in a GenBank dataset, which excluded all flatworm sequences at a cutoff of different BLASTP E values. The numbers within the middle-sized blue and small yellow circles represent S. japonicum CDSs with similarity to the EST data from platyhelminths and schistosomes, respectively, at a cutoff of tBLASTN E value of 10−20. The numbers within the smallest green circles indicate proteins identified by the proteomic approach. (C) S. japonicum CDSs were compared with EST and cluster datasets of S. mansoni using the tBLASTN program at a cutoff of different E values indicated.

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