转录组揭示禁水环境下双峰驼结肠组织适应机制

doi:10.11843/j.issn.0366-6964.2018.11.007

摘要/Abstract

摘要：

旨在了解骆驼属在缺水条件下组织环境适应机制。本研究选取6峰6~9岁的成年阿拉善双峰驼，随机分为2组，第一组为对照组（colon1_3），正常采食饲料与水；第二组为禁水组（colon3），不给骆驼饮水，其他处理（饲草量）与对照组相同，禁水24 d。采用Illumina HiSeq 2000测序平台通过对禁水（试验组）与正常饮水（对照组）条件下双峰驼结肠组织进行转录组测序，并对转录组数据进行质控、比对、差异表达、GO和KEGG分析。结果显示，禁水组与对照组比较共获得差异表达基因2 122个，其中上调表达基因813个，下调表达基因1 309个。GO分析结果显示，禁水组下调表达基因最为显著富集的条目有30条，上调表达基因中未得到统计学意义的富集条目。KEGG富集分析显示，禁水组下调表达基因显著富集到剪接体、蛋白外排、内质网蛋白合成过程、RNA转运、核糖体合成、mRNA检测、RNA降解代谢途径；上调表达基因富集到的通路包含局部细胞黏连、溶酶体功能等。上述结果表明，禁水环境下，结肠组织下调表达基因多于上调表达基因，下调表达基因多参与RNA加工和蛋白质合成，这些功能有利于骆驼在缺水环境下，减少RNA的合成，降低结肠组织的代谢速率。

Abstract:

The aim of this study was to understand the mechanism of tissue environmental adaptation in the absence of water in Camelus. In this study, six 6-9 years old adult Alashan Bactrian camels were randomly divided into 2 groups, the first group was the control group (colon1_3), in which the animals were fed with normal feed and water, the second group was the no drinking water group (colon3), in which the animals were in the absence of water for 24 d, other treatment (forage) was the same as the control group. The Illumina HiSeq 2000 sequencing platform was used to sequence the transcriptome of Bactrian camel colon tissue in the control and no drinking water groups, and the transcriptome data were used to perform quality-controlled, alignment, differentially expressed, GO and KEGG analysis. The results showed that, compared with control group, a total of 2 122 differentially expressed genes were obtained in the no drinking water group, among which 813 genes were up-regulated and 1 309 genes were down-regulated. GO enrichment analysis results showed that 30 terms in the no drinking water group were significantly enriched by down-regulated expression genes. There was no statistically significant enrichment term by the up-regulated expression genes. The KEGG pathway analysis showed that the down-regulated expression genes in no drinking water group were significantly enriched in multiply pathways, including spliceosome, protein export, protein processing in endoplasmic reticulum, RNA transport, ribosome biogenesis in eukaryotes, mRNA detection, RNA degradation metabolic pathways. The up-regulated expression genes in no drinking water group were enriched in focal adhesion, lysosome function, and so on. The results of this study indicate that the number of down-regulated expression genes in colon are more than up-regulated expressed genes in water-deficient environments, and the functions of these down-regulated expression genes are mainly associated with RNA processes and protein synthesis pathways. These genes are favorable for camels to reduce the RNA synthesis and the metabolic rate of colon tissue in water-deficient environments.

中图分类号:

S824.2

凌宇, 齐昱, 曹俊伟, 王申元, 周欢敏, 张焱如. 转录组揭示禁水环境下双峰驼结肠组织适应机制[J]. 畜牧兽医学报, 2018, 49(11): 2359-2370.

LING Yu, QI Yu, CAO Jun-wei, WANG Shen-yuan, ZHOU Huan-min, ZHANG Yan-ru. Transcriptome Reveals the Adapting Mechanism of Colon Tissues of Bactrian Camel in Water-deficient Environment[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2018, 49(11): 2359-2370.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://www.xmsyxb.com/CN/10.11843/j.issn.0366-6964.2018.11.007

https://www.xmsyxb.com/CN/Y2018/V49/I11/2359

参考文献

[1] SEQUENCING T B C G, CONSORTIUM A. Genome sequences of wild and domestic bactrian camels[J]. Nat Commun, 2012, 3(1):1202.
[2] WU H G,GUANG X M,AL-FAGEEH M B,et al.Camelid genomes reveal evolution and adaptation to desert environments[J].Nat Commun,2014,5:5188.
[3] MILLER T L,WOLIN M J.Pathways of acetate,propionate,and butyrate formation by the human fecal microbial flora[J].Appl Environ Microbiol,1996,62(5):1589-1592.
[4] MCNEIL N I.The contribution of the large intestine to energy supplies in man[J].Am J Clin Nutr,1984,39(2):338-342.
[5] WAHL M C,WILL C L,LÜHRMANN R.The spliceosome:design principles of a dynamic RNP machine[J].Cell,2009,136(4):701-718.
[6] RITCHIE D B,SCHELLENBERG M J,MACMILLAN A M.Spliceosome structure:piece by piece[J].Biochim Biophys Acta,2009,1789(9-10):624-633.
[7] NG S Y M,CHABAN B,VANDYKE D J,et al.Archaeal signal peptidases[J].Microbiology,2007,153(Pt2):305-314.
[8] DEJGAARD K,THEBERGE J F,HEATH-ENGEL H,et al.Organization of the Sec61 translocon,studied by high resolution native electrophoresis[J].J Proteome Res,2010,9(4):1763-1771.
[9] MÄÄTTÄNEN P,GEHRING K,BERGERON J J M,et al.Protein quality control in the ER:the recognition of misfolded proteins[J].Semin Cell Dev Biol,2010,21(5):500-511.
[10] STOLZ A,WOLF D H.Endoplasmic reticulum associated protein degradation:a chaperone assisted journey to hell[J].Biochim Biophys Acta,2010,1803(6):694-705.
[11] SUZUKI T,IZUMI H,OHNO M.Cajal body surveillance of U snRNA export complex assembly[J].J Cell Biol,2010,190(4):603-612.
[12] PALANCADE B,DOYE V.Sumoylating and desumoylating enzymes at nuclear pores:underpinning their unexpected duties?[J].Trends Cell Biol,2008,18(4):174-183.
[13] MANDEL C R, BAI Y, TONG L. Protein factors in pre-mRNA 3'-end processing[J]. Cell Mol Life Sci, 2008, 65(7-8):1099-1122.
[14] MAQUAT L E. Nonsense-mediated mRNA decay:splicing, translation and mRNP dynamics[J]. Nat Rev Mol Cell Biol, 2004, 5(2):89-99.
[15] AMRANI N, SACHS M S, JACOBSON A. Early nonsense:mRNA decay solves a translational problem[J]. Nat Rev Mol Cell Biol, 2006, 7(6):415-425.
[16] EULALIO A, BEHM-ANSMANT I, IZAURRALDE E. P bodies:at the crossroads of post-transcriptional pathways[J]. Nat Rev Mol Cell Biol, 2007, 8(1):9-22.
[17] CLEMENT S L, LYKKE-ANDERSEN J. No mercy for messages that mess with the ribosome[J]. Nat Struct Mol Biol, 2006, 13(4):299-301.
[18] CHENG W, CHEN G, JIA H, et al. DDX5 RNA helicases:Emerging roles in viral infection[J]. Int J Mol Sci, 2018, 19(4).
[19] KOKOLO M, BACH-ELIAS M. Downregulation of p68 RNA Helicase (DDX5) activates a survival pathway involving mTOR and MDM2 signals[J]. Folia Biol (Praha), 2017, 63(2):52-59.
[20] MA Z, FENG J, GUO Y, et al. Knockdown of DDX5 inhibits the proliferation and tumorigenesis in esophageal cancer[J]. Oncol Res, 2017, 25(6):887-895.
[21] O'DONNELL J P, MARSH H M, SONDERMANN H, et al. Disrupted hydrogen-bond network and impaired ATPase activity in an Hsc70 cysteine mutant[J]. Biochemistry, 2018, 57(7):1073-1086.
[22] DONG Q, MEN R, DAN X, et al. Hsc70 regulates the IRES activity and serves as an antiviral target of enterovirus A71 infection[J]. Antiviral Res, 2017, 150:39-46.
[23] CHASE A R, LAUDERMILCH E, WANG J, et al. Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1[J]. Mol Biol Cell, 2017, 28(21):2765-2772.
[24] ZHOU R, PARK J W, CHUN R F, et al. Concerted effects of heterogeneous nuclear ribonucleoprotein C1/C2 to control vitamin D-directed gene transcription and RNA splicing in human bone cells[J]. Nucleic Acids Res, 2017, 45(2):606-618.
[25] DECHTAWEWAT T SONGPRAKHON P, LIMJINDAPORN T, et al. Role of human heterogeneous nuclear ribonucleoprotein C1/C2 in dengue virus replication[J]. Virol J, 2015, 12(1):14.
[26] MCCLOSKEY A, TANIGUCHI I, SHINMYOZU K, et al. hnRNP C tetramer measures RNA length to classify RNA polymerase Ⅱ transcripts for export[J]. Science, 2012, 335(6076):1643-1646.
[27] SAKONO M, KIDANI T. ATP-independent inhibition of amyloid beta fibrillation by the endoplasmic reticulum resident molecular chaperone GRP78[J]. Biochem Biophys Res Commun, 2017, 493(1):500-503.
[28] SUN C, HAN C, JIANG Y, et al. Inhibition of GRP78 abrogates radioresistance in oropharyngeal carcinoma cells after EGFR inhibition by cetuximab[J]. PLoS One, 2017, 12(12):e0188932.
[29] ZHANG L, LI Z, DING G, et al. GRP78 plays an integral role in tumor cell inflammation-related migration induced by M2 macrophages[J]. Cell Signal, 2017, 37:136-148.
[30] HETTINGHOUSE A, LIU R H, LIU C J. Multifunctional molecule ERp57:From cancer to neurodegenerative diseases[J]. Pharmacol Ther, 2017, 181:34-48.
[31] LIU M, DU L, HE Z, et al. Increased ERp57 expression in HBV-related hepatocellular carcinoma:Possible correlation and prognosis[J]. Biomed Res Int, 2017, 2017(12):1-8.
[32] WANG I H, BURCKHARDT C J, YAKIMOVICH A, et al. The nuclear export factor CRM1 controls juxta-nuclear microtubule-dependent virus transport[J]. J Cell Sci, 2017,130(13):2185-2195.
[33] CHEN Y, CAMACHO S C, SILVERS T R, et al. Inhibition of the nuclear export receptor XPO1 as a therapeutic target for platinum-resistant ovarian cancer[J]. Clin Cancer Res, 2017, 23(6):1552-1563.
[34] CHUTIWITOONCHAI N, MANO T, KAKISAKA M, et al. Inhibition of CRM1-mediated nuclear export of influenza A nucleoprotein and nuclear export protein as a novel target for antiviral drug development[J]. Virology, 2017, 507:32-39.
[35] ARTS G J, FORNEROD M, MATTAJ I W. Identification of a nuclear export receptor for tRNA[J]. Curr Biol, 1998, 8(6):305-314.
[36] ARTS G J, KUERSTEN S, ROMBY P, et al. The role of exportin-t in selective nuclear export of mature tRNAs[J]. EMBO J, 2014, 17(24):7430-7441.
[37] GELPERIN D, HORTON L, BECKMAN J, et al. Bms1p, a novel GTP-binding protein, and the related Tsr1p are required for distinct steps of 40S ribosome biogenesis in yeast[J]. RNA, 2001, 7(9):1268-1283.