Expression characterisation of cyclophilin BrROC1 during light treatment and abiotic stresses response in Brassica rapa subsp. rapa ‘Tsuda’

2018 ◽  
Vol 45 (12) ◽  
pp. 1223 ◽  
Author(s):  
Haifang Yan ◽  
Bo Zhou ◽  
Wei He ◽  
Yuzhe Nie ◽  
Yuhua Li
Keyword(s):  
Blue Light ◽  
Brassica Rapa ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Transcript Level ◽  
Light Treatment ◽  
Anthocyanin Synthesis ◽  
Root Epidermis ◽  
High Or Low Temperature ◽  
Level Analysis

ROC1 is a prototypic peptidyl prolyl cis/trans isomerase (PPIase) of the plant cytosol belonging to the large subfamily of cyclophilins that are associated with diverse functions through foldase, scaffolding, chaperoning or other unknown activities. Although many functions of plant cyclophilins have been reported, the molecular basis of stress-responsive expression of plant cyclophilins is still largely unknown. To characterise the roles of BrROC1 during light treatment and their responses in various abiotic stresses, we identified BrROC1 genes and characterised their expression patterns in Brassica rapa subsp. rapa ‘Tsuda’. Our results showed that BrROC1 genes are multi-family genes. Transcript level analysis showed BrROC1-2 expressed higher than BrROC1-1 in 0 to 6-day-old seedlings under natural light. Moreover, BrROC1-2 genes were also induced to highly express in the cotyledon, upper hypocotyls and lower hypocotyls of seedlings under UV-A and blue-light treatment. In addition, the transcript level of BrROC1-1 was higher in pigment tissues than that in unpigment tissues (cotyledon and lower hypocotyl) under UV-A and blue-light treatment. Furthermore, when the unpigment epidermis (shaded light) of 2-month-old ‘Tsuda’ turnip roots was exposed to UV-A light, transcript levels of the BrROC1-1 and BrROC1-2 were significantly increased with time prolongation. These two BrROC1 genes might be involved in UV-A-induced anthocyanin synthesis in the root epidermis of ‘Tsuda’ turnip, which accumulates high levels of anthocyanin. These two BrROC1 genes were also induced to be regulated by abiotic stresses such as high or low temperature, dehydration, osmotic and salt stresses. Then, the results indicate that BrROC1 genes are involved in light induction response and may play important roles in adaptation of plants to various environmental stresses.

scholarly journals Gene expression profiling of adp-glucose pyrophosphorylase (AGPase) in sink and source organs of some cassava varieties with different starch contents in Vietnam

2018 ◽  
Vol 14 (4) ◽  
pp. 673-682
Author(s):  
Nguyen Thi Minh Hong ◽  
Le Thu Ngoc ◽  
Nguyen Mau Hung ◽  
Pham Bich Ngoc ◽  
Chu Hoang Ha
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Transcript Level ◽  
Starch Biosynthesis ◽  
Storage Roots ◽  
Genes Encoding ◽  
Adp Glucose Pyrophosphorylase ◽  
Level Analysis ◽  
Starch Production ◽  
Cassava Varieties

Starch is the most widespread and abundant storage carbohydrate in plants. We depend upon starch for our nutrition, exploit its unique properties in industry, and use it as a feedstock for bio-ethanol production. Starch is stored in the form of osmotically inactive, water-insoluble granules in amyloplasts (storage starch) and chloroplasts (transitory starch). The biosynthesis of starch involves not only the production of the composite glucans but also their arrangement into an organized form within the starch granule. Understanding the specific functions played by individual isoforms of enzymes involved in starch biosynthesis pathways will provide important basis for regulation of starch production in plant. A transcript-level analysis of the genes which encode starch-synthesis enzymes is fundamental for assessment of enzyme function and the regulatory mechanism for starch biosynthesis in source and sink organs. In this work, the expression level of the genes encoding ADP-glucose pyrophosphorylase (AGPase) in two local varieties Do Dia Phuong (Do DF) and Trang Hoa Binh (Trang HB) as well as two imported varieties KM94 (Rayong1 X Rayong 90) and KM140 (KM98-1 x KM36) with different starch contents were evaluated by quantitative real-time PCR method. The result of transcript level analysis made the expression profiles of cassava AGPS and AGPL genes (encoding AGPase small and large subunits) during three development periods, 90, 180 and 270 DAP (day after planting). The transcriptional activities of these genes exhibited tissue-specific expression patterns. In particular, AGPS2 and AGPL1 transcripts were predominant in leaves, whereas expression of AGPS1, AGPL2, and AGPL3 appeared to be mostly confined to storage roots. Despite of having disparities between development stages, expression patterns of both AGPS2 and AGPL1 in leaves did not show significant differences amongst investigated cassava varieties. In contrast, transcriptional activities of AGPS1 and AGPL3 in tubers had patterns directly related to the starch contents of the cultivars. These results indicated that AGPS1 and AGPL3 genes likely play an important role in the starch biosynthesis pathway and have potential for regulation of starch production in cassava.

scholarly journals Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Kathleen Greenham ◽  
Ryan C Sartor ◽  
Stevan Zorich ◽  
Ping Lou ◽  
Todd C Mockler ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Network Models ◽  
Transcript Level ◽  
Rapid Expansion ◽  
Genetic Redundancy ◽  
Circadian Expression ◽  
Genome Wide ◽  
Important Challenge

An important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Here we describe the circadian transcriptome in the polyploid crop Brassica rapa. Strikingly, almost three-quarters of the expressed genes exhibited circadian rhythmicity. Genetic redundancy resulting from whole genome duplication is thought to facilitate evolutionary change through sub- and neo-functionalization among paralogous gene pairs. We observed genome-wide expansion of the circadian expression phase among retained paralogous pairs. Using gene regulatory network models, we compared transcription factor targets between B. rapa and Arabidopsis circadian networks to reveal evidence for divergence between B. rapa paralogs that may be driven in part by variation in conserved non-coding sequences (CNS). Additionally, differential drought response among retained paralogous pairs suggests further functional diversification. These findings support the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new approach for assessing paralog activity at the transcript level.

scholarly journals Characterization of Three Chalcone Synthase-like Genes in Dianthus Chinensis 

2021 ◽  
Author(s):  
Jia Liu ◽  
Xi-Long Hao ◽  
Xue-Qin He
Keyword(s):  
Chalcone Synthase ◽  
Expression Patterns ◽  
Tobacco Rattle Virus ◽  
Transcript Level ◽  
Close Relation ◽  
Amino Acid Sequences ◽  
Anthocyanin Synthesis ◽  
Anthocyanin Content ◽  
Virus Induced Gene Silencing ◽  
Floral Bud

Abstract Being an important garden plant, Dianthus chinensis flower has a great variety of colors and color patterns. Chalcone synthase (CHS) is the key enzyme in the anthocyanin biosynthetic pathway. Although CHS genes have been isolated and characterized in ornamental plants, the CHS gene is still unknown in D. chinensis. In our study, three CHS genes, DchCHS1 (KX893854), DchCHS2 (MK404175) and DchCHS3 (MK416198) were isolated in D. chinensis. Their deduced amino acid sequences show high homology with the known CHS sequences in Caryophyllaceae. The phylogenetic tree suggests that the DchCHS1 and the DchCHS3 have a close relation with the known CHS sequences in Caryophyllaceae and the DchCHS2 is different from them. The DchCHSs were characterized by the Tobacco Rattle Virus (TRV)-based virus-induced gene silencing (VIGS) system. We obtained white or pale purple flowers in the DchCHS1-silenced flowers and reducing purple flowers in the DchCHS2-silenced and the DchCHS3-silenced flowers. The anthocyanin content and the transcript level of the silenced DchCHS were significantly reduced in accordance with the silencing phenotypes. The DchCHSs showed different expression patterns during floral bud developments, among flower colors and in organs. Their expression levels in the purple flower were greatly higher than those in the white flower. Compared with DchCHS2 and DchCHS3, DchCHS1 was abundantly expressed at each floral bud stage, in each flower color and in the flower organ. In conclusion, the three DchCHSs are all involved in the anthocyanin synthesis and the flower coloration, and DchCHS1 probably plays a major role in D. chinensis flowers.

scholarly journals Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Yuntian Ye ◽  
Yongqiang Liu ◽  
Xiaolong Li ◽  
Qing Chen ◽  
Yong Zhang ◽  
...  
Keyword(s):  
Blue Light ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Light Treatment ◽  
Rna Seq ◽  
Function Annotation ◽  
Data Resource ◽  
Kegg Pathways ◽  
Flowering Regulation ◽  
Go Terms

Blue light is an important signal that regulates the flowering of strawberry plants. To reveal the mechanism of early flowering under blue light treatment at the transcriptional regulation level, seedlings of cultivated strawberry (Fragaria × ananassa Duch.) “Benihoppe” were subjected to a white light treatment (WL) and blue light treatment (BL) until their flowering. To detect the expression patterns of genes in response to BL, a transcriptome analysis was performed based on RNA-Seq. The results identified a total of 6875 differentially expressed genes (DEGs) that responded to BL, consisting of 3138 (45.64%) downregulated ones and 3737 (54.36%) upregulated ones. These DEGs were significantly enriched into 98 GO terms and 71 KEGG pathways based on gene function annotation. Among the DEGs, the expression levels of genes that might participate in light signaling (PhyB, PIFs, and HY5) and circadian rhythm (FKF1, CCA1, LHY, and CO) in plants were altered under BL. The BBX transcription factors which responded to BL were also identified. The result showed that the FaBBX29, one of strawberry’s BBX family genes, may play an important role in flowering regulation. Our results provide a timely, comprehensive view and a reliable reference data resource for further study of flowering regulation under different light qualities.

scholarly journals Functional examination of lncRNAs in allotetraploid Gossypium hirsutum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Luyao Wang ◽  
Jin Han ◽  
Kening Lu ◽  
Menglin Li ◽  
Mengtao Gao ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Expression Patterns ◽  
Leaf Tissue ◽  
Evolutionary Model ◽  
Cotton Leaf ◽  
Functional Screening ◽  
Virus Induced Gene Silencing ◽  
Individual Gene ◽  
Cotton Species ◽  
Allotetraploid Cotton

Abstract Background An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown. Results We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses. Conclusions Low-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis-regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.

scholarly journals Identification and Characterization of Abiotic Stress Responsive CBL-CIPK Family Genes in Medicago

2021 ◽  
Vol 22 (9) ◽  
pp. 4634
Author(s):  
Wenxuan Du ◽  
Junfeng Yang ◽  
Lin Ma ◽  
Qian Su ◽  
Yongzhen Pang
Keyword(s):  
Abiotic Stress ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Interacting Protein ◽  
Forage Crop ◽  
Cis Acting ◽  
Protein Motifs ◽  
Plant Signal Transduction ◽  
Identification And Characterization

The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) play important roles in plant signal transduction and response to abiotic stress. Plants of Medicago genus contain many important forages, and their growth is often affected by a variety of abiotic stresses. However, studies on the CBL and CIPK family member and their function are rare in Medicago. In this study, a total of 23 CBL and 58 CIPK genes were identified from the genome of Medicago sativa as an important forage crop, and Medicaog truncatula as the model plant. Phylogenetic analysis suggested that these CBL and CIPK genes could be classified into five and seven groups, respectively. Moreover, these genes/proteins showed diverse exon-intron organizations, architectures of conserved protein motifs. Many stress-related cis-acting elements were found in their promoter region. In addition, transcriptional analyses showed that these CBL and CIPK genes exhibited distinct expression patterns in various tissues, and in response to drought, salt, and abscisic acid treatments. In particular, the expression levels of MtCIPK2 (MsCIPK3), MtCIPK17 (MsCIPK11), and MtCIPK18 (MsCIPK12) were significantly increased under PEG, NaCl, and ABA treatments. Collectively, our study suggested that CBL and CIPK genes play crucial roles in response to various abiotic stresses in Medicago.

scholarly journals Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Seung Hee Eom ◽  
Tae Kyung Hyun
Keyword(s):  
Functional Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Physiological Processes ◽  
Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

scholarly journals Single Wavelengths of LED Light Supplement Promote the Biosynthesis of Major Cyclic Monoterpenes in Japanese Mint

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1420
Author(s):  
Takahiro Ueda ◽  
Miki Murata ◽  
Ken Yokawa
Keyword(s):  
Blue Light ◽  
Solid Phase ◽  
Glandular Trichomes ◽  
Red Light ◽  
Glandular Trichome ◽  
Pulse Amplitude ◽  
Light Treatment ◽  
Led Light ◽  
Trichome Formation ◽  
Japanese Mint

Environmental light conditions influence the biosynthesis of monoterpenes in the mint plant. Cyclic terpenes, such as menthol, menthone, pulegone, and menthofuran, are major odor components synthesized in mint leaves. However, it is unclear how light for cultivation affects the contents of these compounds. Artificial lighting using light-emitting diodes (LEDs) for plant cultivation has the advantage of preferential wavelength control. Here, we monitored monoterpene contents in hydroponically cultivated Japanese mint leaves under blue, red, or far-red wavelengths of LED light supplements. Volatile cyclic monoterpenes, pulegone, menthone, menthol, and menthofuran were quantified using the head-space solid phase microextraction method. As a result, all light wavelengths promoted the biosynthesis of the compounds. Remarkably, two weeks of blue-light supplement increased all compounds: pulegone (362% increase compared to the control), menthofuran (285%), menthone (223%), and menthol (389%). Red light slightly promoted pulegone (256%), menthofuran (178%), and menthol (197%). Interestingly, the accumulation of menthone (229%) or menthofuran (339%) was observed with far-red light treatment. The quantification of glandular trichomes density revealed that no increase under light supplement was confirmed. Blue light treatment even suppressed the glandular trichome formation. No promotion of photosynthesis was observed by pulse-amplitude-modulation (PAM) fluorometry. The present result indicates that light supplements directly promoted the biosynthetic pathways of cyclic monoterpenes.

scholarly journals Complete Inactivation of Blood Borne Pathogen Trypanosoma cruzi in Stored Human Platelet Concentrates and Plasma Treated With 405 nm Violet-Blue Light

2020 ◽  
Vol 7 ◽  
Author(s):  
Katarzyna I. Jankowska ◽  
Rana Nagarkatti ◽  
Nirmallya Acharyya ◽  
Neetu Dahiya ◽  
Caitlin F. Stewart ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Human Plasma ◽  
Blue Light ◽  
Chagas Disease ◽  
Light Treatment ◽  
Platelet Concentrates ◽  
Complete Inactivation ◽  
Pathogen Reduction ◽  
Biochemical Indices

The introduction of pathogen reduction technologies (PRTs) to inactivate bacteria, viruses and parasites in donated blood components stored for transfusion adds to the existing arsenal toward reducing the risk of transfusion-transmitted infectious diseases (TTIDs). We have previously demonstrated that 405 nm violet-blue light effectively reduces blood-borne bacteria in stored human plasma and platelet concentrates. In this report, we investigated the microbicidal effect of 405 nm light on one important bloodborne parasite Trypanosoma cruzi that causes Chagas disease in humans. Our results demonstrated that a light irradiance at 15 mWcm−2 for 5 h, equivalent to 270 Jcm−2, effectively inactivated T. cruzi by over 9.0 Log10, in plasma and platelets that were evaluated by a MK2 cell infectivity assay. Giemsa stained T. cruzi infected MK2 cells showed that the light-treated parasites in plasma and platelets were deficient in infecting MK2 cells and did not differentiate further into intracellular amastigotes unlike the untreated parasites. The light-treated and untreated parasite samples were then evaluated for any residual infectivity by injecting the treated parasites into Swiss Webster mice, which did not develop infection even after the animals were immunosuppressed, further demonstrating that the light treatment was completely effective for inactivation of the parasite; the light-treated platelets had similar in vitro metabolic and biochemical indices to that of untreated platelets. Overall, these results provide a proof of concept toward developing 405 nm light treatment as a pathogen reduction technology (PRT) to enhance the safety of stored human plasma and platelet concentrates from bloodborne T. cruzi, which causes Chagas disease.

scholarly journals Identification and Functional Characterization of a Cold-Related Protein, BcHHP5, in Pak-Choi (Brassica rapa ssp. chinensis)

2018 ◽  
Vol 20 (1) ◽  
pp. 93
Author(s):  
Jin Wang ◽  
Feiyi Huang ◽  
Xiong You ◽  
Xilin Hou
Keyword(s):  
Brassica Rapa ◽  
Abiotic Stresses ◽  
Quantitative Polymerase Chain Reaction ◽  
Functional Characterization ◽  
Regulation Mechanism ◽  
Pak Choi ◽  
Negative Effect ◽  
Polymerase Chain ◽  
Related Proteins

In plants, heptahelical proteins (HHPs) have been shown to respond to a variety of abiotic stresses, including cold stress. Up to the present, the regulation mechanism of HHP5 under low temperature stress remains unclear. In this study, BcHHP5 was isolated from Pak-choi (Brassica rapa ssp. chinensis cv. Suzhouqing). Sequence analysis and phylogenetic analysis indicated that BcHHP5 in Pak-choi is similar to AtHHP5 in Arabidopsis thaliana. Structure analysis showed that the structure of the BcHHP5 protein is relatively stable and highly conservative. Subcellular localization indicated that BcHHP5 was localized on the cell membrane and nuclear membrane. Furthermore, real-time quantitative polymerase chain reaction (RT-qPCR) analysis showed that BcHHP5 was induced to express by cold and other abiotic stresses. In Pak-choi, BcHHP5-silenced assay, inhibiting the action of endogenous BcHHP5, indicated that BcHHP5-silenced might have a negative effect on cold tolerance, which was further confirmed. All of these results indicate that BcHHP5 might play a role in abiotic response. This work can serve as a reference for the functional analysis of other cold-related proteins from Pak-choi in the future.

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