Publications by authors named "Iniga George"

9 Publications

  • Page 1 of 1

Shotgun proteomic analysis of photoperiod regulated dormancy induction in grapevine.

J Proteomics 2018 09 29;187:13-24. Epub 2018 May 29.

Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia. Electronic address:

Certain grapevine genotypes become dormant in response to decreasing photoperiod and others require low temperature or both environmental cues to induce dormancy. This study used a proteomic approach to gain an understanding of the underlying molecular events involved in bud dormancy commitment. Two F siblings (F2-110 and F2-040) with differences in photoperiod induced dormancy responsiveness were subjected to long day (LD, 15 h, paradormancy maintenance or dormancy inhibition) or short day (SD, 13 h, endodormancy commitment) treatment. Proteins were extracted at two time points (28 days and 42 days) of LD and SD photoperiod exposure, and label-free quantitative shotgun proteomic analysis was performed for three biological replicates of each treatment and time point. A total of 1577 non-redundant proteins were identified in the combined dataset of eight different conditions (2 genotypes, 2 photoperiods and 2 timepoints, available via ProteomeXchange with identifier PXD001627). Genotype specific patterns of budbreak and protein expression were detected in response to the differential photoperiod treatment at the two time points. Peroxidases, dehydrogenases and superoxide dismutases were more abundant at 42 SD than at 28 SD in the dormancy responsive F2-110, suggesting that oxidative stress response related proteins could be markers of endodormancy commitment in grapevine buds.
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http://dx.doi.org/10.1016/j.jprot.2018.05.014DOI Listing
September 2018

Relative quantification of phosphoproteomic changes in grapevine (Vitis vinifera L.) leaves in response to abscisic acid.

Hortic Res 2016 22;3:16029. Epub 2016 Jun 22.

Department of Biochemistry and Molecular Biology, University of Nevada, Reno , Reno, NV, USA.

In a previous transcriptomic analysis, abscisic acid (ABA) was found to affect the abundance of a number of transcripts in leaves of Cabernet Sauvignon grapevines with roots that had been exposed to 10 μm ABA for 2 h. Other work has indicated that ABA affects protein abundance and protein phosphorylation as well. In this study we investigated changes in protein abundance and phosphorylation of Cabernet Sauvignon grapevine leaves. Protein abundance was assessed by both label-free and isobaric-label quantitive proteomic methods. Each identified common proteins, but also additional proteins not found with the other method. Overall, several thousand proteins were identified and several hundred were quantified. In addition, hundreds of phosphoproteins were identified. Tens of proteins were found to be affected in the leaf after the roots had been exposed to ABA for 2 h, more than half of them were phosphorylated proteins. Many phosphosites were confirmed and several new ones were identified. ABA increased the abundance of some proteins, but the majority of the proteins had their protein abundance decreased. Many of these proteins were involved in growth and plant organ development, including proteins involved in protein synthesis, photosynthesis, sugar and amino-acid metabolism. This study provides new insights into how ABA regulates plant responses and acclimation to water deficits.
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http://dx.doi.org/10.1038/hortres.2016.29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4916266PMC
July 2016

Quantitative proteomic analysis of cabernet sauvignon grape cells exposed to thermal stresses reveals alterations in sugar and phenylpropanoid metabolism.

Proteomics 2015 Sep 15;15(17):3048-60. Epub 2015 Jun 15.

Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, Australia.

Grapes (Vitis vinifera) are a valuable fruit crop and wine production is a major industry. Global warming and expanded range of cultivation will expose grapes to more temperature stresses in future. Our study investigated protein level responses to abiotic stresses, with particular reference to proteomic changes induced by the impact of four different temperature stress regimes, including both hot and cold temperatures, on cultured grape cells. Cabernet Sauvignon cell suspension cultures grown at 26°C were subjected to 14 h of exposure to 34 and 42°C for heat stress, and 18 and 10°C for cold stress. Cells from the five temperatures were harvested in biological triplicates and label-free quantitative shotgun proteomic analysis was performed. A total of 2042 non-redundant proteins were identified from the five temperature points. Fifty-five proteins were only detected in extreme heat stress conditions (42°C) and 53 proteins were only detected at extreme cold stress conditions (10°C). Gene Ontology (GO) annotations of differentially expressed proteins provided insights into the metabolic pathways that are involved in temperature stress in grape cells. Sugar metabolism displayed switching between alternative and classical pathways during temperature stresses. Additionally, nine proteins involved in the phenylpropanoid pathway were greatly increased in abundance at extreme cold stress, and were thus found to be cold-responsive proteins. All MS data have been deposited in the ProteomeXchange with identifier PXD000977 (http://proteomecentral.proteomexchange.org/dataset/PXD000977).
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http://dx.doi.org/10.1002/pmic.201400541DOI Listing
September 2015

Protein identification and quantification from riverbank grape, Vitis riparia: Comparing SDS-PAGE and FASP-GPF techniques for shotgun proteomic analysis.

Proteomics 2015 Sep 22;15(17):3061-5. Epub 2015 Jun 22.

Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia.

Protein sample preparation optimisation is critical for establishing reproducible high throughput proteomic analysis. In this study, two different fractionation sample preparation techniques (in-gel digestion and in-solution digestion) for shotgun proteomics were used to quantitatively compare proteins identified in Vitis riparia leaf samples. The total number of proteins and peptides identified were compared between filter aided sample preparation (FASP) coupled with gas phase fractionation (GPF) and SDS-PAGE methods. There was a 24% increase in the total number of reproducibly identified proteins when FASP-GPF was used. FASP-GPF is more reproducible, less expensive and a better method than SDS-PAGE for shotgun proteomics of grapevine samples as it significantly increases protein identification across biological replicates. Total peptide and protein information from the two fractionation techniques is available in PRIDE with the identifier PXD001399 (http://proteomecentral.proteomexchange.org/dataset/PXD001399).
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http://dx.doi.org/10.1002/pmic.201500085DOI Listing
September 2015

Current perspectives in proteomic analysis of abiotic stress in Grapevines.

Front Plant Sci 2014 8;5:686. Epub 2014 Dec 8.

Department of Chemistry and Biomolecular Sciences, Macquarie University North Ryde, NSW, Australia.

Grapes are an important crop plant which forms the basis of a globally important industry. Grape and wine production is particularly vulnerable to environmental and climatic fluctuations, which makes it essential for us to develop a greater understanding of the molecular level responses of grape plants to various abiotic stresses. The completion of the initial grape genome sequence in 2007 has led to a significant increase in research on grapes using proteomics approaches. In this article, we discuss some of the current research on abiotic stress in grapevines, in the context of abiotic stress research in other plant species. We also highlight some of the current limitations in grapevine proteomics and identify areas with promising scope for potential future research.
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http://dx.doi.org/10.3389/fpls.2014.00686DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258992PMC
December 2014

Manipulating root water supply elicits major shifts in the shoot proteome.

J Proteome Res 2014 Feb 3;13(2):517-26. Epub 2013 Dec 3.

Australian School of Advanced Medicine, Faculty of Human Sciences, Macquarie University , Sydney, New South Wales, Australia.

Substantial reductions in yield caused by drought stress can occur when parts of the root system experience water deficit even though other parts have sufficient access to soil water. To identify proteins associated to drought signaling, rice (Oryza sativa L. cv. IR64.) plants were transplanted into plastic pots with an internal wall dividing each pot into two equal compartments, allowing for equal distribution of soil and the root system between these compartments. The following treatments were applied: either both compartments were watered daily ("wet" roots), or water was withheld from both compartments ("dry" roots), or water was withheld from only one of the two compartments in each pot ("wet" and "dry" roots). The substantial differences in physiological parameters of different growth conditions were accompanied by differential changes in protein abundances. Label-free quantitative shotgun proteomics have resulted in identification of 1383 reproducible proteins across all three conditions. Differentially expressed proteins were categorized within 17 functional groups. The patterns observed were interesting in that in some categories such as protein metabolism and oxidation-reduction, substantial numbers of proteins were most abundant when leaves were receiving signals from "wet" and "dry" roots. In yet other categories such as transport, several key transporters were surprisingly abundant in leaves supported by partially or completely droughted root systems, especially plasma membrane and vacuolar transporters. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soils. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. These results suggest that drought signals are complex interactions and not simply the additive effect of water supply to the roots.
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http://dx.doi.org/10.1021/pr400696uDOI Listing
February 2014

Analysis of rice proteins using SDS-PAGE shotgun proteomics.

Methods Mol Biol 2014 ;1072:289-302

Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia.

In this chapter we describe the workflow used in our laboratory to analyze rice leaf samples using label-free shotgun proteomics based on SDS-PAGE fractionation of proteins. Rice proteomics has benefitted substantially from successful execution of shotgun proteomics techniques. We describe steps on how to proceed starting from rice protein extraction, SDS-PAGE, in-gel protein digestion with trypsin, nanoLC-MS/MS, and database searching using the GPM. Data from these experiments can be used for spectral counting, where simultaneous quantitation of several thousand proteins can be obtained.
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http://dx.doi.org/10.1007/978-1-62703-631-3_21DOI Listing
May 2014

The influence of signals from chilled roots on the proteome of shoot tissues in rice seedlings.

Proteomics 2013 Jun 6;13(12-13):1922-33. Epub 2013 Jun 6.

Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, New South Wales, Australia.

Low root temperature causes a decrease in water uptake, which leads to mineral and nutrient deficiencies with potentially decreased root and shoot growth. Differential temperature effects in plants have been studied extensively, however, the effect of root chilling on the global protein expression in shoots has not been explored. In this study, we imposed chilling temperatures on roots of rice plants while maintaining shoots at optimum atmospheric temperature. Shoot materials (growing zones and leaves) were harvested at five points over a time course of four days, including a two-day recovery period. Proteins were quantified by tandem mass tags and triple stage MS, using a method developed to overcome ratio compression in isobaric-labelled quantitation. Over 3000 proteins in each of the tissues were quantified by multiple peptides. Proteins significantly differentially expressed as compared with the control included abscisic acid-responsive and drought-associated proteins. The data also contained evidence of a possible induction of a sugar signalling pathway.
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http://dx.doi.org/10.1002/pmic.201200475DOI Listing
June 2013

Shotgun proteomic profiling of five species of New Zealand Pachycladon.

Proteomics 2011 Jan 6;11(1):166-71. Epub 2010 Dec 6.

Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia.

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http://dx.doi.org/10.1002/pmic.200900816DOI Listing
January 2011
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