Integrated transcriptomic and proteomic analysis reveals the complex molecular mechanisms underlying stone cell formation in Korla pear

AbstractKorla pear (Pyrus sinkiangensis Yü) is a landrace selected from a hybrid pear species in the Xinjiang Autonomous Region in China. In recent years, pericarp roughening has been one of the major factors that adversely affects fruit quality. Compared with regular fruits, rough-skin fruits have a greater stone cell content. Stone cells compose sclerenchyma tissue that is formed by secondary thickening of parenchyma cell walls. In this work, we determined the main components of stone cells by isolating them from the pulp of rough-skin fruits at the ripening stage. Stone cell staining and apoptosis detection were then performed on fruit samples that were collected at three different developmental stages (20, 50 and 80 days after flowering (DAF)) representing the prime, late and stationary stages of stone cell differentiation, respectively. The same batches of samples were used for parallel transcriptomic and proteomic analysis to identify candidate genes and proteins that are related to SCW biogenesis in Korla pear fruits. The results showed that stone cells are mainly composed of cellulose (52%), hemicellulose (23%), lignin (20%) and a small amount of polysaccharides (3%). The periods of stone cell differentiation and cell apoptosis were synchronous and primarily occurred from 0 to 50 DAF. The stone cell components increased abundantly at 20 DAF but then decreased gradually. A total of 24,268 differentially expressed genes (DEGs) and 1011 differentially accumulated proteins (DAPs) were identified from the transcriptomic and proteomic data, respectively. We screened the DEGs and DAPs that were enriched in SCW-related pathways, including those associated with lignin biosynthesis (94 DEGs and 31 DAPs), cellulose and xylan biosynthesis (46 DEGs and 18 DAPs), S-adenosylmethionine (SAM) metabolic processes (10 DEGs and 3 DAPs), apoplastic ROS production (16 DEGs and 2 DAPs), and cell death (14 DEGs and 6 DAPs). Among the identified DEGs and DAPs, 63 significantly changed at both the transcript and protein levels during the experimental periods. In addition, the majority of these identified genes and proteins were expressed the most at the prime stage of stone cell differentiation, but their levels gradually decreased at the later stages.

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Integrated transcriptomic and proteomic analysis reveal new insights into stone cell formation in Korla pear

10.21203/rs.3.rs-23121/v1 ◽

2020 ◽

Author(s):

Aisajan Mamat ◽

Xiaoli Zhang ◽

Juan Xu ◽

Peng Yan ◽

Chuang Mei ◽

...

Keyword(s):

Function Analysis ◽

Cell Formation ◽

Lignin Biosynthesis ◽

Cell Content ◽

Time Points ◽

Protein Levels ◽

Stone Cell ◽

Fruit Samples ◽

Important Time ◽

Underlying Mechanisms

Abstract Background Korla fragrant pear(P•sinkiangensis Yü)is a famous local variety of Xinjiang China. One difficulty is the high stone cell content of these pears, which causes the formation of rough skins on the fruit. To elucidate the underlying mechanisms of stone cell formation, parallel analyses of the transcriptome and proteome was performed to identify important regulators and pathways involved in stone cell formation.Results Fruit samples were collected at three important time points depending on the stages of stone cell formation (20, 50 and 80 days after flowering). A total of 24268 differentially expressed genes (DEGs) and 1011 differentially accumulated proteins (DAPs) were identified from all the time points. Function analysis of the differential genes/proteins revealed that a set of candidates was associated with stone cell formation. These candidates mainly enriched in pathways involved in lignin biosynthesis, cellulose and xylan biosynthesis, S-adenosylmethionine (SAM) metabolic process, Reactive oxygen species (ROS) production, and cell death. We mined a total of 253 DEGs, and 100 DAPs, 63 of which were significantly changed at both the transcript and protein levels during fruit development.Conclusions Our findings reveal that some intriguing genes/proteins were previously unrecognized related with the sclereid formation, which provided new insights into molecular processes regulating sclereid accumulation in pear pulp.

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The Correlation between Cellular Features and Gene Expression in ‘Korla’ Fragrant Pear

HortScience ◽

10.21273/hortsci14613-19 ◽

2020 ◽

Vol 55 (1) ◽

pp. 8-13

Author(s):

Wen-hui Li ◽

Jian-rong Feng ◽

Shi-kui Zhang ◽

Zhang-hu Tang

Keyword(s):

Cell Wall ◽

Cell Formation ◽

Parenchyma Cell ◽

Wall Thickening ◽

Cell Content ◽

Stone Cell ◽

Cell Wall Development ◽

Highly Correlated ◽

Parenchyma Cell Wall

‘Korla’ fragrant pear (Pyrus sinkiangensis T.T. Yu) variety has shown severe coarse skin in recent years. The intrinsic quality of its coarse fruit shows an increase in the number of stone cells and poor taste. In this study, stone cells and the cell wall of coarse pear (CP) and normal pear (NP) during various development stages were compared using paraffin-sectioning and transmission electron microscopy (TEM), and the relationships between lignin-related genes and stone cell formation and cell wall thickening were also analyzed. Our results show that giant stone cells are formed and distributed in the core of pear, whereas many of these crack 60 days after flowering (DAF). The period of stone cell fragmentation occurs later in CP fruits than in NP fruits. Parenchyma cell wall development in CP and NP fruits varies from 120 DAF to maturity. The parenchyma cell wall of CP fruits thickens, whereas that of NP fruits is thinner during the same period. The expression pattern of five genes (Pp4CL1-l, PpHCT-l, Pp4CL2-l, PpPOD4, and PpPOD25) coincides with changes in stone cell content in the pulp. Correlation analysis demonstrates a significant correlation between stone cell content and the expression level of the five genes (ρ < 0.05). In addition, the expression of those five genes and PpCCR1 genes in CP fruits significantly increases during maturation and is highly correlated with the thickness of the parenchyma cell wall. The aim of this work is to provide insights into the mechanism of stone cell and parenchyma cell wall development in pear fruits and identify important candidate genes to regulate the quality of fruit texture using bioengineering methods.

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HNF4A Regulates the Formation of Hepatic Progenitor Cells from Human iPSC-Derived Endoderm by Facilitating Efficient Recruitment of RNA Pol II

Genes ◽

10.3390/genes10010021 ◽

2018 ◽

Vol 10 (1) ◽

pp. 21 ◽

Cited By ~ 12

Author(s):

Ann DeLaForest ◽

Francesca Di Furio ◽

Ran Jing ◽

Amy Ludwig-Kubinski ◽

Kirk Twaroski ◽

...

Keyword(s):

Cell Differentiation ◽

Chromatin Immunoprecipitation ◽

Molecular Mechanisms ◽

Cell Formation ◽

Rna Pol Ii ◽

Pol Ii ◽

High Throughput Dna Sequencing ◽

Hepatocyte Nuclear Factor 4 ◽

Induced Pluripotent ◽

Human Ipsc

Elucidating the molecular basis of cell differentiation will advance our understanding of organ development and disease. We have previously established a protocol that efficiently produces cells with hepatocyte characteristics from human induced pluripotent stem cells. We previously used this cell differentiation model to identify the transcription factor hepatocyte nuclear factor 4 α (HNF4A) as being essential during the transition of the endoderm to a hepatic fate. Here, we sought to define the molecular mechanisms through which HNF4A controls this process. By combining HNF4A chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) analyses at the onset of hepatic progenitor cell formation with transcriptome data collected during early stages of differentiation, we identified genes whose expression is directly dependent upon HNF4A. By examining the dynamic changes that occur at the promoters of these HNF4A targets we reveal that HNF4A is essential for recruitment of RNA polymerase (RNA pol) II to genes that are characteristically expressed as the hepatic progenitors differentiate from the endoderm.

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CAD Genes: Genome-Wide Identification, Evolution, and Their Contribution to Lignin Biosynthesis in Pear (Pyrus bretschneideri)

Plants ◽

10.3390/plants10071444 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1444

Author(s):

Kaijie Qi ◽

Xiaofei Song ◽

Yazhou Yuan ◽

Jianping Bao ◽

Xin Gong ◽

...

Keyword(s):

Expression Patterns ◽

Lignin Biosynthesis ◽

Gene Families ◽

Cell Number ◽

Segmental Duplications ◽

Pear Fruit ◽

Gene Expressions ◽

Cell Content ◽

Stone Cell ◽

Gene Pairs

The synthetic enzyme cinnamyl alcohol dehydrogenase (CAD) is involved in responses to various stresses during plant growth. It regulates the monolignol biosynthesis and catalyzes hydroxyl cinnamaldehyde reduction to the corresponding alcohols. Although the CAD gene families have been explored in some species, little known is in Rosaceae. In this study, we identified 149 genes in Pyrus bretschneideri (PbrCAD), Malus domestica (MDPCAD), Prunus mume (PmCAD) and Fragaria vesca (mrnaCAD). They were phylogenetically clustered into six subgroups. All CAD genes contained ADH-N and ADH-zinc-N domains and were distributed on chromosomes unevenly. Dispersed and WGD/segmental duplications accounted the highest number of evolutionary events. Eight collinear gene pairs were identified among the four Rosaceae species, and the highest number was recorded in pear as five pairs. The five PbrCAD gene pairs had undergone purifying selection under Ka/Ks analysis. Furthermore, nine genes were identified based on transcriptomic and stone cell content in pear fruit. In qRT-PCR, the expression patterns of PbrCAD1, PbrCAD20, PbrCAD27, and PbrCAD31 were consistent with variation in stone cell content during pear fruit development. These results will provide valuable information for understanding the relationship between gene expressions and stone cell number in fruit.

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Cinnamate-4-Hydroxylase Gene Is Involved in the Step of Lignin Biosynthesis in Chinese White Pear

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.140.6.573 ◽

2015 ◽

Vol 140 (6) ◽

pp. 573-579 ◽

Cited By ~ 8

Author(s):

Shutian Tao ◽

Danyang Wang ◽

Cong Jin ◽

Wei Sun ◽

Xing Liu ◽

...

Keyword(s):

Gene Expression ◽

Lignin Content ◽

Lignin Biosynthesis ◽

Enzymatic Reactions ◽

Cell Content ◽

Stone Cell ◽

Chinese White ◽

Essential Enzyme ◽

Main Component ◽

Lignin Metabolism

Lignin is the main component of stone cells, and stone cell content is one of the crucial factors for fruit quality in chinese white pear (Pyrus ×bretschneideri). The lignin biosynthesis pathway is complex and involves many enzymatic reactions. Cinnamate-4-hydroxylase [C4H (EC.1.14.13.11)] is an essential enzyme in lignin metabolism. This study was conducted to investigate the effect of bagging on lignin metabolism during fruit development in chinese white pear. The study showed that bagging had little effect on stone cell content, lignin content, C4H activity, and C4H gene expression and that there was a positive correlation between C4H gene expression and lignin content as well as stone cell content. Moreover, a full-length complementary DNA (cDNA) encoding C4H (PbrC4H, GenBank accession number KJ577541.1) was isolated from chinese white pear fruit. The cDNA is 1515 bp long and encodes a protein of 504 amino acids. Sequence alignment suggested that the deduced protein belongs to the P450 gene family and that C4H might be located subcellularly in the cell membrane. The results indicate that bagging cannot change the lignin and stone cell content significantly and that C4H catalyzes a step in lignin biosynthesis. These findings provide certain theoretical references and practical criteria for improving the quality of chinese white pear.

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An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging “Golden Delicious” Apple

International Journal of Molecular Sciences ◽

10.3390/ijms20184462 ◽

2019 ◽

Vol 20 (18) ◽

pp. 4462 ◽

Cited By ~ 1

Author(s):

Gaopeng Yuan ◽

Shuxun Bian ◽

Xiaolei Han ◽

Shanshan He ◽

Kai Liu ◽

...

Keyword(s):

Transcription Factors ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Lignin Biosynthesis ◽

Proteome Analysis ◽

Differentially Expressed ◽

Proteomics Data ◽

Absolute Quantitation ◽

Physiological Disorder ◽

Golden Delicious

Apple skin russeting naturally occurs in many varieties, particularly in “Golden Delicious” and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted (non-bagging) and non-russeted (bagging) skin of “Golden Delicious” apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400, and MD17G1225100) involved in lignin biosynthesis are significant changed during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors, may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.

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Integrative Analysis of the Core Fruit Lignification Toolbox in Pear Reveals Targets for Fruit Quality Bioengineering

Biomolecules ◽

10.3390/biom9090504 ◽

2019 ◽

Vol 9 (9) ◽

pp. 504 ◽

Cited By ~ 4

Author(s):

Yunpeng Cao ◽

Xiaoxu Li ◽

Lan Jiang

Keyword(s):

Fruit Quality ◽

Expression Patterns ◽

Lignin Biosynthesis ◽

Integrative Analysis ◽

Bimolecular Fluorescence Complementation ◽

Pear Fruit ◽

Cell Content ◽

Tandem Gene Duplication ◽

Stone Cell ◽

Chinese White

Stone cell content is an important factor affecting pear fruit flavor. Lignin, a major component of pear stone cells, hinders the quality and value of commercial fruit. The completion of the Chinese white pear (Pyrus bretschneideri) genome sequence provides an opportunity to perform integrative analysis of the genes encoding the eleven protein families (i.e., PAL, C4H, 4CL, HCT, C3H, CSE, CCoAOMT, CCR, F5H, COMT, and CAD) in the phenylpropanoid pathway. Here, a systematic study based on expression patterns and phylogenetic analyses was performed to identify the members of each gene family potentially involved in the lignification in the Chinese white pear. The phylogenetic analysis suggested that 35 P. bretschneideri genes belong to bona fide lignification clade members. Compared to other plants, some multigene families are expanded by tandem gene duplication, such as HCT, C3H, COMT, and CCR. RNA sequencing was used to study the expression patterns of the genes in different tissues, including leaf, petal, bud, sepal, ovary, stem, and fruit. Eighteen genes presented a high expression in fruit, indicating that these genes may be involved in the biosynthesis of lignin in pear fruit. Similarly to what has been observed for Populus trichocarpa, a bimolecular fluorescence complementation (BiFC) experiment indicated that P. bretschneideri C3H and C4H might also interact with each other to regulate monolignol biosynthesis in P. bretschneideri, ultimately affecting the stone cell content in pear fruits. The identification of the major genes involved in lignin biosynthesis in pear fruits provides the basis for the development of strategies to improve fruit quality.

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Effects of Metaxenia on Stone Cell Formation in Pear (Pyrus bretschneideri) Based on Transcriptomic Analysis and Functional Characterization of the Lignin-Related Gene PbC4H2

Forests ◽

10.3390/f11010053 ◽

2020 ◽

Vol 11 (1) ◽

pp. 53

Author(s):

Xi Cheng ◽

Jinyun Zhang ◽

Han Wang ◽

Tianzhe Chen ◽

Guohui Li ◽

...

Keyword(s):

Signal Transduction ◽

Cell Wall ◽

Cell Formation ◽

Differentially Expressed ◽

Pollen Parent ◽

Seed Parent ◽

Cell Content ◽

Stone Cell ◽

Lignin Metabolism

The deposition of lignin in flesh parenchyma cells for pear stone cells, and excessive stone cells reduce the taste and quality of the fruit. The effect of metaxenia on the quality of fruit has been heavily studied, but the effect of metaxenia on stone cell formation has not been fully elucidated to date. This study used P. bretschneideri (Chinese white pear) cv. ‘Yali’ (high-stone cell content) and P. pyrifolia (Sand pear) cv. ‘Cuiguan’ (low-stone cell content) as pollination trees to pollinate P. bretschneideri cv. ‘Lianglizaosu’ separately to fill this gap in the literature. The results of quantitative determination, histochemical staining and electron microscopy indicated that the content of stone cells and lignin in YL fruit (‘Yali’ (pollen parent) × ‘Lianglizaosu’ (seed parent)) was significantly higher than that in CL fruit (‘Cuiguan’ (pollen parent) × ‘Lianglizaosu’ (seed parent)). The transcriptome sequencing results that were obtained from the three developmental stages of the two types of hybrid fruits indicated that a large number of differentially expressed genes (DEGs) related to auxin signal transduction (AUX/IAAs and ARFs), lignin biosynthesis, and lignin metabolism regulation (MYBs, LIMs, and KNOXs) between the CL and YL fruits at the early stage of fruit development. Therefore, metaxenia might change the signal transduction process of auxin in pear fruit, thereby regulating the expression of transcription factors (TFs) related to lignin metabolism, and ultimately affecting lignin deposition and stone cell development. In addition, we performed functional verification of a differentially expressed gene, PbC4H2 (cinnamate 4-hydroxylase). Heterologous expression of PbC4H2 in the c4h mutant not only restored its collapsed cell wall, but also significantly increased the lignin content in the inflorescence stem. The results of our research help to elucidate the metaxenia-mediated regulation of pear stone cell development and clarify the function of PbC4H2 in cell wall development and lignin synthesis, which establishes a foundation for subsequent molecular breeding.

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Selenium Increases Fruit Quality By Reducing Ethylene Production And The Stone Cell Content In Pear (Pyrus Ussuriensis)

10.21203/rs.3.rs-626936/v1 ◽

2021 ◽

Author(s):

Chi Yuan ◽

Haidong Bu ◽

Jiaming Zhao ◽

Jiaojiao Liu ◽

Hui Yuan ◽

...

Keyword(s):

Fruit Quality ◽

Ethylene Production ◽

Lignin Biosynthesis ◽

Essential Trace Element ◽

Pear Fruit ◽

Cell Content ◽

Stone Cell ◽

Titratable Acid ◽

Biosynthesis Gene ◽

Key Genes

Abstract Background:Selenium (Se) is an essential trace element for both animals and plants. Se treatment can increase fruit Se concentration and shelf life. However, the mechanism underlying Se-delayed fruit ripening is still unclear.Results:In this research, two groups of Se (A and B treatments) were used to treat ‘Nanhong’ pear fruit. The results showed that these treatments could greatly increase the Se content but decreased the titratable acid content. Treatment A significantly decreased ethylene production, and the key genes controlling ethylene production, PuACSs and PuERF2, were inhibited by Se treatment. In addition, treatment A significantly decreased the stone cell content, and one lignin biosynthesis gene, PuC4H, was downregulated by treatment A.Concusions:Se treatment increased the Se content in pear fruit. In addition, Se decreased ethylene production and the stone cell content. Moreover, the key genes for ethylene production (PuACSs and PuERF2) and lignin biosynthesis (PuC4H) were also inhibited by Se treatment.

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PbCSE1 promotes lignification during stone cell development in pear (Pyrus bretschneideri) fruit

Scientific Reports ◽

10.1038/s41598-021-88825-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jiahui Xu ◽

Xingyu Tao ◽

Zhihua Xie ◽

Xin Gong ◽

Kaijie Qi ◽

...

Keyword(s):

Lignin Content ◽

Cell Formation ◽

Lignin Biosynthesis ◽

Physiological Data ◽

Stone Cell ◽

Key Enzyme ◽

Main Component ◽

Delayed Growth ◽

Lignin Deposition

AbstractPear [Pyrus bretschneideri cv. Dangshan Su] fruit quality is not always satisfactory owing to the presence of stone cells, and lignin is the main component of stone cells in pear fruits. Caffeoyl shikimate esterase (CSE) is a key enzyme in the lignin biosynthesis. Although CSE-like genes have been isolated from a variety of plant species, their orthologs are not characterized in pear. In this study, the CSE gene family (PbCSE) from P. bretschneideri was identified. According to the physiological data and quantitative RT-PCR (qRT-PCR), PbCSE1 was associated with lignin deposition and stone cell formation. The overexpression of PbCSE1 increased the lignin content in pear fruits. Relative to wild-type (WT) Arabidopsis, the overexpression of PbCSE1 delayed growth, increased the lignin deposition and lignin content in stems. Simultaneously, the expression of lignin biosynthetic genes were also increased in pear fruits and Arabidopsis. These results demonstrated that PbCSE1 plays an important role in cell lignification and will provide a potential molecular strategy to improve the quality of pear fruits.

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