Plant iTRAQ‐Based Proteomics

Handakumbura, Pubudu; Hixson, Kim; Purvine, Samuel O.; Jansson, Christer; Paša‐Tolić, Ljiljana

doi:10.1002/cppb.20052

Cited by 5 publications

(3 citation statements)

References 14 publications

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“…Soluble sugars were extracted using ethanol and starch in the pellet was solubilized by an amylase/amyloglucosidase treatment and quantified spectrophotometrically using standard protocols as previously described (Stitt et al ., 1989; Smith and Zeeman, 2006). Metabolites for gas chromatography-mass spectrometry/mass spectrometry (GC-MS), lipidomics, and ion-mobility spectroscopy (IMS) were extracted using a methanol-chloroform extraction as previously described (Handakumbura et al ., 2017). Leaf tissue samples from sampling days D2, D3, and D4 were analyzed by GC-MS, lipidomics, and IMS.…”

Section: Supplemental Materialsmentioning

confidence: 99%

“…Metabolites for gas chromatography-mass spectrometry/mass spectrometry (GC-MS), lipidomics, and ion-mobility spectroscopy (IMS) were extracted using a methanol-chloroform extraction as previously described (Handakumbura et al, 2017). Leaf tissue samples from sampling days D2, D3, and D4 were analyzed by GC-MS, lipidomics, and IMS.…”

Section: Metabolite Extraction and Quantificationmentioning

confidence: 99%

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Metabolomic, photoprotective, and photosynthetic acclimatory responses to post-flowering drought in sorghum

Baker

Patel

Cole

et al. 2022

Preprint

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Climate change is globally affecting rainfall patterns, necessitating the improvement of drought tolerance in crops. Sorghum bicolor is a drought-tolerant cereal capable of producing high yields under water scarcity conditions. Functional stay-green sorghum genotypes can maintain green leaf area and efficient grain filling in terminal post-flowering water deprivation, a period of ~10 weeks. To obtain molecular insights into these characteristics, two drought-tolerant genotypes, BTx642 and RTx430, were grown in control and terminal post-flowering drought field plots in the Central Valley of California. Photosynthetic, photoprotective, water dynamics, and biomass traits were quantified and correlated with metabolomic data collected from leaves, stems, and roots at multiple timepoints during drought. Physiological and metabolomic data was then compared to longitudinal RNA sequencing data collected from these two genotypes. The metabolic response to drought highlights the uniqueness of the post-flowering drought acclimation relative to pre-flowering drought. The functional stay-green genotype BTx642 specifically induced photoprotective responses in post-flowering drought supporting a putative role for photoprotection in the molecular basis of the functional stay-green trait. Specific genes are highlighted that may contribute to post-flowering drought tolerance and that can be targeted in crops to maximize yields under limited water input conditions.

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Section: Supplemental Materialsmentioning

confidence: 99%

Section: Metabolite Extraction and Quantificationmentioning

confidence: 99%

Metabolomic, photoprotective, and photosynthetic acclimatory responses to post-flowering drought in sorghum

Baker

Patel

Cole

et al. 2022

Preprint

Self Cite

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“…These reagents have been shown to commonly interfere with LC based quantitative proteomics techniques (Isaacson et al 2006). iTRAQ analysis has been used to study aluminium tolerance and drought tolerance in sorghum (Zhou et al 2016;Handakumbura et al 2017). However, the protein extraction and preparation method cited therein still uses reagents that can interfere with downstream analysis.…”

Section: Label-free Proteomic Identification and Quantification Of Somentioning

confidence: 99%

Method for Label-Free Quantitative Proteomics for Sorghum bicolor L. Moench

Sharan

Nikam

Jaleel

et al. 2018

Tropical Plant Biol.

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Sorghum (Sorghum bicolor L. Moench) is a rapidly emerging high biomass feedstock for bioethanol and lignocellulosic biomass production. The robust varietal germplasm of sorghum and its completed genome sequence provide the necessary genetic and molecular tools to study and engineer the biotic/abiotic stress tolerance. Traditional proteomics approaches for outlining the sorghum proteome have many limitations like, demand for high protein amounts, reproducibility and identification of only few differential proteins. In this study, we report a gel-free, quantitative proteomic method for in-depth coverage of the sorghum proteome. This novel method combining phenol extraction and methanol chloroform precipitation gives high total protein yields for both mature sorghum root and leaf tissues. We demonstrate successful application of this method in comparing proteomes of contrasting cultivars of sorghum, at two different phenological stages. Protein identification and relative quantification analyses were performed by a label-free liquid chromatography tandem mass spectrometry (LC/MS-MS) analyses. Several unique proteins were identified respectively from sorghum tissues, specifically 271 from leaf and 774 from root tissues, with 193 proteins common in both tissues. Using gene ontology analysis, the differential proteins identified were finely corroborated with their leaf/root tissue specific functions. This method of protein extraction and analysis would contribute substantially to generate in-depth differential protein data in sorghum as well as related species. It would also increase the repertoire of methods uniquely suited for gel-free plant proteomics that are increasingly being developed for studying abiotic and biotic stress responses.

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