Comparison of sample preparation methods suitable for poplar leaf proteomics

doi:10.3969/j.issn.1000-2006.201706063

ZHEN Yan, ZHENG Xiuhua, SHI Jisen

Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 2018, Vol. 42 ›› Issue (02) : 33-39.

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Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 2018, Vol. 42 ›› Issue (02) : 33-39. DOI: 10.3969/j.issn.1000-2006.201706063

Comparison of sample preparation methods suitable for poplar leaf proteomics

ZHEN Yan, ZHENG Xiuhua, SHI Jisen^*

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Abstract

【Objective】In order to improve the detection of low abundance proteins in plant leaves, the effective extraction methods were established in poplar leaves for proteomics analysis.【Method】 Trichloroacetic acid(TCA)-acetone coupled with polyethylene glycol(PEG)fractionation and sodium dodecyl sulfate(SDS)-phenol coupled with PEG fractionation were evaluated, combined with SDS-polyacrylamide gel electrophoresis(SDS-PAGE)and two-dimensional electrophoresis(2-DE).【Result】The SDS-PAGE results showed that TCA-acetone coupled with PEG fractionation is superior to SDS-phenol coupled with the PEG fractionation method. Further, proteins with PEG fractionation and no PEG fractionation coupled with TCA-acetone were compared by using 2-DE, and the gel maps displayed that PEG fractionation is a good way to deplete the Rubiscos and improve the detection of low abundant proteins. The PEG fractionation method can detect nearly 90 more spots than nonfractionation can. 【Conclusion】LTQ-Orbitrap XL was used to identify several proteins from the PEG fractionation coupled with TCA-acetone. The TCA-acetone coupled with PEG fractionation is an effective approach for the detection of 2-DE analysis and mass spectroscopy(MS)identification of lower abundance proteins.

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ZHEN Yan, ZHENG Xiuhua, SHI Jisen. Comparison of sample preparation methods suitable for poplar leaf proteomics[J]. Journal of Nanjing Forestry University (Natural Sciences Edition）. 2018, 42(02): 33-39 https://doi.org/10.3969/j.issn.1000-2006.201706063

References

[1] CELLAR N A, KUPPANNAN K, LANGHORST M L, et al. Cross species applicability of abundant protein depletion columns for ribulose-1,5-bisphosphate carboxylase-oxygenase [J]. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences, 2008, 861(1):29-39. DOI:10.1016-j.jchromb.2007.11.024.
[2] GIAVALISCO P, NORDHOFF E, KREITLER T, et al. Proteome analysis of Arabidopsis thaliana by two-dimensional gel electrophoresis and matrix-assisted laser desorption-ionisation-time of flight mass spectrometry [J]. Proteomics, 2005, 5(7):1902-1913. DOI:10.1002-pmic.200401062.
[3] LEE D G, AHSAN N, LEE S H, et al. An approach to identify cold-induced low-abundant proteins in rice leaf [J]. Comptes Rendus Biologies, 2007, 330(3):215-225.
[4] WIDJAJA I, NAUMANN K, ROTH U, et al. Combining subproteome enrichment and Rubisco depletion enables identification of low abundance proteins differentially regulated during plant defense [J]. Proteomics, 2009, 9(1):138-147. DOI:10.1016-j.crvi.2007.01.001.
[5] ATHA D H, INGHAM K C. Mechanism of precipitation of proteins by polyethylene glycols: analysis in terms of excluded volume [J]. The Journal of Biological Chemistry, 1981, 256(23):12108-12117. PMID:7298647
[6] JUCKES I R. Fractionation of proteins and viruses with polyethylene glycol[J]. Biochimica et Biophysica Acta, 1971, 229(3):535-546. PMID:5103022
[7] XI J, WANG X, LI S, et al. Polyethylene glycol fractionation improved detection of low-abundant proteins by two-dimensional electrophoresis analysis of plant proteome [J]. Phytochemistry, 2006, 67(21):2341-2348. DOI:10.1016-j.phytochem.2006.08.005.
[8] AHSAN N, LEE D G, LEE S H, et al. A comparative proteomic analysis of tomato leaves in response to waterlogging stress [J]. Physiologia Plantarum, 2007, 131(4):555-570. DOI:10.1111-j.1399-3054.2007.00980.x.
[9] FALVO S, ACQUADRO A, ALBO A G, et al. Proteomic analysis of PEG fractionated UV-C stress-response proteins in globe Artichoke[J]. Plant Molecular Biology Reporter, 2012, 30(1):111-122. DOI.org-10.1007-s11105-011-0325-2
[10] KIM S T, CHO K S, JANG Y S, et al. Two-dimensional electrophoretic analysis of rice proteins by polyethylene glycol fractionation for protein arrays [J]. Electrophoresis, 2001, 22(10):2103-2109. DOI:10.1002-1522-2683(200106)22:10<2103::AID-ELPS2103>3.0.CO; 2-W.
[11] ZHANG A, LU Q, YIN Y, et al. Comparative proteomic analysis provides new insights into the regulation of carbon metabolism during leaf senescence of rice grown under field conditions[J]. Journal of Plant Physiology, 2010, 167(16):1380-1389. DOI:10.1016-j.jplph.2010.05.011
[12] SHEN J W, BUKO A. Rapid identification of proteins in polyethylene glycol-containing samples using capillary electrophoresis electrospray mass spectrometry[J]. Analytical Biochemistry, 2002, 311(1):80-83. PMID:12441156
[13] HESSE A M, MARCELO P, ROSSIER J, et al. Simple and universal tool to remove on-line impurities in mono-or two-dimensional liquid chromatography-mass spectrometry analysis [J]. Journal of Chromatography A, 2008, 1189(1/2):175-182. DOI:10.1016-j.chroma.2007.12.060.
[14] ARYAL U K, KROCHKO J E, ROSS A R S. Identification of phosphoproteins in Arabidopsis thaliana leaves using polyethylene glycol fractionation, immobilized metal-ion affinity chromatography, two-dimensional gel electrophoresis and mass spectrometry [J]. Journal of Proteome Research, 2012, 11(1):425-437. DOI:10.1021-pr200917t.
[15] ZHEN Y, QI J L, WANG S S, et al. Comparative proteome analysis of differentially expressed proteins induced by Al toxicity in soybean [J]. Physiologia Plantarum, 2007, 131(4):542-554. DOI:10.1111-j.1399-3054.2007.00979.x.
[16] UEMATSU K, SUZUKI N, IWAMAE T, et al. Increased fructose 1,6-bisphosphate aldolase in plastids enhances growth and photosynthesis of tobacco plants [J]. Journal of Experimental Botany, 2012, 63(8):3001-3009. DOI:10.1093-jxb-ers004.
[17]PARK J I, ISHIMIZU T, SUWABE K, et al. UDP-Glucose pyrophosphorylase is rate limiting in vegetative and reproductive phases in Arabidopsis thaliana [J]. Plant and Cell Physiology, 2010, 51(6):981-996. DOI:10.1093-pcp-pcq057.
[18] CHIVASA S, TOME D F A, SLABAS A R. UDP-Glucose pyrophosphorylase is a novel plant cell death regulator [J]. Journal of Proteome Research, 2013, 12(4):1743-1753. DOI:10.1021-pr3010887.

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