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Proteomics in commercial crops: An overview

Tan BC, Lim YS, Lau SE

J Proteomics, 2017 10 03;169:176-188.
PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018

Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement.
SIGNIFICANCE: Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.
Fulltext Impact of sea-salt on morpho-physiological and biochemical responses in banana (Musa acuminata cv. Berangan)

Mazumdar P, Lau SE, Singh P, Takhtgahi HM, Harikrishna JA

Physiol Mol Biol Plants, 2019 May;25(3):713-726.
PMID: 31168234 DOI: 10.1007/s12298-019-00659-3

Banana is often grown in coastal-regions, and while known for its sensitivity towards seawater, little is documented on the effect of sea-salt on the growth, physiology and metal homeostasis. Here we report that banana plantlets exposed to sea-salt at extreme (average seawater concentration; 52.7 dS m-1), severe (28.5 dS m-1) or moderate (10.2 dS m-1) salinity levels had reduced root length (2.0-6.0-fold), plant height (1.2-1.6-fold), leaf number (2.0-2.3-fold) and leaf area (3.3-4.0-fold) compared to control plantlets. Degradation of pigments (total chlorophyll: 1.3-12.3-fold, chlorophyll a: 1.3-9.2-fold; chlorophyll b: 1.3-6.9-fold lower and carotenoids: 1.4-3.7-fold lower) reflected vulnerability of photosystems to salt stress. Relative water content showed a maximum decrease of 1.5-fold in salt stress. MDA analysis showed sea-salt exposure triggers 2.3-3.5-fold higher lipid peroxidation. Metal content analysis showed a 73-fold higher Na value from roots exposed to extreme salinity compared to control plantlets. While phenotype was clearly affected, moderate salinity showed no significant alteration of macro (N, P, K and Ca) and micro (Fe, Mn and Cu) metal content. The antioxidant enzymes: SOD (3.2-fold), CAT (1.7-fold) and GR (6-fold) showed higher activity at moderate salinity level compared to control plantlets but lower activity at severe (SOD: 1.3-fold; CAT: 1.5-fold; GR: 2-fold lower) and extreme seawater salinity (SOD: 1.5; CAT: 1.9; GR: 1.3-fold lower). Mild changes in growth and physiology at sea-salt levels equivalent to moderate seawater flooding, indicate that banana will survive such flooding, while extreme seawater inundation will be lethal. This data provides a reference for future salinity-mediated work in banana.
Fulltext dsRNA silencing of an R2R3-MYB transcription factor affects flower cell shape in a Dendrobium hybrid

Lau SE, Schwarzacher T, Othman RY, Harikrishna JA

BMC Plant Biol, 2015;15:194.
PMID: 26260631 DOI: 10.1186/s12870-015-0577-3

The R2R3-MYB genes regulate pigmentation and morphogenesis of flowers, including flower and cell shape, and therefore have importance in the development of new varieties of orchids. However, new variety development is limited by the long breeding time required in orchids. In this study, we identified a cDNA, DhMYB1, that is expressed during flower development in a hybrid orchid, Dendrobium hybrida (Dendrobium bobby messina X Dendrobium chao phraya) then used the direct application of dsRNA to observe the effect of gene silencing on flower phenotype and floral epidermal cell shape.
Ectopic expression of a Musa acuminata root hair defective 3 (MaRHD3) in Arabidopsis enhances drought tolerance

Wong GR, Mazumdar P, Lau SE, Harikrishna JA

J Plant Physiol, 2018 Dec;231:219-233.
PMID: 30292098 DOI: 10.1016/j.jplph.2018.09.018

Genetic improvement is an important approach for crop improvement towards yield stability in stress-prone areas. Functional analysis of candidate stress response genes can provide key information to allow the selection and modification of improved crop varieties. In this study, the constitutive expression of a banana cDNA, MaRHD3 in Arabidopsis improved the ability of transgenic lines to adapt to drought conditions. Transgenic Arabidopsis plants expressing MaRHD3 had roots with enhanced branching and more root hairs when challenged with drought stress. The MaRHD3 plants had higher biomass accumulation, higher relative water content, higher chlorophyll content and an increase in activity of reactive oxygen species (ROS) scavenging enzymes; SOD, CAT, GR, POD and APX with reduced water loss rates compared to control plants. The analysis of oxidative damage indicated lower cell membrane damage in transgenic lines compared to control plants. These findings, together with data from higher expression of ABF-3 and higher ABA content of drought-stressed transgenic MaRHD3 expressing plants, support the involvement of the ABA signal pathway and ROS scavenging enzyme systems in MaRHD3 mediated drought tolerance.
Fulltext High-quality RNA isolation from pigment-rich Dendrobium flowers

Khairul-Anuar MA, Mazumdar P, Lau SE, Tan TT, Harikrishna JA

3 Biotech, 2019 Oct;9(10):371.
PMID: 31588395 DOI: 10.1007/s13205-019-1898-y

Isolation of high-quality RNA from Dendrobium flowers is challenging because of the high levels of pigment, polysaccharides, and polyphenols. In the present study, an efficient CTAB method for RNA extraction from the pigment-rich flowers of Dendrobium was optimised. The optimised method yielded high quantities of RNA (10.1-12.9 µg/g). Spectrophotometric values of A260/280 in the range of 2.2 to 2.4 and A260/230 values of 2.0 suggested that the isolated RNA was free of polyphenols, polysaccharides, and protein contaminants. RNA integrity numbers determined by microfluidics were in the range of 7.9-8.9 indicative of intact RNA. In the improved method, the addition of 3 M NaCl and 3% PVP-10 in the extraction buffer, followed by an incubation period of 45 min at 65 °C, eliminated most of the polysaccharides, polyphenolic compounds, and denatured protein. Extraction with phenol:chloroform:isoamyl alcohol (125:24:1) effectively removed pigments from the aqueous phase, while the precipitation of RNA with lithium chloride minimised the co-precipitation of protein, DNA, and polysaccharide and resulted in the extraction of high quality of RNA. The suitability of the RNA for downstream processing was confirmed via RT-PCR amplification of Chalcone synthase gene from cDNA prepared from RNA isolated from different developmental stages of the flower of a Dendrobium hybrid. The present method will be highly useful for the isolation of RNA from pigment, polyphenol, and polysaccharide-rich plant tissues.
Fulltext Plant Nitric Oxide Signaling under Drought Stress

Lau SE, Hamdan MF, Pua TL, Saidi NB, Tan BC

Plants (Basel), 2021 Feb 13;10(2).
PMID: 33668545 DOI: 10.3390/plants10020360

Water deficit caused by drought is a significant threat to crop growth and production. Nitric oxide (NO), a water- and lipid-soluble free radical, plays an important role in cytoprotection. Apart from a few studies supporting the role of NO in drought responses, little is known about this pivotal molecular amendment in the regulation of abiotic stress signaling. In this review, we highlight the knowledge gaps in NO roles under drought stress and the technical challenges underlying NO detection and measurements, and we provide recommendations regarding potential avenues for future investigation. The modulation of NO production to alleviate abiotic stress disturbances in higher plants highlights the potential of genetic manipulation to influence NO metabolism as a tool with which plant fitness can be improved under adverse growth conditions.
Fulltext Osmotic stress in banana is relieved by exogenous nitric oxide

Mohd Amnan MA, Pua TL, Lau SE, Tan BC, Yamaguchi H, Hitachi K, et al.

PeerJ, 2021;9:e10879.
PMID: 33614294 DOI: 10.7717/peerj.10879

Drought is one of the severe environmental stresses threatening agriculture around the globe. Nitric oxide plays diverse roles in plant growth and defensive responses. Despite a few studies supporting the role of nitric oxide in plants under drought responses, little is known about its pivotal molecular amendment in the regulation of stress signaling. In this study, a label-free nano-liquid chromatography-mass spectrometry approach was used to determine the effects of sodium nitroprusside (SNP) on polyethylene glycol (PEG)-induced osmotic stress in banana roots. Plant treatment with SNP improved plant growth and reduced the percentage of yellow leaves. A total of 30 and 90 proteins were differentially identified in PEG+SNP against PEG and PEG+SNP against the control, respectively. The majority of proteins differing between them were related to carbohydrate and energy metabolisms. Antioxidant enzyme activities, such as superoxide dismutase and ascorbate peroxidase, decreased in SNP-treated banana roots compared to PEG-treated banana. These results suggest that the nitric oxide-induced osmotic stress tolerance could be associated with improved carbohydrate and energy metabolism capability in higher plants.