scholarly journals Insights on seed abortion (endosperm and embryo development failure) from the transcriptome analysis of the wild type plant species Paeonia lutea

2020 ◽  
Vol 16 (8) ◽  
pp. 638-651 ◽  
Author(s):  
Shanshan Zhang ◽  
Keyword(s):  
Plant Species ◽  
Embryo Development ◽  
Transcriptome Analysis ◽  
Wild Type Plant ◽  
Seed Abortion ◽  
Wild Type ◽  
Development Failure

Genome-wide transcriptome analysis of rice genes responsive to chilling stress

2012 ◽  
Vol 92 (3) ◽  
pp. 447-460 ◽  
Author(s):  
Hyun Yong Cho ◽  
Sun-Goo Hwang ◽  
Dong Sub Kim ◽  
Cheol Seong Jang
Keyword(s):  
Abiotic Stress ◽  
Transcriptome Analysis ◽  
Chilling Stress ◽  
Stress Conditions ◽  
Functional Enrichment ◽  
Wild Type Plant ◽  
Wild Type ◽  
Tolerant Plants ◽  
Genome Wide ◽  
Inducible Genes

Cho, H. Y., Hwang, S.-G., Kim, D. S. and Jang, C. S. 2012. Genome-wide transcriptome analysis of rice genes responsive to chilling stress. Can. J. Plant Sci. 92: 447–460. Low temperature is known to be one of the major challenges to rice production. We have selected chilling-tolerant TILLING of Donganbyeo, which showed significantly vigorous growth relative to wild-type plants under chilling stress conditions (10–12°C). We performed a comparative transcriptome analysis using a chilling-tolerant line and wild-type plant with the objective to evaluate genomic responses to chilling stress and to identify chilling inducible genes. Functional enrichment analysis results demonstrated that a large proportion of chilling-inducible genes were associated with certain biological pathways, e.g., monosaccharide catabolic processes, reflecting the energy requirements necessary for adaptation to sub-optimal temperatures in plants. Extremely low correlation coefficients in a range of −0.07 to 0.04 were detected between plant responses to chilling stress and different abiotic stress conditions such as drought, salt, cold, and heat; these results imply that plants might exploit strikingly different response mechanisms against stress conditions. The largest subnetwork, which was composed of 78 chilling-specific inducible genes, was found in the tolerant plants, but not in the wild-type plants, which probably implies the existence of a delicate and harmonious signaling pathway setup in the tolerant plants. Expression patterns of 20 chilling-responsive genes were assessed via abiotic stress treatments and phytohormone treatments. About 80% of the tested chilling-inducible genes were upregulated by exogenous abscisic acid (ABA) treatment. The results of this study may prove useful in elucidating the chilling-response pathway and in the development of chilling-tolerant rice varieties.

Novel Metabolism of Nitrogen in Plants

2005 ◽  
Vol 60 (3-4) ◽  
pp. 265-271 ◽  
Author(s):  
Hiromichi Morikawa ◽  
Misa Takahashi ◽  
Atsushi Sakamoto ◽  
Manami Ueda-Hashimoto ◽  
Toshiyuki Matsubara ◽  
...  
Keyword(s):  
Plant Species ◽  
Reactive Nitrogen Species ◽  
Organic Nitrogen ◽  
Nitrate Nitrogen ◽  
Nitro Compounds ◽  
Wild Type Plant ◽  
Wild Type ◽  
Physiological Relevance ◽  
Kjeldahl Method ◽  
Β Carotene

Abstract Our previous study showed that approximately one-third of the nitrogen of 15N-labeled NO2 taken up into plants was converted to a previously unknown organic nitrogen (hereafter designated UN) that was not recoverable by the Kjeldahl method (Morikawa et al., 2004). In this communication, we discuss metabolic and physiological relevance of the UN based on our newest experimental results. All of the 12 plant species were found to form UN derived from NO2 (about 10-30% of the total nitrogen derived from NO2). The UN was formed also from nitrate nitrogen in various plant species. Thus, UN is a common metabolite in plants. The amount of UN derived from NO2 was greatly increased in the transgenic tobacco clone 271 (Vaucheret et al., 1992) where the activity of nitrite reductase is suppressed less than 5% of that of the wild-type plant. On the other hand, the amount of this UN was significantly decreased by the overexpression of S-nitrosoglutathione reductase (GSNOR). These findings strongly suggest that nitrite and other reactive nitrogen species are involved in the formation of the UN, and that the UN-bearing compounds are metabolizable. A metabolic scheme for the formation of UN-bearing compounds was proposed, in which nitric oxide and peroxynitrite derived from NO2 or endogenous nitrogen oxides are involved for nitrosation and/or nitration of organic compounds in the cells to form nitroso and nitro compounds, including N-nitroso and S-nitroso ones. Participation of non-symbiotic haemoglobin bearing peroxidase-like activity (Sakamoto et al., 2004) and GSNOR (Sakamoto et al., 2002) in the metabolism of the UN was discussed. The UN-bearing compounds identified to date in the extracts of the leaves of Arabidopsis thaliana fumigated with NO2 include a ⊿2- 1,2,3-thiadiazoline derivative (Miyawaki et al., 2004) and 4-nitro-β-carotene.

scholarly journals Transcriptome Analysis Provides Insights into the Mechanism of Astaxanthin Enrichment in a Mutant of the Ridgetail White Prawn Exopalaemon carinicauda

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 618
Author(s):  
Yue Jin ◽  
Shihao Li ◽  
Yang Yu ◽  
Chengsong Zhang ◽  
Xiaojun Zhang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Underlying Mechanism ◽  
Biological Processes ◽  
Wild Type ◽  
Expression Levels ◽  
In The Wild ◽  
Cuticle Proteins ◽  
Apolipoprotein D ◽  
High Level ◽  
Lower Expression

A mutant of the ridgetail white prawn, which exhibited rare orange-red body color with a higher level of free astaxanthin (ASTX) concentration than that in the wild-type prawn, was obtained in our lab. In order to understand the underlying mechanism for the existence of a high level of free astaxanthin, transcriptome analysis was performed to identify the differentially expressed genes (DEGs) between the mutant and wild-type prawns. A total of 78,224 unigenes were obtained, and 1863 were identified as DEGs, in which 902 unigenes showed higher expression levels, while 961 unigenes presented lower expression levels in the mutant in comparison with the wild-type prawns. Based on Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis, as well as further investigation of annotated DEGs, we found that the biological processes related to astaxanthin binding, transport, and metabolism presented significant differences between the mutant and the wild-type prawns. Some genes related to these processes, including crustacyanin, apolipoprotein D (ApoD), cathepsin, and cuticle proteins, were identified as DEGs between the two types of prawns. These data may provide important information for us to understand the molecular mechanism of the existence of a high level of free astaxanthin in the prawn.

scholarly journals CAND2/PMTR1 Is Required for Melatonin-Conferred Osmotic Stress Tolerance in Arabidopsis

2021 ◽  
Vol 22 (8) ◽  
pp. 4014
Author(s):  
Lin-Feng Wang ◽  
Ting-Ting Li ◽  
Yu Zhang ◽  
Jia-Xing Guo ◽  
Kai-Kai Lu ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
Stress Tolerance ◽  
Wild Type Plant ◽  
Wild Type ◽  
Melatonin Receptor ◽  
Ros Scavenging ◽  
Exogenous Melatonin ◽  
Osmotic Stress Tolerance ◽  
Osmotic Stress Response ◽  
In The Wild

Osmotic stress severely inhibits plant growth and development, causing huge loss of crop quality and quantity worldwide. Melatonin is an important signaling molecule that generally confers plant increased tolerance to various environmental stresses, however, whether and how melatonin participates in plant osmotic stress response remain elusive. Here, we report that melatonin enhances plant osmotic stress tolerance through increasing ROS-scavenging ability, and melatonin receptor CAND2 plays a key role in melatonin-mediated plant response to osmotic stress. Upon osmotic stress treatment, the expression of melatonin biosynthetic genes including SNAT1, COMT1, and ASMT1 and the accumulation of melatonin are increased in the wild-type plants. The snat1 mutant is defective in osmotic stress-induced melatonin accumulation and thus sensitive to osmotic stress, while exogenous melatonin enhances the tolerance of the wild-type plant and rescues the sensitivity of the snat1 mutant to osmotic stress by upregulating the expression and activity of catalase and superoxide dismutase to repress H2O2 accumulation. Further study showed that the melatonin receptor mutant cand2 exhibits reduced osmotic stress tolerance with increased ROS accumulation, but exogenous melatonin cannot revert its osmotic stress phenotype. Together, our study reveals that CADN2 functions necessarily in melatonin-conferred osmotic stress tolerance by activating ROS-scavenging ability in Arabidopsis.

scholarly journals Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yang Dong ◽  
Morgan Newman ◽  
Stephen M. Pederson ◽  
Karissa Barthelson ◽  
Nhi Hin ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Oxidative Phosphorylation ◽  
Transcriptome Analysis ◽  
Iron Homeostasis ◽  
Late Onset ◽  
Wild Type ◽  
Familial Alzheimer’S Disease ◽  
Zebrafish Larvae ◽  
Familial Alzheimer's Disease

Abstract Background Early-onset familial Alzheimer’s disease (EOfAD) is promoted by dominant mutations, enabling the study of Alzheimer’s disease (AD) pathogenic mechanisms through generation of EOfAD-like mutations in animal models. In a previous study, we generated an EOfAD-like mutation, psen1Q96_K97del, in zebrafish and performed transcriptome analysis comparing entire brains from 6-month-old wild type and heterozygous mutant fish. We identified predicted effects on mitochondrial function and endolysosomal acidification. Here we aimed to determine whether similar effects occur in 7 day post fertilization (dpf) zebrafish larvae that might be exploited in screening of chemical libraries to find ameliorative drugs. Results We generated clutches of wild type and heterozygous psen1Q96_K97del 7 dpf larvae using a paired-mating strategy to reduce extraneous genetic variation before performing a comparative transcriptome analysis. We identified 228 differentially expressed genes and performed various bioinformatics analyses to predict cellular functions. Conclusions Our analyses predicted a significant effect on oxidative phosphorylation, consistent with our earlier observations of predicted effects on ATP synthesis in adult heterozygous psen1Q96_K97del brains. The dysregulation of minichromosome maintenance protein complex (MCM) genes strongly contributed to predicted effects on DNA replication and the cell cycle and may explain earlier observations of genome instability due to PSEN1 mutation. The upregulation of crystallin gene expression may be a response to defective activity of mutant Psen1 protein in endolysosomal acidification. Genes related to extracellular matrix (ECM) were downregulated, consistent with previous studies of EOfAD mutant iPSC neurons and postmortem late onset AD brains. Also, changes in expression of genes controlling iron ion transport were observed without identifiable changes in the prevalence of transcripts containing iron responsive elements (IREs) in their 3′ untranslated regions (UTRs). These changes may, therefore, predispose to the apparent iron dyshomeostasis previously observed in 6-month-old heterozygous psen1Q96_K97del EOfAD-like mutant brains.

scholarly journals Degradation of trinitrotoluene by transgenic nitroreductase in Arabidopsis plants

2018 ◽  
Vol 64 (No. 8) ◽  
pp. 379-385 ◽  
Author(s):  
Zhu Bo ◽  
Han Hongjuan ◽  
Fu Xiaoyan ◽  
Li Zhenjun ◽  
Gao Jianjie ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Transgenic Arabidopsis ◽  
Environmental Pollutant ◽  
Specific Rate ◽  
Wild Type Plant ◽  
Wild Type ◽  
Fresh Weight ◽  
Human Carcinogen ◽  
Specific Rate Constant ◽  
Nitroreductase Activity

The explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic and persistent environmental pollutant. TNT is toxic to many organisms, it is known to be a potential human carcinogen, and is persistent in the environment. This study presents a system of phytoremediation by Arabidopsis plants developed on the basis of overexpression of NAD(P)H-flavin nitroreductase (NFSB) from the Sulfurimonas denitrificans DSM1251. The resulting transgenic Arabidopsis plants demonstrated significantly enhanced TNT tolerance and a strikingly higher capacity to remove TNT from their media. The highest specific rate constant of TNT disappearance rate was 1.219 and 2.297 mL/g fresh weight/h for wild type and transgenic plants, respectively. Meanwhile, the nitroreductase activity in transgenic plant was higher than wild type plant. All this indicates that transgenic plants show significantly enhanced tolerances to TNT; transgenic plants also exhibit strikingly higher capabilities of removing TNT from their media and high efficiencies of transformation.

scholarly journals Plant Hormone Metabolome and Transcriptome Analysis of Dwarf and Wild-type Banana

2021 ◽  
Author(s):  
Biao Deng ◽  
Xuan Wang ◽  
Xing Long ◽  
Ren Fang ◽  
Shuangyun Zhou ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
Feedback Regulation ◽  
Wild Type ◽  
Hormone Levels ◽  
Transporter Protein ◽  
Repressor Proteins ◽  
Differential Gene ◽  
The Relationship

AbstractGibberellin (GA), auxin (IAA) and brassinosteroid (BR) are indispensable in the process of plant growth and development. Currently, research on the regulatory mechanism of phytohormones in banana dwarfism is mainly focused on GA, and few studies are focused on IAA and BR. In this study, we measured the contents of endogenous GA, IAA and BR and compared the transcriptomes of wild-type Williams banana and its dwarf mutant across five successive growth periods. We investigated the relationship between hormones and banana dwarfism and explored differential gene expression through transcriptome analysis, thus revealing the possible metabolic regulatory mechanism. We inferred a complex regulatory network of banana dwarfing. In terms of endogenous hormone levels, GA and IAA had significant effects on banana dwarfing, while BR had little effect. The key gene in GA biosynthesis of is GA2ox, and the key genes in IAA biosynthesis are TDC and YUCCA. The differential expression of these genes might be the main factor affecting hormone levels and plant height. In terms of hormone signal transduction, DELLA and AUX/IAA repressor proteins were the core regulators of GA and IAA, respectively. They inhibited the process of signal transduction and had feedback regulation on hormone levels. Finally, the transporter protein PIN, AUX1/LAX protein family and ABCB subfamily played supplementary roles in the transport of IAA. These results provide new insights into GA and IAA regulation of banana growth and a reliable foundation for the improvement of dwarf varieties.

scholarly journals Transcriptome Analysis of Rice Roots in Response to Root-Knot Nematode Infection

2020 ◽  
Vol 21 (3) ◽  
pp. 848
Author(s):  
Yuan Zhou ◽  
Di Zhao ◽  
Li Shuang ◽  
Dongxue Xiao ◽  
Yuanhu Xuan ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Gene Annotation ◽  
Oryza Sativa L ◽  
Development Stage ◽  
Post Inoculation ◽  
Rna Seq ◽  
Wild Type ◽  
Root Knot Nematode ◽  
Rice Roots ◽  
Invasion Stage

Meloidogyne incognita and Meloidogyne graminicola are root-knot nematodes (RKNs) infecting rice (Oryza sativa L.) roots and severely decreasing yield, whose mechanisms of action remain unclear. We investigated RKN invasion and development in rice roots through RNA-seq transcriptome analysis. The results showed that 952 and 647 genes were differently expressed after 6 (invasion stage) and 18 (development stage) days post inoculation, respectively. Gene annotation showed that the differentially expressed genes were classified into diverse metabolic and stress response categories. Furthermore, phytohormone, transcription factor, redox signaling, and defense response pathways were enriched upon RKN infection. RNA-seq validation using qRT-PCR confirmed that CBL-interacting protein kinase (CIPK) genes (CIPK5, 8, 9, 11, 14, 23, 24, and 31) as well as brassinosteroid (BR)-related genes (OsBAK1, OsBRI1, D2, and D11) were altered by RKN infection. Analysis of the CIPK9 mutant and overexpressor indicated that the RKN populations were smaller in cipk9 and larger in CIPK9 OX, while more galls were produced in CIPK9 OX plant roots than the in wild-type roots. Significantly fewer numbers of second-stage infective juveniles (J2s) were observed in the plants expressing the BR biosynthesis gene D2 mutant and the BR receptor BRI1 activation-tagged mutant (bri1-D), and fewer galls were observed in bri1-D roots than in wild-type roots. The roots of plants expressing the regulator of ethylene signaling ERS1 (ethylene response sensor 1) mutant contained higher numbers of J2s and developed more galls compared with wild-type roots, suggesting that these signals function in RKN invasion or development. Our findings broaden our understanding of rice responses to RKN invasion and provide useful information for further research on RKN defense mechanisms.

scholarly journals The Arabidopsis TRM61/TRM6 complex is a bona fide tRNA N1-methyladenosine methyltransferase

2020 ◽  
Vol 71 (10) ◽  
pp. 3024-3036
Author(s):  
Jun Tang ◽  
Pengfei Jia ◽  
Peiyong Xin ◽  
Jinfang Chu ◽  
Dong-Qiao Shi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Embryo Development ◽  
Protein Biosynthesis ◽  
Seed Abortion ◽  
Bona Fide ◽  
The Stability

Abstract tRNA molecules, which contain the most abundant post-transcriptional modifications, are crucial for proper gene expression and protein biosynthesis. Methylation at N1 of adenosine 58 (A58) is critical for maintaining the stability of initiator methionyl-tRNA (tRNAiMet) in bacterial, archaeal, and eukaryotic tRNAs. However, although research has been conducted in yeast and mammals, it remains unclear how A58 in plant tRNAs is modified and involved in development. In this study, we identify the nucleus-localized complex AtTRM61/AtTRM6 in Arabidopsis as tRNA m1A58 methyltransferase. Deficiency or a lack of either AtTRM61 or AtTRM6 leads to embryo arrest and seed abortion. The tRNA m1A level decreases in conditionally complemented Attrm61/LEC1pro::AtTRM61 plants and this is accompanied by reduced levels of tRNAiMet, indicating the importance of the tRNA m1A modification for tRNAiMet stability. Taken together, our results demonstrate that tRNA m1A58 modification is necessary for tRNAiMet stability and is required for embryo development in Arabidopsis.

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