Advertisement

Plant Molecular Biology

, Volume 96, Issue 6, pp 641–653 | Cite as

Tracking the elusive 5′ exonuclease activity of Chlamydomonas reinhardtii RNase J

  • Anna Liponska
  • Ailar Jamalli
  • Richard Kuras
  • Loreto Suay
  • Enrico Garbe
  • Francis-André Wollman
  • Soumaya Laalami
  • Harald Putzer
Article

Abstract

Key message

Chlamydomonas RNase J is the first member of this enzyme family that has endo- but no intrinsic 5′ exoribonucleolytic activity. This questions its proposed role in chloroplast mRNA maturation.

Abstract

RNA maturation and stability in the chloroplast are controlled by nuclear-encoded ribonucleases and RNA binding proteins. Notably, mRNA 5′ end maturation is thought to be achieved by the combined action of a 5′ exoribonuclease and specific pentatricopeptide repeat proteins (PPR) that block the progression of the nuclease. In Arabidopsis the 5′ exo- and endoribonuclease RNase J has been implicated in this process. Here, we verified the chloroplast localization of the orthologous Chlamydomonas (Cr) RNase J and studied its activity, both in vitro and in vivo in a heterologous B. subtilis system. Our data show that Cr RNase J has endo- but no significant intrinsic 5′ exonuclease activity that would be compatible with its proposed role in mRNA maturation. This is the first example of an RNase J ortholog that does not possess a 5′ exonuclease activity. A yeast two-hybrid screen revealed a number of potential interaction partners but three of the most promising candidates tested, failed to induce the latent exonuclease activity of Cr RNase J. We still favor the hypothesis that Cr RNase J plays an important role in RNA metabolism, but our findings suggest that it rather acts as an endoribonuclease in the chloroplast.

Keywords

RNase J Chlamydomonas reinhardtii Endoribonuclease Exoribonuclease RNA metabolism 

Notes

Acknowledgements

We thank Saravuth Ngo for efficient technical assistance. We are grateful to Jacqueline Plumbridge for useful discussions and critical reading of the manuscript. CNRS and University Paris Diderot, Sorbonne Paris Cité provided funding to the Research Unit UMR8261. A.L. received a doctoral fellowship from the “Initiative d’Excellence” program from the French State (Grant DYNAMO, ANR-11-LABX-0011) and the Edmond de Rothschild Foundations.

Author contributions

AL did the cloning, protein purification and in vitro and in vivo analysis of RNase J; AJ carried out cloning of certain RNase J variants and their in vitro tests; RK and LS did the chloroplast isolation and RNase J localization experiment; EG purified and tested potential RNase J partner proteins; FAW, SL and HP were involved in experimental design, data analysis and supervision of the project. HP wrote the manuscript with support from SL.

Supplementary material

11103_2018_720_MOESM1_ESM.pdf (755 kb)
Supplementary material 1 (PDF 754 KB)

References

  1. Barkan A (2011) Expression of plastid genes: organelle-specific elaborations on a prokaryotic scaffold. Plant Physiol 155:1520–1532CrossRefPubMedPubMedCentralGoogle Scholar
  2. Barkan A, Small I (2014) Pentatricopeptide repeat proteins in plants. Annu Rev Plant Biol 65:415–442CrossRefPubMedGoogle Scholar
  3. Callebaut I, Moshous D, Mornon JP, de Villartay JP (2002) Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family. Nucleic Acids Res 30:3592–3601CrossRefPubMedPubMedCentralGoogle Scholar
  4. Clouet-d’Orval B, Rinaldi D, Quentin Y, Carpousis AJ (2010) Euryarchaeal beta-CASP proteins with homology to bacterial RNase J Have 5′- to 3′-exoribonuclease activity. J Biol Chem 285:17574–17583CrossRefPubMedPubMedCentralGoogle Scholar
  5. Collins JA, Irnov I, Baker S, Winkler WC (2007) Mechanism of mRNA destabilization by the glmS ribozyme. Genes Dev 21:3356–3368CrossRefPubMedPubMedCentralGoogle Scholar
  6. Emanuelsson O, Nielsen H, von Heijne G (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8:978–984CrossRefPubMedPubMedCentralGoogle Scholar
  7. Even S, Pellegrini O, Zig L, Labas V, Vinh J, Brechemmier-Baey D, Putzer H (2005) Ribonucleases J1 and J2: two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Res 33:2141–2152CrossRefPubMedPubMedCentralGoogle Scholar
  8. Figaro S, Durand S, Gilet L, Cayet N, Sachse M, Condon C (2013) Knockouts of the genes encoding ribonucleases RNase Y and J1 are viable in B. subtilis, with major defects in cell morphology, sporulation and competence. J Bacteriol 195:2340–2348CrossRefPubMedPubMedCentralGoogle Scholar
  9. Harris E (1989) The Chlamydomonas sourcebook: a comprehensive guide to biology and laboratory use. Academic Press, San DiegoGoogle Scholar
  10. Hausmann S, Guimaraes VA, Garcin D, Baumann N, Linder P, Redder P (2017) Both exo- and endo-nucleolytic activities of RNase J1 from Staphylococcus aureus are manganese dependent and active on triphosphorylated 5′-ends. RNA Biol 14:1431–1443CrossRefPubMedPubMedCentralGoogle Scholar
  11. Jamalli A, Hebert A, Zig L, Putzer H (2014) Control of expression of the RNases J1 and J2 in Bacillus subtilis. J Bacteriol 196:318–324CrossRefPubMedPubMedCentralGoogle Scholar
  12. Kuras R, Wollman FA (1994) The assembly of cytochrome b6/f complexes: an approach using genetic transformation of the green alga Chlamydomonas reinhardtii. EMBO J 13:1019–1027PubMedPubMedCentralGoogle Scholar
  13. Laalami S, Zig L, Putzer H (2014) Initiation of mRNA decay in bacteria. Cell Mol Life Sci 71:1799–1828CrossRefPubMedGoogle Scholar
  14. Li dela, Sierra-Gallay I, Zig L, Jamalli A, Putzer H (2008) Structural insights into the dual activity of RNase. J Nat Struct Mol Biol 15:206–212CrossRefGoogle Scholar
  15. Loiselay C, Gumpel NJ, Girard-Bascou J, Watson AT, Purton S, Wollman FA, Choquet Y (2008) Molecular identification and function of cis- and trans-acting determinants for petA transcript stability in Chlamydomonas reinhardtii chloroplasts. Mol Cell Biol 28:5529–5542CrossRefPubMedPubMedCentralGoogle Scholar
  16. Luro S, Germain A, Sharwood RE, Stern DB (2013) RNase J participates in a pentatricopeptide repeat protein-mediated 5′ end maturation of chloroplast mRNAs. Nucleic Acids Res 41:9141–9151CrossRefPubMedPubMedCentralGoogle Scholar
  17. Mathy N, Benard L, Pellegrini O, Daou R, Wen T, Condon C (2007) 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129:681–692CrossRefPubMedGoogle Scholar
  18. Mathy N, Hebert A, Mervelet P, Benard L, Dorleans A, Li de la Sierra-Gallay I, Noirot P, Putzer H, Condon C (2010) Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol Microbiol 75:489–498CrossRefPubMedGoogle Scholar
  19. Mayford M, Weisblum B (1989) Conformational alterations in the ermC transcript in vivo during induction. Embo J 8:4307–4314PubMedPubMedCentralGoogle Scholar
  20. Nickelsen J, Kuck U (2000) The unicellular green alga Chlamydomonas reinhardtii as an experimental system to study chloroplast RNA metabolism. Naturwissenschaften 87:97–107CrossRefPubMedGoogle Scholar
  21. Rudner DZ, Breger KS, Rio DC (1998) Molecular genetic analysis of the heterodimeric splicing factor U2AF: the RS domain on either the large or small Drosophila subunit is dispensable in vivo. Genes Dev 12:1010–1021CrossRefPubMedPubMedCentralGoogle Scholar
  22. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  23. Shahbabian K, Jamalli A, Zig L, Putzer H (2009) RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J 28:3523–3533CrossRefPubMedPubMedCentralGoogle Scholar
  24. Sharwood RE, Halpert M, Luro S, Schuster G, Stern DB (2011) Chloroplast RNase J compensates for inefficient transcription termination by removal of antisense RNA. RNA 17:2165–2176CrossRefPubMedPubMedCentralGoogle Scholar
  25. Spizizen J (1958) Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc Natl Acad Sci USA 44:407–408CrossRefGoogle Scholar
  26. Stern DB, Goldschmidt-Clermont M, Hanson MR (2010) Chloroplast RNA metabolism. Annu Rev Plant Biol 61:125–155CrossRefPubMedGoogle Scholar
  27. Tardif M, Atteia A, Specht M, Cogne G, Rolland N, Brugiere S, Hippler M, Ferro M, Bruley C, Peltier G, Vallon O, Cournac L (2012) PredAlgo: a new subcellular localization prediction tool dedicated to green algae. Mol Biol Evol 29:3625–3639CrossRefPubMedGoogle Scholar
  28. Taverniti V, Forti F, Ghisotti D, Putzer H (2011) Mycobacterium smegmatis RNase J is a 5′-3′ exo-/endoribonuclease and both RNase J and RNase E are involved in ribosomal RNA maturation. Mol Microbiol 82:1260–1276CrossRefPubMedGoogle Scholar
  29. Uhart M, Bustos DM (2013) Human 14-3-3 paralogs differences uncovered by cross-talk of phosphorylation and lysine acetylation. PLoS ONE 8:e55703CrossRefPubMedPubMedCentralGoogle Scholar
  30. Zerges W, Rochaix JD (1998) Low density membranes are associated with RNA-binding proteins and thylakoids in the chloroplast of Chlamydomonas reinhardtii. J Cell Biol 140:101–110CrossRefPubMedPubMedCentralGoogle Scholar
  31. Zhao Y, Lu M, Zhang H, Hu J, Zhou C, Xu Q, Ul Hussain Shah AM, Xu H, Wang L, Hua Y (2015) Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J. Nucleic Acids Res 43:5550–5559CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Anna Liponska
    • 1
  • Ailar Jamalli
    • 1
    • 3
  • Richard Kuras
    • 2
  • Loreto Suay
    • 2
  • Enrico Garbe
    • 1
  • Francis-André Wollman
    • 2
  • Soumaya Laalami
    • 1
  • Harald Putzer
    • 1
  1. 1.CNRS UMR8261 - Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-ChimiqueParisFrance
  2. 2.CNRS UMR7141 (Associated with Université Pierre et Marie Curie), Institut de Biologie Physico-ChimiqueParisFrance
  3. 3.Laboratory Science Research CenterGolestan University of Medical SciencesGorganIran

Personalised recommendations