PONE-D-19-29130

Target Of Rapamycin pathway in the white-rot fungus Phanerochaete chrysosporium

PLOS ONE

Dear Dr sormani,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

We were able to secure only one review. Accordingly, the decision is based on that reviewer's comments and my own reading of the manuscript. I generally concur with the reviewer's points, particularly the clarity of the proteomic methods and analysis.  Please consider revising these sections and, in addition to the reviewer's suggestions, clearly describe the experimental details. For example, precisely how many replicates were processed? I understand that the data may not lend itself for quantitative (statistical) analyses, but an explanation of the scoring (Table 2S) would be helpful to many readers. Consider footnotes to the supplemental table. 

In addition to the reviewer, please also consider these minor suggestions:

Line 54. Replace with ref #17

Line 150. This is confusing.  What "rap mutants"?

Line 168. "fumigate"?

Line 227. Consider colored highlighting of AGR57_3808 in table S2.

Line 334. Consider "more closely related to"

Line 354. Consider "S. pombe relative to S. cerevisiae"

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Daniel Cullen

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

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Reviewer #1: No

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Reviewer #1: Yes

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5. Review Comments to the Author

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Reviewer #1: In this manuscript the authors investigate the conservation of the TOR signaling network in the white-rot fungus Phanerochaete chrysosporium. They observe that rapamycin blocks conidia germination and hyphal growth. They also provide preliminary data to suggest that the composition of proteins secreted by this organism is altered by carbon source and rapamycin.

Main concern:

The proteomics experiments are not well described. How quantitative are these results? What is the FDR rate? Said another way, how can one be sure that proteins observed in one condition are really only present in that condition? This point needs to be readdressed prior to acceptance.

Specific comments

i) line 183: Is the exponential phase really 30.9 hours? There seems to be a shift at about 25hrs. How is exponential phase defined?

ii) Paragraph starting on line 211: Until line 217, I do not see how the specific numbers cited correspond to the Venn diagram in Figure 2E. Shouldn’t a main point here be that 16 proteins are secreted only in the presence of rapamycin and/or 17 are secreted only in the absence of rapamycin?

iii) Why does Table S2 list sucrose as the carbon source?

iv) Line 221 ACR57 should be AGR57

v) Paragraph starting on line 284 – a more current review of TORC2 functions can be found here: https://doi.org/10.3390/biom7030066

vi) Reference 16 is now outdated.

Use this for ortholog searches

https://www.cell.com/cell-metabolism/pdfExtended/S1550-4131(17)30422-9

From line 292 on the paragraph needs to be rewritten for comprehensibility. Note that Tco89 and Bit61 orthologs exist in S. pombe; Ego1 and Ego3 are conserved in metazoans but are difficult to detect in sequence searches.

What about orthologs of SEACIT, SEACAT, Lst4/7? Tip41, Ypk1 and Ypk3?

vii) Legend for figure 3 is not clearly written. Line 495 does not accurately describe figure which has structures from other organisms. Line 502 – where are W89 and F96 in the figure? Why are the red numbers in 3D so discordant with the red numbers in E and F? The species origins for each protein domain should be labelled directly in the figure.

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Reviewer #1: No

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Target Of Rapamycin pathway in the white-rot fungus Phanerochaete chrysosporium

PONE-D-19-29130R1

Dear Dr. sormani,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

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With kind regards,

Daniel Cullen

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: