Short hairpin RNA-mediated knockdown of protein expression in Entamoeba histolytica

BMC Microbiology

Volumn 9, Issue , 2009, Pages

  Linford, Alicia S ^a   Moreno, Heriberto ^a   Good, Katelyn R ^b   Zhang, Hanbang ^c   Singh, Upinder ^c   Petri, William A ^a,b  

^a UNIVERSITY OF VIRGINIA   (United States)

^b UNIVERSITY OF VIRGINIA   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTOZOAL PROTEIN; PROTOZOAL RNA; RNA; RNA PRIMERS; SMALL INTERFERING RNA;

ANIMAL; ARTICLE; ENTAMOEBA HISTOLYTICA; GENE; GENE EXPRESSION REGULATION; GENE SILENCING; GENETIC TRANSFECTION; GENETICS; METABOLISM; PROMOTER REGION; RNA INTERFERENCE;

ANIMALS; ENTAMOEBA HISTOLYTICA; GENE EXPRESSION REGULATION; GENE KNOCKDOWN TECHNIQUES; GENES, PROTOZOAN; PROMOTER REGIONS, GENETIC; PROTOZOAN PROTEINS; RNA; RNA INTERFERENCE; RNA, PROTOZOAN; RNA, SMALL INTERFERING; TRANSFECTION;

EID: 61849145256     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-9-38     Document Type: Article

References (55)

1. Comparative genomics of Dictyostelium discoideum and Entamoeba histolytica. L Eichinger AA Noegel, Curr Opin Microbiol 2005 8 5 606 611 10.1016/j.mib.2005.08.009 16125444
2. The genome of the protist parasite Entamoeba histolytica. B Loftus I Anderson R Davies UC Alsmark J Samuelson P Amedeo P Roncaglia M Berriman RP Hirt BJ Mann, Nature 2005 433 7028 865 868 10.1038/nature03291 15729342
3. The bittersweet interface of parasite and host: lectin-carbohydrate interactions during human invasion by the parasite Entamoeba histolytica. WA Petri Jr R Haque BJ Mann, Annu Rev Microbiol 2002 56 39 64 10.1146/annurev. micro.56.012302.160959 12142490
4. Amoebiasis. Wkly Epidemiol Rec 1997 72 14 97 99 9100475
5. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. A Fire S Xu MK Montgomery SA Kostas SE Driver CC Mello, Nature 1998 391 6669 806 811 10.1038/35888 9486653
6. The RNAi revolution. CD Novina PA Sharp, Nature 2004 430 6996 161 164 10.1038/430161a 15241403
7. RNA silencing: the genome's immune system. RH Plasterk, Science 2002 296 5571 1263 1265 10.1126/science.1072148 12016302
8. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. PD Zamore T Tuschl PA Sharp DP Bartel, Cell 2000 101 1 25 33 10.1016/S0092-8674(00)80620-0 10778853
9. Role for a bidentate ribonuclease in the initiation step of RNA interference. E Bernstein AA Caudy SM Hammond GJ Hannon, Nature 2001 409 6818 363 366 10.1038/35053110 11201747
10. RNA interference is mediated by 21- and 22-nucleotide RNAs. SM Elbashir W Lendeckel T Tuschl, Genes Dev 2001 15 2 188 200 11157775 10.1101/gad.862301
11. RNA interference: biology, mechanism, and applications. N Agrawal PV Dasaradhi A Mohmmed P Malhotra RK Bhatnagar SK Mukherjee, Microbiol Mol Biol Rev 2003 67 4 657 685 14665679 10.1128/MMBR.67.4.657-685.2003
12. Killing the messenger: short RNAs that silence gene expression. DM Dykxhoorn CD Novina PA Sharp, Nat Rev Mol Cell Biol 2003 4 6 457 467 10.1038/nrm1129 12778125
13. Distinct populations of primary and secondary effectors during RNAi in C. elegans. J Pak A Fire, Science 2007 315 5809 241 244 10.1126/science.1132839 17124291
14. On the role of RNA amplification in dsRNA-triggered gene silencing. T Sijen J Fleenor F Simmer KL Thijssen S Parrish L Timmons RH Plasterk A Fire, Cell 2001 107 4 465 476 10.1016/S0092-8674(01)00576-1 11719187
15. Entamoeba histolytica : computational identification of putative microRNA candidates. S De D Pal SK Ghosh, Exp Parasitol 2006 113 4 239 243 10.1016/j.exppara.2006.01.009 16515787
16. Molecular characterization of Entamoeba histolytica RNase III and AGO2, two RNA interference hallmark proteins. M Abed S Ankri, Exp Parasitol 2005 110 3 265 269 10.1016/j.exppara.2005.02.023 15955322
17. Transcriptional profiling of Entamoeba histolytica trophozoites. RC MacFarlane PH Shah U Singh, Int J Parasitol 2005 35 5 533 542 10.1016/j.ijpara.2005.02.006 15826645
18. Inhibition of gene expression with double strand RNA interference in Entamoeba histolytica. G Kaur A Lohia, Biochem Biophys Res Commun 2004 320 4 1118 1122 10.1016/j.bbrc.2004.06.064 15249205
19. The cell cycle of Entamoeba histolytica. A Lohia, Mol Cell Biochem 2003 253 217 222 10.1023/A:1026055631421 14619972
20. Double-stranded RNA mediates homology-dependent gene silencing of gamma-tubulin in the human parasite Entamoeba histolytic a. L Vayssie M Vargas C Weber N Guillen, Mol Biochem Parasitol 2004 138 1 21 28 10.1016/j.molbiopara. 2004.07.005 15500912
21. Applying antisense technology to the study of Entamoeba histolytica pathogenesis. WA Petri G Ramakrishnan, Trends Microbiol 1999 7 12 471 474 10.1016/S0966-842X(99)01626-1 10603478
22. Delinking of S phase and cytokinesis in the protozoan parasite Entamoeba histolytica. S Das A Lohia, Cell Microbiol 2002 4 1 55 60 10.1046/j.1462-5822. 2002.00165.x 11856173
23. Heterogeneity of DNA content and expression of cell cycle genes in axenically growing Entamoeba histolytica HM1:IMSS clone A. SS Gangopadhyay SS Ray K Kennady G Pande A Lohia, Mol Biochem Parasitol 1997 90 1 9 20 10.1016/S0166-6851(97)00156-4 9497028
24. Inhibition of gene expression in Entamoeba by the transcription of antisense RNA: effect of 5' and 3' regulatory elements. R Bracha Y Nuchamowitz D Mirelman, Mol Biochem Parasitol 2000 107 1 81 90 10.1016/S0166-6851(00)00181-X 10717304
25. Eh Klp5 is a divergent member of the kinesin 5 family that regulates genome content and microtubular assembly in Entamoeba histolytica. PG Dastidar S Majumder A Lohia, Cell Microbiol 2007 9 2 316 328 10.1111/j.1462-5822.2006. 00788.x 16925786
26. Identification of an Entamoeba histolytica serine-, threonine-, and isoleucine-rich protein with roles in adhesion and cytotoxicity. RC MacFarlane U Singh, Eukaryot Cell 2007 6 11 2139 2146 17827347 10.1128/EC.00174-07
27. RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. JY Yu SL DeRuiter DL Turner, Proc Natl Acad Sci USA 2002 99 9 6047 6052 11972060 10.1073/pnas.092143499
28. A system for stable expression of short interfering RNAs in mammalian cells. TR Brummelkamp R Bernards R Agami, Science 2002 296 5567 550 553 10.1126/science.1068999 11910072
29. Upstream regulatory elements are necessary and sufficient for transcription of a U6 RNA gene by RNA polymerase III. G Das D Henning D Wright R Reddy, EMBO J 1988 7 2 503 512 3366121
30. Gene silencing in mammalian cells by PCR-based short hairpin RNA. D Gou N Jin L Liu, FEBS Lett 2003 548 1-3 113 118 10.1016/S0014-5793(03)00630-6 12885417
31. Second-generation shRNA libraries covering the mouse and human genomes. JM Silva MZ Li K Chang W Ge MC Golding RJ Rickles D Siolas G Hu PJ Paddison MR Schlabach, Nat Genet 2005 37 11 1281 1288 16200065
32. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. DH Kim MA Behlke SD Rose MS Chang S Choi JJ Rossi, Nat Biotechnol 2005 23 2 222 226 10.1038/nbt1051 15619617
33. Identification of the 150-kDa surface antigen of Entamoeba histolytica as a galactose- and N-acetyl-D-galactosamine-inhibitable lectin. XJ Cheng H Tsukamoto Y Kaneda H Tachibana, Parasitol Res 1998 84 8 632 639 10.1007/s004360050462 9747935
34. Intermediate subunit of the Gal/GalNAc lectin of Entamoeba histolytica is a member of a gene family containing multiple CXXC sequence motifs. XJ Cheng MA Hughes CD Huston B Loftus CA Gilchrist LA Lockhart S Ghosh V Miller-Sims BJ Mann WA Petri Jr, Infect Immun 2001 69 9 5892 5898 11500468 10.1128/IAI.69.9. 5892-5898.2001
35. Identification and gene expression analysis of a large family of transmembrane kinases related to the Gal/GalNAc lectin in Entamoeba histolytica. DL Beck DR Boettner B Dragulev K Ready T Nozaki WA Petri Jr, Eukaryot Cell 2005 4 4 722 732 15821132 10.1128/EC.4.4.722-732.2005
36. Calcium modulates promoter occupancy by the Entamoeba histolytica Ca2+-binding transcription factor URE3-BP. CA Gilchrist M Leo CG Line BJ Mann WA Petri Jr, J Biol Chem 2003 278 7 4646 4653 10.1074/jbc.M211271200 12466263
37. Kinetics and strain variation of phagosome proteins of Entamoeba histolytica by proteomic analysis. M Okada CD Huston M Oue BJ Mann WA Petri Jr K Kita T Nozaki, Mol Biochem Parasitol 2006 145 2 171 183 10.1016/j.molbiopara. 2005.10.001 16290089
38. The C2 domain calcium-binding motif: structural and functional diversity. EA Nalefski JJ Falke, Protein Science 1996 5 2375 2390 8976547 10.1002/pro.5560051201
39. Entamoeba histolytica phagocytosis of human erythrocytes involves PATMK, a member of the transmembrane kinase family. DR Boettner CD Huston AS Linford SN Buss E Houpt NE Sherman WA Petri Jr, PLoS Pathog 2008 4 1 e8 18208324 10.1371/journal.ppat.0040008
40. Identification and analysis of the u6 small nuclear RNA gene from Entamoeba histolytica. R Miranda LM Salgado R Sanchez-Lopez A Alagon PM Lizardi, Gene 1996 180 1-2 37 42 10.1016/S0378-1119(96)00397-6 8973344
41. Stable episomal transfection of Entamoeba histolytica. RR Vines JE Purdy BD Ragland J Samuelson BJ Mann WA Petri Jr, Mol Biochem Parasitol 1995 71 2 265 267 10.1016/0166-6851(95)00057-8 7477110
42. Tetracycline-controlled gene expression in Entamoeba histolytica. L Hamann H Buss E Tannich, Mol Biochem Parasitol 1997 84 1 83 91 10.1016/S0166-6851(96)02771-5 9041523
43. Transfection and continuous expression of heterologous genes in the protozoan parasite Entamoeba histolytica. L Hamann R Nickel E Tannich, Proc Natl Acad Sci USA 1995 92 19 8975 8979 7568055 10.1073/pnas.92.19.8975
44. Effect of target secondary structure on RNAi efficiency. Y Shao CY Chan A Maliyekkel CE Lawrence IB Roninson Y Ding, RNA 2007 13 1631 1640 17684233 10.1261/rna.546207
45. Impact of target mRNA structure on siRNA silencing efficiency: a large-scale study. JA Gredell AK Berger SP Walton, Biotechnol Bioeng 2008 100 744 755 10.1002/bit.21798 18306428
46. Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome. CA Gilchrist E Houpt N Trapaidze Z Fei O Crasta A Asgharpour C Evans S Martino-Catt DJ Baba S Stroup, Mol Biochem Parasitol 2006 147 2 163 176 10.1016/j.molbiopara.2006.02.007 16569449
47. A new medium for the axenic cultivation of Entamoeba histolytica and other Entamoeba. LS Diamond DR Harlow CC Cunnick, Trans R Soc Trop Med Hyg 1978 72 4 431 432 10.1016/0035-9203(78)90144-X 212851
48. Apoptotic killing and phagocytosis of host cells by the parasite Entamoeba histolytica. CD Huston DR Boettner V Miller-Sims WA Petri Jr, Infect Immun 2003 71 2 964 972 12540579 10.1128/IAI.71.2.964-972.2003
49. A tetracycline-inducible gene expression system in Entamoeba histolytica. G Ramakrishnan RR Vines BJ Mann WA Petri Jr, Mol Biochem Parasitol 1997 84 1 93 100 10.1016/S0166-6851(96)02784-3 9041524
50. Comparison between constitutive and inducible plasmid vectors used for gene expression in Entamoeba histolytica. U Katz R Bracha Y Nuchamowitz O Milstein D Mirelman, Mol Biochem Parasitol 2003 128 2 229 233 10.1016/S0166-6851(03)00076-8 12742589
51. The Ambion/Applied Biosystems siRNA Target Finder. http://www.ambion.com/ techlib/misc/siRNA-finder.html
52. TIGR Database Entamoeba histolytica Genome Project. http://www.tigr.org/ tdb/e2k1/eha1/
53. GraphPad QuickCalcs. http://www.graphpad.com/quickcalcs
54. Relative quantification of mRNA: comparison of methods currently used for real-time PCR data analysis. S Cikos A Bukovska J Koppel, BMC Mol Biol 2007 8 113 18093344 10.1186/1471-2199-8-113
55. Real-Time PCR: M. Teyfik Dorak, MD, PhD. http://www.dorak.info/genetics/ realtime.html