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Research article
Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage
Xin Li
Henan University of Science and Technology
Corresponding Author
ORCiD: https://orcid.org/0000-0002-5976-2988
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
Background: It was demonstrated in our previous research that trypsin scavenges superoxide anions. In this study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus.
Results: Trypsin significantly delayed the weight loss and decreased the levels of ROS and membrane lipid peroxidation. Transcriptome profiles of H. undatus treated with trypsin revealed the pathways and regulatory mechanisms of ROS genes that were up- or downregulated following trypsin treatment by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses. The current results showed that through the regulation of the expression of hub redox enzymes, especially thioredoxin-related proteins, trypsin can maintain low levels of endogenous active oxygen species, reduce malondialdehyde content and delay fruit aging. In addition, the results of protein-protein interaction networks suggested that the downregulated NAD(P)H and lignin pathways might be the key regulatory mechanisms governed by trypsin.
Conclusions: Trypsin significantly prolonged the storage life of H. undatus through regulatory on the endogenous ROS metabolism. As a new biopreservative, trypsin is highly efficient, safe and economical. Therefore, trypsin possesses technical feasibility for the quality control of fruit storage.
Keywords
GO; KEGG; Hylocereus undatus (H. undatus); Reactive oxygen species (ROS); Protein-protein interaction (PPI); Storage; Trypsin
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This is a list of supplementary files associated with this preprint. Click to download.
- TableS4KEGGEvalue1e4.xlsx
- TableS1Totalnumofdatabases.xlsx
- TableS3COG.xlsx
- TableS6VennVennofROSgenes.xlsx
- TableS7ROS85GOenrichment.xlsx
- TableS8FulllistofROSrelatinggenes.xlsx
- TableS2Commonunigenesinpublicdatabases.xlsx
- TableS9PPIROS11172000edgesignificbycytoscape.xlsx
- TableS5Volcano1703.xlsx
- TableS12ClustersofROS1117byMCODE.xlsx
- TableS13RankHubs.xlsx
- TableS14Hubs.xlsx
- TableS10PPIROS1117up2000edgebycytoscape.xlsx
- TableS15Annotationofhubnodes.xlsx
- TableS16Informationofhubgenes.xlsx
- TableS11PPIROS1117down2000edgebycytoscape.xlsx
- Graphicfortableofcontents.tif
- Fig.S13map04016.jpg
- Fig.S12map00940.jpg
- Supplementaryfigures111.docx
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CURRENT STATUS: Published
Version 3
Posted 19 Jun, 2020
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Editorial decision: Minor revision
On 16 Jun, 2020
Review #2 received
Received 12 Jun, 2020
Review #1 received
Received 09 Jun, 2020
Reviewer #2 agreed
On 02 Jun, 2020
Editor assigned
On 01 Jun, 2020
Reviewers invited
Invitations sent on 01 Jun, 2020
Reviewer #1 agreed
On 01 Jun, 2020
Submission checks complete
On 31 May, 2020
Editor invited
On 31 May, 2020
No comments provided
Editorial decision: Major revision
On 26 May, 2020
Review #2 received
Received 12 May, 2020
Reviewer #2 agreed
On 01 May, 2020
Review #1 received
Received 14 Feb, 2020
Reviewers invited
Invitations sent on 01 Oct, 2019
Reviewer #1 agreed
On 01 Oct, 2019
Submission checks complete
On 02 Sep, 2019
Editor invited
On 02 Sep, 2019
Editor assigned
On 27 Aug, 2019
First submitted
On 24 Aug, 2019
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PDF Downloads: ...
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Subject Areas
Epigenetics & Genomics
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage
Xin Li
Henan University of Science and Technology
Corresponding Author
ORCiD: https://orcid.org/0000-0002-5976-2988
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 3
Posted 19 Jun, 2020
No comments provided
Editorial decision: Minor revision
On 16 Jun, 2020
Review #2 received
Received 12 Jun, 2020
Review #1 received
Received 09 Jun, 2020
Reviewer #2 agreed
On 02 Jun, 2020
Editor assigned
On 01 Jun, 2020
Reviewers invited
Invitations sent on 01 Jun, 2020
Reviewer #1 agreed
On 01 Jun, 2020
Submission checks complete
On 31 May, 2020
Editor invited
On 31 May, 2020
No comments provided
Editorial decision: Major revision
On 26 May, 2020
Review #2 received
Received 12 May, 2020
Reviewer #2 agreed
On 01 May, 2020
Review #1 received
Received 14 Feb, 2020
Reviewers invited
Invitations sent on 01 Oct, 2019
Reviewer #1 agreed
On 01 Oct, 2019
Submission checks complete
On 02 Sep, 2019
Editor invited
On 02 Sep, 2019
Editor assigned
On 27 Aug, 2019
First submitted
On 24 Aug, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
Background: It was demonstrated in our previous research that trypsin scavenges superoxide anions. In this study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus.
Results: Trypsin significantly delayed the weight loss and decreased the levels of ROS and membrane lipid peroxidation. Transcriptome profiles of H. undatus treated with trypsin revealed the pathways and regulatory mechanisms of ROS genes that were up- or downregulated following trypsin treatment by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses. The current results showed that through the regulation of the expression of hub redox enzymes, especially thioredoxin-related proteins, trypsin can maintain low levels of endogenous active oxygen species, reduce malondialdehyde content and delay fruit aging. In addition, the results of protein-protein interaction networks suggested that the downregulated NAD(P)H and lignin pathways might be the key regulatory mechanisms governed by trypsin.
Conclusions: Trypsin significantly prolonged the storage life of H. undatus through regulatory on the endogenous ROS metabolism. As a new biopreservative, trypsin is highly efficient, safe and economical. Therefore, trypsin possesses technical feasibility for the quality control of fruit storage.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6