scholarly journals Unique transcriptome features of pea (Pisum sativum L.) lines with differing responses to beneficial soil microorganisms

2021 ◽  
Vol 19 (2) ◽  
pp. 131-141
Author(s):  
Alexey M. Afonin ◽  
Emma S. Gribchenko ◽  
Evgeny A. Zorin ◽  
Anton S. Sulima ◽  
Daria A. Romanyuk ◽  
...  
Keyword(s):  
Pisum Sativum ◽  
Mycorrhizal Fungi ◽  
Soil Microorganisms ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Arbuscular Mycorrhizal ◽  
Plant Responses ◽  
Single Nucleotide Variants ◽  
Interaction Efficiency

BACKGROUND: Garden pea (Pisum sativum L.) possesses the ability to form beneficial symbioses with various soil microorganisms. However, different pea cultivars, genotypes, and lines gain more or less benefit from these interactions, so the trait named efficiency of interaction with soil microorganisms (EIBSM) was suggested to describe this phenomenon. The molecular mechanisms underlying the manifestation of the EIBSM trait are not properly studied, and only few works focusing on plant responses to combined microbial preparations have been published to date. METHODS: Eight pea lines previously described as contrasting in manifestation of the EIBSM trait were grown in pots with soil under combined inoculation with nodule bacteria and arbuscular mycorrhizal fungi, and the transcriptome profiles of the whole root systems of the plants were investigated using 3'MACE RNA sequencing. RESULTS: The relatedness of the lines inferred from the analysis of transcripts SNVs (Single Nucleotide Variants) corresponded to the manifestation of the EIBSM trait: three high-EIBSM lines and three low-EIBSM lines formed two distinct clusters. Thus, the gene expression profiles were compared between these two clusters, which enabled identification of transcriptome signatures characteristic for each group. The lines previously described as high-EIBSM have lower symbiotic activity, and the expression levels of pathogen response genes were elevated compared to the lines with low EIBSM. CONCLUSION: This result suggests that the mechanism of high interaction efficiency may be connected to stricter host control of symbionts, allowing such plants to expend less on the symbioses.

scholarly journals Profiling of Seed Proteome in Pea (Pisum sativum L.) Lines Characterized with High and Low Responsivity to Combined Inoculation with Nodule Bacteria and Arbuscular Mycorrhizal Fungi

Molecules ◽  
2019 ◽  
Vol 24 (8) ◽  
pp. 1603 ◽  
Author(s):  
Mamontova ◽  
Afonin ◽  
Ihling ◽  
Soboleva ◽  
Lukasheva ◽  
...  
Keyword(s):  
Pisum Sativum ◽  
Soil Microorganisms ◽  
Molecular Mechanisms ◽  
High Efficiency ◽  
Arbuscular Mycorrhizal ◽  
Cellular Respiration ◽  
Food Protein ◽  
Pisum Sativum L ◽  
Productivity Gain ◽  
Seed Proteome

Legume crops represent the major source of food protein and contribute to human nutrition and animal feeding. An essential improvement of their productivity can be achieved by symbiosis with beneficial soil microorganisms—rhizobia (Rh) and arbuscular mycorrhizal (AM) fungi. The efficiency of these interactions depends on plant genotype. Recently, we have shown that, after simultaneous inoculation with Rh and AM, the productivity gain of pea (Pisum sativum L) line K-8274, characterized by high efficiency of interaction with soil microorganisms (EIBSM), was higher in comparison to a low-EIBSM line K-3358. However, the molecular mechanisms behind this effect are still uncharacterized. Therefore, here, we address the alterations in pea seed proteome, underlying the symbiosis-related productivity gain, and identify 111 differentially expressed proteins in the two lines. The high-EIBSM line K-8274 responded to inoculation by prolongation of seed maturation, manifested by up-regulation of proteins involved in cellular respiration, protein biosynthesis, and down-regulation of late-embryogenesis abundant (LEA) proteins. In contrast, the low-EIBSM line K-3358 demonstrated lower levels of the proteins, related to cell metabolism. Thus, we propose that the EIBSM trait is linked to prolongation of seed filling that needs to be taken into account in pulse crop breeding programs. The raw data have been deposited to the ProteomeXchange with identifier PXD013479.

Temporal dynamics of mycorrhizal fungal communities and co-associations with grassland plant communities following experimental manipulation of rainfall

2019 ◽  
Author(s):  
Coline Deveautour ◽  
Sally Power ◽  
Kirk Barnett ◽  
Raul Ochoa-Hueso ◽  
Suzanne Donn ◽  
...  
Keyword(s):  
Community Composition ◽  
Plant Community ◽  
Plant Communities ◽  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Temporal Dynamics ◽  
Arbuscular Mycorrhizal ◽  
Fungal Communities ◽  
Plant Responses ◽  
Rainfall Regimes

Climate models project overall a reduction in rainfall amounts and shifts in the timing of rainfall events in mid-latitudes and sub-tropical dry regions, which threatens the productivity and diversity of grasslands. Arbuscular mycorrhizal fungi may help plants to cope with expected changes but may also be impacted by changing rainfall, either via the direct effects of low soil moisture on survival and function or indirectly via changes in the plant community. In an Australian mesic grassland (former pasture) system, we characterised plant and arbuscular mycorrhizal (AM) fungal communities every six months for nearly four years to two altered rainfall regimes: i) ambient, ii) rainfall reduced by 50% relative to ambient over the entire year and iii) total summer rainfall exclusion. Using Illumina sequencing, we assessed the response of AM fungal communities sampled from contrasting rainfall treatments and evaluated whether variation in AM fungal communities was associated with variation in plant community richness and composition. We found that rainfall reduction influenced the fungal communities, with the nature of the response depending on the type of manipulation, but that consistent results were only observed after more than two years of rainfall manipulation. We observed significant co-associations between plant and AM fungal communities on multiple dates. Predictive co-correspondence analyses indicated more support for the hypothesis that fungal community composition influenced plant community composition than vice versa. However, we found no evidence that altered rainfall regimes were leading to distinct co-associations between plants and AM fungi. Overall, our results provide evidence that grassland plant communities are intricately tied to variation in AM fungal communities. However, in this system, plant responses to climate change may not be directly related to impacts of altered rainfall regimes on AM fungal communities. Our study shows that AM fungal communities respond to changes in rainfall but that this effect was not immediate. The AM fungal community may influence the composition of the plant community. However, our results suggest that plant responses to altered rainfall regimes at our site may not be resulting via changes in the AM fungal communities.

scholarly journals Modulation of the Immune Response by Deferasirox in Myelodysplastic Syndrome Patients

2021 ◽  
Vol 14 (1) ◽  
pp. 41
Author(s):  
Hana Votavova ◽  
Zuzana Urbanova ◽  
David Kundrat ◽  
Michaela Dostalova Merkerova ◽  
Martin Vostry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Blood Cell ◽  
Myelodysplastic Syndrome ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Adaptive Immune Response ◽  
Gene Expression Profiles ◽  
Iron Chelator ◽  
Multiple Cancer

Deferasirox (DFX) is an oral iron chelator used to reduce iron overload (IO) caused by frequent blood cell transfusions in anemic myelodysplastic syndrome (MDS) patients. To study the molecular mechanisms by which DFX improves outcome in MDS, we analyzed the global gene expression in untreated MDS patients and those who were given DFX treatment. The gene expression profiles of bone marrow CD34+ cells were assessed by whole-genome microarrays. Initially, differentially expressed genes (DEGs) were determined between patients with normal ferritin levels and those with IO to address the effect of excessive iron on cellular pathways. These DEGs were annotated to Gene Ontology terms associated with cell cycle, apoptosis, adaptive immune response and protein folding and were enriched in cancer-related pathways. The deregulation of multiple cancer pathways in iron-overloaded patients suggests that IO is a cofactor favoring the progression of MDS. The DEGs between patients with IO and those treated with DFX were involved predominantly in biological processes related to the immune response and inflammation. These data indicate DFX modulates the immune response mainly via neutrophil-related genes. Suppression of negative regulators of blood cell differentiation essential for cell maturation and upregulation of heme metabolism observed in DFX-treated patients may contribute to the hematopoietic improvement.

scholarly journals Characterization of Interactions between the Soybean Salt-Stress Responsive Membrane-Intrinsic Proteins GmPIP1 and GmPIP2

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1312
Author(s):  
Jia Liu ◽  
Weicong Qi ◽  
Haiying Lu ◽  
Hongbo Shao ◽  
Dayong Zhang
Keyword(s):  
Plasma Membrane ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Early Gene ◽  
Plant Responses ◽  
Constitutive Overexpression ◽  
Important Trait

Salt tolerance is an important trait in soybean cultivation and breeding. Plant responses to salt stress include physiological and biochemical changes that affect the movement of water across the plasma membrane. Plasma membrane intrinsic proteins (PIPs) localize to the plasma membrane and regulate the water and solutes flow. In this study, quantitative real-time PCR and yeast two-hybridization were engaged to analyze the early gene expression profiles and interactions of a set of soybean PIPs (GmPIPs) in response to salt stress. A total of 20 GmPIPs-encoding genes had varied expression profiles after salt stress. Among them, 13 genes exhibited a downregulated expression pattern, including GmPIP1;6, the constitutive overexpression of which could improve soybean salt tolerance, and its close homologs GmPIP1;7 and 1;5. Three genes showed upregulated patterns, including the GmPIP1;6 close homolog GmPIP1;4, when four genes with earlier increased and then decreased expression patterns. GmPIP1;5 and GmPIP1;6 could both physically interact strongly with GmPIP2;2, GmPIP2;4, GmPIP2;6, GmPIP2;8, GmPIP2;9, GmPIP2;11, and GmPIP2;13. Definite interactions between GmPIP1;6 and GmPIP1;7 were detected and GmPIP2;9 performed homo-interaction. The interactions of GmPIP1;5 with GmPIP2;11 and 2;13, GmPIP1;6 with GmPIP2;9, 2;11 and GmPIP2;13, and GmPIP2;9 with itself were strengthened upon salt stress rather than osmotic stress. Taken together, we inferred that GmPIP1 type and GmPIP2 type could associate with each other to synergistically function in the plant cell; a salt-stress environment could promote part of their interactions. This result provided new clues to further understand the soybean PIP–isoform interactions, which lead to potentially functional homo- and heterotetramers for salt tolerance.

scholarly journals Cooperation among phosphate-solubilizing bacteria, humic acids and arbuscular mycorrhizal fungi induces soil microbiome shifts and enhances plant nutrient uptake

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Vincenza Cozzolino ◽  
Hiarhi Monda ◽  
Davide Savy ◽  
Vincenzo Di Meo ◽  
Giovanni Vinci ◽  
...  
Keyword(s):  
Microbial Community ◽  
Arbuscular Mycorrhizal Fungi ◽  
Humic Acids ◽  
Mycorrhizal Fungi ◽  
Soil Microorganisms ◽  
Microbial Community Composition ◽  
Arbuscular Mycorrhizal ◽  
Soil Microbiome ◽  
Phosphate Solubilizing Bacteria ◽  
Saprotrophic Fungi

Abstract Background Increasing the presence of beneficial soil microorganisms is a promising sustainable alternative to support conventional and organic fertilization and may help to improve crop health and productivity. If the application of single bioeffectors has shown satisfactory results, further improvements may arise by combining multiple beneficial soil microorganisms with natural bioactive molecules. Methods In the present work, we investigated in a pot experiment under greenhouse conditions whether inoculation of two phosphate-solubilizing bacteria, Pseudomonas spp. (B2) and Bacillus amyloliquefaciens (B3), alone or in combination with a humic acids (HA) extracted from green compost and/or a commercial inoculum (M) of arbuscular mycorrhizal fungi (AMF), may affect maize growth and soil microbial community. Phospholipid fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) fingerprinting analysis were performed to detect changes in the microbial community composition. Results Plant growth, N and P uptake, and mycorrhizal root colonization were found to be larger in all inoculated treatments than in the uninoculated control. The greatest P uptake was found when B. amyloliquefaciens was applied in combination with both HA and arbuscular mycorrhizal fungi (B3HAM), and when Pseudomonas was combined with HA (B2HA). The PLFA-based community profile revealed that inoculation changed the microbial community composition. Gram+/Gram− bacteria, AMF/saprotrophic fungi and bacteria/fungi ratios increased in all inoculated treatments. The greatest values for the AMF PLFA marker (C16:1ω5) and AMF/saprotrophic fungi ratio were found for the B3HAM treatment. Permutation test based on DGGE data confirmed a similar trend, with most significant variations in both bacterial and fungal community structures induced by inoculation of B2 or B3 in combination with HA and M, especially in B3HAM. Conclusions The two community-based datasets indicated changes in the soil microbiome of maize induced by inoculation of B2 or B3 alone or when combined with humic acids and mycorrhizal inoculum, leading to positive effects on plant growth and improved nutrient uptake. Our study implies that appropriate and innovative agricultural management, enhancing the potential contribution of beneficial soil microorganisms as AMF, may result in an improved nutrient use efficiency in plants.

scholarly journals LysM Receptor-Like Kinase LYK9 of Pisum Sativum L. May Regulate Plant Responses to Chitooligosaccharides Differing in Structure

2021 ◽  
Vol 22 (2) ◽  
pp. 711
Author(s):  
Irina V. Leppyanen ◽  
Olga A. Pavlova ◽  
Maria A. Vashurina ◽  
Andrey D. Bovin ◽  
Alexandra V. Dolgikh ◽  
...  
Keyword(s):  
Immune Response ◽  
Pisum Sativum ◽  
Binding Capacity ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Phytopathogenic Fungi ◽  
Plant Responses ◽  
Pisum Sativum L ◽  
Receptor Like Kinase ◽  
Pea Mutants

This study focused on the interactions of pea (Pisum sativum L.) plants with phytopathogenic and beneficial fungi. Here, we examined whether the lysin-motif (LysM) receptor-like kinase PsLYK9 is directly involved in the perception of long- and short-chain chitooligosaccharides (COs) released after hydrolysis of the cell walls of phytopathogenic fungi and identified in arbuscular mycorrhizal (AM) fungal exudates. The identification and analysis of pea mutants impaired in the lyk9 gene confirmed the involvement of PsLYK9 in symbiosis development with AM fungi. Additionally, PsLYK9 regulated the immune response and resistance to phytopathogenic fungi, suggesting its bifunctional role. The existence of co-receptors may provide explanations for the potential dual role of PsLYK9 in the regulation of interactions with pathogenic and AM fungi. Co-immunoprecipitation assay revealed that PsLYK9 and two proposed co-receptors, PsLYR4 and PsLYR3, can form complexes. Analysis of binding capacity showed that PsLYK9 and PsLYR4, synthesized as extracellular domains in insect cells, were able to bind the deacetylated (DA) oligomers CO5-DA–CO8-DA. Our results suggest that the receptor complex consisting of PsLYK9 and PsLYR4 can trigger a signal pathway that stimulates the immune response in peas. However, PsLYR3 seems not to be involved in the perception of CO4-5, as a possible co-receptor of PsLYK9.

Dorsal Root Ganglion Neuron Types and Their Functional Specialization

2018 ◽  
pp. 127-155 ◽  
Author(s):  
Edward C. Emery ◽  
Patrik Ernfors
Keyword(s):  
Chronic Pain ◽  
Dorsal Root Ganglion ◽  
Sensory Neurons ◽  
Dorsal Root ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Drg Neurons ◽  
Low Threshold

Primary sensory neurons of the dorsal root ganglion (DRG) respond and relay sensations that are felt, such as those for touch, pain, temperature, itch, and more. The ability to discriminate between the various types of stimuli is reflected by the existence of specialized DRG neurons tuned to respond to specific stimuli. Because of this, a comprehensive classification of DRG neurons is critical for determining exactly how somatosensation works and for providing insights into cell types involved during chronic pain. This article reviews the recent advances in unbiased classification of molecular types of DRG neurons in the perspective of known functions as well as predicted functions based on gene expression profiles. The data show that sensory neurons are organized in a basal structure of three cold-sensitive neuron types, five mechano-heat sensitive nociceptor types, four A-Low threshold mechanoreceptor types, five itch-mechano-heat–sensitive nociceptor types and a single C–low-threshold mechanoreceptor type with a strong relation between molecular neuron types and functional types. As a general feature, each neuron type displays a unique and predicable response profile; at the same time, most neuron types convey multiple modalities and intensities. Therefore, sensation is likely determined by the summation of ensembles of active primary afferent types. The new classification scheme will be instructive in determining the exact cellular and molecular mechanisms underlying somatosensation, facilitating the development of rational strategies to identify causes for chronic pain.

scholarly journals Transcriptome-wide gene expression plasticity in Stipa grandis in response to grazing intensity differences

2020 ◽  
Author(s):  
Zhenhua Dang ◽  
Yuanyuan Jia ◽  
Yunyun Tian ◽  
Jiabin Li ◽  
Yanan Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Pathways ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Grazing Intensity ◽  
Glycolate Oxidase ◽  
Bisphosphate Carboxylase ◽  
Grazing Intensities

Organisms have evolved effective and distinct adaptive strategies to survive. Stipa grandis is one of the widespread dominant species on the typical steppe of the Inner Mongolian Plateau, and is regarded as a suitable species for studying the effects of grazing in this region. Although phenotypic (morphological and physiological) variations in S. grandis in response to long-term grazing have been identified, the molecular mechanisms underlying adaptations and plastic responses remain largely unknown. Accordingly, we performed a transcriptomic analysis to investigate changes in gene expression of S. grandis under four different grazing intensities. A total of 2,357 differentially expressed genes (DEGs) were identified among the tested grazing intensities, suggesting long-term grazing resulted in gene expression plasticity that affected diverse biological processes and metabolic pathways in S. grandis. DEGs were identified that indicated modulation of Calvin–Benson cycle and photorespiration metabolic pathways. The key gene´expression profiles encoding various proteins (e.g., Ribulose-1,5-bisphosphate carboxylase/oxygenase, fructose-1,6-bisphosphate aldolase, glycolate oxidase etc.) involved in these pathways suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of S. grandis. Our findings provide scientific clues for improving grassland use and protection, and identify important questions to address in future transcriptome studies.

scholarly journals Transcriptome resequencing analysis of the responses of Ty-5-Mediated resistance to TYLCV via in resistant vs. susceptible tomato cultivars

2018 ◽  
Author(s):  
Qingqi Chen ◽  
Xiangyang Xu ◽  
Jingbin Jiang ◽  
Jingfu Li
Keyword(s):  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Glutathione Metabolism ◽  
Functional Classification ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Tomato Cultivars ◽  
Susceptible Tomato

Tomato yellow leaf curl virus (TYLCV) is one of the most devastating viruses of cultivated tomato in both tropical and subtropical regions. Five major genes (Ty-1, Ty-2, Ty-3, Ty-4 and Ty-5) from wild tomato species have been associated with resistance to TYLCV. Researchers have recently attempted to determine the functions of these resistance genes, but molecular mechanisms underlying the observed resistance remain unclear. Here, resistant (cv. CLN3212A-23, carrying Ty-5) and susceptible (cv. Moneymaker) plants were either left untreated (R and S, respectively) or artificially inoculated with TYLCV via Agrobacterium-mediated transformation (RT and ST, respectively). The transcriptomes of the plants in the four groups were then analyzed by RNA-Seq, and the results identified 8,639 differentially expressed genes (DEGs) between the R and RT groups, 2,818 DEGs between the RT and ST groups, 8,899 DEGs between the S and ST groups, and 707 DEGs between the R and S groups. The gene expression profiles in both the resistant and susceptible tomato cultivars appeared to undergo notable changes after viral inoculation, and functional classification revealed that most DEGs were associated with 18 GO terms. Moreover, the functional classification of the response of Ty-5-carrying tomato plants to TYLCV infection identified the importance of the GO term “response to stimulus” in the BP category, which is related to disease resistance. In addition, 28 genes were significantly enriched in the “Plant hormone signal transduction”, “Carbon metabolism”, “ Carbon fixation in photosynthetic organisms ” and “ Glutathione metabolism ” pathways. The differential expression levels of 12 select genes were confirmed by quantitative real-time PCR. The present study indicates that the Ty-5 gene activates the expression of multiple genes involved in the resistance process and will aid a more in-depth understanding of the effects of the Ty-5 gene on resistance based on its molecular mechanism with the aim of improving TYLCV disease management in tomato.

scholarly journals Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

2018 ◽  
Author(s):  
Ivan D. Mateus ◽  
Frédéric G. Masclaux ◽  
Consolée Aletti ◽  
Edward C. Rojas ◽  
Romain Savary ◽  
...  
Keyword(s):  
Mycorrhizal Fungi ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Arbuscular Mycorrhizal ◽  
Mycorrhizal Symbiosis ◽  
Rna Seq ◽  
Plant Host ◽  
Transcriptional Responses ◽  
Plant Genes ◽  
Fungal Genetic

AbstractArbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organisation during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation plays a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype x genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.

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