TMT-Based Quantitative Proteomic Analysis Reveals the Physiological Regulatory Networks of Embryo Dehydration Protection in Lotus (Nelumbo nucifera)

Lotus is an aquatic plant that is sensitive to water loss, but its seeds are longevous after seed embryo dehydration and maturation. The great difference between the responses of vegetative organs and seeds to dehydration is related to the special protective mechanism in embryos. In this study, tandem mass tags (TMT)-labeled proteomics and parallel reaction monitoring (PRM) technologies were used to obtain novel insights into the physiological regulatory networks during lotus seed dehydration process. Totally, 60,266 secondary spectra and 32,093 unique peptides were detected. A total of 5,477 proteins and 815 differentially expressed proteins (DEPs) were identified based on TMT data. Of these, 582 DEPs were continuously downregulated and 228 proteins were significantly up-regulated during the whole dehydration process. Bioinformatics and protein-protein interaction network analyses indicated that carbohydrate metabolism (including glycolysis/gluconeogenesis, galactose, starch and sucrose metabolism, pentose phosphate pathway, and cell wall organization), protein processing in ER, DNA repair, and antioxidative events had positive responses to lotus embryo dehydration. On the contrary, energy metabolism (metabolic pathway, photosynthesis, pyruvate metabolism, fatty acid biosynthesis) and secondary metabolism (terpenoid backbone, steroid, flavonoid biosynthesis) gradually become static status during lotus embryo water loss and maturation. Furthermore, non-enzymatic antioxidants and pentose phosphate pathway play major roles in antioxidant protection during dehydration process in lotus embryo. Abscisic acid (ABA) signaling and the accumulation of oligosaccharides, late embryogenesis abundant proteins, and heat shock proteins may be the key factors to ensure the continuous dehydration and storage tolerance of lotus seed embryo. Stress physiology detection showed that H2O2 was the main reactive oxygen species (ROS) component inducing oxidative stress damage, and glutathione and vitamin E acted as the major antioxidant to maintain the REDOX balance of lotus embryo during the dehydration process. These results provide new insights to reveal the physiological regulatory networks of the protective mechanism of embryo dehydration in lotus.

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Faculty Opinions recommendation of Convergent evolution of zoonotic Brucella species toward the selective use of the pentose phosphate pathway.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.738798441.793579509 ◽

2020 ◽

Author(s):

Jean Celli

Keyword(s):

Pentose Phosphate Pathway ◽

Convergent Evolution ◽

Pentose Phosphate ◽

Brucella Species

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Systematic Identification of Regulators of Oxidative Stress Reveals Non-canonical Roles for Peroxisomal Import and the Pentose Phosphate Pathway

Cell Reports ◽

10.1016/j.celrep.2020.01.013 ◽

2020 ◽

Vol 30 (5) ◽

pp. 1417-1433.e7 ◽

Cited By ~ 7

Author(s):

Michael M. Dubreuil ◽

David W. Morgens ◽

Kanji Okumoto ◽

Masanori Honsho ◽

Kévin Contrepois ◽

...

Keyword(s):

Oxidative Stress ◽

Pentose Phosphate Pathway ◽

Pentose Phosphate ◽

Systematic Identification

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Resolving the TCA cycle and pentose-phosphate pathway of Clostridium acetobutylicum ATCC 824: Isotopomer analysis, in vitro activities and expression analysis

Biotechnology Journal ◽

10.1002/biot.201000282 ◽

2010 ◽

Vol 6 (3) ◽

pp. 300-305 ◽

Cited By ~ 69

Author(s):

Scott B. Crown ◽

Dinesh C. Indurthi ◽

Woo Suk Ahn ◽

Jungik Choi ◽

Eleftherios T. Papoutsakis ◽

...

Keyword(s):

Expression Analysis ◽

Pentose Phosphate Pathway ◽

Clostridium Acetobutylicum ◽

Tca Cycle ◽

Pentose Phosphate ◽

The Tca Cycle ◽

Isotopomer Analysis ◽

Clostridium Acetobutylicum Atcc 824

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Geranylgeranylacetone attenuates cerebral ischemia–reperfusion injury in rats through the augmentation of HSP 27 phosphorylation: a preliminary study

BMC Neuroscience ◽

10.1186/s12868-021-00614-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Kazuya Matsuo ◽

Kohkichi Hosoda ◽

Jun Tanaka ◽

Yusuke Yamamoto ◽

Taichiro Imahori ◽

...

Keyword(s):

Cerebral Ischemia ◽

Reperfusion Injury ◽

Pentose Phosphate Pathway ◽

Ischemia Reperfusion Injury ◽

Ischemia Reperfusion ◽

Pentose Phosphate ◽

Cerebral Ischemia Reperfusion ◽

Hsp27 Phosphorylation ◽

Cerebral Ischemia Reperfusion Injury ◽

Preliminary Study

Abstract Background We previously reported that heat shock protein 27 (HSP27) phosphorylation plays an important role in the activation of glucose-6-phosphate dehydrogenase (G6PD), resulting in the upregulation of the pentose phosphate pathway and antioxidant effects against cerebral ischemia–reperfusion injury. The present study investigated the effect of geranylgeranylacetone, an inducer of HSP27, on ischemia–reperfusion injury in male rats as a preliminary study to see if further research of the effects of geranylgeranylacetone on the ischemic stroke was warranted. Methods In all experiments, male Wistar rats were used. First, we conducted pathway activity profiling based on a gas chromatography–mass spectrometry to identify ischemia–reperfusion-related metabolic pathways. Next, we investigated the effects of geranylgeranylacetone on the pentose phosphate pathway and ischemia–reperfusion injury by real-time polymerase chain reaction (RT-PCR), immunoblotting, and G6PD activity, protein carbonylation and infarct volume analysis. Geranylgeranylacetone or vehicle was injected intracerebroventricularly 3 h prior to middle cerebral artery occlusion or sham operation. Results Pathway activity profiling demonstrated that changes in the metabolic state depended on reperfusion time and that the pentose phosphate pathway and taurine-hypotaurine metabolism pathway were the most strongly related to reperfusion among 137 metabolic pathways. RT-PCR demonstrated that geranylgeranylacetone did not significantly affect the increase in HSP27 transcript levels after ischemia–reperfusion. Immunoblotting showed that geranylgeranylacetone did not significantly affect the elevation of HSP27 protein levels. However, geranylgeranylacetone significantly increase the elevation of phosphorylation of HSP27 after ischemia–reperfusion. In addition, geranylgeranylacetone significantly affected the increase in G6PD activity, and reduced the increase in protein carbonylation after ischemia–reperfusion. Accordingly, geranylgeranylacetone significantly reduced the infarct size (median 31.3% vs 19.9%, p = 0.0013). Conclusions As a preliminary study, these findings suggest that geranylgeranylacetone may be a promising agent for the treatment of ischemic stroke and would be worthy of further study. Further studies are required to clearly delineate the mechanism of geranylgeranylacetone-induced HSP27 phosphorylation in antioxidant effects, which may guide the development of new approaches for minimizing the impact of cerebral ischemia–reperfusion injury.

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Pentose Phosphate Pathway Reactions in Photosynthesizing Cells

Cells ◽

10.3390/cells10061547 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1547

Author(s):

Thomas D. Sharkey

Keyword(s):

Pentose Phosphate Pathway ◽

Strong Association ◽

Pentose Phosphate ◽

Critical Component ◽

Reaction Sequence ◽

Response To Stress ◽

Labeling Pattern

The pentose phosphate pathway (PPP) is divided into an oxidative branch that makes pentose phosphates and a non-oxidative branch that consumes pentose phosphates, though the non-oxidative branch is considered reversible. A modified version of the non-oxidative branch is a critical component of the Calvin–Benson cycle that converts CO2 into sugar. The reaction sequence in the Calvin–Benson cycle is from triose phosphates to pentose phosphates, the opposite of the typical direction of the non-oxidative PPP. The photosynthetic direction is favored by replacing the transaldolase step of the normal non-oxidative PPP with a second aldolase reaction plus sedoheptulose-1,7-bisphosphatase. This can be considered an anabolic version of the non-oxidative PPP and is found in a few situations other than photosynthesis. In addition to the strong association of the non-oxidative PPP with photosynthesis metabolism, there is recent evidence that the oxidative PPP reactions are also important in photosynthesizing cells. These reactions can form a shunt around the non-oxidative PPP section of the Calvin–Benson cycle, consuming three ATP per glucose 6-phosphate consumed. A constitutive operation of this shunt occurs in the cytosol and gives rise to an unusual labeling pattern of photosynthetic metabolites while an inducible shunt in the stroma may occur in response to stress.

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Fine tuning the glycolytic flux ratio of EP-bifido pathway for mevalonate production by enhancing glucose-6-phosphate dehydrogenase (Zwf) and CRISPRi suppressing 6-phosphofructose kinase (PfkA) in Escherichia coli

Microbial Cell Factories ◽

10.1186/s12934-021-01526-1 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Ying Li ◽

He Xian ◽

Ya Xu ◽

Yuan Zhu ◽

Zhijie Sun ◽

...

Keyword(s):

Pentose Phosphate Pathway ◽

Conversion Rate ◽

Metabolic Flux ◽

Flux Ratio ◽

Reducing Power ◽

Pentose Phosphate ◽

Fine Tuning ◽

High Yield ◽

Glycolytic Flux ◽

Acetyl Coa

Abstract Background Natural glycolysis encounters the decarboxylation of glucose partial oxidation product pyruvate into acetyl-CoA, where one-third of the carbon is lost at CO2. We previously constructed a carbon saving pathway, EP-bifido pathway by combining Embden-Meyerhof-Parnas Pathway, Pentose Phosphate Pathway and “bifid shunt”, to generate high yield acetyl-CoA from glucose. However, the carbon conversion rate and reducing power of this pathway was not optimal, the flux ratio of EMP pathway and pentose phosphate pathway (PPP) needs to be precisely and dynamically adjusted to improve the production of mevalonate (MVA). Result Here, we finely tuned the glycolytic flux ratio in two ways. First, we enhanced PPP flux for NADPH supply by replacing the promoter of zwf on the genome with a set of different strength promoters. Compared with the previous EP-bifido strains, the zwf-modified strains showed obvious differences in NADPH, NADH, and ATP synthesis levels. Among them, strain BP10BF accumulated 11.2 g/L of MVA after 72 h of fermentation and the molar conversion rate from glucose reached 62.2%. Second, pfkA was finely down-regulated by the clustered regularly interspaced short palindromic repeats interference (CRISPRi) system. The MVA yield of the regulated strain BiB1F was 8.53 g/L, and the conversion rate from glucose reached 68.7%. Conclusion This is the highest MVA conversion rate reported in shaken flask fermentation. The CRISPRi and promoter fine-tuning provided an effective strategy for metabolic flux redistribution in many metabolic pathways and promotes the chemicals production.

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