Abstract
Relation between animals and bacteria is just like marriage made by evolution . For Caenorhabditis elegans, bacteria are part of their food as well as the environments. In recent decades, C. elegans has been extensively used as a model organism for studying host–microbiota interactions. As dsRNAs expressed in E. coli , which is the laboratory food of C. elegans, can trigger RNAi in the worm, it is possible that bacteria could use their own RNAs to affect the physiology of C. elegans. The recent studies provide insights into these speculations. Our lab have demonstrated that some of the noncoding RNAs of E. coli modulate gene expression and regulate the life span and sensory response of C. elegans. These noncoding RNAs may be processed into tiny RNAs of ~17–18 nucleotides (nt) and utilize a distinct although partially overlapping pathway with the canonical feeding RNAi, which is triggered by exogenous double-stranded RNAs. There is a need for more studies and discussions about the interaction between C. elegans and RNAs in the environments, as a lot of details and mechanisms are still unknown.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Akay A, Sarkies P, Miska EA (2015) E. coli OxyS non-coding RNA does not trigger RNAi in C. elegans. Sci Rep 5:9597. doi:10.1038/srep09597
Castel SE, Martienssen RA (2013) RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet 14(2):100–112. doi:10.1038/nrg3355
Dalzell JJ, McVeigh P, Warnock ND, Mitreva M, Bird DM, Abad P, Fleming CC, Day TA, Mousley A, Marks NJ, Maule AG (2011) RNAi effector diversity in nematodes. PLoS Negl Trop Dis 5(6):e1176. doi:10.1371/journal.pntd.0001176
Feinberg EH, Hunter CP (2003) Transport of dsRNA into cells by the transmembrane protein SID-1. Science 301(5639):1545–1547. doi:10.1126/science.1087117
Fire A, Albertson D, Harrison SW, Moerman DG (1991) Production of antisense RNA leads to effective and specific inhibition of gene expression in C. elegans muscle. Development 113(2):503–514
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811. doi:10.1038/35888
Fischer SE (2010) Small RNA-mediated gene silencing pathways in C. elegans. Int J Biochem Cell Biol 42(8):1306–1315. doi:10.1016/j.biocel.2010.03.006
Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrin-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL (2007) Draft genome of the filarial nematode parasite Brugia malayi. Science 317(5845):1756–1760. doi:10.1126/science.1145406
Gottesman S, Storz G (2011) Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 3(12). doi:10.1101/cshperspect.a003798
Hinas A, Wright AJ, Hunter CP (2012) SID-5 is an endosome-associated protein required for efficient systemic RNAi in C. elegans. Curr Biol 22(20):1938–1943. doi:10.1016/j.cub.2012.08.020
Hu S, Wu J, Chen L, Shan G (2012) Signals from noncoding RNAs: unconventional roles for conventional pol III transcripts. Int J Biochem Cell Biol 44(11):1847–1851. doi:10.1016/j.biocel.2012.07.013
Jose AM, Smith JJ, Hunter CP (2009) Export of RNA silencing from C. elegans tissues does not require the RNA channel SID-1. Proc Natl Acad Sci USA 106(7):2283–2288. doi:10.1073/pnas.0809760106
Jose AM, Kim YA, Leal-Ekman S, Hunter CP (2012) Conserved tyrosine kinase promotes the import of silencing RNA into Caenorhabditis elegans cells. Proc Natl Acad Sci USA 109(36):14520–14525. doi:10.1073/pnas.1201153109
Kiontke K, Sudhaus W (2006) Ecology of Caenorhabditis species. WormBook:1–14. doi:10.1895/wormbook.1.37.1
Kong Y, Ruan L, Ma L, Cui Y, Wang JM, Le Y (2007) RNA interference as a novel and powerful tool in immunopharmacological research. Int Immunopharmacol 7(4):417–426. doi:10.1016/j.intimp.2006.12.011
Lalaouna D, Simoneau-Roy M, Lafontaine D, Masse E (2013) Regulatory RNAs and target mRNA decay in prokaryotes. Biochim Biophys Acta 1829(6–7):742–747. doi:10.1016/j.bbagrm.2013.02.013
Lee JT (2012) Epigenetic regulation by long noncoding RNAs. Science 338(6113):1435–1439. doi:10.1126/science.1231776
Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, Yu B, Hu W, Dai L, Zhu P, Chang Z, Wu Q, Zhao Y, Jia Y, Xu P, Liu H, Shan G (2015) Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol 22(3):256–264. doi:10.1038/nsmb.2959
Liu H, Wang X, Wang HD, Wu J, Ren J, Meng L, Wu Q, Dong H, Kao TY, Ge Q, Wu ZX, Yuh CH, Shan G (2012) Escherichia coli noncoding RNAs can affect gene expression and physiology of Caenorhabditis elegans. Nat Commun 3:1073. doi:10.1038/ncomms2071
McEwan DL, Weisman AS, Hunter CP (2012) Uptake of extracellular double-stranded RNA by SID-2. Mol Cell 47(5):746–754. doi:10.1016/j.molcel.2012.07.014
Meng LF, Chen L, Li ZY, Wu ZX, Shan G (2013) Environmental RNA interference in animals. Chin Sci Bull 35:4418–4425
Saleh MC, van Rij RP, Hekele A, Gillis A, Foley E, O’Farrell PH, Andino R (2006) The endocytic pathway mediates cell entry of dsRNA to induce RNAi silencing. Nat Cell Biol 8(8):793–802. doi:10.1038/ncb1439
Tabara H, Grishok A, Mello CC (1998) RNAi in C. elegans: soaking in the genome sequence. Science 282(5388):430–431
Timmons L, Fire A (1998) Specific interference by ingested dsRNA. Nature 395(6705):854. doi:10.1038/27579
Ulitsky I, Bartel DP (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154(1):26–46. doi:10.1016/j.cell.2013.06.020
Whangbo JS, Hunter CP (2008) Environmental RNA interference. Trends Genet 24(6):297–305. doi:10.1016/j.tig.2008.03.007
Winston WM, Molodowitch C, Hunter CP (2002) Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science 295(5564):2456–2459. doi:10.1126/science.1068836
Winston WM, Sutherlin M, Wright AJ, Feinberg EH, Hunter CP (2007) Caenorhabditis elegans SID-2 is required for environmental RNA interference. Proc Natl Acad Sci USA 104(25):10565–10570. doi:10.1073/pnas.0611282104
Acknowledgments
We thank Bin Yu and other members of the Ge Shan lab for discussions. This work was supported by the National Basic Research Program of China (2015CB943000), National Natural Science Foundation of China (31471225 and 91519333), and the Fundamental Research Funds for the Central Universities (WK2070000034).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Waqas, A., Shan, G. (2016). Uptake and Reaction of C. elegans to Environmental RNAs. In: Leitão, A., Enguita, F. (eds) Non-coding RNAs and Inter-kingdom Communication. Springer, Cham. https://doi.org/10.1007/978-3-319-39496-1_7
Download citation
DOI: https://doi.org/10.1007/978-3-319-39496-1_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-39494-7
Online ISBN: 978-3-319-39496-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)