PONE-D-19-34496

A long noncoding RNA acts as a post-transcriptional regulator of heat shock protein 70 kDa synthesis in the cold hardy Diamesa tonsa under heat shock

PLOS ONE

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PLOS ONE

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1. Thank you for inlcuding your funding statement; "This work was partially supported by the Cassa di Risparmio di Trento e Rovereto Foundation within the RACE-TN Project (“Valutazione del rischio ambientale dei contaminanti emergenti nei fiumi trentini: effetti sulla vita selvatica e sull’uomo”/“Environmental Risk assessment of emerging contaminants in Trentino rivers: effects on wildlife and human health”, Grant CARITRO n. 2015.0199; October 2015-January 2018). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The funder supported 1 m/m of the contract of the first author (Paola Bernabò) and the purchase of some consumables."

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Reviewer #1: Yes

Reviewer #2: Partly

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: In this manuscript, the authors show how a stenothermal organism controls gene expression at the transcriptional, translational, and protein levels. They identify a novel pseudogene hsp70, encoding a putative lncRNA that exhibits a post-transcriptional control on HSP70 protein levels. The authors have carried out an extensive study to show that pseudogenes, indeed, are important regulators of gene regulation and should not be considered as junk DNA. In this context, the authors are requested to include this recent review in their references:

https://www.ncbi.nlm.nih.gov/pubmed/31848477

All the experiments have been carried out meticulously with the proper controls and statistical analysis. However, a couple of questions need to be addressed and a few minor changes.

1. I was wondering if the pseugodene encoded lncRNA can be knocked out using siRNA? If so, what effect would that have on the post-transcriptional control of HSP70? Have the authors tried checking this? Alternatively, they could try and include a couple of sentences in the discussion section.

2. The authors have looked at the gene expression in the polysome fractions. Have they looked at the protein expression of the hsp proteins in the polysome fractions?

3. Optional: Could the lncRNA be specifically localizing to the nucleolus especially since these are centers of ribosome production and since the authors show that Dt-Ps-hsp70 acts as a ribosome sponge to modulate the protein synthesis of HSP70. Maybe the authors could include a couple of sentences to discuss this, if possible.

Minor:

Title: Remove "kDa" and include the abbreviated form in brackets (e.e.g HSP70)

Page 5...Line 100...Replace "cox1" with "COX1"

Page 12...Line 274...Replace "long nc-RNAs" with "lncRNAs".

Page 16...Line 366...Is hsc70-x one of the cognate hsc genes or is it a typo?

Reviewer #2: In this manuscript the authors have proposed existence of a long noncoding RNA as post-transcriptional regulator of HSP 70 in Diamesa tonsa under heat shock. While authors provide compelling evidence of pseudo-hsp 70 modulating heat thermal stress response, more functional analysis is needed to prove the correlation. Have the authors tried genome editing tools to maybe try to silence the ps-hsp 70 and then examine its effect on hsp70? Or maybe even try to overexpress it.

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Reviewer #1: No

Reviewer #2: No

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A long noncoding RNA acts as a post-transcriptional regulator of heat shock protein (HSP70) synthesis in the cold hardy Diamesa tonsa under heat shock

PONE-D-19-34496R1

Dear Dr. Lencioni,

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,

Swati Palit Deb

Academic Editor

PLOS ONE

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