The APC/C Activator Cdh1p Plays a Role in Mitochondrial Metabolic Remodelling in Yeast

Round 1

Reviewer 1 Report

In the manuscript "The APC/C activator Cdh1p plays a role in mitochondrial metabolic remodelling in yeast" the authors report the role of the cell-cycle related protein Cdh1 in regulating the expression of the mitochondrial proteins. The authors demonstrate that Cdh1 remodel the mitochondrial proteome by acting on transcription factors. Although they provide evidence of the role of two transcription factors, Yap1 and Rpn4, they do not demonstrate the molecular mechanism linking Cdh1 to their activity.

The manuscript is valid, interesting and well-written but a few points need to be addressed.

• The link between ROS increase in Cdh1D and Yap1 activation should be investigated in more detail and clarified. Is Yap1 activated if cells are treated with antioxidants or if antioxidant enzymes are more expressed? In general the proposed interplay between Cdh1, ROS and Yap1 is not clear. Do the authors propose that Yap1 is the transcription factor triggering the mitochondrial proteome remodelling and the resulting increase in respiration determines an increase in ROS production or do they think that Yap1 expression is triggered by the increase in ROS production determined by the increase in respiration? Is it possible for example, that Yap1 expression is triggered by ROS and thus it determines an increase in mitochondrial activity by protecting them rather than triggering the increase in respiration?
• Important. The authors discuss very briefly what would be the physiological role of Cdh1 in regulating mitochondrial activity. Is there any hypothesis about the physiological role of Chd1 (of course for what concerns the regulation of mitochondrial activity)? Is there enough time for mitochondrial protein remodelling during cell cycle? In which conditions is CDH1 more expressed or when is the encoded protein more active? Experiments performed over-expressing CDH1 would have been helpful in this regard.
• The increase in protein abundance of Log2(FC)=0.3 means a FC=1.2 which is a quite low cut-off.
• The NAO experiment suggests that in addition to a remodelling also the mitochondrial mass was increased. The authors should develop this point. Does Cdh1 deletion triggers more a remodelling or an increase of mitochondrial mass?
• Figure 3 A and related text: looking at the numbers there is not a significant difference between the transcription factor predicted binding sites in the up-regulated and down-regulated proteins. All of them seem almost always found in the promoters of the affected genes. The authors should reinforce their findings demonstrating that this is not the case of other, possibly mitochondrial-related, transcription factors or by looking at the promoters of the genes encoding proteins not affected by CDH1 deletion.
• Important. The effect of Cdh1 on Dnm1 was surprisingly neglected by the authors. What about the mitochondrial network morphology in cdh1D? This point should be investigated in more detail.

MINOR POINTS

• INTRODUCTION: “cdh1Δ cells exhibit a prolonged cell cycle and are sensitive to different types of stress…”. Which kind of stress? This is important considering the data provided about the increase in oxidative stress
• Icl2 is not strictly involved in lipid metabolism but in the methyl-citrate pathway
• I am not familiar with AUC used to assess yeast growth. Why not using the measurement of the growth rate and biomass accumulated at the stationary phase? What is the advantage of using AUC?
• “…9Myc protein was expressed from a vector under the regulation of its native promoter…”; is this a low-copy vector?
• Please explain in more detail why cdh1D cells should be more sensitive to MMS

 

 

 

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

Dear Authors!

Mu comments are in attached file.

Comments for author File: Comments.pdf

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

The authors have addressed my concerns

Reviewer 2 Report

Dear Authors!

I thank you for your work on the revision of the manuscript. All my comments have been clarified. From the editorial recommendations - the captions for figures 6 and 7 are not in place.