scholarly journals Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut

2021 ◽  
Vol 23 (1) ◽  
pp. 246
Author(s):  
Bin Tong ◽  
Yusun Shi ◽  
Aaron Ntambiyukuri ◽  
Xia Li ◽  
Jie Zhan ◽  
...  
Keyword(s):  
Cell Death ◽  
Stress Response ◽  
Programmed Cell Death ◽  
Target Genes ◽  
Ketone Bodies ◽  
Acid Soil ◽  
Arable Land ◽  
Differentially Expressed ◽  
Degradome Sequencing ◽  
Al Stress

Peanut is one of the most important oil crops in the world. In China, the peanut is highly produced in its southern part, in which the arable land is dominated by acid soil. At present, miRNAs have been identified in stress response, but their roles and mechanisms are not clear, and no miRNA studies have been found related to aluminum (Al)-induced programmed cell death (PCD). In the present study, transcriptomics, sRNAs, and degradome analysis in the root tips of two peanut cultivars ZH2 (Al-sensitive, S) and 99-1507 (Al-tolerant, T) were carried out. Here, we generated a comprehensive resource focused on identifying key regulatory miRNA-target circuits that regulate PCD under Al stress. Through deep sequencing, 2284 miRNAs were identified and 147 miRNAs were differentially expressed under Al stress. Furthermore, 19237 target genes of 749 miRNAs were validated by degradome sequencing. GO and KEGG analyses of differential miRNA targets showed that the pathways of synthesis and degradation of ketone bodies, citrate cycle (TCA cycle), and peroxisome were responded to Al stress. The combined analysis of the degradome data sets revealed 89 miRNA-mRNA interactions that may regulate PCD under Al stress. Ubiquitination may be involved in Al-induced PCD in peanut. The regulatory networks were constructed based on the differentially expressed miRNAs and their targets related to PCD. Our results will provide a useful platform to research on PCD induced by Al and new insights into the genetic engineering for plant stress response.

scholarly journals Flight muscles degenerate by programmed cell death after migration in the wheat aphid, Sitobion avenae

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Honglin Feng ◽  
Xiao Guo ◽  
Hongyan Sun ◽  
Shuai Zhang ◽  
Jinghui Xi ◽  
...  
Keyword(s):  
Cell Death ◽  
Programmed Cell Death ◽  
Molecular Mechanism ◽  
Differentially Expressed Genes ◽  
Flight Muscle ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Terminal Deoxynucleotidyl Transferase ◽  
Muscle Degeneration ◽  
Flight Muscles

Abstract Objective Previous studies showed that flight muscles degenerate after migration in some aphid species; however, the underlying molecular mechanism remains virtually unknown. In this study, using the wheat aphid, Sitobion avenae, we aim to investigate aphid flight muscle degeneration and the underlying molecular mechanism. Results Sitobion avenae started to differentiate winged or wingless morphs at the second instar, the winged aphids were fully determined at the third instar, and their wings were fully developed at the fourth instar. After migration, the aphid flight muscles degenerated via programmed cell death, which is evidenced by a Terminal deoxynucleotidyl transferase dUTP-biotin nick-end labeling assay. Then, we identified a list of differentially expressed genes before and after tethered flights using differential-display reverse transcription-PCR. One of the differentially expressed genes, ubiquitin-ribosomal S27a, was confirmed using qPCR. Ubiquitin-ribosomal S27a is drastically up regulated following the aphids’ migration and before the flight muscle degeneration. Our data suggested that aphid flight muscles degenerate after migration. During flight muscle degeneration, endogenous proteins may be degraded to reallocate energy for reproduction.

scholarly journals Flight muscles degenerate by programmed cell death after migration in the wheat aphid, Sitobion avenae

2019 ◽  
Author(s):  
Honglin Feng ◽  
Xiao Guo ◽  
Hongyan Sun ◽  
Shuai Zhang ◽  
Jinghui Xi ◽  
...  
Keyword(s):  
Cell Death ◽  
Programmed Cell Death ◽  
Differentially Expressed Genes ◽  
Flight Muscle ◽  
Aphid Species ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Terminal Deoxynucleotidyl Transferase ◽  
Muscle Degeneration ◽  
Flight Muscles

Abstract Objective Previous studies showed that flight muscles degenerate after migration in some aphid species; however, the underlying molecular mechanism remains virtually unknown. In this study, using the wheat aphid, Sitobion avenae , we aim to investigate aphid flight muscle degeneration and the underlying molecular mechanism.Results S. avenae started to differentiate winged or wingless lines at the second instar, the winged aphids were fully determined at the third instar, and their wings were fully developed at the fourth instar. After migration, the aphid flight muscles degenerated via programmed cell death, which is evidenced by a Terminal deoxynucleotidyl transferase dUTP-biotin nick end labeling assay. Then, we identified a list of differentially expressed genes before and after tethered flights using differential-display reverse transcription-PCR. One of the differentially expressed genes, ubiquitin-ribosomal S27a, was confirmed using qPCR. Ubiquitin-ribosomal S27a is drastically up regulated following the aphids’ migration and before the flight muscle degeneration. Our data suggested that aphid flight muscles degenerate after migration. During flight muscle degeneration, endogenous proteins may be degraded to reallocate energy for reproduction.

scholarly journals Screening and identification of miRNAs related to sexual differentiation of strobili in Ginkgo biloba by integration analysis of small RNA, mRNA, and degradome sequencing

2020 ◽  
Author(s):  
Xiao-Meng Liu ◽  
Shui-Yuan Cheng ◽  
Jia-Bao Ye ◽  
Ze-Xiong Chen ◽  
Yong-Ling Liao ◽  
...  
Keyword(s):  
Small Rna ◽  
Ginkgo Biloba ◽  
Sexual Differentiation ◽  
Target Genes ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Multiple Perspectives ◽  
Juvenile Period ◽  
Degradome Sequencing ◽  
Screening And Identification

Abstract Background: Ginkgo biloba, a typical dioecious plant, is a traditional medicinal plant widely planted. However, it has a long juvenile period, which severely affected the breeding and cultivation of superior ginkgo varieties.Results: In order to clarify the complex mechanism of sexual differentiation in G. biloba strobili. Here, a total of 3,293 miRNAs were identified in buds and strobili of G. biloba, including 1,085 conserved miRNAs and 2,208 novel miRNAs using the three sequencing approaches of transcriptome, small RNA, and degradome. Comparative transcriptome analysis screened 4,346 and 7,087 differentially expressed genes (DEGs) in MB _vs_ FB and MS _vs_ OS, respectively. A total of 6,032 target genes were predicted for differentially expressed miRNA. The combined analysis of both small RNA and transcriptome datasets identified 51 miRNA-mRNA interaction pairs that may be involved in the process of G. biloba strobili sexual differentiation, of which 15 pairs were verified in the analysis of degradome sequencing. Conclusions: The comprehensive analysis of the small RNA, RNA and degradome sequencing data in this study provided candidate genes and clarified the regulatory mechanism of sexual differentiation of G. biloba strobili from multiple perspectives.

scholarly journals Glucocorticoid and progesterone inhibit involution and programmed cell death in the mouse mammary gland.

1995 ◽  
Vol 131 (4) ◽  
pp. 1095-1103 ◽  
Author(s):  
Z Feng ◽  
A Marti ◽  
B Jehn ◽  
H J Altermatt ◽  
G Chicaiza ◽  
...  
Keyword(s):  
Cell Death ◽  
Mammary Gland ◽  
Programmed Cell Death ◽  
Hormone Receptors ◽  
Target Genes ◽  
Mouse Mammary Gland ◽  
Binding Activity ◽  
Steroid Hormone Receptors ◽  
Mrna Levels ◽  
Glucocorticoid Hormone

Milk production during lactation is a consequence of the suckling stimulus and the presence of glucocorticoids, prolactin, and insulin. After weaning the glucocorticoid hormone level drops, secretory mammary epithelial cells die by programmed cell death and the gland is prepared for a new pregnancy. We studied the role of steroid hormones and prolactin on the mammary gland structure, milk protein synthesis, and on programmed cell death. Slow-release plastic pellets containing individual hormones were implanted into a single mammary gland at lactation. At the same time the pups were removed and the consequences of the release of hormones were investigated histologically and biochemically. We found a local inhibition of involution in the vicinity of deoxycorticosterone- and progesterone-release pellets while prolactin-release pellets were ineffective. Dexamethasone, a very stable and potent glucocorticoid hormone analogue, inhibited involution and programmed cell death in all the mammary glands. It led to an accumulation of milk in the glands and was accompanied by an induction of protein kinase A, AP-1 DNA binding activity and elevated c-fos, junB, and junD mRNA levels. Several potential target genes of AP-1 such as stromelysin-1, c-jun, and SGP-2 that are induced during normal involution were strongly inhibited in dexamethasone-treated animals. Our results suggest that the cross-talk between steroid hormone receptors and AP-1 previously described in cells in culture leads to an impairment of AP-1 activity and to an inhibition of involution in the mammary gland implying that programmed cell death in the postlactational mammary gland depends on functional AP-1.

scholarly journals Plasmodium falciparum Replication factor C subunit 1 is involved in genotoxic stress response

2020 ◽  
Author(s):  
O Sheriff ◽  
Y Aniweh ◽  
Soak-Kuan Lai ◽  
HL Loo ◽  
S. K Sze ◽  
...  
Keyword(s):  
Dna Damage ◽  
Cell Death ◽  
Dna Repair ◽  
Plasmodium Falciparum ◽  
Stress Response ◽  
Programmed Cell Death ◽  
Genotoxic Stress ◽  
Antimalarial Drugs ◽  
Protein Levels ◽  
Factor C

AbstractAbout half the world’s population is at risk of malaria, with Plasmodium falciparum malaria being responsible for the most malaria related deaths globally. Antimalarial drugs such as chloroquine and artemisinin are directed towards the proliferating intra-erythrocytic stages of the parasite, which is responsible for all the clinical symptoms of the disease. These antimalarial drugs have been reported to function via multiple pathways, one of which induces DNA damage via the generation of free radicals and reactive oxygen species. An urgent need to understand the mechanistic details of drug response and resistance is highlighted by the decreasing clinical efficacy of the front line drug, Artemisinin.The replication factor C subunit 1 protein is an important component of the DNA replication machinery and DNA damage response mechanism. Here we show the translocation of PfRFC1 from an intranuclear localization to the nuclear periphery indicating an orchestrated progression of distinct patterns of replication in the developing parasites. PfRFC1 responds to genotoxic stress via elevated protein levels in soluble and chromatin bound fractions.Reduction of PfRFC1 protein levels upon treatment with antimalarials suggests an interplay of replication and DNA repair pathways leading to cell death. Additionally, mislocalization of the endogenously tagged protein confirmed its essential role in parasites’ replication and DNA repair. This study provides key insights into DNA replication, DNA damage response and cell death in plasmodium falciparum.ImportanceFrontline drugs have been found to induce DNA damage in the human malaria parasite Plasmodium falciparum. The genotoxic stress response in Plasmodium and the interplay between DNA damage repair, replication and activation of programmed cell death pathways remains largely undescribed. This study shows a distinct pattern of localization of PfRFC1 during replication and DNA repair. PfRFC1 responds to genotoxic stress with an increase in protein expression. Interfering with the RFC complex formation or mislocalization of PfRFC1 is associated with disrupted genotoxic stress response. Additionally, a reduction of PfRFC1 protein levels is observed upon treatment with antimalarial drugs or under apoptosis like conditions, highlighting the role of DEVD/G like motif in mediating programmed cell death in these parasites. This study sheds light on the role of PfRFC1 in differentially responding to replication, genotoxic stress and programmed cell death in Plasmodium parasites.

Evidence for programmed cell death and activation of specific caspase-like enzymes in the tomato fruit heat stress response

Planta ◽  
2009 ◽  
Vol 229 (6) ◽  
pp. 1269-1279 ◽  
Author(s):  
Gui-Qin Qu ◽  
Xiang Liu ◽  
Ya-Li Zhang ◽  
Dan Yao ◽  
Qiu-Min Ma ◽  
...  
Keyword(s):  
Cell Death ◽  
Heat Stress ◽  
Stress Response ◽  
Programmed Cell Death ◽  
Tomato Fruit ◽  
Heat Stress Response

scholarly journals Identification of miRNAs and Their Target Genes Involved in Cucumber Fruit Expansion Using Small RNA and Degradome Sequencing

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 483 ◽  
Author(s):  
Sun ◽  
Luo ◽  
Chang ◽  
Li ◽  
Zhou ◽  
...  
Keyword(s):  
Small Rna ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Complex Biological Process ◽  
Cucumber Fruit ◽  
Differentially Expressed Mirnas

Fruit expansion is an essential and very complex biological process. Regulatory roles of microRNAs (miRNAs) and miRNA–mRNA modules in the cucumber fruit expansion are not yet to be investigated. In this work, 1253 known and 1269 novel miRNAs were identified from nine cucumber fruit small RNA (sRNA) libraries through high-throughput sequencing. A total of 105 highly differentially expressed miRNAs were recognized in the fruit on five days post anthesis with pollination (EXP_5d) sRNA library. Further, expression patterns of 11 differentially expressed miRNAs were validated by quantitative real-time PCR (qRT-PCR). The expression patterns were similar to sRNAs sequencing data. Transcripts of 1155 sequences were predicted as target genes of differentially expressed miRNAs by degradome sequencing. Gene Ontology (GO) enrichment showed that these target genes were involved in 24 biological processes, 15 cell components and nine molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that these target genes were significantly enriched in 19 pathways and the enriched KEGG pathways were associated with environmental adaptation, signal transduction and translation. Based on the functional prediction of miRNAs and target genes, our findings suggest that miRNAs have a potential regulatory role in cucumber fruit expansion by targeting their target genes, which provide important data for understanding the miRNA-mediated regulatory networks controlling fruit expansion in cucumber. Specific miRNAs could be selected for further functional research and molecular breeding in cucumber.

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