Mitotic checkpoint gene expression is tuned by codon usage bias

Abstract

The mitotic checkpoint (also called spindle assembly checkpoint, SAC) is a signaling pathway that safeguards proper chromosome segregation. Correct functioning of the SAC depends on adequate protein concentrations and appropriate stoichiometries between SAC proteins. Yet very little is known about the regulation of SAC gene expression. Here, we show in the fission yeast Schizosaccharomyces pombe that a combination of short mRNA half-lives and long protein half-lives supports stable SAC protein levels. For the SAC genes mad2 + and mad3 + , their short mRNA half-lives are caused, in part, by a high frequency of nonoptimal codons. In contrast, mad1 + mRNA has a short half-life despite a higher frequency of optimal codons, and despite the lack of known RNAdestabilizing motifs. Hence, different SAC genes employ different strategies of expression. We further show that Mad1 homodimers form co-translationally, which may necessitate a certain codon usage pattern. Taken together, we propose that the codon usage of SAC genes is fine-tuned to ensure proper SAC function. Our work shines light on gene expression features that promote spindle assembly checkpoint function and suggests that synonymous mutations may weaken the checkpoint.

Size-Dependent Expression of the Fission Yeast Cdc13 Cyclin is Conferred by Translational Regulation

“…We did so by blocking their synthesis, with cycloheximide or thiolutin, respectively, and assaying their levels over time to infer their decay rates (Figures 1B, C). The half life of Cdc13 is about 30 minutes, consistent with previous reports (Christiano et al, 2014; Esposito et al, 2022), and it does not change much with cell size (Figure 1C). The difference between cells averaging 10.7±0.3 µm in length and those averaging 21.2±1.3 µm is only 28% (Figure 1C).…”

The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian

“…The Mad1 and Mad2 proteins form an extremely tight 2:2 complex ( 53, 54 ). The Mad1 dimer at the core of this complex assembles co-translationally ( 45, 121 ). We consider it possible that the binding of Mad2 to the Mad1 dimer also needs to be co-translational.…”

“…SAC genes mad1 , mad2 , mad3 , and bub1 were tagged with ymEGFP at the endogenous locus without inserting any other exogenous sequences ( 45 ). This was accomplished either by replacement of the counter-selectable rpl42-hphNT1 cassette in an rpl42::cyh R (sP56Q) strain ( 122 ) or by using CRISPR-mediated targeting ( 123 ).…”

“…We used rad21, which is a cell cycle-regulated gene whose Fano factor can increase to around 12 during expression late in the cell cycle (Fig. 5B; S6A,B) [72][73][74] , and nmt1, 9 which is a thiamine-responsive, highly variable gene 12,45 . When expressing rad21 and nmt1 from the mad2 and mad3 promoter, the cell cycle-regulation of rad21 disappeared (Fig.…”

“…To shed additional light on low-noise gene expression, we have investigated a group of constitutively expressed S. pombe genes, that are important for cell division and show low mRNA and protein noise ( 44, 45 ). The protein products of these genes contribute to the spindle assembly checkpoint (SAC, also known as mitotic checkpoint).…”