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.

scholarly journals The global mass and average rate of rubisco

2019 ◽  
Vol 116 (10) ◽  
pp. 4738-4743 ◽  
Author(s):  
Yinon M. Bar-On ◽  
Ron Milo
Keyword(s):  
Total Mass ◽  
Carbon Fixation ◽  
Average Rate ◽  
Carbon Assimilation ◽  
Dry Weight ◽  
Effective Rate ◽  
Terrestrial Plants ◽  
Bisphosphate Carboxylase ◽  
Catalytic Rate

Photosynthetic carbon assimilation enables energy storage in the living world and produces most of the biomass in the biosphere. Rubisco (d-ribulose 1,5-bisphosphate carboxylase/oxygenase) is responsible for the vast majority of global carbon fixation and has been claimed to be the most abundant protein on Earth. Here we provide an updated and rigorous estimate for the total mass of Rubisco on Earth, concluding it is ≈0.7 Gt, more than an order of magnitude higher than previously thought. We find that >90% of Rubisco enzymes are found in the ≈2 × 1014m2of leaves of terrestrial plants, and that Rubisco accounts for ≈3% of the total mass of leaves, which we estimate at ≈30 Gt dry weight. We use our estimate for the total mass of Rubisco to derive the effective time-averaged catalytic rate of Rubisco of ≈0.03 s−1on land and ≈0.6 s−1in the ocean. Compared with the maximal catalytic rate observed in vitro at 25 °C, the effective rate in the wild is ≈100-fold slower on land and sevenfold slower in the ocean. The lower ambient temperature, and Rubisco not working at night, can explain most of the difference from laboratory conditions in the ocean but not on land, where quantification of many more factors on a global scale is needed. Our analysis helps sharpen the dramatic difference between laboratory and wild environments and between the terrestrial and marine environments.

scholarly journals Quantitative proteomic analysis of aberrant expressed lysine acetylation in gastrointestinal stromal tumors

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Bo Wang ◽  
Long Zhao ◽  
Zhidong Gao ◽  
Jianyuan Luo ◽  
Haoran Zhang ◽  
...  
Keyword(s):  
Risk Group ◽  
Risk Groups ◽  
Quantitative Information ◽  
Differentially Expressed ◽  
High Rate ◽  
Lysine Acetylation ◽  
Kegg Pathways ◽  
Tandem Mass Tag ◽  
Cell Components ◽  
Nih Classification

Abstract Background Gastrointestinal stromal tumor (GIST) is a common digestive tract tumor with high rate of metastasis and recurrence. Currently, we understand the genome, transcriptome and proteome in GIST. However, posttranscriptional modification features in GIST remain unclear. In the present study, we aimed to construct a complete profile of acetylome in GIST. Methods Five common protein modifications, including acetylation, succinylation, crotonylation, 2-hydroxyisobutyrylation, and malonylation were tested among GIST subgroups and significantly differentially- expressed lysine acetylation was found. The acetylated peptides labeled with Tandem Mass Tag (TMT)under high sensitive mass spectrometry, and some proteins with acetylation sites were identified. Subsequently, these proteins and peptides were classified into high/moderate (H/M) risk and low (L) risk groups according to the modified NIH classification standard. Furthermore, cell components, molecular function, biological processes, KEGG pathways and protein interaction networks were analyzed. Results A total of 2904 acetylation sites from 1319 proteins were identified, of which quantitative information of 2548 sites from 1169 proteins was obtained. Finally, the differentially-expressed lysine acetylation sites were assessed and we found that 42 acetylated sites of 38 proteins were upregulated in the H/M risk group compared with the L risk group, while 48 acetylated sites of 44 proteins were downregulated, of which Ki67 K1063Ac and FCHSD2 K24Ac were the two acetylated proteins that were most changed. Conclusions Our novel findings provide further understanding of acetylome in GIST and might demonstrate the possibility in the acetylation targeted diagnosis and therapy of GIST.

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 Photosynthetic efficiency and production of cowpea cultivars under deficit irrigation

2018 ◽  
Vol 13 (5) ◽  
pp. 1 ◽  
Author(s):  
Alberto Soares de Melo ◽  
Allisson Rafael Ferreira da Silva ◽  
Alexson Filgueiras Dutra ◽  
Wellison Filgueiras Dutra ◽  
Marcos Eric Barbosa Brito ◽  
...  
Keyword(s):  
Water Deficit ◽  
Deficit Irrigation ◽  
Photosynthetic Efficiency ◽  
Arid Regions ◽  
Carbon Fixation ◽  
Management Strategies ◽  
Carbon Assimilation ◽  
Green Beans ◽  
Gas Exchanges ◽  
Cowpea Cultivars

Cowpea is a crop with great economic, social and food importance in semi-arid regions, but its production is drastically reduced by the water deficit in these regions, requiring better management strategies that allow the crop’s production. This study therefore aimed to evaluate the photosynthetic efficiency and production of cowpea cultivars under deficit irrigation replacement levels. The experiment tested three cowpea genotypes (G1 = ‘BRS Aracé’, G2 = ‘BR 17 Gurguéia’ and G3 = ‘BRS Marataoã’) and four irrigation depths (40, 60, 80 and 100% of ETc), resulting in a 3 x 4 factorial scheme, arranged in randomized complete blocks design with four replicates. During the experiment, the gas exchanges, chlorophyll a fluorescence and production of the cowpea genotypes under deficit irrigation were evaluated. Carbon fixation in the photosynthetic metabolism of cowpea plants was reduced by accentuated water deficit, regardless of the genotype. The low stress severity was indicated by the lack of effects on chlorophyll fluorescence, indicating that the reduction in the rate of carbon assimilation was due to the stomatal effects. The irrigation with 80% of ETc can be used in the cultivation of the respective cultivars, but with small losses in the production. Among the genotypes, ‘BRS Marataoã’ stands out with respect to yield, with higher values for weight of pods and green beans.

scholarly journals Transcriptomic responses of Microcystis aeruginosa under electromagnetic radiation exposure

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chao Tang ◽  
Ziyan Zhang ◽  
Shen Tian ◽  
Peng Cai
Keyword(s):  
Energy Metabolism ◽  
Electromagnetic Radiation ◽  
Differentially Expressed Genes ◽  
Microcystis Aeruginosa ◽  
Carbon Fixation ◽  
Biological Effects ◽  
Differentially Expressed ◽  
Ecological Environment ◽  
Inhibit Protein Synthesis ◽  
Potential Threat

AbstractElectromagnetic radiation is an important environmental factor. It has a potential threat to public health and ecological environment. However, the mechanism by which electromagnetic radiation exerts these biological effects remains unclear. In this study, the effect of Microcystis aeruginosa under electromagnetic radiation (1.8 GHz, 40 V/m) was studied by using transcriptomics. A total of 306 differentially expressed genes, including 121 upregulated and 185 downregulated genes, were obtained in this study. The differentially expressed genes were significantly enriched in the ribosome, oxidative phosphorylation and carbon fixation pathways, indicating that electromagnetic radiation may inhibit protein synthesis and affect cyanobacterial energy metabolism and photosynthesis. The total ATP synthase activity and ATP content significantly increased, whereas H+K+-ATPase activity showed no significant changes. Our results suggest that the energy metabolism pathway may respond positively to electromagnetic radiation. In the future, systematic studies on the effects of electromagnetic radiation based on different intensities, frequencies, and exposure times are warranted; to deeply understand and reveal the target and mechanism of action of electromagnetic exposure on organisms.

scholarly journals Design and in vitro realization of carbon-conserving photorespiration

2018 ◽  
Vol 115 (49) ◽  
pp. E11455-E11464 ◽  
Author(s):  
Devin L. Trudeau ◽  
Christian Edlich-Muth ◽  
Jan Zarzycki ◽  
Marieke Scheffen ◽  
Moshe Goldsmith ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Calvin Cycle ◽  
Computational Design ◽  
Carbon Loss ◽  
Fixation Rate ◽  
Bisphosphate Carboxylase ◽  
Stoichiometric Model ◽  
Synthetic Routes ◽  
Coa Reductase

Photorespiration recycles ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenation product, 2-phosphoglycolate, back into the Calvin Cycle. Natural photorespiration, however, limits agricultural productivity by dissipating energy and releasing CO2. Several photorespiration bypasses have been previously suggested but were limited to existing enzymes and pathways that release CO2. Here, we harness the power of enzyme and metabolic engineering to establish synthetic routes that bypass photorespiration without CO2 release. By defining specific reaction rules, we systematically identified promising routes that assimilate 2-phosphoglycolate into the Calvin Cycle without carbon loss. We further developed a kinetic–stoichiometric model that indicates that the identified synthetic shunts could potentially enhance carbon fixation rate across the physiological range of irradiation and CO2, even if most of their enzymes operate at a tenth of Rubisco’s maximal carboxylation activity. Glycolate reduction to glycolaldehyde is essential for several of the synthetic shunts but is not known to occur naturally. We, therefore, used computational design and directed evolution to establish this activity in two sequential reactions. An acetyl-CoA synthetase was engineered for higher stability and glycolyl-CoA synthesis. A propionyl-CoA reductase was engineered for higher selectivity for glycolyl-CoA and for use of NADPH over NAD+, thereby favoring reduction over oxidation. The engineered glycolate reduction module was then combined with downstream condensation and assimilation of glycolaldehyde to ribulose 1,5-bisphosphate, thus providing proof of principle for a carbon-conserving photorespiration pathway.

scholarly journals Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

2020 ◽  
Author(s):  
Changbing Huang ◽  
Chun Jiang ◽  
limin Jin ◽  
Huanchao Zhang
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Stress Responses ◽  
Target Genes ◽  
Low Temperature Stress ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas ◽  
Cold Tolerant

Abstract Background:Hemerocallis fulva is a perennial herb belonging to Hemerocallis of Hemerocallis. Because of the large and bright colors, it is often used as a garden ornamental plant. But most varieties of H. fulva on the market will wither in winter, which will affect their beauty. It is very important to study the effect of low temperature stress on the physiological indexes of H. fulva and understand the cold tolerance of different H. fulva. MiRNA is a kind of endogenous non coding small molecular RNA with length of 21-24nt. It mainly inhibits protein translation by cutting target genes, and plays an important role in the development of organisms, gene expression and biological stress. Low temperature is the main abiotic stress affecting the production of H. fulva in China, which hinders the growth and development of plants. A comprehensive understanding of the expression pattern of microRNA in H. fulva under low temperature stress can improve our understanding of microRNA mediated stress response. Although there are many studies on miRNAs of various plants under cold stress at home and abroad, there are few studies on miRNAs related to cold stress of H. fulva. It is of great significance to explore the cold stress resistant gene resources of H. fulva, especially the identification and functional research of miRNA closely related to cold stress, for the breeding of excellent H. fulva.Results A total of 5619 cold-responsive miRNAs, 315 putative novel and 5 304 conserved miRNAs, were identified from the leaves and roots of two different varieties ‘Jinyan’ (cold-tolerant) and ‘Lucretius ’ (cold-sensitive), which were stressed under -4 oC for 24 h. Twelve conserved and three novel miRNAs (novel-miR10, novel-miR19 and novel-miR48) were differentially expressed in leaves of ‘Jinyan’ under cold stress. Novel-miR19, novel-miR29 and novel-miR30 were up-regulated in roots of ‘Jinyan’ under cold stress. Thirteen and two conserved miRNAs were deferentially expressed in leaves and roots of ‘Lucretius’ after cold stress. The deferentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR156, miR166 and miR319 families. A total of 6 598 target genes for 6 516 known miRNAs and 82 novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Ten differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR(q-PCR), and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR156a-3-p, miR319a, and novel-miR19) may play important roles in plant response to cold stress.Conclusions Our study indicates that some putative target genes and miRNA mediated metabolic processes and stress responses are significant to cold tolerance in H. fulva.

scholarly journals Photoperiod, Carbon Partitioning, and Reproductive Development in Rabbiteye Blueberry

1991 ◽  
Vol 116 (5) ◽  
pp. 856-860 ◽  
Author(s):  
Rebecca L. Darnell
Keyword(s):  
Carbon Fixation ◽  
Carbon Assimilation ◽  
Reproductive Development ◽  
Carbon Partitioning ◽  
Stem Tissue ◽  
Flower Buds ◽  
Vaccinium Ashei ◽  
Bloom Period ◽  
Short Days

Containerized `Climax' and `Beckyblue' rabbiteye blueberry plants (Vaccinium ashei Reade) were exposed to 5 weeks of natural daylengths or shortened daylengths starting 30 Sept. `Beckyblue' plants exposed to short daylengths in the fall initiated more flower buds and had a shorter, more concentrated bloom period than did plants exposed to natural fall daylengths. Reproductive development of `Climax' was not influenced by photoperiod treatments. Leaf carbon assimilation of both cultivars increased under short days. Partitioning of translocated 14C-labeled assimilates to stem tissue increased under short photoperiods for `Beckyblue'; however, partitioning patterns in `Climax' were not affected. Increased carbon fixation and increased partitioning of carbon to stem tissue under short days may contribute to the observed effect of short days on enhancing reproductive development in `Beckyblue'.

scholarly journals The keystone species of Precambrian deep bedrock biosphere belong to <i>Burkholderiales</i> and <i>Clostridiales</i>

2015 ◽  
Vol 12 (21) ◽  
pp. 18103-18150 ◽  
Author(s):  
L. Purkamo ◽  
M. Bomberg ◽  
R. Kietäväinen ◽  
H. Salavirta ◽  
M. Nyyssönen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Carbon Fixation ◽  
Keystone Species ◽  
Carbon Assimilation ◽  
Sugar Metabolism ◽  
Archaeal Community ◽  
Amino Sugar ◽  
Amplicon Sequencing ◽  
Fracture Zones ◽  
Crystalline Bedrock

Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180–2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments.

scholarly journals CO2 Assimilation, Photosynthetic Enzymes, and Carbohydrates of `Concord' Grape Leaves in Response to Iron Supply

2004 ◽  
Vol 129 (5) ◽  
pp. 738-744 ◽  
Author(s):  
Li-Song Chen ◽  
Brandon R. Smith ◽  
Lailiang Cheng
Keyword(s):  
Sucrose Concentration ◽  
Calvin Cycle ◽  
Sucrose Phosphate Synthase ◽  
Nonstructural Carbohydrates ◽  
Bisphosphate Carboxylase ◽  
Chl A ◽  
Photosynthetic Enzymes ◽  
Fe Content ◽  
Significant Difference ◽  
Assimilation Capacity

Own-rooted 1-year-old `Concord' grapevines (Vitis labruscana Bailey) were fertigated twice weekly for 11 weeks with 1, 10, 20, 50, or 100 μm iron (Fe) from ferric ethylenediamine di (o-hydroxyphenylacetic) acid (Fe-EDDHA) in a complete nutrient solution. As Fe supply increased, leaf total Fe content did not show a significant change, whereas active Fe (extracted by 2,2′-dipyridyl) content increased curvilinearly. Chlorophyll (Chl) content increased as Fe supply increased, with a greater response at the lower Fe rates. Chl a: b ratio remained relatively constant over the range of Fe supply, except for a slight increase at the lowest Fe treatment. Both CO2 assimilation and stomatal conductance increased curvilinearly with increasing leaf active Fe, whereas intercellular CO2 concentrations decreased linearly. Activities of key enzymes in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), NADP-glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoribulokinase (PRK), stromal fructose-1,6-bisphosphatase (FBPase), and a key enzyme in sucrose synthesis, cytosolic FBPase, all increased linearly with increasing leaf active Fe. No significant difference was found in the activities of ADP-glucose pyrophosphorylase (AGPase) and sucrose phosphate synthase (SPS) of leaves between the lowest and the highest Fe treatments, whereas slightly lower activities of AGPase and SPS were observed in the other three Fe treatments. Content of 3-phosphoglycerate (PGA) increased curvilinearly with increasing leaf active Fe, whereas glucose-6-phosphate (G6P), fructose-6-phosphate (F6P), and the ratio of G6P: F6P remained unchanged over the range of Fe supply. Concentrations of glucose, fructose, sucrose, starch, and total nonstructural carbohydrates (TNC) at both dusk and predawn increased with increasing leaf active Fe. Concentrations of starch and TNC at any given leaf active Fe content were higher at dusk than at predawn, but both glucose and fructose showed the opposite trend. No difference in sucrose concentration was found at dusk or predawn. The export of carbon from starch breakdown during the night, calculated as the difference between dusk and predawn measurements, increased as leaf active Fe content increased. The ratio of starch to sucrose at both dusk and predawn also increased with increasing leaf active Fe. In conclusion, Fe limitation reduces the activities of Rubisco and other photosynthetic enzymes, and hence CO2 assimilation capacity. Fe-deficient grapevines have lower concentrations of nonstructural carbohydrates in source leaves and, therefore, are source limited.

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