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Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3′-UTR

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Abstract

Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3′-untranslated region (3′-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3′-UTR of rice genes. Of 249 genes that conserved the consensus in their 3′-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication protein A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3′-UTRs to achieve the faithful transition of germ cells to meiosis.

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Abbreviations

3′-UTR:

3′-untranslated region

CAF1:

CCR4 associated factor 1

DAZ:

Deleted in azospermia

DAZAP1:

DAZ-associated protein1

DMC1:

DNA meiotic recombinase 1

DSBs:

Double strand breaks

eIF:

Elongation initiation factors

EMSA:

Electrophoresis mobility shift assay

Hsp90:

Heat shock protein 90

HuR:

Hu antigen R

MEL2:

MEIOSIS ARRESTED AT LEPTOTENE2

PABP:

Poly(A) binding protein

PMT:

Photomultiplier

Prrp:

Proline-rich protein

RPA1a:

Replication protein A 1a

RRM:

RNA recognition motif

SCF complex:

SKP1-cullin-F-box protein complex

SDS:

Solo dancers

SELEX:

Systematic evolution of ligands by exponential enrichment

YB-1:

Y-box-binding protein 1

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Acknowledgments

We thank M. Nakano, N. Furuya, M. Eiguchi, Y. Tamaki, M. Mochizuki and S. Saeki for help with experimental work and growing plants. We also appreciate the valuable discussions with Dr. T. Nishino (NIG, SOKENDAI) and Dr. Y. Ninomiya (NIG) for protein and statistics works. This work was supported by Japan Society for the Promotion of Science (JSPS), KAKENHI (Grants-in-Aid for Scientific Research) Nos. 21678001, 24770048 and 25252004, and by JSPS Bilateral Program.

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Author notes

  1. Saori Miyazaki

    Present address: Office for the Promotion of Global Education Programs, Shizuoka University, Jyouhoku, Nakaku, Hamamatsu, Shizuoka, 432-8561, Japan

  2. Tomoya Asano

    Present address: Wakasa Seikatsu Co. Ltd, 22 Naginataboko-cho, Shijo-Karasuma, Shimogyo-ku, Kyoto, 600-8008, Japan

Authors and Affiliations

  1. Experimental Farm, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan

    Saori Miyazaki & Ken-Ichi Nonomura

  2. Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan

    Saori Miyazaki & Ken-Ichi Nonomura

  3. Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan

    Yutaka Sato & Yoshiaki Nagamura

  4. Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Takaramachi, Kanazawa, 920-0934, Japan

    Tomoya Asano

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  1. Saori Miyazaki
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Correspondence to Saori Miyazaki or Ken-Ichi Nonomura.

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Authors’ contributions

SM and KN designed experiments and wrote the manuscript. SM and TA performed experiments. SM, YS and AT analyzed data. YN supervised the gene expression data analyses. All authors read and approved the final manuscript.

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Miyazaki, S., Sato, Y., Asano, T. et al. Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3′-UTR. Plant Mol Biol 89, 293–307 (2015). https://doi.org/10.1007/s11103-015-0369-z

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