Nitrogen Transfer Play an Important Role of Differentially Expressed Protein of Roots in Eucalyptus Urophylla × E. grandis and Dalbergia Odorifera Nursery Seedlings Intercropping System

Abstract Background: The mixing of Eucalyptus with N2-fixing trees is a frequently successful and sustainable cropping practice. In this study, we evaluated nitrogen transfer and conducted a proteomic analysis on seedlings of Eucalyptus and a N2-fixing tree, Dalbergia (D.) odorifera, from intercropping and monocropping systems, to elucidate the physiological effecting and the molecular mechanisms on N transfer of Eucalyptus mixed with D. odorifera. Results: We demonstrated the following: (1) Nitrogen transfer occurred from D. odorifera to E. urophylla × E. grandis by 14.6 %. Interspecific facilitation of N uptake and root growth in E. urophylla × E. grandis was increased in the intercropping system, but the root growth and N absorption of D. odorifera were inhibited. (2) Among differentially expressed proteins was greater than 1.5 times, E. urophylla × E. grandis were found to be up-regulated several proteins for the nitrogen assimilation and enhancing the nitrogen competition, such as the proteins related to tricarboxylic acid/organic transformation, nitrogen metabolism and nitrogen assimilation; it also up-regulated the expression of stress resistant protein for its adaptability. However, the assimilation and metabolism of nitrogen was promoted in D. odorifera through the up-regulation of amino acid metabolism related proteins, and increased the key enzyme abundance of glycolysis pathway in D. odorifera. (3) Importantly, E. urophylla × E. grandis was the beneficiary in the process of N transfer, there were more different proteins involved in the synthesis pathway than that of the metabolic pathway, but there were more functional proteins involved in metabolic degradation in D. odorifera. Additionaly, the two groups of nitrogen compound transporter were found in E. urophylla × E. grandis, i.e. the molecular mechanism of the N transfer from D. odorifera to E. urophylla × E. grandis was explained by proteomics. Conclusions: Our study suggests that N transfer occurred from D. odorifera to E. urophylla × E. grandis and it was affected by the variations in the differentially expressed protein. We anticipate the result can be verified in field experiments for the sustainable development of Eucalyptus plantations.

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The physiological and molecular mechanisms of N transfer in Eucalyptus and Dalbergia odorifera intercropping systems using root proteomics

BMC Plant Biology ◽

10.1186/s12870-021-02969-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xianyu Yao ◽

Liangning Liao ◽

Yongzhen Huang ◽

Ge Fan ◽

Mei Yang ◽

...

Keyword(s):

Stress Resistance ◽

Molecular Mechanisms ◽

Field Experiments ◽

N Uptake ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

N Transfer ◽

The Sustainable Development ◽

Dalbergia Odorifera ◽

Root Proteomics

Abstract Background The mixing of Eucalyptus with N2-fixing trees species (NFTs) is a frequently successful and sustainable cropping practice. In this study, we evaluated nitrogen (N) transfer and conducted a proteomic analysis of the seedlings of Eucalyptus urophylla × E. grandis (Eucalyptus) and an NFT, Dalbergia (D.) odorifera, from intercropping and monocropping systems to elucidate the physiological effects and molecular mechanisms of N transfer in mixed Eucalyptus and D. odorifera systems. Results N transfer occurred from D. odorifera to Eucalyptus at a rate of 14.61% in the intercropping system, which increased N uptake and growth in Eucalyptus but inhibited growth in D. odorifera. There were 285 and 288 differentially expressed proteins by greater than 1.5-fold in Eucalyptus and D. odorifera roots with intercropping vs monoculture, respectively. Introduction of D. odorifera increased the stress resistance ability of Eucalyptus, while D. odorifera stress resistance was increased by increasing levels of jasmonic acid (JA). Additionally, the differentially expressed proteins of N metabolism, such as glutamine synthetase nodule isozyme (GS), were upregulated to enhance N competition in Eucalyptus. Importantly, more proteins were involved in synthetic pathways than in metabolic pathways in Eucalyptus because of the benefit of N transfer, and the two groups of N compound transporters were found in Eucalyptus; however, more functional proteins were involved in metabolic degradation in D. odorifera; specifically, the molecular mechanism of the transfer of N from D. odorifera to Eucalyptus was explained by proteomics. Conclusions Our study suggests that N transfer occurred from D. odorifera to Eucalyptus and was affected by the variations in the differentially expressed proteins. We anticipate that these results can be verified in field experiments for the sustainable development of Eucalyptus plantations.

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Role of root exudates and root turnover in the below-ground N transfer from Canavalia ensiformis (jackbean) to the associated Musa acuminata (banana)

Crop and Pasture Science ◽

10.1071/cp08215 ◽

2009 ◽

Vol 60 (3) ◽

pp. 289 ◽

Cited By ~ 9

Author(s):

Jorge Sierra ◽

Lucienne Desfontaines

Keyword(s):

Root Exudates ◽

N Uptake ◽

Root Traits ◽

Box Model ◽

Root Turnover ◽

Nitrogen Transfer ◽

N Transfer ◽

Donor Plant ◽

Feeding Method ◽

N Release

Jackbean is an annual legume frequently used as green manure in tropical intercropping systems with bananas. Although the beneficial effect of nitrogen (N) release from above-ground residues on banana nutrition is well known, little information is available on the N transfer from jackbean roots before and after the above-ground harvest. The aim of this study was to assess the relative contribution of exudates and root turnover in the N transfer from jackbean to banana in a greenhouse experiment. Nitrogen transfer was studied in a 6-month trial using the 15N leaf feeding method, and estimated with a box model of 15N dilution based on the observed data of 15N content in exudates and decomposing roots. For the sowing–harvest period, the amount of N transferred from jackbean exudates represented 16% of banana N uptake and 0.7% of jackbean N uptake. Therefore, the N transfer flux via exudates was 23 times higher in terms of N input for the recipient plant than in terms of N output for the donor plant. This value, which is an index of the effectiveness of N transfer, was lower than those reported previously for other soil–plant systems in greenhouse conditions. This would be due to differences in root traits of the recipient plants. The amount of transferred N from root turnover after jackbean harvest represented 52% of banana N uptake in that period. The box model described N transfer from both legume N sources adequately (r2 = 0.92). For the whole experiment, 38% of banana N uptake was derived from jackbean (6% from exudates and 32% from root turnover), and 62% from soil N. The results indicated that N transfer from root exudates of jackbean would be a useful but minor process compared with N release from root turnover in soil. The experimental and theoretical approach proposed in this study may be useful in screening studies to assess the capability of herbaceous legumes to transfer N.

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Analysis of differentially expressed genes induced by drought stress in tef (Eragrostistef) root

Nigerian Journal of Biotechnology ◽

10.4314/njb.v36i2.17 ◽

2020 ◽

Vol 36 (2) ◽

pp. 167-187

Author(s):

Hewan Demissie Degu

Keyword(s):

Drought Stress ◽

Root Growth ◽

Molecular Mechanisms ◽

Rna Binding ◽

Expression Profiles ◽

Differentially Expressed ◽

Eragrostis Tef ◽

Direct Role ◽

Functional Roles ◽

Related Transcription Factor

Drought stress is one of the major abiotic stresses which induces root growth in tef. Molecular mechanisms underlying the elongation of roots under drought stress are not known. Therefore, we aimed to study the tef root system to uncover the expression profiles for drought stress using Agilent gene chip of rice. One hundred seventy-five expressed genes were found to be differentially expressed after eight days of drought stress with Eragrostis tef- resistant genotype, Kaye Murri. The drought-responsive genes were isolated and classified into nine categories according to the functional roles in plant metabolic pathways, such as defense, signal transduction, cell wall fortification, oxidative stress, photosynthesis, development, cell maintenance, RNA binding, and unknown functions. The profiles of tef root genes, responsive to drought stress shared common identities with other expression profiles known to be elicited by diverse stresses, including pathogenesis, abiotic stress, and wounding. Well-known drought-related transcription factor-like, WRKY and bHLH were up-regulated. Cell transport-related regulators such as potassium transporter 22-like, auxin transporter-like protein 1, and wall-associated receptor kinase were also involved in the expression profile of tef root under drought stress. Their expression had enhanced the drought-responsive genes, which, have a direct role to maintain root growth under drought stress. Key words: Drought, Genome, Microarray, Root, Tef

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Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323666200402085832 ◽

2020 ◽

Vol 23 (6) ◽

pp. 546-553

Author(s):

Hongyuan Cui ◽

Mingwei Zhu ◽

Junhua Zhang ◽

Wenqin Li ◽

Lihui Zou ◽

...

Keyword(s):

Papillary Thyroid Carcinoma ◽

Thyroid Carcinoma ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Cellular Proliferation ◽

Mrna Level ◽

Thyroid Tissue ◽

Differentially Expressed ◽

Thyroid Tumors ◽

Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

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Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

Current Bioinformatics ◽

10.2174/1574893614666190204152500 ◽

2019 ◽

Vol 14 (7) ◽

pp. 591-601 ◽

Cited By ~ 1

Author(s):

Aravind K. Konda ◽

Parasappa R. Sabale ◽

Khela R. Soren ◽

Shanmugavadivel P. Subramaniam ◽

Pallavi Singh ◽

...

Keyword(s):

Expression Pattern ◽

Gene Networks ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Wrky Transcription Factor ◽

Functional Enrichment ◽

Differentially Expressed ◽

Callose Deposition ◽

Significant Probability

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

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Comparative transcriptomic and metabolomic analyses of carotenoid biosynthesis reveal the basis of white petal color in Brassica napus

Planta ◽

10.1007/s00425-020-03536-6 ◽

2021 ◽

Vol 253 (1) ◽

Author(s):

Ledong Jia ◽

Junsheng Wang ◽

Rui Wang ◽

Mouzheng Duan ◽

Cailin Qiao ◽

...

Keyword(s):

Brassica Napus ◽

Molecular Mechanisms ◽

Flower Color ◽

Carotenoid Biosynthesis ◽

Differentially Expressed ◽

Transcriptome Data ◽

Oilseed Crops ◽

Qrt Pcr ◽

Carotenoid Metabolism ◽

Rapeseed Cultivar

Abstract Main conclusion The molecular mechanism underlying white petal color in Brassica napus was revealed by transcriptomic and metabolomic analyses. Abstract Rapeseed (Brassica napus L.) is one of the most important oilseed crops worldwide, but the mechanisms underlying flower color in this crop are known less. Here, we performed metabolomic and transcriptomic analyses of the yellow-flowered rapeseed cultivar ‘Zhongshuang 11’ (ZS11) and the white-flowered inbred line ‘White Petal’ (WP). The total carotenoid contents were 1.778-fold and 1.969-fold higher in ZS11 vs. WP petals at stages S2 and S4, respectively. Our findings suggest that white petal color in WP flowers is primarily due to decreased lutein and zeaxanthin contents. Transcriptome analysis revealed 10,116 differentially expressed genes with a fourfold or greater change in expression (P-value less than 0.001) in WP vs. ZS11 petals, including 1,209 genes that were differentially expressed at four different stages and 20 genes in the carotenoid metabolism pathway. BnNCED4b, encoding a protein involved in carotenoid degradation, was expressed at abnormally high levels in WP petals, suggesting it might play a key role in white petal formation. The results of qRT-PCR were consistent with the transcriptome data. The results of this study provide important insights into the molecular mechanisms of the carotenoid metabolic pathway in rapeseed petals, and the candidate genes identified in this study provide a resource for the creation of new B. napus germplasms with different petal colors.

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Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

International Journal of Molecular Sciences ◽

10.3390/ijms22052481 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2481

Author(s):

Jodi Callwood ◽

Kalpalatha Melmaiee ◽

Krishnanand P. Kulkarni ◽

Amaranatha R. Vennapusa ◽

Diarra Aicha ◽

...

Keyword(s):

Heat Stress ◽

Molecular Mechanisms ◽

Stomatal Closure ◽

Enrichment Analysis ◽

Leaf Size ◽

Vaccinium Corymbosum ◽

Climatic Conditions ◽

Differentially Expressed ◽

Transcriptomic Changes ◽

Go Terms

Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, and help in understanding the complex mechanisms involved in heat stress tolerance.

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The Alterations in Methylene Blue/Light-Treated Frozen Plasma Proteins Revealed by Proteomics

Transfusion Medicine and Hemotherapy ◽

10.1159/000515119 ◽

2021 ◽

pp. 1-8

Author(s):

Tiange Wu ◽

Xiaoning Wang ◽

Kai Ren ◽

Xiaochen Huang ◽

Jiankai Liu

Keyword(s):

Mass Spectrometry ◽

Methylene Blue ◽

Western Blot ◽

Blue Light ◽

Differentially Expressed ◽

Enzyme Linked Immunosorbent Assay ◽

Differentially Expressed Protein ◽

Significant Difference ◽

Modified Proteins ◽

Frozen Plasma

Introduction: The aim of this study was to investigate the modified proteins in methylene blue/light-treated frozen plasma (MB-FP) compared with fresh frozen plasma (FFP) in order to gain a better application of MB/light-treated plasma in clinic transfusion. Methods: MB-FP and FFP were collected from Changchun central blood station, and a trichloroacetic acid/acetone precipitation method was used to remove albumin for the enrichment of lower abundance proteins. The plasma protein in MB-FP and FFP were separated using two-dimensional gel electrophoresis (2-DE) and the differentially expressed protein spots were analyzed using mass spectrometry. Finally, the differentially expressed proteins were tested using Western blot and enzyme-linked immunosorbent assay (ELISA). Results: Approximately 14 differentially expressed protein spots were detected in the MB-FP, and FFP was chosen as the control. After 2-DE comparison analysis and mass spectrometry, 8 significantly differentially expressed protein spots were identified, corresponding to 6 different proteins, including complement C1r subcomponent (C1R), inter-alpha-trypsin inhibitor heavy chain H4 (ITI-H4), keratin, type II cytoskeletal 1 (KRT1), hemopexin (HPX), fibrinogen gamma chain (FGG), and transthyretin (TTR). Western blot showed no significant difference in the expression level of KRT1 between MB-FP and FFP (p > 0.05). Both Western blot and ELISA indicated that the level of HPX was significantly higher in FFP than in MB-FP (p < 0.05). Conclusion: This comparative proteomics study revealed that some significantly modified proteins occur in MB-FP, such as C1R, ITI-H4, KRT1, HPX, FGG, and TTR. Our findings provide more theoretical data for using MB-FP in transfusion medicine. However, the relevance of the data for the transfusion of methylene blue/light-treated plasma remains unclear. The exact modification of these proteins and the effects of these modified proteins on their functions and their effects in clinical plasma infusion need to be further studied.

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Comprehensive Analysis of Transcriptome and Metabolome Reveals the Flavonoid Metabolic Pathway Is Associated with Fruit Peel Coloration of Melon

Molecules ◽

10.3390/molecules26092830 ◽

2021 ◽

Vol 26 (9) ◽

pp. 2830

Author(s):

Aiai Zhang ◽

Jing Zheng ◽

Xuemiao Chen ◽

Xueyin Shi ◽

Huaisong Wang ◽

...

Keyword(s):

Molecular Mechanisms ◽

Comprehensive Analysis ◽

Differentially Expressed ◽

Integrated Analysis ◽

Fruit Peel ◽

External Quality ◽

Color Formation ◽

Peel Color ◽

Dark Green

The peel color is an important external quality of melon fruit. To explore the mechanisms of melon peel color formation, we performed an integrated analysis of transcriptome and metabolome with three different fruit peel samples (grey-green ‘W’, dark-green ‘B’, and yellow ‘H’). A total of 40 differentially expressed flavonoids were identified. Integrated transcriptomic and metabolomic analyses revealed that flavonoid biosynthesis was associated with the fruit peel coloration of melon. Twelve differentially expressed genes regulated flavonoids synthesis. Among them, nine (two 4CL, F3H, three F3′H, IFS, FNS, and FLS) up-regulated genes were involved in the accumulation of flavones, flavanones, flavonols, and isoflavones, and three (2 ANS and UFGT) down-regulated genes were involved in the accumulation of anthocyanins. This study laid a foundation to understand the molecular mechanisms of melon peel coloration by exploring valuable genes and metabolites.

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Impact of Mycorrhization on Phosphorus Utilization Efficiency of Acacia gummifera and Retama monosperma under Salt Stress

Forests ◽

10.3390/f12050611 ◽

2021 ◽

Vol 12 (5) ◽

pp. 611

Author(s):

Abdessamad Fakhech ◽

Martin Jemo ◽

Najat Manaut ◽

Lahcen Ouahmane ◽

Mohamed Hafidi

Keyword(s):

Salt Stress ◽

Root Growth ◽

N Uptake ◽

P Uptake ◽

Utilization Efficiency ◽

Legume Species ◽

Growth Responses ◽

Phosphorus Utilization ◽

Phosphorus Utilization Efficiency ◽

Shoot And Root Growth

The impact of salt stress on the growth and phosphorus utilization efficiency (PUE) of two leguminous species: Retama monosperma and Acacia gummifera was studied. The effectiveness of arbuscular mycorrhizal fungi (AMF) to mitigate salt stress was furthermore assessed. Growth, N and P tissue concentrations, mycorrhizal root colonization frequency and intensity, and P utilization efficiency (PUE) in the absence or presence of AMF were evaluated under no salt (0 mM L−1) and three salt (NaCl) concentrations of (25, 50 and 100 mM L−1) using a natural sterilized soil. A significant difference in mycorrhizal colonization intensity, root-to-shoot ratio, P uptake, PUE, and N uptake was observed between the legume species. Salt stress inhibited the shoot and root growth, and reduced P and N uptake by the legume species. Mycorrhizal inoculation aided to mitigate the effects of salt stress with an average increase of shoot and root growth responses by 35% and 32% in the inoculated than in the non-inoculated A. gummifera treatments. The average shoot and root growth responses were 37% and 45% higher in the inoculated compared to the non-inoculated treatments of R. monosperma. Average mycorrhizal shoot and root P uptake responses were 66% and 68% under A. gummifera, and 40% and 95% under R. monosperma, respectively. Mycorrhizal inoculated treatments consistently maintained lower PUE in the roots. The results provide insights for further investigations on the AMF conferred mechanisms to salt stress tolerance response by A. gummifera and R. monosperma, to enable the development of effective technologies for sustainable afforestation and reforestation programs in the Atlantic coast of Morocco.

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