Evolutionary Plasticity of the NHL Domain Underlies Distinct Solutions to RNA Recognition

Overview

Journal Nat Commun

Specialty Biology

Date 2018 Apr 21

PMID 29674686

Citations 23

Authors

Pooja Kumari

Florian Aeschimann

Dimos Gaidatzis

Jeremy J Keusch

Pritha Ghosh

Anca Neagu

Katarzyna Pachulska-Wieczorek

Janusz M Bujnicki

Heinz Gut

Helge Grosshans

Rafal Ciosk

Affiliations

Soon will be listed here.

Abstract

RNA-binding proteins regulate all aspects of RNA metabolism. Their association with RNA is mediated by RNA-binding domains, of which many remain uncharacterized. A recently reported example is the NHL domain, found in prominent regulators of cellular plasticity like the C. elegans LIN-41. Here we employ an integrative approach to dissect the RNA specificity of LIN-41. Using computational analysis, structural biology, and in vivo studies in worms and human cells, we find that a positively charged pocket, specific to the NHL domain of LIN-41 and its homologs (collectively LIN41), recognizes a stem-loop RNA element, whose shape determines the binding specificity. Surprisingly, the mechanism of RNA recognition by LIN41 is drastically different from that of its more distant relative, the fly Brat. Our phylogenetic analysis suggests that this reflects a rapid evolution of the domain, presenting an interesting example of a conserved protein fold that acquired completely different solutions to RNA recognition.

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References

Slack F, Basson M, Liu Z, Ambros V, Horvitz H, Ruvkun G . The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol Cell. 2000; 5(4):659-69. DOI: 10.1016/s1097-2765(00)80245-2. View

Fraser A, Kamath R, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J . Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature. 2000; 408(6810):325-30. DOI: 10.1038/35042517. View

Edgar R, Domrachev M, Lash A . Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2001; 30(1):207-10. PMC: 99122. DOI: 10.1093/nar/30.1.207. View

Kurowski M, Bujnicki J . GeneSilico protein structure prediction meta-server. Nucleic Acids Res. 2003; 31(13):3305-7. PMC: 168964. DOI: 10.1093/nar/gkg557. View

Edwards T, Wilkinson B, Wharton R, Aggarwal A . Model of the brain tumor-Pumilio translation repressor complex. Genes Dev. 2003; 17(20):2508-13. PMC: 218144. DOI: 10.1101/gad.1119403. View

Lancman J, Caruccio N, Harfe B, Pasquinelli A, Schageman J, Pertsemlidis A . Analysis of the regulation of lin-41 during chick and mouse limb development. Dev Dyn. 2005; 234(4):948-60. DOI: 10.1002/dvdy.20591. View

Law M, Rice A, Lin P, Laird-Offringa I . The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA. RNA. 2006; 12(7):1168-78. PMC: 1484440. DOI: 10.1261/rna.75206. View

Skrisovska L, Bourgeois C, Stefl R, Grellscheid S, Kister L, Wenter P . The testis-specific human protein RBMY recognizes RNA through a novel mode of interaction. EMBO Rep. 2007; 8(4):372-9. PMC: 1852761. DOI: 10.1038/sj.embor.7400910. View

Krissinel E, Henrick K . Inference of macromolecular assemblies from crystalline state. J Mol Biol. 2007; 372(3):774-97. DOI: 10.1016/j.jmb.2007.05.022. View

10.

Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F, Artus-Revel C . MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol. 2008; 15(3):259-67. DOI: 10.1038/nsmb.1391. View

11.

Loer B, Bauer R, Bornheim R, Grell J, Kremmer E, Kolanus W . The NHL-domain protein Wech is crucial for the integrin-cytoskeleton link. Nat Cell Biol. 2008; 10(4):422-8. DOI: 10.1038/ncb1704. View

12.

Bowman S, Rolland V, Betschinger J, Kinsey K, Emery G, Knoblich J . The tumor suppressors Brat and Numb regulate transit-amplifying neuroblast lineages in Drosophila. Dev Cell. 2008; 14(4):535-46. PMC: 2988195. DOI: 10.1016/j.devcel.2008.03.004. View

13.

Pei J, Tang M, Grishin N . PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Res. 2008; 36(Web Server issue):W30-4. PMC: 2447800. DOI: 10.1093/nar/gkn322. View

14.

Frokjaer-Jensen C, Davis M, Hopkins C, Newman B, Thummel J, Olesen S . Single-copy insertion of transgenes in Caenorhabditis elegans. Nat Genet. 2008; 40(11):1375-83. PMC: 2749959. DOI: 10.1038/ng.248. View

15.

Berrow N, Alderton D, Owens R . The precise engineering of expression vectors using high-throughput In-Fusion PCR cloning. Methods Mol Biol. 2008; 498:75-90. DOI: 10.1007/978-1-59745-196-3_5. View

16.

Abdulrahman W, Uhring M, Kolb-Cheynel I, Garnier J, Moras D, Rochel N . A set of baculovirus transfer vectors for screening of affinity tags and parallel expression strategies. Anal Biochem. 2008; 385(2):383-5. DOI: 10.1016/j.ab.2008.10.044. View

17.

Maller Schulman B, Liang X, Stahlhut C, DelConte C, Stefani G, Slack F . The let-7 microRNA target gene, Mlin41/Trim71 is required for mouse embryonic survival and neural tube closure. Cell Cycle. 2008; 7(24):3935-42. PMC: 2895810. DOI: 10.4161/cc.7.24.7397. View

18.

Deigan K, Li T, Mathews D, Weeks K . Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci U S A. 2008; 106(1):97-102. PMC: 2629221. DOI: 10.1073/pnas.0806929106. View

19.

Schwamborn J, Berezikov E, Knoblich J . The TRIM-NHL protein TRIM32 activates microRNAs and prevents self-renewal in mouse neural progenitors. Cell. 2009; 136(5):913-25. PMC: 2988196. DOI: 10.1016/j.cell.2008.12.024. View

20.

Gibson D, Young L, Chuang R, Venter J, Hutchison 3rd C, Smith H . Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009; 6(5):343-5. DOI: 10.1038/nmeth.1318. View