Các bản sao chức năng liên quan có mô típ RNA chung cho các protein gắn RNA đặc hiệu trong trypanosomes

Springer Science and Business Media LLC - Tập 9 - Trang 1-19 - 2008
Griselda Noé1, Javier G De Gaudenzi1, Alberto C Frasch1
1Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús, UNSAM-CONICET, Av. Gral. Paz 5445, Provincia de Buenos Aires, Argentina

Tóm tắt

Trypanosom chủ yếu điều khiển biểu hiện gen thông qua các sự kiện sau phiên mã, chẳng hạn như điều chỉnh độ ổn định của mRNA và hiệu quả phiên dịch. Các cơ chế này liên quan đến các protein gắn RNA (RBP), các protein này liên kết với các bản sao để tạo thành các phức hợp ribonucleoprotein thông điệp (mRNP). Trong nghiên cứu này, chúng tôi báo cáo việc xác định các mục tiêu mRNA cho RBP 1 giàu U của Trypanosoma cruzi (Tc UBP1) và RBP 3 của T. cruzi (Tc RBP3), hai protein bảo tồn về mặt phát sinh loài giữa các Kinetoplastida. Các RNA liên kết với RBP được đồng phân tách và được chiết xuất từ các phức hợp mRNP, và việc liên kết của các RBP với một số mục tiêu đã được xác nhận bởi các thử nghiệm độc lập. Phân tích trình tự mục tiêu transcript cho phép xác định các mô típ RNA đặc trưng khác nhau cho mỗi protein. Các yếu tố cis để liên kết RBP có cấu trúc thân vòng từ 30–35 base và được đại diện nhiều hơn trong vùng không dịch mã 3' (UTR) của mRNA. Việc chèn các phần tử RNA đã gấp đúng vào một mRNA không đặc hiệu đã biến nó thành một bản sao mục tiêu, trong khi việc thay thế các phần tử RNA đã làm giảm tương tác RBP. Ngoài ra, các RBP đã cạnh tranh cho các vị trí liên kết RNA phù hợp với sự phân bố của các mô típ khác nhau và chồng chéo trong vùng UTR 3' của các mRNA chung. Các bản sao liên quan chức năng được liên kết ưu tiên với một RBP nhất định; các mục tiêu Tc UBP1 giàu có trong các gen mã hóa protein liên quan đến chuyển hóa, trong khi các bản sao mã hóa protein ribosome là nhóm lớn nhất trong các mục tiêu Tc RBP3. Tổng thể, những kết quả này cho thấy sự kiểm soát phối hợp của các tập hợp mRNA khác nhau ở mức độ sau phiên mã bởi các RBP cụ thể.

Từ khóa


Tài liệu tham khảo

Barrett MP, Burchmore RJ, Stich A, Lazzari JO, Frasch AC, Cazzulo JJ, Krishna S: The trypanosomiases. Lancet 2003, 362(9394):1469-1480. Fenn K, Matthews KR: The cell biology of Trypanosoma brucei differentiation. Curr Opin Microbiol 2007, 10(6):539-546. Palenchar JB, Bellofatto V: Gene transcription in trypanosomes. Mol Biochem Parasitol 2006, 146(2):135-141. Liang XH, Haritan A, Uliel S, Michaeli S: trans and cis splicing in trypanosomatids: mechanism, factors, and regulation. Eukaryot Cell 2003, 2(5):830-840. Boothroyd JC, Cross GA: Transcripts coding for variant surface glycoproteins of Trypanosoma brucei have a short, identical exon at their 5' end. Gene 1982, 20(2):281-289. van der Ploeg LH, Liu AY, Michels PA, De Lange T, Borst P, Majumder HK, Weber H, Veeneman GH, van Boom J: RNA splicing is required to make the messenger RNA for a variant surface antigen in trypanosomes. Nucleic Acids Res 1982, 10(12):3591-3604. Matthews KR, Tschudi C, Ullu E: A common pyrimidine-rich motif governs trans -splicing and polyadenylation of tubulin polycistronic pre-mRNA in trypanosomes. Genes Dev 1994, 8(4):491-501. Gilinger G, Bellofatto V: Trypanosome spliced leader RNA genes contain the first identified RNA polymerase II gene promoter in these organisms. Nucleic Acids Res 2001, 29(7):1556-1564. Campbell DA, Thomas S, Sturm NR: Transcription in kinetoplastid protozoa: why be normal? Microbes Infect 2003, 5(13):1231-1240. Matthews KR, Ellis JR, Paterou A: Molecular regulation of the life cycle of African trypanosomes. Trends Parasitol 2004, 20(1):40-47. Schwede A, Ellis L, Luther J, Carrington M, Stoecklin G, Clayton C: A role for Caf1 in mRNA deadenylation and decay in trypanosomes and human cells. Nucleic Acids Res 2008, 36(10):3374-3388. Milone J, Wilusz J, Bellofatto V: Characterization of deadenylation in trypanosome extracts and its inhibition by poly(A)-binding protein Pab1p. Rna 2004, 10(3):448-457. Clayton C, Schwede A, Stewart M, Robles A, Benz C, Po J, Wurst M, Quieroz R, Archer S: Control of mRNA degradation in trypanosomes. Biochem Soc Trans 2008, 36(Pt 3):520-521. Li CH, Irmer H, Gudjonsdottir-Planck D, Freese S, Salm H, Haile S, Estevez AM, Clayton C: Roles of a Trypanosoma brucei 5'->3' exoribonuclease homolog in mRNA degradation. Rna 2006, 12(12):2171-2186. Estevez AM, Kempf T, Clayton C: The exosome of Trypanosoma brucei . Embo J 2001, 20(14):3831-3839. Shi H, Djikeng A, Tschudi C, Ullu E: Argonaute protein in the early divergent eukaryote Trypanosoma brucei : control of small interfering RNA accumulation and retroposon transcript abundance. Mol Cell Biol 2004, 24(1):420-427. Ullu E, Tschudi C, Chakraborty T: RNA interference in protozoan parasites. Cell Microbiol 2004, 6(6):509-519. Webb H, Burns R, Kimblin N, Ellis L, Carrington M: A novel strategy to identify the location of necessary and sufficient cis -acting regulatory mRNA elements in trypanosomes. Rna 2005, 11(7):1108-1116. Clayton C, Shapira M: Post-transcriptional regulation of gene expression in trypanosomes and leishmanias. Mol Biochem Parasitol 2007, 156(2):93-101. Keene JD: Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc Natl Acad Sci USA 2001, 98(13):7018-7024. Maris C, Dominguez C, Allain FH: The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. Febs J 2005, 272(9):2118-2131. El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran AN, Ghedin E, Worthey EA, Delcher AL, Blandin G, et al.: The genome sequence of Trypanosoma cruzi , etiologic agent of Chagas disease. Science 2005, 309(5733):409-415. Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, et al.: The genome of the African trypanosome Trypanosoma brucei . Science 2005, 309(5733):416-422. Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E, Aert R, et al.: The genome of the kinetoplastid parasite Leishmania major . Science 2005, 309(5733):436-442. De Gaudenzi J, Frasch AC, Clayton C: RNA-binding domain proteins in Kinetoplastids: a comparative analysis. Eukaryot Cell 2005, 4(12):2106-2114. De Gaudenzi JG, D'Orso I, Frasch AC: RNA Recognition Motif-type RNA-binding Proteins in Trypanosoma cruzi Form a Family Involved in the Interaction with Specific Transcripts in Vivo. J Biol Chem 2003, 278(21):18884-18894. D'Orso I, Frasch AC: TcUBP-1, an mRNA destabilizing factor from trypanosomes, homodimerizes and interacts with novel AU-rich element- and Poly(A)-binding proteins forming a ribonucleoprotein complex. J Biol Chem 2002, 277(52):50520-50528. Volpon L, D'Orso I, Young CR, Frasch AC, Gehring K: NMR Structural Study of Tc UBP1, a Single RRM Domain Protein from Trypanosoma cruzi : Contribution of a beta Hairpin to RNA Binding. Biochemistry 2005, 44(10):3708-3717. Hartmann C, Benz C, Brems S, Ellis L, Luu VD, Stewart M, D'Orso I, Busold C, Fellenberg K, Frasch AC, et al.: Small trypanosome RNA-binding proteins Tb UBP1 and Tb UBP2 influence expression of F-box protein mRNAs in bloodstream trypanosomes. Eukaryot Cell 2007, 6(11):1964-1978. Hartmann C, Clayton C: Regulation of a transmembrane protein gene family by the small RNA-binding proteins Tb UBP1 and Tb UBP2. Mol Biochem Parasitol 2008, 157(1):112-115. Nagai K, Oubridge C, Jessen TH, Li J, Evans PR: Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. Nature 1990, 348(6301):515-520. Jessen TH, Oubridge C, Teo CH, Pritchard C, Nagai K: Identification of molecular contacts between the U1 A small nuclear ribonucleoprotein and U1 RNA. Embo J 1991, 10(11):3447-3456. Lopez de Silanes I, Galban S, Martindale JL, Yang X, Mazan-Mamczarz K, Indig FE, Falco G, Zhan M, Gorospe M: Identification and functional outcome of mRNAs associated with RNA-binding protein TIA-1. Mol Cell Biol 2005, 25(21):9520-9531. Kim HS, Kuwano Y, Zhan M, Pullmann R Jr, Mazan-Mamczarz K, Li H, Kedersha N, Anderson P, Wilce MC, Gorospe M, et al.: Elucidation of a C-rich signature motif in target mRNAs of RNA-binding protein TIAR. Mol Cell Biol 2007, 27(19):6806-6817. Cassola A, De Gaudenzi JG, Frasch AC: Recruitment of mRNAs to cytoplasmic ribonucleoprotein granules in trypanosomes. Mol Microbiol 2007, 65(3):655-670. Mili S, Steitz JA: Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. Rna 2004, 10(11):1692-1694. Eddy SR, Durbin R: RNA sequence analysis using covariance models. Nucleic Acids Res 1994, 22(11):2079-2088. Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan A, Cheung F, Quackenbush J: The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res 2005, (33 Database):D71-74. Keene JD, Komisarow JM, Friedersdorf MB: RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nature protocols 2006, 1(1):302-307. Beach DL, Keene JD: Ribotrap: targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs. Methods Mol Biol 2008, 419: 69-91. Khaladkar M, Patel V, Bellofatto V, Wilusz J, Wang JT: Detecting conserved secondary structures in RNA molecules using constrained structural alignment. Comput Biol Chem 2008. Khaladkar M, Bellofatto V, Wang JT, Tian B, Shapiro BA: RADAR: a web server for RNA data analysis and research. Nucleic Acids Res 2007, (35 Web Server):W300-304. Sanchez-Diaz P, Penalva LO: Post-transcription meets post-genomic: the saga of RNA binding proteins in a new era. RNA Biol 2006, 3(3):101-109. Caro F, Bercovich N, Atorrasagasti C, Levin MJ, Vazquez MP: Trypanosoma cruzi : analysis of the complete PUF RNA-binding protein family. Exp Parasitol 2006, 113(2):112-124. Luu VD, Brems S, Hoheisel JD, Burchmore R, Guilbride DL, Clayton C: Functional analysis of Trypanosoma brucei PUF1. Mol Biochem Parasitol 2006, 150(2):340-349. Dallagiovanna B, Correa A, Probst CM, Holetz F, Smircich P, de Aguiar AM, Mansur F, da Silva CV, Mortara RA, Garat B, et al.: Functional genomic characterization of mRNAs associated with TcPUF6, a pumilio-like protein from Trypanosoma cruzi . J Biol Chem 2008, 283(13):8266-8273. Haile S, Papadopoulou B: Developmental regulation of gene expression in trypanosomatid parasitic protozoa. Curr Opin Microbiol 2007, 10(6):569-577. Irmer H, Clayton C: Degradation of the unstable EP1 mRNA in Trypanosoma brucei involves initial destruction of the 3'-untranslated region. Nucleic Acids Res 2001, 29(22):4707-4715. Hehl A, Vassella E, Braun R, Roditi I: A conserved stem-loop structure in the 3' untranslated region of procyclin mRNAs regulates expression in Trypanosoma brucei . Proc Natl Acad Sci USA 1994, 91(1):370-374. Boucher N, Wu Y, Dumas C, Dube M, Sereno D, Breton M, Papadopoulou B: A common mechanism of stage-regulated gene expression in Leishmania mediated by a conserved 3'-untranslated region element. J Biol Chem 2002, 277(22):19511-19520. Mayho M, Fenn K, Craddy P, Crosthwaite S, Matthews K: Post-transcriptional control of nuclear-encoded cytochrome oxidase subunits in Trypanosoma brucei : evidence for genome-wide conservation of life-cycle stage-specific regulatory elements. Nucleic Acids Res 2006, 34(18):5312-5324. Gerber AP, Luschnig S, Krasnow MA, Brown PO, Herschlag D: Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster . Proc Natl Acad Sci USA 2006, 103(12):4487-4492. Jackson JS Jr, Houshmandi SS, Lopez Leban F, Olivas WM: Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast. Rna 2004, 10(10):1625-1636. Ulbricht RJ, Olivas WM: Puf1p acts in combination with other yeast Puf proteins to control mRNA stability. Rna 2008, 14(2):246-262. Lal A, Mazan-Mamczarz K, Kawai T, Yang X, Martindale JL, Gorospe M: Concurrent versus individual binding of HuR and AUF1 to common labile target mRNAs. Embo J 2004, 23(15):3092-3102. Gama-Carvalho M, Barbosa-Morais NL, Brodsky AS, Silver PA, Carmo-Fonseca M: Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome Biol 2006, 7(11):R113. Hook BA, Goldstrohm AC, Seay DJ, Wickens M: Two yeast PUF proteins negatively regulate a single mRNA. J Biol Chem 2007, 282(21):15430-15438. Gerber AP, Herschlag D, Brown PO: Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol 2004, 2(3):E79. Keene JD, Lager PJ: Post-transcriptional operons and regulons co-ordinating gene expression. Chromosome Res 2005, 13(3):327-337. Keene JD: RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 2007, 8(7):533-543. Inada M, Guthrie C: Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs. Proc Natl Acad Sci USA 2004, 101(2):434-439. Duttagupta R, Tian B, Wilusz CJ, Khounh DT, Soteropoulos P, Ouyang M, Dougherty JP, Peltz SW: Global analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Mol Cell Biol 2005, 25(13):5499-5513. Zingales B, Pereira ME, Oliveira RP, Almeida KA, Umezawa ES, Souto RP, Vargas N, Cano MI, da Silveira JF, Nehme NS, et al.: Trypanosoma cruzi genome project: biological characteristics and molecular typing of clone CL Brener. Acta Trop 1997, 68(2):159-173. Di Noia JM, D'Orso I, Sanchez DO, Frasch AC: AU-rich elements in the 3'-untranslated region of a new mucin-type gene family of Trypanosoma cruzi confers mRNA instability and modulates translation efficiency. J Biol Chem 2000, 275(14):10218-10227. Benz C, Nilsson D, Andersson B, Clayton C, Guilbride DL: Messenger RNA processing sites in Trypanosoma brucei . Mol Biochem Parasitol 2005, 143(2):125-134. Stern AL, Burgos E, Salmon L, Cazzulo JJ: Ribose 5-phosphate isomerase type B from Trypanosoma cruzi : kinetic properties and site-directed mutagenesis reveal information about the reaction mechanism. Biochem J 2007, 401(1):279-285. Gorodkin J, Stricklin SL, Stormo GD: Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res 2001, 29(10):2135-2144. Yao Z, Weinberg Z, Ruzzo WL: CMfinder – a covariance model based RNA motif finding algorithm. Bioinformatics 2006, 22(4):445-452. Hofacker IL: Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31(13):3429-3431. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673-4680.