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Current Genetics

, Volume 65, Issue 2, pp 561–573 | Cite as

Co-evolution of spliceosomal disassembly interologs: crowning J-protein component with moonlighting RNA-binding activity

  • S. Raut
  • K. Yadav
  • A. K. Verma
  • Y. Tak
  • P. Waiker
  • C. SahiEmail author
Original Article
  • 177 Downloads

Abstract

Spliceosome disassembly is catalyzed by the NineTeen-related (NTR) complex, which is constituted by several proteins, including Cwc23, Ntr1, and Ppr43. Cwc23 is an essential J-protein in Saccharomyces cerevisiae that recruits Ntr1, an NTC-related G-patch protein, to the spliceosome. Ntr1 interacts with Prp43, a DExD/H box RNA helicase protein, which facilitates the disassembly of spliceosomal intermediates. The interaction between Ntr1 and Prp43 is conserved and crucial for the disassembly process. However, the J-protein component of this complex is not studied in other eukaryotes. In silico analysis supported by results of yeast complementation and two-hybrid studies suggests that while Prp43 is highly conserved, both Ntr1 and Cwc23 are co-evolving components of the disassembly triad. The J-domain of Cwc23, which is otherwise dispensable for its function, is highly conserved, whereas the functionally critical C-terminus has significantly diverged in Cwc23 orthologs. Some eukaryotic orthologs of Cwc23 contain a distinct RNA recognition motif at their C-terminus and are able to bind RNA in vitro. Based on the results presented in this study, we propose that RNA-binding activity in some eukaryotic orthologs of Cwc23 might provide additional functional diversity or robustness to the J-protein/Hsp70 machine in spliceosomal remodelling processes.

Keywords

J-proteins S. cerevisiae K. lactis S. pombe Spliceosome Co-evolution RRM 

Notes

Acknowledgements

We would like to thank Prof. Elizabeth Craig (University of Wisconsin–Madison), and Prof. R.S. Tomar (Indian Institute of Science Education and Research, Bhopal) for yeast strains, plasmids, and antibodies. We thank C.S. lab members for critical comments. We thank the reviewers for their valuable suggestions which really helped in improving this manuscript. S.R. and A.K.V. thank the Indian Ministry of Human Resource Development for a Graduate Aptitude Test in Engineering fellowship; K.Y. and Y.T. thank Council of Scientific and Industrial Research, Government of India, for fellowship. This work was supported by project grants from the Department of Biotechnology (BT/PR12149/BRB/10/1348/2014), Government of India to C.S. We thank IISER Bhopal for intramural funds and the Central Instrumentation Facility.

Supplementary material

294_2018_906_MOESM1_ESM.tif (2 mb)
Supplementary Fig. S1 Kl-Cwc23 can completely substitute for Sc-Cwc23. (A) Equal volume of tenfold serial dilutions of cwc23Δ cells harbouring wild-type or mutants versions of Cwc23 (Sc-Cwc23, Sc-Cwc23-ΔC) or Kl-Cwc23 were spotted on drop-out media (Trp DO plates) and incubated at the indicated temperatures. (B-C) Growth of cwc23Δ cells harbouring wild-type or mutants versions of Cwc23 (Sc-Cwc23, Sc-Cwc23-ΔC) or Kl-Cwc23 was recorded in liquid drop-out media (Trp DO) at indicated temperatures for 24 h using an automated plate reader. The average cell density (OD600) of three independent isolates per genotype with error bar was plotted against different time points and the growth curve was obtained (TIF 2079 KB)
294_2018_906_MOESM2_ESM.tif (1.2 mb)
Supplementary Fig. S2 Inter and intra-species interaction between disassembly triad interologs. Cartoon representation of intra and inter-species interaction amongst the spliceosome disassembly triad. Lines with arrows depict positive interaction while blunt ends represent non-interactors (TIF 1227 KB)
294_2018_906_MOESM3_ESM.tif (3 mb)
Supplementary Fig. S3 Phylogenetic distribution of spliceosome disassembly factors across species. (A, B, C) Phylogenetic tree of Cwc23, Ntr1 and Prp43 orthologs from various eukaryotic species. The approximately-maximum-likelihood trees generated in FastTree with branch length values indicated for each branch. Orthologs from species belonging to different kingdoms are highlighted with different colours; Fungi (Blue), Plantae (Green) and Animalia (Pink) (TIF 3048 KB)
294_2018_906_MOESM4_ESM.docx (37 kb)
Supplementary material 4 (DOCX 37 KB)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • S. Raut
    • 1
  • K. Yadav
    • 1
  • A. K. Verma
    • 1
  • Y. Tak
    • 1
  • P. Waiker
    • 1
    • 2
  • C. Sahi
    • 1
    Email author
  1. 1.Chaperone and Stress Biology Lab, Department of Biological SciencesIndian Institute of Science Education and Research (IISER) BhopalBhopalIndia
  2. 2.Department of BiologyUniversity of North Carolina at GreensboroGreensboroUSA

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