scholarly journals Full-length transcriptome and targeted metabolome analyses provide insights into defense mechanisms of Malus sieversii against Agrilus mali

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8992
Author(s):  
Chuang Mei ◽  
Jie Yang ◽  
Peng Yan ◽  
Ning Li ◽  
Kai Ma ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Full Length ◽  
Metabolome Analysis ◽  
Insect Feeding ◽  
Illumina Hiseq ◽  
Malus Sieversii ◽  
Long Reads ◽  
Transcriptional Changes

Malus sieversii is the wild progenitor for many cultivars of domesticated apple and an important germplasm resource for breeding. However, this valuable species faces a significant threat in the areas north of the Tianshan Mountains in China, by the invasion of Agrilus mali, a destructive pest of apple trees belonging to the family Buprestidae. Our preliminary study has has shown that there may be resistance to this insect in M. sieversii plants in the field, but the corresponding molecular mechanisms remain unclear. In this study, we compared the response of insect-resistant and insect-susceptible plants of M. sieversii to insect feeding using full-length transcriptome and targeted metabolome. 112,103 non-chimeric full-length reads (FLNC) totaling 10.52 Gb of data were generating with Pacific Biosciences SingleMolecule, Real-Time (PacBio SMRT) sequencing. A total of 130.06 Gb data of long reads were acquired with an Illumina HiSeq. Function annotation indicated that the different expressed genes (DEGs) were mainly involved in signal transduction pathway of plant hormones and in the synthesis of compounds such as terpenes, quinones, flavonoids, and jasmonic acid. Through targeted metabolome analysis resistant strains showed higher levels of trans-cinnamic acid, caffeine and ferulic acid after pest infestation. This study helps to decipher the transcriptional changes and related signaling paths in M. sieversii after an insect feeding, which lays a foundation for further research on molecular mechanisms of insect resistance in apples.

scholarly journals Molecular Mechanisms for Microbe Recognition and Defense by the Red Seaweed Laurencia dendroidea

mSphere ◽  
2017 ◽  
Vol 2 (6) ◽  
Author(s):  
Louisi Souza de Oliveira ◽  
Diogo Antonio Tschoeke ◽  
Ana Carolina Rubem Magalhães Lopes ◽  
Daniela Bueno Sudatti ◽  
Pedro Milet Meirelles ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Bacterial Infections ◽  
Large Scale ◽  
Marine Bacterium ◽  
Molecular Mechanisms ◽  
Disease Outbreaks ◽  
Red Seaweed ◽  
Content Type ◽  
Transcriptional Changes ◽  
Molecular Components

ABSTRACT Marine bacteria are part of the healthy microbiota associated with seaweeds, but some species, such as Vibrio spp., are frequently associated with disease outbreaks, especially in economically valuable cultures. In this context, the ability of seaweeds to recognize microbes and, when necessary, activate defense mechanisms is essential for their survival. However, studies dedicated to understanding the molecular components of the immune response in seaweeds are rare and restricted to indirect stimulus. This work provides an unprecedentedly large-scale evaluation of the transcriptional changes involved in microbe recognition, cellular signaling, and defense in the red seaweed Laurencia dendroidea in response to the marine bacterium Vibrio madracius. By expanding knowledge about seaweed-bacterium interactions and about the integrated defensive system in seaweeds, this work offers the basis for the development of tools to increase the resistance of cultured seaweeds to bacterial infections. The ability to recognize and respond to the presence of microbes is an essential strategy for seaweeds to survive in the marine environment, but understanding of molecular seaweed-microbe interactions is limited. Laurencia dendroidea clones were inoculated with the marine bacterium Vibrio madracius. The seaweed RNA was sequenced, providing an unprecedentedly high coverage of the transcriptome of Laurencia, and the gene expression levels were compared between control and inoculated samples after 24, 48, and 72 h. Transcriptomic changes in L. dendroidea in the presence of V. madracius include the upregulation of genes that participate in signaling pathways described here for the first time as a response of seaweeds to microbes. Genes coding for defense-related transcription activators, reactive oxygen species metabolism, terpene biosynthesis, and energy conversion pathways were upregulated in inoculated samples of L. dendroidea, indicating an integrated defensive system in seaweeds. This report contributes significantly to the current knowledge about the molecular mechanisms involved in the highly dynamic seaweed-bacterium interactions. IMPORTANCE Marine bacteria are part of the healthy microbiota associated with seaweeds, but some species, such as Vibrio spp., are frequently associated with disease outbreaks, especially in economically valuable cultures. In this context, the ability of seaweeds to recognize microbes and, when necessary, activate defense mechanisms is essential for their survival. However, studies dedicated to understanding the molecular components of the immune response in seaweeds are rare and restricted to indirect stimulus. This work provides an unprecedentedly large-scale evaluation of the transcriptional changes involved in microbe recognition, cellular signaling, and defense in the red seaweed Laurencia dendroidea in response to the marine bacterium Vibrio madracius. By expanding knowledge about seaweed-bacterium interactions and about the integrated defensive system in seaweeds, this work offers the basis for the development of tools to increase the resistance of cultured seaweeds to bacterial infections.

scholarly journals Syndecan-1 Promotes Hepatocyte-Like Differentiation of Hepatoma Cells Targeting Ets-1 and AP-1

Biomolecules ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1356
Author(s):  
Péter Hollósi ◽  
Lóránd Váncza ◽  
Katalin Karászi ◽  
Katalin Dobos ◽  
Bálint Péterfia ◽  
...  
Keyword(s):  
Cell Surface ◽  
Heparan Sulfate ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Normal Liver ◽  
Surface Expression ◽  
Hepatoma Cells ◽  
Full Length ◽  
Cell Surface Expression ◽  
Gene Assay

Syndecan-1 is a transmembrane heparan sulfate proteoglycan which is indispensable in the structural and functional integrity of epithelia. Normal hepatocytes display strong cell surface expression of syndecan-1; however, upon malignant transformation, they may lose it from their cell surfaces. In this study, we demonstrate that re-expression of full-length or ectodomain-deleted syndecan-1 in hepatocellular carcinoma cells downregulates phosphorylation of ERK1/2 and p38, with the truncated form exerting an even stronger effect than the full-length protein. Furthermore, overexpression of syndecan-1 in hepatoma cells is associated with a shift of heparan sulfate structure toward a highly sulfated type specific for normal liver. As a result, cell proliferation and proteolytic shedding of syndecan-1 from the cell surface are restrained, which facilitates redifferentiation of hepatoma cells to a more hepatocyte-like phenotype. Our results highlight the importance of syndecan-1 in the formation and maintenance of differentiated epithelial characteristics in hepatocytes partly via the HGF/ERK/Ets-1 signal transduction pathway. Downregulation of Ets-1 expression alone, however, was not sufficient to replicate the phenotype of syndecan-1 overexpressing cells, indicating the need for additional molecular mechanisms. Accordingly, a reporter gene assay revealed the inhibition of Ets-1 as well as AP-1 transcription factor-induced promoter activation, presumably an effect of the heparan sulfate switch.

scholarly journals Complete genome sequence of Sphingomonas paucimobilis AIMST S2, a xenobiotic-degrading bacterium

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Suganniiya K. Ravintheran ◽  
Sumitra Sivaprakasam ◽  
Stella Loke ◽  
Su Yin Lee ◽  
Ravichandran Manickam ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Molecular Mechanisms ◽  
Sphingomonas Paucimobilis ◽  
Growth Promoters ◽  
Illumina Hiseq ◽  
Degrading Bacterium ◽  
Long Reads ◽  
Gene Expression Studies

AbstractComplete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its’ potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation.

scholarly journals Differential Regulation of Anthocyanins in Green and Purple Turnips Revealed by Combined De Novo Transcriptome and Metabolome Analysis

2019 ◽  
Vol 20 (18) ◽  
pp. 4387 ◽  
Author(s):  
Hongmei Zhuang ◽  
Qian Lou ◽  
Huifang Liu ◽  
Hongwei Han ◽  
Qiang Wang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Skin Pigmentation ◽  
Anthocyanin Content ◽  
Anthocyanidin Synthase ◽  
De Novo Transcriptome ◽  
Metabolome Analysis ◽  
Transcriptional Changes ◽  
The Difference

Purple turnip Brassica rapa ssp. rapa is highly appreciated by consumers but the metabolites and molecular mechanisms underlying the root skin pigmentation remain open to study. Herein, we analyzed the anthocyanin composition in purple turnip (PT) and green turnip (GT) at five developmental stages. A total of 21 anthocyanins were detected and classified into the six major anthocynanin aglycones. Distinctly, PT contains 20 times higher levels of anthocyanins than GT, which explain the difference in the root skin pigmentation. We further sequenced the transcriptomes and analyzed the differentially expressed genes between the two turnips. We found that PT essentially diverts dihydroflavonols to the biosynthesis of anthocyanins over flavonols biosynthesis by strongly down-regulating one flavonol synthase gene, while strikingly up-regulating dihydroflavonol 4-reductase (DFR), anthocyanidin synthase and UDP-glucose: flavonoid-3-O-glucosyltransferase genes as compared to GT. Moreover, a nonsense mutation identified in the coding sequence of the DFR gene may lead to a nonfunctional protein, adding another hurdle to the accumulation of anthocyanin in GT. We also uncovered several key members of MYB, bHLH and WRKY families as the putative main drivers of transcriptional changes between the two turnips. Overall, this study provides new tools for modifying anthocyanin content and improving turnip nutritional quality.

scholarly journals Transcriptomic analysis of melon/squash graft junction reveals molecular mechanisms potentially underlying the graft union development

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12569
Author(s):  
Chuanqiang Xu ◽  
Ying Zhang ◽  
Mingzhe Zhao ◽  
Yiling Liu ◽  
Xin Xu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Healing Process ◽  
Signal Transduction Pathway ◽  
Lignin Biosynthesis ◽  
Graft Healing ◽  
Oriental Melon ◽  
Future Production ◽  
Grafting Technique ◽  
Phenylpropanoid Biosynthesis ◽  
Transcriptional Changes

Oriental melon (Cucumis melo var. makuwa Makino) has become a widely planted horticultural crop in China especially in recent years and has been subjected to the grafting technique for the improvement of cultivation and stress resistance. Although grafting has a long history in horticulture, there is little known about the molecular mechanisms of the graft healing process in oriental melon. This study aims to reveal the molecular changes involved in the graft healing process. In the present work, anatomical observations indicated that the 2, 6, and 9 DAG were three critical stages for the graft healing and therefore, were selected for the subsequent high-throughput RNA-seq analysis. A total of 1,950 and 1,313 DEGs were identified by comparing IL vs. CA and CA vs. VB libraries, respectively. More DEGs in the melon scion exhibited abundant transcriptional changes compared to the squash rootstock, providing increased metabolic activity and thus more material basis for the graft healing formation in the scion. Several DEGs were enriched in the plant hormone signal transduction pathway, phenylpropanoid biosynthesis, and carbon metabolism. In addition, the results showed that concentrations of IAA, GA3, and ZR were induced in the graft junctions. In conclusion, our study determined that genes involved in the hormone-signaling pathway and lignin biosynthesis played the essential roles during graft healing. These findings expand our current understandings of the molecular basis of the graft junction formation and facilitate the improvement and success of melon grafting in future production.

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