Integrated analysis of transcriptomic and metabolomic data reveals critical metabolic pathways involved in polyphenol biosynthesis in Nicotiana tabacum under chilling stress

2019 ◽  
Vol 46 (1) ◽  
pp. 30 ◽  
Author(s):  
Peilu Zhou ◽  
Qiyao Li ◽  
Guangliang Liu ◽  
Na Xu ◽  
Yinju Yang ◽  
...  
Keyword(s):  
Nicotiana Tabacum ◽  
Chilling Stress ◽  
Lignin Biosynthesis ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Integrated Analysis ◽  
Limiting Factor ◽  
Active Metabolites ◽  
Cold Temperatures ◽  
Flight Mass Spectrometry ◽  
Key Steps

Chilling stress increases the amount of polyphenols, especially lignin, which protects tobacco (Nicotiana tabacum L. cv. k326) from chilling stress. To clarify the molecular biosynthesis mechanism of the key representative compounds, specifically lignin, RNA sequencing and ultra-high pressure liquid chromatography coupled to quadrupole-time of flight mass spectrometry technologies were used to construct transcriptomic and metabolomic libraries from the leaves of tobacco plants subjected to normal (25°C) and chilling (4°C) temperature treatments. Transcriptomic libraries from the different samples were sequenced, generating more than 40million raw reads. Among nine samples, metabolomic analysis identified a total of 97 encoding enzymes that function in the key steps of pathways related to polyphenol biosynthesis, where 42 metabolites were also located. An integrated analysis of metabolic and transcriptomic data revealed that most of the intermediate metabolites and enzymes related to lignin biosynthesis were synthesised in the leaves under chilling stress, which suggests that the biosynthesis of lignin plays an important role in the response of tobacco leaves to cold temperatures. In addition, the cold insensitivity of chalcone synthase genes might be considered to be an important rate-limiting factor in the process of precursor substance flow to flavonoid biosynthesis under chilling stress. Furthermore, the upregulated expression of phenylalanine ammonia lyase (PAL), hydroxycinnamoyl transferase (HCT) and cinnamyl-alcohol dehydrogenase (CAD) under chilling stress is the key to an increase in lignin synthesis. This study provides a hypothetical basis for the screening of new active metabolites and the metabolic engineering of polyphenols in tobacco.

scholarly journals Altered lignocellulose chemical structure and molecular assembly in CINNAMYL ALCOHOL DEHYDROGENASE-deficient rice

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Andri Fadillah Martin ◽  
Yuki Tobimatsu ◽  
Ryosuke Kusumi ◽  
Naoyuki Matsumoto ◽  
Takuji Miyamoto ◽  
...  
Keyword(s):  
Alcohol Dehydrogenase ◽  
Supramolecular Structure ◽  
Lignin Biosynthesis ◽  
Total Content ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Molecular Assembly ◽  
Limiting Factor ◽  
Cinnamyl Alcohol ◽  
Chemical Structures ◽  
Rice Mutant

AbstractLignin is a complex phenylpropanoid polymer deposited in plant cell walls. Lignin has long been recognized as an important limiting factor for the polysaccharide-oriented biomass utilizations. To mitigate lignin-associated biomass recalcitrance, numerous mutants and transgenic plants that produce lignocellulose with reduced lignin contents and/or lignins with altered chemical structures have been produced and characterised. However, it is not fully understood how altered lignin chemistry affects the supramolecular structure of lignocellulose, and consequently, its utilization properties. Herein, we conducted comprehensive chemical and supramolecular structural analyses of lignocellulose produced by a rice cad2 mutant deficient in CINNAMYL ALCOHOL DEHYDROGENASE (CAD), which encodes a key enzyme in lignin biosynthesis. By using a solution-state two-dimensional NMR approach and complementary chemical methods, we elucidated the structural details of the altered lignins enriched with unusual hydroxycinnamaldehyde-derived substructures produced by the cad2 mutant. In parallel, polysaccharide assembly and the molecular mobility of lignocellulose were investigated by solid-state 13C MAS NMR, nuclear magnetic relaxation, X-ray diffraction, and Simon’s staining analyses. Possible links between CAD-associated lignin modifications (in terms of total content and chemical structures) and changes to the lignocellulose supramolecular structure are discussed in the context of the improved biomass saccharification efficiency of the cad2 rice mutant.

scholarly journals Reactive Oxygen Species and the Redox-Regulatory Network in Cold Stress Acclimation

Antioxidants ◽  
2018 ◽  
Vol 7 (11) ◽  
pp. 169 ◽  
Author(s):  
Anna Dreyer ◽  
Karl-Josef Dietz
Keyword(s):  
Reactive Oxygen Species ◽  
Cold Stress ◽  
Regulatory Network ◽  
Chilling Stress ◽  
Nicotinamide Adenine Dinucleotide Phosphate ◽  
Reactive Oxygen ◽  
Cold Climate ◽  
Oxygen Species ◽  
Cold Temperatures ◽  
Stress Acclimation

Cold temperatures restrict plant growth, geographical extension of plant species, and agricultural practices. This review deals with cold stress above freezing temperatures often defined as chilling stress. It focuses on the redox regulatory network of the cell under cold temperature conditions. Reactive oxygen species (ROS) function as the final electron sink in this network which consists of redox input elements, transmitters, targets, and sensors. Following an introduction to the critical network components which include nicotinamide adenine dinucleotide phosphate (NADPH)-dependent thioredoxin reductases, thioredoxins, and peroxiredoxins, typical laboratory experiments for cold stress investigations will be described. Short term transcriptome and metabolome analyses allow for dissecting the early responses of network components and complement the vast data sets dealing with changes in the antioxidant system and ROS. This review gives examples of how such information may be integrated to advance our knowledge on the response and function of the redox regulatory network in cold stress acclimation. It will be exemplarily shown that targeting the redox network might be beneficial and supportive to improve cold stress acclimation and plant yield in cold climate.

scholarly journals Analysis of Active Metabolites of Sophora flavescens for Indoleamine 2,3-dioxygenase and Monoamine Oxidases using Ultra-Performance Liquid Chromatography-Quadrupole time-of-Flight Mass Spectrometry

2018 ◽  
Vol 13 (12) ◽  
pp. 1934578X1801301 ◽  
Author(s):  
Mi Hyeon Park ◽  
Seong Mi Lee ◽  
Sung-Kyun Ko ◽  
Kyeong Yeol Oh ◽  
Jung-Hee Kim ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
High Performance ◽  
Time Of Flight ◽  
Sophora Flavescens ◽  
Active Metabolites ◽  
Ongoing Research ◽  
Monoamine Oxidases ◽  
Indoleamine 2,3 Dioxygenase ◽  
Flight Mass Spectrometry

As part of ongoing research on natural products derived from medicinal plants for enzyme inhibition, known dibenzoyl derivatives (1–3, 11 and 20), pterocarpans (4, 15 and 19), flavanones (5, 7, 10, 12–14, 18, 21–24, 26, 27, 29, 31–33, 35, 36, and 38–46), flavones (6, 16, 28, 30 and 37), isoflavones (8 and 17), furocoumarins (9), and chalcones (25 and 34) have been tentatively identified within fractions of Sophora flavescens roots (SFR) using the ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTof-MS) technique. The extract and column fractions inhibited indoleamine 2,3-dioxygenase (IDO) and monoamine oxidases (MAOs) differently depending on the metabolite groups. The majority of rich fractions were shown to have residual activities of 49–59% at 10 μg/mL (IDO) and 11.7–34.9% at 50 μg/mL (MAOs) or below. In the total ion current (TIC) chromatogram, significant markers for the metabolites of the bioactive-guided fractions were identified; pterocarpans (4, 15 and 19), flavanones (5, 10, 12–14, 18, 21–23, 26, 29 31–33, 35, 36, and 38–46), isoflavones (8 and 17), furocoumarins (9), dibenzoyl derivatives (11 and 20), flavones (16, 28, 30 and 37), and chalcones (25 and 34) were evaluated among forty-six analyzed metabolites. Possible bioactive markers could be deduced using a data library and previous references, and information regarding spectroscopic characterization and optimal target metabolites was obtained.

scholarly journals Integrated Proteo-Transcriptomic Analyses Reveal Insights into Regulation of Pollen Development Stages and Dynamics of Cellular Response to Apple Fruit Crinkle Viroid (AFCVd)-Infection in Nicotiana tabacum

2020 ◽  
Vol 21 (22) ◽  
pp. 8700
Author(s):  
Ankita Shrestha ◽  
Ajay Kumar Mishra ◽  
Jaroslav Matoušek ◽  
Lenka Steinbachová ◽  
David Potěšil ◽  
...  
Keyword(s):  
Nicotiana Tabacum ◽  
Pollen Development ◽  
Apple Fruit ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Pairwise Comparisons ◽  
Development Stages ◽  
Gradual Process ◽  
Three Stages ◽  
Pollen Stage

Tobacco (Nicotiana tabacum) pollen is a well-suited model for studying many fundamental biological processes owing to its well-defined and distinct development stages. It is also one of the major agents involved in the transmission of infectious viroids, which is the primary mechanism of viroid pathogenicity in plants. However, some viroids are non-transmissible and may be possibly degraded or eliminated during the gradual process of pollen development maturation. The molecular details behind the response of developing pollen against the apple fruit crinkle viroid (AFCVd) infection and viroid eradication is largely unknown. In this study, we performed an integrative analysis of the transcriptome and proteome profiles to disentangle the molecular cascade of events governing the three pollen development stages: early bicellular pollen (stage 3, S3), late bicellular pollen (stage 5, S5), and 6 h-pollen tube (PT6). The integrated analysis delivered the molecular portraits of the developing pollen against AFCVd infection, including mechanistic insights into the viroid eradication during the last steps of pollen development. The isobaric tags for label-free relative quantification (iTRAQ) with digital gene expression (DGE) experiments led us to reliably identify subsets of 5321, 5286, and 6923 proteins and 64,033, 60,597, and 46,640 expressed genes in S3, S5, and PT6, respectively. In these subsets, 2234, 2108 proteins and 9207 and 14,065 mRNAs were differentially expressed in pairwise comparisons of three stages S5 vs. S3 and PT6 vs. S5 of control pollen in tobacco. Correlation analysis between the abundance of differentially expressed mRNAs (DEGs) and differentially expressed proteins (DEPs) in pairwise comparisons of three stages of pollen revealed numerous discordant changes in mRNA/protein pairs. Only a modest correlation was observed, indicative of divergent transcription, and its regulation and importance of post-transcriptional events in the determination of the fate of early and late pollen development in tobacco. The functional and enrichment analysis of correlated DEGs/DEPs revealed the activation in pathways involved in carbohydrate metabolism, amino acid metabolism, lipid metabolism, and cofactor as well as vitamin metabolism, which points to the importance of these metabolic pathways in pollen development. Furthermore, the detailed picture of AFCVd-infected correlated DEGs/DEPs was obtained in pairwise comparisons of three stages of infected pollen. The AFCVd infection caused the modulation of several genes involved in protein degradation, nuclear transport, phytohormone signaling, defense response, and phosphorylation. Intriguingly, we also identified several factors including, DNA-dependent RNA-polymerase, ribosomal protein, Argonaute (AGO) proteins, nucleotide binding proteins, and RNA exonucleases, which may plausibly involve in viroid stabilization and eradication during the last steps of pollen development. The present study provides essential insights into the transcriptional and translational dynamics of tobacco pollen, which further strengthens our understanding of plant-viroid interactions and support for future mechanistic studies directed at delineating the functional role of candidate factors involved in viroid elimination.

scholarly journals The climatic rhythm and blooms of cyanobacteria in a tropical reservoir in São Paulo, Brazil

2014 ◽  
Vol 74 (1) ◽  
pp. 72-78 ◽  
Author(s):  
I Ogashawara ◽  
JA Zavattini ◽  
JG Tundisi
Keyword(s):  
Water Quality ◽  
Meteorological Data ◽  
Polar Front ◽  
Sao Paulo ◽  
Cyanobacterial Blooms ◽  
Metropolitan Region ◽  
Integrated Analysis ◽  
Limiting Factor ◽  
São Paulo ◽  
Tropical Reservoir

The present study sought to develop a methodology to analyse water quality based on the concepts and methods of climate and climatology. Accordingly, we attempted to relate hydro- and limnometeorological techniques and methodologies to a rhythmic analysis technique developed within the context of the Brazilian geographical climatology. Our goal was to assess and analyse cyanobacterial blooms, the main index of water quality for the reservoirs of the “Alto Tietê” Basin and, consequently, the Metropolitan Region of São Paulo, an area of high environmental complexity due to its high degree of development and high population density. The meteorological data used were collected by the Institute of Astronomy, Geophysics and Atmospheric Sciences at the University of São Paulo meteorological station, and the limnological data were collected through the Hydrological Monitoring System implemented by SABESP in the Billings and Guarapiranga Reservoirs and the laboratory of the same entity. The rhythmic and integrated analysis showed that the process of cyanobacterial blooms is dependent on a combination of meteorological factors as temperature and wind intensity that may disrupt the stability of the reservoir, providing the conditions necessary for the development of cyanobacteria during the stabilisation process. The pace of the Atlantic Polar Front Entrance during the winter in São Paulo is a limiting factor for the growth of cyanobacteria because of their high frequency, thus maintaining the balance of the reservoir throughout this period. The weather types those could cause a instability in the water column were: Cold Front entrance (66.67%), conflict between masses (22.22%) and the Tropical Instability Line (11.11%). The possibility for prevention and forecasting periods advise when these reservoirs should not be used, mainly with regard to recreational activities.

scholarly journals Isolation and Characterization of Full-Length Phenylalanine Ammonium Lyase and Cinnamyl Alcohol Dehydrogenase Genes Involved in Lignin Biosynthesis of Erianthus Arundinaceus

Proceedings ◽  
2020 ◽  
Vol 36 (1) ◽  
pp. 174
Author(s):  
Lakshmi Kasirajan ◽  
Prathima Perumal Thirugnanasambandam ◽  
Agnelo Furtado ◽  
Frikkie C. Botha ◽  
Robert J. Henry
Keyword(s):  
Alcohol Dehydrogenase ◽  
Untranslated Region ◽  
Plant Cell Wall ◽  
Lignin Content ◽  
Lignin Biosynthesis ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Raw Material ◽  
Sequence Information ◽  
Cinnamyl Alcohol ◽  
Isolation And Characterization

Lignocellulosic biomasses available in abundance is the most promising raw material for alternate energy production considering the issues of dwindling oil prices, and global warming. Recently, Erianthus arundinaceous has been identified as a potential target for second generation biofuel crop due to its high biomass production, and adaptability to extreme growth environments. Lignin is a major plant cell wall polymer indispensable for plant growth and development, however it hinders the saccharification of lignocellulosic biomass. Based on the previous transcriptome studies in a set of sugarcane genotypes differing for lignin content, genes encoding cinnamyl alcohol dehydrogenase (CAD), and Phenylalanine ammonia lyase (PAL) genes playing major roles in genetic regulation of lignin production have been cloned and characterized from an Erianthus clone IK 76-81. The genomic region of EriCAD was 3524 bp sequence containing four exons and three introns, among which the exon 1&2 of 88 and 80 bp were conserved with sorghum and Miscanthus CADs. The coding region of CAD was identified with 1086 bp open reading frame (ORF), a 68 bp 5′ untranslated region (UTR), and a 86 bp 3′ untranslated region (UTR). In the PROSITE analysis, a zinc-containing alcohol dehydrogenase signature (GHEVVGEVVEVGPEV) and an NADP-binding domain motif (GLGGLG) was identified. Similarly sequence analysis of PAL showed an ORF of 2106 bp encoding for 702 amino acid residues. It was flanked by 172 bp of 5′ UTR and 121 bp of 3′ UTR. This sequence information on PAL and CAD from Erianthus might be useful for subsequent research on lignin modification for improved biomass conversion.

scholarly journals Tubulin recycling limits cold tolerance

2019 ◽  
Author(s):  
Gabriella Li ◽  
Jeffrey K. Moore
Keyword(s):  
Cold Tolerance ◽  
Low Temperatures ◽  
Conformational Dynamics ◽  
Limiting Factor ◽  
Cold Temperatures ◽  
Nucleation Sites ◽  
Tubulin Binding ◽  
Microtubule Networks ◽  
Almost All ◽  
In Cells

AbstractAlthough cold temperatures have long been used to depolymerize microtubules, how temperature specifically affects the polymerization and depolymerization activities of tubulin proteins and how these lead to changes in microtubule networks in cells has not been established. We investigated these questions in budding yeast, an organism found in diverse environments and therefore predicted to exhibit dynamic microtubules across a broad range of temperatures. We measured the dynamics of GFP-labeled microtubules in living cells and found that lowering the temperature from 37°C to 10°C decreased the rates of both polymerization and depolymerization, decreased the amount of polymer assembled before catastrophes and decreased the frequency of microtubule emergence from nucleation sites. Lowering to 4°C caused rapid loss of almost all microtubule polymer. We provide evidence that these effects on microtubule dynamics may be explained in part by changes in the co-factor-dependent conformational dynamics of tubulin proteins. Ablation of tubulin-binding co-factors further sensitizes cells and their microtubules to low temperatures, and we highlight a specific role for TBCB/Alf1 in microtubule maintenance at low temperatures. Finally, we show that inhibiting the maturation cycle of tubulin by using a point mutant in β-tubulin confers hyper-stable microtubules at low temperatures, rescues the requirement for TBCB/Alf1, and improves the cold tolerance of the yeast. Together, these results reveal an unappreciated step in the tubulin cycle in cells and suggest that this step may be a key limiting factor in the thermal tolerance of organisms.

scholarly journals Overexpression of Pear (Pyrus pyrifolia) CAD2 in Tomato Affects Lignin Content

Molecules ◽  
2019 ◽  
Vol 24 (14) ◽  
pp. 2595 ◽  
Author(s):  
Mingtong Li ◽  
Chenxia Cheng ◽  
Xinfu Zhang ◽  
Suping Zhou ◽  
Lixia Li ◽  
...  
Keyword(s):  
Lignin Content ◽  
Lignin Biosynthesis ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Transformation Method ◽  
Transgenic Tomato ◽  
Pyrus Pyrifolia ◽  
Tomato Plants ◽  
Over Expression ◽  
Transgenic Tomato Plants ◽  
Vessel Elements

PpCAD2 was originally isolated from the ‘Wangkumbae’ pear (Pyrus pyrifolia Nakai), and it encodes for cinnamyl alcohol dehydrogenase (CAD), which is a key enzyme in the lignin biosynthesis pathway. In order to verify the function of PpCAD2, transgenic tomato (Solanum lycopersicum) ‘Micro-Tom’ plants were generated using over-expression constructs via the agrobacterium-mediated transformation method. The results showed that the PpCAD2 over-expression transgenic tomato plant had a strong growth vigor. Furthermore, these PpCAD2 over-expression transgenic tomato plants contained a higher lignin content and CAD enzymatic activity in the stem, leaf and fruit pericarp tissues, and formed a greater number of vessel elements in the stem and leaf vein, compared to wild type tomato plants. This study clearly indicated that overexpressing PpCAD2 increased the lignin deposition of transgenic tomato plants, and thus validated the function of PpCAD2 in lignin biosynthesis.

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