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Transcriptional profiling analysis of individual kinase-deletion strains of fission yeast in response to nitrogen starvation

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Abstract

Nitrogen starvation (NS) induces sexual development when mating partners are available or enter into quiescent state (G0) in heterothallic background in fission yeast. However, little is known whether the two processes share common signaling molecules or cells defective in the two processes share common transcriptional signatures. To address these questions, we first assessed 77 kinase-deletion strains for NS-induced G0-arrest phenotypes. Our result indicated that 10 out of 77 kinase-deletion strains exhibited defect in G0-arrest, only 3 of which were defective in sexual development based on a previous study, suggesting that the two processes hardly share common signaling components. We subsequently performed transcriptional profiling analysis. Our result indicated that NS-induced transcriptional change was so robust that it prevailed the alteration by individual kinase-deletion alleles. Based on comparison between kinase-deletion strains proficient and deficient in sexual development or G0-arrest, we identified subsets of genes that were associated with sexual development-deficient or G0-arrest-deficient kinase-deletion strains. Multiple pairing analyses allowed grouping of functional related kinases. Furthermore, we showed that Pka1-mediated pathways were required for upregulation of NS-induced genes upon NS and downregulation of the same set of genes under the N-replete conditions. Taken together, our analyses indicate that sexual development and NS-induced G0-arrest are unrelated; and sexual development-deficient and G0-arrest-deficient kinase-deletion strains possess distinct transcriptional signatures. We propose that Pka1 is a key regulator of nitrogen metabolic pathways and Pka1-mediated signaling pathways play roles in regulation of NS-induced genes under both N-depleted and N-replete conditions.

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Abbreviations

NS:

Nitrogen starvation

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Acknowledgments

The authors would like to thank X. Peng and R. Krishnan for manufacturing the S. pombe 50-mer oligonucleotide-based DNA microarrays and L. Zhu and R. K. M. Karuturi for assistance in bioinformatics analysis. This work is initiated in GIS, Singapore and completed in the Zhejiang University, Zhejiang, China.

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Author notes

  1. Yonghui Jia

    Present address: Brigham and Women’s Hospital, Boston, MA, 02115, USA

  2. Juntao Li

    Present address: SingHealth Translational Immunology and Inflammation Centre, Singapore, Singapore

Authors and Affiliations

  1. Ocean Research Centre of Zhoushan, Zhejiang University, 10 Tiyu Road, Room 502, Zhoushan, 310058, ZJ, China

    Jianhua Liu

  2. Collaborative Innovation Center of Deep Sea Biology, Ocean College, Zhejiang University, Hangzhou, 310058, ZJ, China

    Jianhua Liu

  3. Genome Institute of Singapore, Singapore, 138672, Singapore

    Yonghui Jia & Juntao Li

  4. Shanghai Chenshan Plant Science Research Center, SIBS, CAS, Shanghai Chenshan Botanic Garden, Songjiang, 201602, SH, China

    Zhaoqing Chu

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  1. Jianhua Liu
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  2. Yonghui Jia
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Correspondence to Jianhua Liu or Zhaoqing Chu.

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Communicated by T. Ito.

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Liu, J., Jia, Y., Li, J. et al. Transcriptional profiling analysis of individual kinase-deletion strains of fission yeast in response to nitrogen starvation. Mol Genet Genomics 290, 1067–1083 (2015). https://doi.org/10.1007/s00438-014-0966-6

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  • DOI: https://doi.org/10.1007/s00438-014-0966-6

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