Integrated proteome and transcriptome analyses revealed key factors involved in tomato (<i>Solanum lycopersicum</i>) under high temperature stress

Ding, Haidong; Mo, Shuangrong; Qian, Ying; Yuan, Guibo; Wu, Xiaoxia; Ge, Cailin

doi:10.1002/fes3.239

Cited by 37 publications

(24 citation statements)

References 62 publications

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“…Thus, the transcriptome and proteome data used in the present analyses were obtained from different sets of patients. Although, the number of co‐differentially expressed genes/proteins identified in the present study were higher as compared to those reported in previous studies ( 51 – 53 ). We select the DEPs based on P and Log2FC values ( 27 , 28 ).…”

Section: Discussioncontrasting

confidence: 87%

“…Since the present study utilized publicly available transcriptomics databases and proteomics results from the current assessment, this 122 co-differentially expressed genes/proteins might be considered as representative of altered biological processes. In previous studies using transcriptomics and proteomics data, obtained from the same sample for both techniques, reported co‐differential expression of genes/proteins in the range of 31–149 ( 51 – 53 ).…”

Section: Discussionmentioning

confidence: 99%

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Combined Transcriptome and Proteome Leukocyte’s Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis

et al. 2021

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Sepsis is a global health emergency, which is caused by various sources of infection that lead to changes in gene expression, protein-coding, and metabolism. Advancements in “omics” technologies have provided valuable tools to unravel the mechanisms involved in the pathogenesis of this disease. In this study, we performed shotgun mass spectrometry in peripheral blood mononuclear cells (PBMC) from septic patients (N=24) and healthy controls (N=9) and combined these results with two public microarray leukocytes datasets. Through combination of transcriptome and proteome profiling, we identified 170 co‐differentially expressed genes/proteins. Among these, 122 genes/proteins displayed the same expression trend. Ingenuity Pathway Analysis revealed pathways related to lymphocyte functions with decreased status, and defense processes that were predicted to be strongly increased. Protein-protein interaction network analyses revealed two densely connected regions, which mainly included down‐regulated genes/proteins that were related to the transcription of RNA, translation of proteins, and mitochondrial translation. Additionally, we identified one module comprising of up‐regulated genes/proteins, which were mainly related to low-density neutrophils (LDNs). LDNs were reported in sepsis and in COVID-19. Changes in gene expression level were validated using quantitative real-time PCR in PBMCs from patients with sepsis. To further support that the source of the upregulated module of genes/proteins found in our results were derived from LDNs, we identified an increase of this population by flow cytometry in PBMC samples obtained from the same cohort of septic patients included in the proteomic analysis. This study provides new insights into a reprioritization of biological functions in response to sepsis that involved a transcriptional and translational shutdown of genes/proteins, with exception of a set of genes/proteins related to LDNs and host‐defense system.

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Section: Discussioncontrasting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Combined Transcriptome and Proteome Leukocyte’s Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis

et al. 2021

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“…In contrast, other genes maintained upregulation patterns for protein processing in ER and ubiquitination ( Derlin , Sec 61 , OS9 , Ubx , p97 , Ufd1 , UbcH5 , HRD1 , SAR1 ) in V. darrowii at 6-h stress, and a few specific genes showed upregulation ( Ubx , Ufd1 , and Sec23/24 , cull ) and downregulation ( eLF2 ) patterns at 9-h stress. Previous studies reported DEGs involved in protein processing in ER such as protein homeostasis (sHSF), luminal chaperon ( NEF, GRP94 ), chaperon binding protein (BiP), protein folding machinery ( CRT , CNX , PDIs , UGGT , HSPs), protein translocation ( Sec 61, 23/24), and ubiquitination ( Derlin , OS9 , Ubx , p97, Ufd1 , UbcH5 , HRD1 , SAR1 ) and other mechanisms involved in the heat stress response in plants [ 33 , 34 , 35 , 36 , 37 ]. The differential expression patterns of protein processing genes in ER suggest a prevalence in differential response and possible protein homeostasis and repair mechanisms under heat stress in blueberry species.…”

Section: Resultsmentioning

confidence: 99%

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

Callwood

Melmaiee

Kulkarni

et al. 2021

IJMS

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Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, andhelp in understanding the complex mechanisms involved in heat stress tolerance.

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“…The extraction of biologically meaningful patterns using data integration is now emerging as one of the most evolving fields in modern data science but there are very few such studies for plants ( Ding et al, 2020 ; Zhang et al, 2020 ). This work began with an aim to identify and investigate the plant prionome in order to explore a general role in memory based on the previous but limited reports of PrLPs having a role in flowering and plant memory.…”

Section: Discussionmentioning

confidence: 99%

Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants

et al. 2021

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Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant stress and memory remains unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive meta-analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species and term the full complement of PrLPs in a genome as its “prionome.” In particular, we found the rice prionome being significantly enriched in transposons/retrotransposons (Ts/RTRs) and identified over 60 rice PrLPs that were differentially regulated in stress and developmental responses. This prompted us to explore whether and to what extent PrLPs may build stress memory. By integrating the available rice interactome, transcriptome, and regulome data sets, we could find links between stress and memory pathways that would not have otherwise been discernible. Regulatory inferences derived from the superimposition of these data sets revealed a complex network and cross talk between PrLPs, transcription factors (TFs), and the genes involved in stress priming. This integrative meta-analysis connects transient and transgenerational memory mechanisms in plants with PrLPs, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. Taken together, our work provides important insights into the anticipated role of prion-like candidates in stress and memory, paving the way for more focused studies for validating the role of the identified PrLPs in memory acclimation.

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Integrated proteome and transcriptome analyses revealed key factors involved in tomato (Solanum lycopersicum) under high temperature stress

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 37 publications

References 62 publications

Combined Transcriptome and Proteome Leukocyte’s Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis

Combined Transcriptome and Proteome Leukocyte’s Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants

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