Genomic-bioinformatic analysis of transcripts enriched in the third-stage larva of the parasitic nematode Ascaris suum.
Genomic-bioinformatic analysis of transcripts enriched in the third-stage larva of the parasitic nematode Ascaris suum.
复制标题
寄生性猪蛔虫第三期幼虫富集转录本的基因组生物信息学分析
DOI：
10.1371/journal.pntd.0000246
复制
发表时间：
2008-06-18
影响因子：
3.8
通讯作者：
Zhu XQ
中科院分区：
文献类型：
--
作者：
Huang CQ;Gasser RB;Cantacessi C;Nisbet AJ;Zhong W;Sternberg PW;Loukas A;Mulvenna J;Lin RQ;Chen N;Zhu XQ
利用基因组生物信息学方法研究了猪蛔虫的差异转录。一个富含感染性的第三期幼虫（L3）分子的cDNA档案。利用抑制性消减杂交（SSH）技术构建了猪曲霉（A. suum）的cDNA克隆，并利用来自不同发育阶段的RNA的cDNA探针对来自3075个克隆的cDNA进行了微阵列分析。suum。对通过微阵列分析显示在L3中富集的cDNA（n =498）进行测序，并使用半自动流水线（ESTExplorer）进行生物信息学分析。 使用基因本体（GO），这些分子中的235个被分配到“生物过程”（n = 68），“细胞成分”（n = 50），或“分子功能”（n = 117）。 在组装的91个分子簇中，56个分子（61.5%）在自由生活的线虫秀丽隐杆线虫和C. Briggsae和/或其他生物体，而35个（38.5%）与当前基因数据库中的任何序列均无显著相似性。编码蛋白激酶、蛋白磷酸酶（及其前体）和烯醇化酶的转录本在A.例如，参与细胞过程的分子，如泛素化和蛋白酶体功能，基因转录，蛋白质-蛋白质相互作用和功能。计算机模拟分析推断C. elegans直向同源物/同源物（n = 50）参与细胞凋亡和胰岛素信号传导（2%）、ATP合成（2%）、碳代谢（6%）、脂肪酸生物合成（2%）、间隙连接（2%）、葡萄糖代谢（6%）或卟啉代谢（2%），尽管其中34个（68%）不能被映射到特定的代谢途径。 这50种分子中的一小部分被预测为分泌（10%）、锚定（2%）和/或跨膜（12%）蛋白。在功能上，其中17个（34%）被预测与C中（非野生型）RNAi表型相关。其中以胚胎致死型（Emb）（13种，占58.8%）、幼虫停滞型（Lva）（23.5%）和幼虫致死型（Lvl）（47%）为主。预测了这17个C. elegans直系同源物，揭示了与胚胎和幼虫发育（66.9%），信息存储和处理（5.1%），细胞加工和信号（15.2%），代谢（6.1%）和未知功能（6.7%）相关的9个分子的高度显着相互作用。这些分子在发展中的潜在作用进行了讨论，其同源物/直系同源物在C。秀丽线虫和一些其他线虫。本研究的结果为进一步的功能基因组学研究奠定了基础，以阐明控制中华绒螯蟹幼虫发育过程的分子机制。suum和/或过渡到寄生。
Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3) of A. suum was constructed by suppressive-subtractive hybridization (SSH), and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498) shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer). Using gene ontology (GO), 235 of these molecules were assigned to ‘biological process’ (n = 68), ‘cellular component’ (n = 50), or ‘molecular function’ (n = 117). Of the 91 clusters assembled, 56 molecules (61.5%) had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5%) had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors), and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein–protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50) to be involved in apoptosis and insulin signaling (2%), ATP synthesis (2%), carbon metabolism (6%), fatty acid biosynthesis (2%), gap junction (2%), glucose metabolism (6%), or porphyrin metabolism (2%), although 34 (68%) of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%), anchored (2%), and/or transmembrane (12%) proteins. Functionally, 17 (34%) of them were predicted to be associated with (non-wild-type) RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb) (13 types; 58.8%), larval arrest (Lva) (23.5%) and larval lethality (Lvl) (47%). A genetic interaction network was predicted for these 17 C. elegans orthologues, revealing highly significant interactions for nine molecules associated with embryonic and larval development (66.9%), information storage and processing (5.1%), cellular processing and signaling (15.2%), metabolism (6.1%), and unknown function (6.7%). The potential roles of these molecules in development are discussed in relation to the known roles of their homologues/orthologues in C. elegans and some other nematodes. The results of the present study provide a basis for future functional genomic studies to elucidate molecular aspects governing larval developmental processes in A. suum and/or the transition to parasitism.
登录
查看更多内容
影响因子：
4
作者：
Brand, A;Hawdon, JM
通讯作者：
Hawdon, JM
影响因子：
1.3
作者：
DOUVRES, FW;TROMBA, FG;MALAKATIS, GM
通讯作者：
MALAKATIS, GM
影响因子：
2.4
作者：
Cottee, P. A.;Nisbet, A. J.;Gasser, R. B.
通讯作者：
Gasser, R. B.
影响因子：
2.4
作者：
Gilleard, J. S.;Beech, R. N.
通讯作者：
Beech, R. N.
影响因子：
9.6
作者：
Foster, JM;Zhang, YH;Carlow, CKS
通讯作者：
Carlow, CKS