scholarly journals Transcriptome Analysis to Elucidate the Enhanced Cold Resistance of Phoebe zhennan Pretreated with Exogenous Calcium

2021 ◽  
Vol 25 (01) ◽  
pp. 151-159
Author(s):  
Bo Deng,
Keyword(s):  
Cold Stress ◽  
Cold Resistance ◽  
Abiotic Factors ◽  
Soluble Sugar ◽  
Resistance Mechanism ◽  
Enrichment Analysis ◽  
Calcium Dependent ◽  
Timber Tree ◽  
Phoebe Zhennan ◽  
Relative Electrical Conductivity

Phoebe zhennan is a high-quality timber tree species, and cold stress is one of the most remarkable abiotic factors limiting its growth and development. In this study, effects of exogenous CaCl2 on cold resistance of P. Zhennan were surveyed. CaCl2-pretreatment increased the levels of abscisic acid, peroxidase, catalase, proline, and soluble sugar, while decreased the levels of malondialdehyde and relative electrical conductivity. In addition, RNA-sequencing was used to investigate global transcriptome responses to cold stress. A total of 4245 differentially expressed genes were identified, including 477 up-regulated and 3768 down-regulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that these DEGs were associated to the plant-pathogen interaction pathway, in which calcium-dependent protein kinase (CDPK) play key role for improving the cold resistance of P. zhennan. Our results can be useful to understand the Ca2+-mediated cold resistance mechanism for improving cold stress tolerance in P. Zhennan seedlings. © 2021 Friends Science Publishers

scholarly journals Comparative Transcriptome Analysis Reveals Potential Gene Modules Associated with Cold Tolerance in Sugarcane (Saccharum officinarum L.)

2021 ◽  
Author(s):  
Xing Huang ◽  
Yongsheng Liang ◽  
Baoqing Zhang ◽  
Xiupeng Song ◽  
Yangrui Li ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Cold Resistance ◽  
Soluble Sugar ◽  
Resistance Mechanism ◽  
Saccharum Officinarum ◽  
Calcium Signal ◽  
Protein Kinase Activity ◽  
Comparative Transcriptome ◽  
Climate Conditions

AbstractSugarcane is an important crop worldwide, and most sugar is derived directly from sugarcane. Due to its thermophilic nature, the yield of sugarcane is largely influenced by extreme climate conditions, especially cold stress. Therefore, the development of sugarcane with improved cold tolerance is an important goal. However, little is known about the multiple mechanisms underlying cold acclimation at the bud stage in sugarcane. In this study, we emphasized that sensitivity to cold stress was higher for the sugarcane variety ROC22 than for GT42, as determined by physical signs, including bud growth capacity, relative conductivity, malonaldehyde contents, and soluble sugar contents. To understand the factors contributing to the difference in cold tolerance between ROC22 and GT42, comparative transcriptome analyses were performed. We found that genes involved in the regulation of the stability of the membrane system were the relative determinants of difference in cold tolerance. Additionally, genes related to protein kinase activity, starch metabolism, and calcium signal transduction were associated with cold tolerance. Finally, 25 candidate genes, including 23 variety-specific and 2 common genes, and 7 transcription factors were screened out for understanding the possible cold resistance mechanism. The findings of this study provide candidate gene resources for cold resistance and will improve our understanding of the regulation of cold tolerance at the bud stage in sugarcane.

scholarly journals Physiological Responses and Proteomic Analysis on the Cold Stress Responses of Annual Pitaya (Hylocereus spp.) Branches

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Junliang Zhou ◽  
Lijuan Wang ◽  
Tujian Xiao ◽  
Zhuang Wang ◽  
Yongya Mao ◽  
...  
Keyword(s):  
Cold Stress ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Cold Resistance ◽  
Physiological Responses ◽  
Soluble Sugar ◽  
Multivariate Statistical ◽  
Chlorophyll Contents ◽  
Proteomic Approach ◽  
Related Proteins

In this study, the physiological response of the annual branches of three varieties of pitaya (Xianmi, Fulong, and Zihonglong) in cold stress was investigated using a multivariate statistical method. Physiological change results showed that cold stress could decrease the moisture and chlorophyll contents, on the contrary, increase the relative electric conductivity, the contents of malonadehyde, soluble protein, soluble sugar, and free proline, and enhance the enzyme activities of peroxidase, superoxide dismutase, and catalase. Meanwhile, a comparative proteomic approach was also conducted to clarify the cold resistance-related proteins and pathways in annual pitaya branches. Proteomics results concluded that the cold tolerance of annual pitaya branches could be improved by modulating autophagy. Therefore, we hypothesized that an increased autophagy ability may be an important characteristic of the annual pitaya branches in response to cold stress conditions. Our results provide a good understanding of the physiological responses and molecular mechanisms of the annual pitaya branches in response to cold stress.

scholarly journals Comparative Study on Cold Resistance Physiology of Red Pulp Pitaya and White Pulp Pitaya

2019 ◽  
Vol 131 ◽  
pp. 01113
Author(s):  
Yan Gong ◽  
Xiaoyi Bi ◽  
Lijun Deng ◽  
Juan Hu ◽  
Shan Jiang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Room Temperature ◽  
Cold Resistance ◽  
Sugar Content ◽  
Soluble Sugar ◽  
White Pulp ◽  
White Crystal ◽  
Soluble Protein Content ◽  
Malondialdehyde Content ◽  
Red Pulp

The red pulp pitaya variety ’Taiwan No. 2’ and the white pulp pitaya variety ’white crystal’ were used as experimental materials, which were cold stressed at low temperature of 3 °C for 48h, 96h, and recovering at room temperature after 96h cold stress for control. The relative conductivity (REC), malondialdehyde content (MDA), soluble sugar content (SS), soluble protein content (SP), free proline content (Pro), activity of superoxide dismutase (SOD), and catalase (CAT) were determined and the cold resistance were analyzed. The results showed that, after cold stress, the SP, Pro content and SOD and CAT activities of ’White Crystal’ pitaya were higher than that of ’Taiwan No. 2’ pitaya. It showed that the cold resistance of ’White Crystal’ white pulp pitaya was stronger than that of ’Taiwan No. 2’ red pulp pitaya.

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

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 470
Author(s):  
Min Zhang ◽  
Hongyuan Zhang ◽  
Jie Tan ◽  
Shuping Huang ◽  
Xia Chen ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Expression Profiles ◽  
Resistance Mechanism ◽  
Solanum Melongena ◽  
Enrichment Analysis ◽  
Nematode Resistance ◽  
Differentially Expressed ◽  
Root Knot Nematode ◽  
Solanum Torvum ◽  
Plant Nematode

Eggplant (Solanum melongena L.), which belongs to the Solanaceae family, is an important vegetable crop. However, its production is severely threatened by root-knot nematodes (RKNs) in many countries. Solanum torvum, a wild relative of eggplant, is employed worldwide as rootstock for eggplant cultivation due to its resistance to soil-borne diseases such as RKNs. In this study, to identify the RKN defense mechanisms, the transcriptomic profiles of eggplant and Solanum torvum were compared. A total of 5360 differentially expressed genes (DEGs) were identified for the response to RKN infection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that these DEGs are mainly involved in the processes of response to stimulus, protein phosphorylation, hormone signal transduction, and plant-pathogen interaction pathways. Many phytohormone-related genes and transcription factors (MYB, WRKY, and NAC) were differentially expressed at the four time points (ck, 7, 14, and 28 days post-infection). The abscisic acid signaling pathway might be involved in plant-nematode interactions. qRT-PCR validated the expression levels of some of the DEGs in eggplant. These findings demonstrate the nematode-induced expression profiles and provide some insights into the nematode resistance mechanism in eggplant.

scholarly journals Gain-of-Function Mutations in the Phospholipid Flippase MprF Confer Specific Daptomycin Resistance

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Christoph M. Ernst ◽  
Christoph J. Slavetinsky ◽  
Sebastian Kuhn ◽  
Janna N. Hauser ◽  
Mulugeta Nega ◽  
...  
Keyword(s):  
Surface Charge ◽  
Bacterial Resistance ◽  
Resistance Mechanism ◽  
Point Mutations ◽  
Content Type ◽  
Calcium Dependent ◽  
Lipopeptide Antibiotics ◽  
Lipopeptide Antibiotic ◽  
Positively Charged ◽  
Phospholipid Flippase

ABSTRACTDaptomycin, a calcium-dependent lipopeptide antibiotic whose full mode of action is still not entirely understood, has become a standard-of-care agent for treating methicillin-resistantStaphylococcus aureus(MRSA) infections. Daptomycin-resistant (DAP-R)S. aureusmutants emerge during therapy, featuring isolates which in most cases possess point mutations in themprFgene. MprF is a bifunctional bacterial resistance protein that synthesizes the positively charged lipid lysyl-phosphatidylglycerol (LysPG) and translocates it subsequently from the inner membrane leaflet to the outer membrane leaflet. This process leads to increased positiveS. aureussurface charge and reduces susceptibility to cationic antimicrobial peptides and cationic antibiotics. We characterized the most commonly reported MprF mutations in DAP-RS. aureusstrains in a defined genetic background and found that only certain mutations, including the frequently reported T345A single nucleotide polymorphism (SNP), can reproducibly cause daptomycin resistance. Surprisingly, T345A did not alter LysPG synthesis, LysPG translocation, or theS. aureuscell surface charge. MprF-mediated DAP-R relied on a functional flippase domain and was restricted to daptomycin and a related cyclic lipopeptide antibiotic, friulimicin B, suggesting that the mutations modulate specific interactions with these two antibiotics. Notably, the T345A mutation led to weakened intramolecular domain interactions of MprF, suggesting that daptomycin and friulimicin resistance-conferring mutations may alter the substrate range of the MprF flippase to directly translocate these lipopeptide antibiotics or other membrane components with crucial roles in the activity of these antimicrobials. Our study points to a new mechanism used byS. aureusto resist calcium-dependent lipopeptide antibiotics and increases our understanding of the bacterial phospholipid flippase MprF.IMPORTANCEEver since daptomycin was introduced to the clinic, daptomycin-resistant isolates have been reported. In most cases, the resistant isolates harbor point mutations in MprF, which produces and flips the positively charged phospholipid LysPG. This has led to the assumption that the resistance mechanism relies on the overproduction of LysPG, given that increased LysPG production may lead to increased electrostatic repulsion of positively charged antimicrobial compounds, including daptomycin. Here we show that the resistance mechanism is highly specific and relies on a different process that involves a functional MprF flippase, suggesting that the resistance-conferring mutations may enable the flippase to accommodate daptomycin or an unknown component that is crucial for its activity. Our report provides a new perspective on the mechanism of resistance to a major antibiotic.

scholarly journals Comparative transcriptome analysis of the cold resistance of the sterile rice line 33S

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0261822
Author(s):  
Hongjun Xie ◽  
Mingdong Zhu ◽  
Yaying Yu ◽  
Xiaoshan Zeng ◽  
Guohua Tang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Resistance ◽  
Temperature Response ◽  
Enrichment Analysis ◽  
Abiotic Factor ◽  
Comparative Transcriptome ◽  
Important Species ◽  
Expression Of Genes ◽  
Nutrient Reserve ◽  
Cold Tolerant

Rice (Oryza sativa L.) is one of the most important species for food production worldwide. Low temperature is a major abiotic factor that affects rice germination and reproduction. Here, the underlying regulatory mechanism in seedlings of a TGMS variety (33S) and a cold-sensitive variety (Nipponbare) was investigated by comparative transcriptome. There were 795 differentially expressed genes (DEGs) identified only in cold-treated 33S, suggesting that 33S had a unique cold-resistance system. Functional and enrichment analysis of these DEGs revealed that, in 33S, several metabolic pathways, such as photosynthesis, amino acid metabolism, secondary metabolite biosynthesis, were significantly repressed. Moreover, pathways related to growth and development, including starch and sucrose metabolism, and DNA biosynthesis and damage response/repair, were significantly enhanced. The expression of genes related to nutrient reserve activity were significantly up-regulated in 33S. Finally, three NAC and several ERF transcription factors were predicted to be important in this transcriptional reprogramming. This present work provides valuable information for future investigations of low-temperature response mechanisms and genetic improvement of cold-tolerant rice seedlings.

scholarly journals Antioxidant Responses and Gene Expression in Bermudagrass under Cold Stress

2014 ◽  
Vol 139 (6) ◽  
pp. 699-705 ◽  
Author(s):  
Jibiao Fan ◽  
Jing Ren ◽  
Weixi Zhu ◽  
Erick Amombo ◽  
Jinmin Fu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Molecular Mechanisms ◽  
Cynodon Dactylon ◽  
Sugar Content ◽  
Soluble Sugar ◽  
Molecular Alteration ◽  
Antioxidant Genes ◽  
Dramatic Decline ◽  
Malondialdehyde Content ◽  
Key Factor

Cold stress is a key factor limiting resource use in bermudagrass (Cynodon dactylon). Under cold stress, bermudagrass growth is severely inhibited and the leaves undergo chlorosis. Therefore, rigorous investigation on the physiological and molecular mechanisms of cold stress in this turf species is urgent. The objective of this study was to investigate the physiological and molecular alteration in wild bermudagrass under cold stress, particularly the changes of transpiration rate, soluble sugar content, enzyme activities, and expression of antioxidant genes. Wild bermudagrass (C. dactylon) was planted in plastic pots (each 10 cm tall and 8 cm in diameter) filled with matrix (brown coal soil:sand 1:1) and treated with 4 °C in a growth chamber. The results displayed a dramatic decline in the growth and transpiration rates of the wild bermudagrass under 4 °C temperature. Simultaneously, cold severely destabilized the cell membrane as indicated by increased malondialdehyde content and electrolyte leakage value. Superoxide dismutase and peroxidase activities were higher in the cold regime than the control. The expression of antioxidant genes including MnSOD, Cu/ZnSOD, POD, and APX was vividly up-regulated after cold stress. In summary, our results contributed to the understanding of the role of the antioxidant system in bermudagrass’ response to cold.

scholarly journals Variation in Morphological and Quality Parameters in Garlic (Allium sativum L.) Bulb Influenced by Different Photoperiod, Temperature, Sowing and Harvesting Time

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 155 ◽  
Author(s):  
Muhammad Jawaad Atif ◽  
Bakht Amin ◽  
Muhammad Imran Ghani ◽  
Muhammad Ali ◽  
Zhihui Cheng
Keyword(s):  
Abiotic Factors ◽  
Soluble Sugar ◽  
Growth Period ◽  
Sowing Date ◽  
Quality Parameters ◽  
Plant Age ◽  
Bulb Formation ◽  
Garlic Bulb ◽  
Soluble Solid ◽  
Higher Temperature

Photoperiod (light) and temperature as abiotic factors having significant impact on the garlic bulb morphology and quality. In various bulb plants including garlic, bulbing is affected by photoperiod, temperature, sowing date and the plant age. In this backdrop experiments were performed to understand the effect of different photoperiods (10 h/14 h, 12 h/12 h and 14 h/10 h (light/dark)), temperatures (25 °C/18 °C and 30 °C/20 °C (light/dark)), sowing dates (D0801: 1st August, D0901: 1st September and D1001: 1st October) and plant ages (A80, A60 and A40: 80, 60 and 40 days after planting) on garlic cultivars viz; G103, G024 and G2011-5. Parameters including morphological (plant height, fresh weight and pseudostem diameter), bulb attributes (diameter, weight, height and bulbing index), growth period and bulb quality related traits (total soluble solid (TSS), contents of soluble protein, soluble sugar, total sugar, glucose, sucrose, fructose, starch, total phenol and total flavonoid) were assayed. Longer photoperiod (14 h), higher temperature (30 °C), early sowing (D0801) and maximum plant age (A80) had maximum morphological and bulb quality related traits for cv. G103. These results showed that early sowing, maximum plant age, longer photoperiod and higher temperature are important for garlic bulb formation and quality. Moreover, the regulation of garlic bulb morphology and quality is achievable over the switch of sowing date, plant age, light and growth temperature.

scholarly journals Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 434 ◽  
Author(s):  
Daniil S. Wiebe ◽  
Nadezhda A. Omelyanchuk ◽  
Aleksei M. Mukhin ◽  
Ivo Grosse ◽  
Sergey A. Lashin ◽  
...  
Keyword(s):  
Abiotic Factors ◽  
Transcriptional Response ◽  
Enrichment Analysis ◽  
R Package ◽  
Fold Change ◽  
Functional Gene ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Go Terms ◽  
Singular Enrichment Analysis

Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-Change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome data with respect to their fold changes. FSEA identifies Gene Ontology (GO) terms, which are shared by the group of genes with a similar magnitude of response, and assesses these changes. GO terms found by FSEA are fold-change-specifically (e.g., weakly, moderately, or strongly) affected by a stimulus under investigation. We demonstrate that many responses to abiotic factors, mutations, treatments, and diseases occur in a fold-change-specific manner. FSEA analyses suggest that there are two prevailing responses of functionally-related gene groups, either weak or strong. Notably, some of the fold-change-specific GO terms are invisible by classical algorithms for functional gene enrichment, Singular Enrichment Analysis (SEA), and Gene Set Enrichment Analysis (GSEA). These are GO terms not enriched compared to the genome background but strictly regulated by a factor within specific fold-change intervals. FSEA analysis of a cancer-related transcriptome suggested that the gene groups with a tightly coordinated response can be the valuable source to search for possible regulators, markers, and therapeutic targets in oncogenic processes. Availability and Implementation: FSEA is implemented as the FoldGO Bioconductor R package and a web-server.

scholarly journals Comprehensive Proteome and Lysine Acetylome Analysis Reveals the Widespread Involvement of Acetylation in Cold Resistance of Pepper (Capsicum annuum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhoubin Liu ◽  
Jingshuang Song ◽  
Wu Miao ◽  
Bozhi Yang ◽  
Zhuqing Zhang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Carbon Fixation ◽  
Cold Resistance ◽  
Triosephosphate Isomerase ◽  
Carbon Assimilation ◽  
Differentially Expressed ◽  
Lysine Acetylation ◽  
Bisphosphate Carboxylase ◽  
Pepper Leaves ◽  
Assimilation Capacity

Pepper is a typical warmth-loving vegetable that lacks a cold acclimation mechanism and is sensitive to cold stress. Lysine acetylation plays an important role in diverse cellular processes, but limited knowledge is available regarding acetylation modifications in the resistance of pepper plants to cold stress. In this study, the proteome and acetylome of two pepper varieties with different levels of cold resistance were investigated by subjecting them to cold treatments of varying durations followed by recovery periods. In total, 6,213 proteins and 4,574 lysine acetylation sites were identified, and this resulted in the discovery of 3,008 differentially expressed proteins and 768 differentially expressed acetylated proteins. A total of 1,988 proteins were identified in both the proteome and acetylome, and the functional differences in these co-identified proteins were elucidated through GO enrichment. KEGG analysis showed that 397 identified acetylated proteins were involved in 93 different metabolic pathways. The dynamic changes in the acetylated proteins in photosynthesis and the “carbon fixation in the photosynthetic organisms” pathway in pepper under low-temperature stress were further analyzed. It was found that acetylation of the PsbO and PsbR proteins in photosystem II and the PsaN protein in photosystem I could regulate the response of pepper leaves to cold stress. The acetylation levels of key carbon assimilation enzymes, such as ribulose bisphosphate carboxylase, fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, glyceraldehyde 3-phosphate dehydrogenase, phosphoribulokinase, and triosephosphate isomerase decreased, leading to decreases in carbon assimilation capacity and photosynthetic efficiency, reducing the cold tolerance of pepper leaves. This study is the first to identify the acetylome in pepper, and it greatly expands the catalog of lysine acetylation substrates and sites in Solanaceae crops, providing new insights for posttranslational modification studies.

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