Wheat grain proteomic and protein–metabolite interactions analyses provide insights into plant growth promoting bacteria–arbuscular mycorrhizal fungi–wheat interactions

Yadav, Radheshyam; Chakraborty, Sudip; Ramakrishna, Wusirika

doi:10.1007/s00299-022-02866-x

Cited by 12 publications

(6 citation statements)

References 146 publications

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“…Studies on gene expression have mainly focused on the expression assay of genes in plants in interaction with PGPB ( Sheibani-Tezerji et al, 2015 ). The expression of genes, proteome, and metabolome in different hosts while interacting with PGPB have been assessed in several studies ( Wang et al, 2005 ; Kwon et al, 2016 ; Kazemi-Oskuei et al, 2018 ; Gamez et al, 2019 ; Yoo et al, 2019 ; Malviya et al, 2020 ; Gozalia et al, 2021 ; Kataoka et al, 2021 ; Li et al, 2021 ; Mellidou et al, 2021 ; Gao et al, 2022 ; Samaras et al, 2022 ; Wiggins et al, 2022 ; Xu et al, 2022 ; Yadav et al, 2022 ).…”

Section: Omics Methods For Assaying Molecular Mechanisms Of Pgpbmentioning

confidence: 99%

Salinity stress endurance of the plants with the aid of bacterial genes

et al. 2023

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The application of plant growth-promoting bacteria (PGPB) is vital for sustainable agriculture with continuous world population growth and an increase in soil salinity. Salinity is one of the severe abiotic stresses which lessens the productivity of agricultural lands. Plant growth-promoting bacteria are key players in solving this problem and can mitigate salinity stress. The highest of reported halotolerant Plant growth-promoting bacteria belonged to Firmicutes (approximately 50%), Proteobacteria (40%), and Actinobacteria (10%), respectively. The most dominant genera of halotolerant plant growth-promoting bacteria are Bacillus and Pseudomonas. Currently, the identification of new plant growth-promoting bacteria with special beneficial properties is increasingly needed. Moreover, for the effective use of plant growth-promoting bacteria in agriculture, the unknown molecular aspects of their function and interaction with plants must be defined. Omics and meta-omics studies can unreveal these unknown genes and pathways. However, more accurate omics studies need a detailed understanding of so far known molecular mechanisms of plant stress protection by plant growth-promoting bacteria. In this review, the molecular basis of salinity stress mitigation by plant growth-promoting bacteria is presented, the identified genes in the genomes of 20 halotolerant plant growth-promoting bacteria are assessed, and the prevalence of their involved genes is highlighted. The genes related to the synthesis of indole acetic acid (IAA) (70%), siderophores (60%), osmoprotectants (80%), chaperons (40%), 1-aminocyclopropane-1-carboxylate (ACC) deaminase (50%), and antioxidants (50%), phosphate solubilization (60%), and ion homeostasis (80%) were the most common detected genes in the genomes of evaluated halotolerant plant growth-promoting and salinity stress-alleviating bacteria. The most prevalent genes can be applied as candidates for designing molecular markers for screening of new halotolerant plant growth-promoting bacteria.

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Section: Omics Methods For Assaying Molecular Mechanisms Of Pgpbmentioning

confidence: 99%

Salinity stress endurance of the plants with the aid of bacterial genes

et al. 2023

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“…Prabhukarthikeyan et al (2022) validated that inoculation of B. megaterium strain BS11 upregulated proteins associated with plant metabolism, transcription, transporter, signaling, defense and stress responses in rice plants using proteomic analysis. Proteome profiling of field soil supplied with B. subtilis CP4 and Arbuscular mycorrhizal fungi (AMF) microbial consortia divulged the promotion of differentially abundant proteins (DAP) including histones, glutenin, avenin, and ATP synthase in abiotic stressed wheat, resulting in better yield and biofortification (Yadav et al, 2022). An integrated proteomics and transcriptomics study successfully identified 64 DAP participating in "carbon fixation in photosynthetic organisms" as well as few amino acid metabolism pathways that may be related to C and N allocations and AMF-mediated Suaeda salsa adaptation in moderate saline conditions (100 mM NaCl) (Diao et al, 2022).…”

Section: Proteomic Studiesmentioning

confidence: 99%

Plant growth-promoting rhizobacteria: Salt stress alleviators to improve crop productivity for sustainable agriculture development

et al. 2023

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Soil salinity, a growing issue worldwide, is a detrimental consequence of the ever-changing climate, which has highlighted and worsened the conditions associated with damaged soil quality, reduced agricultural production, and decreasing land areas, thus resulting in an unsteady national economy. In this review, halo-tolerant plant growth-promoting rhizo-microbiomes (PGPRs) are evaluated in the salinity-affected agriculture as they serve as excellent agents in controlling various biotic–abiotic stresses and help in the augmentation of crop productivity. Integrated efforts of these effective microbes lighten the load of agro-chemicals on the environment while managing nutrient availability. PGPR-assisted modern agriculture practices have emerged as a green strategy to benefit sustainable farming without compromising the crop yield under salinity as well as salinity-affected supplementary stresses including increased temperature, drought, salinity, and potential invasive plant pathogenicity. PGPRs as bio-inoculants impart induced systemic tolerance (IST) to plants by the production of volatile organic compounds (VOCs), antioxidants, osmolytes, extracellular polymeric substances (EPS), phytohormones, and ACC-deaminase and recuperation of nutritional status and ionic homeostasis. Regulation of PGPR-induced signaling pathways such as MAPK and CDPK assists in salinity stress alleviation. The “Next Gen Agriculture” consists of the application of designer crop microbiomes through gene editing tools, for instance, CRISPR, and engineering of the metabolic pathways of the microbes so as to gain maximum plant resistance. The utilization of omics technologies over the traditional approaches can fulfill the criteria required to increase crop yields in a sustainable manner for feeding the burgeoning population and augment plant adaptability under climate change conditions, ultimately leading to improved vitality. Furthermore, constraints such as the crop specificity issue of PGPR, lack of acceptance by farmers, and legal regulatory aspects have been acknowledged while also discussing the future trends for product commercialization with the view of the changing climate.

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“…Notwithstanding non-plant hits, pathways symptomatic of grains were accurately captured in this experiment such as the carbon metabolism (42, 6%), glycolysis/gluconeogenesis (25, 4%), as well as the starch and sucrose metabolism (18, 3%) (Supplementary Figure S12D-F). Despite the constraint raised above, KEGG remains a database widely employed to explore plant proteomes, including wheat grain proteins (41,(145)(146)(147). Mapping our 390 LMA-associated biomarkers (Supplementary Table S5) highlighted that many up-regulated peptides came from OFFICIAL OFFICIAL ribosomal proteins (Figure 6D) while several down-regulated peptides belonged to enzymes acting in the biosynthesis of AAs (Figure 6I).…”

Section: Kegg To Retrieve Pathway Brite and Module Namesmentioning

confidence: 99%

Finding the LMA needle in the wheat proteome haystack

Vincent

Bui

Ram

et al. 2023

Preprint

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Late maturity alpha-amylase (LMA) is a wheat genetic defect causing the synthesis of high isoelectric point (pI) alpha-amylase in the aleurone as a result of a temperature shock during mid-grain development or prolonged cold throughout grain development leading to an unacceptable low falling numbers (FN) at harvest or during storage. High pI alpha-amylase is normally not synthesized until after maturity in seeds when they may sprout in response to rain or germinate following sowing the next season crop. Whilst the physiology is well understood, the biochemical mechanisms involved in grain LMA response remain unclear. We have employed high-throughput proteomics to analyse thousands of wheat flours displaying a range of LMA values. We have applied an array of statistical analyses to select LMA-responsive biomarkers and we have mined them using a suite of tools applicable to wheat proteins. To our knowledge, this is not only the first proteomics study tackling the wheat LMA issue, but also the largest plant-based proteomics study published to date. Logistics, technicalities, requirements, and bottlenecks of such an ambitious large-scale high-throughput proteomics experiment along with the challenges associated with big data analyses are discussed. We observed that stored LMA-affected grains activated their primary metabolisms such as glycolysis and gluconeogenesis, TCA cycle, along with DNA- and RNA binding mechanisms, as well as protein translation. This logically transitioned to protein folding activities driven by chaperones and protein disulfide isomerase, as well as protein assembly via dimerisation and complexing. The secondary metabolism was also mobilised with the up-regulation of phytohormones, chemical and defense responses. LMA further invoked cellular structures among which ribosomes, microtubules, and chromatin. Finally, and unsurprisingly, LMA expression greatly impacted grain starch and other carbohydrates with the up-regulation of alpha-gliadins and starch metabolism, whereas LMW glutenin, stachyose, sucrose, UDP-galactose and UDP-glucose were down-regulated. This work demonstrates that proteomics deserves to be part of the wheat LMA molecular toolkit and should be adopted by LMA scientists and breeders in the future.

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Wheat grain proteomic and protein–metabolite interactions analyses provide insights into plant growth promoting bacteria–arbuscular mycorrhizal fungi–wheat interactions

Cited by 12 publications

References 146 publications

Salinity stress endurance of the plants with the aid of bacterial genes

Salinity stress endurance of the plants with the aid of bacterial genes

Plant growth-promoting rhizobacteria: Salt stress alleviators to improve crop productivity for sustainable agriculture development

Finding the LMA needle in the wheat proteome haystack

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