Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage

Abstract 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.

Download Full-text

Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage

10.21203/rs.2.14059/v2 ◽

2020 ◽

Author(s):

Xin Li ◽

Liu Xueru ◽

Pang Xinyue ◽

Yin Yong ◽

Yu Huichun ◽

...

Keyword(s):

Active Oxygen Species ◽

Membrane Lipid ◽

Regulatory Mechanisms ◽

Trypsin Treatment ◽

Fruit Storage ◽

Protein Protein Interaction ◽

Ros Metabolism ◽

Malondialdehyde Content ◽

Hylocereus Undatus ◽

Related Proteins

Abstract 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.

Download Full-text

Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage

BMC Genomics ◽

10.1186/s12864-020-06850-1 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Xin Li ◽

Xueru Liu ◽

Xinyue Pang ◽

Yong Yin ◽

Huichun Yu ◽

...

Keyword(s):

Transcriptomic Analysis ◽

Trypsin Treatment ◽

Hub Genes ◽

Ros Metabolism ◽

Hylocereus Undatus ◽

Superoxide Scavenger

Download Full-text

Chance, contingency, and necessity in the experimental evolution of ancestral proteins

10.1101/2020.08.29.273581 ◽

2020 ◽

Author(s):

Victoria Cochran Xie ◽

Jinyue Pu ◽

Brian P.H. Metzger ◽

Joseph W. Thornton ◽

Bryan C. Dickinson

Keyword(s):

Protein Evolution ◽

Experimental Evolution ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Sequence Evolution ◽

Protein Protein Interaction ◽

Evolutionary Trajectories ◽

Historical Moment ◽

Related Proteins ◽

Ancestral Protein

SUMMARYThe extent to which chance and contingency shaped the sequence outcomes of protein evolution is largely unknown. To directly characterize the causes and consequences of chance and contingency, we combined directed evolution with ancestral protein reconstruction. By repeatedly selecting a phylogenetic series of ancestral proteins in the B-cell lymphoma-2 family to evolve the same protein-protein interaction specificities that existed during history, we show that contingency and chance interact to make sequence evolution almost entirely unpredictable over the timescale of metazoan evolution. At any historical moment, multiple sets of mutations can alter or maintain specificity, and chance decides which ones occur. Contingency arises because historical sequence substitutions epistatically altered which mutations are compatible with new or ancestral functions. Evolutionary trajectories launched from different ancestors therefore lead to dramatically different outcomes over phylogenetic time, with virtually no mutations occurring repeatedly in distantly related proteins, even under identical selection conditions.

Download Full-text

PPInfer: a Bioconductor package for inferring functionally related proteins using protein interaction networks

F1000Research ◽

10.12688/f1000research.12947.1 ◽

2017 ◽

Vol 6 ◽

pp. 1969

Author(s):

Dongmin Jung ◽

Xijin Ge

Keyword(s):

Protein Interaction ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Biological Processes ◽

Bioconductor Package ◽

Biological Functions ◽

Ppi Network ◽

Protein Protein Interaction ◽

Ppi Networks ◽

Related Proteins

Interactions between proteins occur in many, if not most, biological processes. This fact has motivated the development of a variety of experimental methods for the identification of protein-protein interaction (PPI) networks. Leveraging PPI data available STRING database, we use network-based statistical learning methods to infer the putative functions of proteins from the known functions of neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions. The package is freely available at the Bioconductor web site (http://bioconductor.org/packages/PPInfer/).

Download Full-text

PPInfer: a Bioconductor package for inferring functionally related proteins using protein interaction networks

F1000Research ◽

10.12688/f1000research.12947.3 ◽

2018 ◽

Vol 6 ◽

pp. 1969 ◽

Cited By ~ 3

Author(s):

Dongmin Jung ◽

Xijin Ge

Keyword(s):

Protein Interaction ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Biological Processes ◽

Bioconductor Package ◽

Biological Functions ◽

Ppi Network ◽

Protein Protein Interaction ◽

Ppi Networks ◽

Related Proteins

Interactions between proteins occur in many, if not most, biological processes. This fact has motivated the development of a variety of experimental methods for the identification of protein-protein interaction (PPI) networks. Leveraging PPI data available in the STRING database, we use a network-based statistical learning methods to infer the putative functions of proteins from the known functions of neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions. The package is freely available at the Bioconductor web site (http://bioconductor.org/packages/PPInfer/).

Download Full-text

A network-based approach reveals novel invasion and Maurer's clefts-related proteins in Plasmodium falciparum

Molecular Omics ◽

10.1039/c9mo00124g ◽

2019 ◽

Vol 15 (6) ◽

pp. 431-441 ◽

Cited By ~ 1

Author(s):

Dibyajyoti Das ◽

Sowmya Ramaswamy Krishnan ◽

Arijit Roy ◽

Gopalakrishnan Bulusu

Keyword(s):

Plasmodium Falciparum ◽

Protein Interaction ◽

Protein Interaction Network ◽

Interaction Network ◽

Disease Pathogenesis ◽

Protein Protein Interaction ◽

Novel Proteins ◽

Maurer's Clefts ◽

Related Proteins ◽

Protein Protein Interaction Network

To understand disease pathogenesis, all the disease-related proteins must be identified. In this work, known proteins were used to identify related novel proteins using RWR method on a dynamic P. falciparum protein–protein interaction network.

Download Full-text

A three-gene signature from protein-protein interaction network of LOXL2 - and actin-related proteins for esophageal squamous cell carcinoma prognosis

Cancer Medicine ◽

10.1002/cam4.1096 ◽

2017 ◽

Vol 6 (7) ◽

pp. 1707-1719 ◽

Cited By ~ 10

Author(s):

Xiu-hui Zhan ◽

Ji-wei Jiao ◽

Hai-feng Zhang ◽

Chun-quan Li ◽

Jian-mei Zhao ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Protein Interaction ◽

Protein Interaction Network ◽

Interaction Network ◽

Gene Signature ◽

Protein Protein Interaction ◽

Related Proteins ◽

Protein Protein Interaction Network

Download Full-text

The regulation of the cardiac potassium channel (HERG) by caveolin-1

Biochemistry and Cell Biology ◽

10.1139/o08-118 ◽

2008 ◽

Vol 86 (5) ◽

pp. 405-415 ◽

Cited By ~ 18

Author(s):

Jijin Lin ◽

Shuguang Lin ◽

Patrick C. Choy ◽

Xiuzhang Shen ◽

Chunyu Deng ◽

...

Keyword(s):

Protein Interaction ◽

Membrane Lipid ◽

Current Amplitude ◽

Cellular Proteins ◽

Herg Channel ◽

Caveolin 1 ◽

Tail Current ◽

Protein Protein Interaction ◽

Herg Current ◽

Herg Channels

Protein–protein interaction plays a key role in the regulation of biological processes. The human potassium (HERG) channel is encoded by the ether-à-go-go-related gene (herg), and its activity may be regulated by association with other cellular proteins. To identify cellular proteins that might play a role in the regulation of the HERG channel, we screened a human heart cDNA library with the N terminus of HERG using a yeast 2-hybrid system, and identified caveolin-1 as a potential HERG partner. The interaction between these 2 proteins was confirmed by coimmunoprecipitation assay, and their overlapping subcellular localization was demonstrated by fluorescence immunocytochemistry. The physiologic implication of the protein–protein interaction was studied in whole-cell patch-clamp electrophysiology experiments. A significant increase in HERG current amplitude and a faster deactivation of tail current were observed in HEK293/HERG cells in a membrane lipid rafts disruption model and caveolin-1 knocked down cells by RNA interference. Alternatively, when caveolin-1 was overexpressed, the HERG current amplitude was significantly reduced and the tail current was deactivated more slowly. Taken together, these data indicate that HERG channels interact with caveolin-1 and are negatively regulated by this interaction. The finding from this study clearly demonstrates the regulatory role of caveolin-1 on HERG channels, and may help to understand biochemical events leading to arrhythmogenesis in the long QT syndrome in cardiac patients.

Download Full-text

Functional Segments on Intrinsically Disordered Regions in Disease-Related Proteins

Biomolecules ◽

10.3390/biom9030088 ◽

2019 ◽

Vol 9 (3) ◽

pp. 88 ◽

Cited By ~ 6

Author(s):

Hiroto Anbo ◽

Masaya Sato ◽

Atsushi Okoshi ◽

Satoshi Fukuchi

Keyword(s):

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Protein Protein Interaction ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Protein Protein Interaction Networks ◽

Digestive System Diseases ◽

To Come ◽

Related Proteins ◽

Disordered Regions

One of the unique characteristics of intrinsically disordered proteins (IPDs) is the existence of functional segments in intrinsically disordered regions (IDRs). A typical function of these segments is binding to partner molecules, such as proteins and DNAs. These segments play important roles in signaling pathways and transcriptional regulation. We conducted bioinformatics analysis to search these functional segments based on IDR predictions and database annotations. We found more than a thousand potential functional IDR segments in disease-related proteins. Large fractions of proteins related to cancers, congenital disorders, digestive system diseases, and reproductive system diseases have these functional IDRs. Some proteins in nervous system diseases have long functional segments in IDRs. The detailed analysis of some of these regions showed that the functional segments are located on experimentally verified IDRs. The proteins with functional IDR segments generally tend to come and go between the cytoplasm and the nucleus. Proteins involved in multiple diseases tend to have more protein-protein interactors, suggesting that hub proteins in the protein-protein interaction networks can have multiple impacts on human diseases.

Download Full-text