Adaptive transcription-splicing resynchronization upon losing an essential splicing factor

Abstract

Essential genes form the core of a genome and are therefore thought to be indispensable for cellular viability. However, recent findings have challenged this notion in that cells may survive in the absence of some essential genes provided that relevant genetic modifiers are in existence. We therefore hypothesized that the loss of an essential gene may not always be fatefully detrimental; instead, it may pave the way towards genome evolution. We experimentally tested this hypothesis in the context of pre-messenger RNA splicing by evolving yeast cells harbouring a permanent loss of the essential splicing factor Prp28 in the presence of a genetic modifier. Here, we show that cellular fitness can be restored by compensatory mutations that alter either the splicing machinery per se or the Spt–Ada–Gcn5 acetyltransferase transcription co-activator complex in the cells with no Prp28. Biochemical and genetic analysis revealed that slowing down transcription compensates for splicing deficiency, which in turn boosts cellular fitness. In addition, we found that inefficient splicing also conversely decreases nascent RNA production. Taken together, our data suggest that transcription-splicing synchronization contributes to robustness in the gene-expression pathway and argue that the intrinsic interconnectivity within a biological system can be exploited for compensatory evolution and system re-optimization.

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Fig. 1: Evolved cells improved fitness and splicing.
Fig. 2: Attenuation of transcription improves fitness and splicing efficiency in the ancestor.
Fig. 3: Four additional evolved lines restored splicing efficiency and decreased nascent RNA production.
Fig. 4: Ancestral reconstruction of the adaptive alleles.

Data availability

Genome sequencing and RNA-Seq data that support the findings of this study have been deposited in GenBank under BioProject identifier PRJNA431703.

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Acknowledgements

We thank S.-Y. Tung, Y.-N. Chen and S.-T. Yu for help with genome sequencing, C. Kaplan for the rpb1 strains, J.-Y. Leu for the Cas9 plasmids, C.-F. Kao for advice on nascent transcript analysis, and M. J. McDonald, J.-Y. Leu, M. Ares, M.-C. Yao and members of the Yao and Chang laboratories for commenting on the manuscript. S.-L.C. was supported by an Academia Sinica Postdoctoral Fellowship. T.-H.C. was supported by grants from the Ministry of Science and Technology (MOST 105-2627-M-001-002 and 105-2311-B-001-059), Academia Sinica and MOST (MOST 106-0210-01-15-02 and 107-0210-01-19-01), and the Academia Sinica Thematic Project (AS-103-TP-B12).

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S.-L.C. and T.-H.C. conceived the project. S.-L.C. designed and conducted the experiments. S.-L.C. and H.-K.W. conducted the bioinformatics analysis. S.-L.C., L.T. and T.-H.C. analysed the data. S.-L.C. and T.-H.C. wrote the paper.

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Correspondence to Tien-Hsien Chang.

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Chang, S., Wang, H., Tung, L. et al. Adaptive transcription-splicing resynchronization upon losing an essential splicing factor. Nat Ecol Evol 2, 1818–1823 (2018). https://doi.org/10.1038/s41559-018-0684-2

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