The Sequence Selectivity of KSRP Explains Its Flexibility in the Recognition of the RNA Targets

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2008 Aug 8

PMID 18684992

Citations 32

Authors

Maria Flor Garcia-Mayoral

Irene Diaz-Moreno

David Hollingworth

Andres Ramos

Affiliations

Soon will be listed here.

Abstract

K-homology (KH) splicing regulator protein (KSRP) is a multi-domain RNA-binding protein that regulates different steps of mRNA metabolism, from mRNA splicing to mRNA decay, interacting with a broad range of RNA sequences. To understand how KSRP recognizes its different RNA targets it is necessary to define the general rules of KSRP-RNA interaction. We describe here a complete scaffold-independent analysis of the RNA-binding potential of the four KH domains of KSRP. The analysis shows that KH3 binds to the RNA with a significantly higher affinity than the other domains and recognizes specifically a G-rich target. It also demonstrates that the other KH domains of KSRP display different sequence preferences explaining the broad range of targets recognized by the protein. Further, KSRP shows a strong negative selectivity for sequences containing several adjacent Cytosines limiting the target choice of KSRP within single-stranded RNA regions. The in-depth analysis of the RNA-binding potential of the KH domains of KSRP provides us with an understanding of the role of low sequence specificity domains in RNA recognition by multi-domain RNA-binding proteins.

Citing Articles

Expanding the Functions of KHSRP Protein: Insights into DNA G-Quadruplex Binding.

Russomanno P, Zizza P, Cerofolini L, DAria F, Iachettini S, Di Vito S Adv Sci (Weinh). 2025; 12(8):e2410086.

PMID: 39763191 PMC: 11848572. DOI: 10.1002/advs.202410086.

Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes.

Hasan M, Jeannine Brady L J Struct Biol X. 2024; 10:100106.

PMID: 39040530 PMC: 11261784. DOI: 10.1016/j.yjsbx.2024.100106.

DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning.

Wang J, Horlacher M, Cheng L, Winther O Bioinformatics. 2024; 40(2).

PMID: 38317052 PMC: 10879750. DOI: 10.1093/bioinformatics/btae065.

Identification of proteins that bind extracellular microRNAs secreted by the parasitic nematode Trichinella spiralis.

Brown A, Selkirk M, Sarkies P Biol Open. 2023; 12(11).

PMID: 37906081 PMC: 10660789. DOI: 10.1242/bio.060096.

K-Homology Type Splicing Regulatory Protein: Mechanism of Action in Cancer and Immune Disorders.

Leavenworth J, Yusuf N, Hassan Q Crit Rev Eukaryot Gene Expr. 2023; 34(1):75-87.

PMID: 37824394 PMC: 11003564. DOI: 10.1615/CritRevEukaryotGeneExpr.2023048085.

References

Chen C, Gherzi R, Ong S, Chan E, Raijmakers R, Pruijn G . AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell. 2001; 107(4):451-64. DOI: 10.1016/s0092-8674(01)00578-5. View

Lopez de Silanes I, Zhan M, Lal A, Yang X, Gorospe M . Identification of a target RNA motif for RNA-binding protein HuR. Proc Natl Acad Sci U S A. 2004; 101(9):2987-92. PMC: 365732. DOI: 10.1073/pnas.0306453101. View

Beuth B, Garcia-Mayoral M, Taylor I, Ramos A . Scaffold-independent analysis of RNA-protein interactions: the Nova-1 KH3-RNA complex. J Am Chem Soc. 2007; 129(33):10205-10. DOI: 10.1021/ja072365q. View

Delaglio F, Grzesiek S, Vuister G, Zhu G, Pfeifer J, Bax A . NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR. 1995; 6(3):277-93. DOI: 10.1007/BF00197809. View

Gherzi R, Lee K, Briata P, Wegmuller D, Moroni C, Karin M . A KH domain RNA binding protein, KSRP, promotes ARE-directed mRNA turnover by recruiting the degradation machinery. Mol Cell. 2004; 14(5):571-83. DOI: 10.1016/j.molcel.2004.05.002. View

Min H, Turck C, Nikolic J, Black D . A new regulatory protein, KSRP, mediates exon inclusion through an intronic splicing enhancer. Genes Dev. 1997; 11(8):1023-36. DOI: 10.1101/gad.11.8.1023. View

Pan F, Huttelmaier S, Singer R, Gu W . ZBP2 facilitates binding of ZBP1 to beta-actin mRNA during transcription. Mol Cell Biol. 2007; 27(23):8340-51. PMC: 2169170. DOI: 10.1128/MCB.00972-07. View

Shamoo Y, Abdul-Manan N, Patten A, CRAWFORD J, Pellegrini M, Williams K . Both RNA-binding domains in heterogenous nuclear ribonucleoprotein A1 contribute toward single-stranded-RNA binding. Biochemistry. 1994; 33(27):8272-81. DOI: 10.1021/bi00193a014. View

Lunde B, Moore C, Varani G . RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol. 2007; 8(6):479-90. PMC: 5507177. DOI: 10.1038/nrm2178. View

10.

Martin S, Biekofsky R, Skinner M, Guerrini R, Salvadori S, Feeney J . Interaction of calmodulin with the phosphofructokinase target sequence. FEBS Lett. 2004; 577(1-2):284-8. DOI: 10.1016/j.febslet.2004.10.023. View

11.

Bakheet T, Williams B, Khabar K . ARED 3.0: the large and diverse AU-rich transcriptome. Nucleic Acids Res. 2005; 34(Database issue):D111-4. PMC: 1347415. DOI: 10.1093/nar/gkj052. View

12.

Auweter S, Oberstrass F, Allain F . Sequence-specific binding of single-stranded RNA: is there a code for recognition?. Nucleic Acids Res. 2006; 34(17):4943-59. PMC: 1635273. DOI: 10.1093/nar/gkl620. View

13.

Garcia-Mayoral M, Hollingworth D, Masino L, Diaz-Moreno I, Kelly G, Gherzi R . The structure of the C-terminal KH domains of KSRP reveals a noncanonical motif important for mRNA degradation. Structure. 2007; 15(4):485-98. DOI: 10.1016/j.str.2007.03.006. View

14.

Makeyev A, Eastmond D, Liebhaber S . Targeting a KH-domain protein with RNA decoys. RNA. 2002; 8(9):1160-73. PMC: 1370330. DOI: 10.1017/s135583820202808x. View

15.

Rehbein M, Wege K, Buck F, Schweizer M, Richter D, Kindler S . Molecular characterization of MARTA1, a protein interacting with the dendritic targeting element of MAP2 mRNAs. J Neurochem. 2002; 82(5):1039-46. DOI: 10.1046/j.1471-4159.2002.01058.x. View