References for plant and algae Protein Extraction Methods 

Collection of articles describing protein extraction from different species/organs

• Laing and Christeller (2004).  Extraction of protein from plant tissues. Curr Protoc Protein Sci. 2004 Nov:Chapter 4:4.7.1-4.7.7. doi: 10.1002/0471140864.ps0407s38.
• Plaxton (2019). Avoiding Proteolysis during the Extraction and Purification of Active Plant Enzymes. Plant Cell Physiol.  1;60(4):715-724.
• Francisco Campos et al. (2011). A general method of protein purification for recombinant unstructured non-acidic proteins. Protein Expr Purif . 80(1):47-51.
• Romero-Pérez et al. (2023). Protein Expr Purif. 202:106183.
• Cahoon et al. (1992). Expression of a coriander desaturase results in petroselinic acid production in transgenic tobacco. Proc Natl Acad Sci U S A . 89(23):11184-8.  (phenol protein extraction method)
  
  
  

• Colmenero-Flores et al. (1999). Pvlea-18, a member of a new late-embryogenesis-abundant protein family that accumulates during water stress and in the growing regions of well-irrigated bean seedlings. Plant Physiol . 1999 May;120(1):93-104. 

• Rahman et al. (2021). A Single Seed Protein Extraction Protocol for Characterizing Brassica Seed Storage Proteins. Agronomy 2021, 11, 107. 
• Heidorn-Czarna et al. (2018). Targeted proteomics approach toward understanding the role of the mitochondrial protease FTSH4 in the biogenesis of OXPHOS during Arabidopsis seed germination. Front Plant Sci. 15:9:821. 
• Rajjou et al. (2006). Proteomic investigation of the effect of salicylic acid on Arabidopsis seed germination and establishment of early defense mechanisms. Plant Physiol. 141(3):910-23. 
• Mikołajczyk et al. (2000). Osmotic Stress Induces Rapid Activation of a Salicylic Acid–Induced Protein Kinase and a Homolog of Protein Kinase ASK1 in Tobacco Cells. Plant Cell . 2000 Jan;12(1):165-78. 
• Colmenero-Flores et al. (1999). Pvlea-18, a member of a new late-embryogenesis-abundant protein family that accumulates during water stress and in the growing regions of well-irrigated bean seedlings. Plant Physiol. 1999 May;120(1):93-104. 

• Zienkiewicz et al. (2014). A Protocol for Protein Extraction from Lipid-Rich Plant Tissues Suitable for Electrophoresis. Methods Mol Biol . 2014:1072:85-91. 

• Charras et al. (2024). An efficient protocol for extracting thylakoid membranes and total leaf proteins from Posidonia oceanica and other polyphenol-rich plants. Plant Methods. 11;20(1):38. 

• Gawarecka and Hoon Ahn (2024). RuBisCO Depletion and Subcellular Fractionation for Enhanced Florigen Detection in Arabidopsis. Methods Mol Biol. 2795:227-238.
• Matsushima and Matsuo (2024). Removal of plant endogenous proteins from tobacco leaf extract by freeze-thaw treatment for purification of recombinant proteins. Plant Sci . 2024 Feb:339:111953. doi: 10.1016/j.plantsci.2023.111953. 

• Pu et al. (2023). Protein Preparation for Proteomic Analysis of the Unfolded Protein Response in Arabidopsis thaliana. Methods Mol Biol. 2022 ; 2378: 279–289. doi:10.1007/978-1-0716-1732-8_18.
• Zhao et al. (2022). Fractionation and Extraction of Crude Nuclear Proteins From Arabidopsis Seedlings. Bio-protocol 12(02): e4296. DOI:10.21769/BioProtoc.4296.

• Okegawa et al. (2023). x- and y-type thioredoxins maintain redox homeostasis on photosystem I acceptor side under fluctuating light. Plant Physiol . 2023 Nov 22;193(4):2498-2512. 
• Tang et al. /2022). Native protein purification of ferroxidase LPR1 from leaf extracts of a transgenic Arabidopsis thaliana line. STAR Protocols Volume 3, Issue 4, 16 December 2022, 101733.
• Wan et al. (2022). Arabidopsis ubiquitin-conjugating enzymes UBC4, UBC5, and UBC6 have major functions in sugar metabolism and leaf senescence. Int J Mol Sci . 23(19):11143. 

• Goto et al. (2019). Comprehensive nuclear proteome of Arabidopsis obtained by sequential extraction. NUCLEUS 2019, VOL. 10, NO. 1, 81–92.

• Roosjen et al. (2023). RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell. 4;187(1):130-148.e17.

• Luís et al. (2016). Selection of an Appropriate Protein Extraction Method to Study the Phosphoproteome of Maize Photosynthetic Tissue. PLoS One . 2016 Oct 11;11(10):e0164387. 

• Busch et al. (2007). Increased air temperature during simulated autumn conditions does not increase photosynthetic carbon gain but affects the dissipation of excess energy in seedlings of the evergreen conifer Jack pine. Plant Physiol . 2007 Mar;143(3):1242-51. 

• Karthikaichamy et al. (2017). Time for Multiple Extraction Methods in Proteomics? A Comparison of Three Protein Extraction Methods in the Eustigmatophyte Alga Microchloropsis gaditana CCMP526. Comparative Study OMICS. Nov;21(11):678-683. 

• Fagerlund et al. (2020). Stabilization of Photosystem II by the PsbT protein impacts photodamage, repair and biogenesis. Biochim Biophys Acta Bioenerg. 1861(10):148234. 
• Behle. (2019). Cell lysis and extraction of total protein from Synechocystis sp. PCC 6803.
• Brown et al. (2008). Flux capacities and acclimation costs in Trichodesmiumfrom the Gulf of Mexico. Marine Biology: Volume 154, pages 413–422.
• Six et al. (2007). Light variability illuminates niche-partitioning among marine Picocyanobacteria. PLoS One.  19;2(12):e1341. 

Articles describing the preparation of different cellular fractions

• Chen et al. (2022).  Isolation of Extracellular Vesicles from Arabidopsis. Curr. Protoc. 2022 January ; 2(1): e352. doi:10.1002/cpz1.352. 

• Lang et al. (2011). Simultaneous isolation of pure and intact chloroplasts and mitochondria from moss as the basis for sub-cellular proteomics. Plant Cell Rep . 2011 Feb;30(2):205-15. 

• Arunima et al. (2024). Improved methods for total and chloroplast protein extraction from Cajanus species for two-dimensional gel electrophoresis and mass spectrometry. PLoS One. 2024 Aug 15;19(8):e0308909.  
• Adamiec et al. (2022). Stress-related expression of the chloroplast EGY3 pseudoprotease and its possible impact on chloroplasts’ proteome composition. Front Plant Sci. 2022; 13: 965143. 
• Majeran et al. (2005). Functional differentiation of bundle sheath and mesophyll maize chloroplasts determined by comparative proteomics. Comparative Study Plant Cell. 17(11):3111-40. 

• Blomqvist et al. (2008). Proteomic analysis of highly purified prolamellar bodies reveals their significance in chloroplast development. Photosynth Res.96(1):37-50. 

• Charras et al. (2024). An efficient protocol for extracting thylakoid membranes and total leaf proteins from Posidonia oceanica and other polyphenol-rich plants. Methodology, Volume 20, article number 38.
• Brady et al. (2023). Protein Extraction Efficiency and Selectivity of Esterified Styrene–Maleic Acid Copolymers in Thylakoid Membranes. Biomacromolecules . 2021 Jun 14;22(6):2544-2553. 
• Korotych et al. (2021). Poly(styrene-co-maleic acid)-mediated isolation of supramolecular membrane protein complexes from plant thylakoids. Biochim Biophys Acta Bioenerg;1862(3):148347.

• Hao and Malnoë (2023). A Simple Sonication Method to Isolate the Chloroplast Lumen in Arabidopsis thaliana. Bio Protoc.13(15):e4756.
• Hall et al. (2011). Preparation of Stroma, Thylakoid Membrane, and Lumen Fractions from Arabidopsis thaliana Chloroplasts for Proteomic Analysis. Methods Mol Biol . 2011:775:207-22. 

• Graça et al. (2021). High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction. Sci Rep. 2021 Jul 30;11(1):15534. 

• LaMontagne et al. (2016). Isolation of Microsomal Membrane Proteins from Arabidopsis thaliana. Curr Protoc Plant Biol . 1(1):217-234. 

• Johansen et al. (2023). Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie . 2023 Feb:205:3-26. 
• Choy et al. (2021). A 10-year meta-analysis of membrane protein structural biology: Detergents, membrane mimetics, and structure determination techniques. Biochim Biophys Acta Biomembr. 1863(3):183533.
• Zhang and Cherezov (2019). Chemical Tools for Membrane Protein Structural Biology. Curr Opin Struct Biol. 58: 278–285. 
• Chae et al. (2021). A New Class of Amphiphiles Bearing Rigid Hydrophobic Groups for Solubilization and Stabilization of Membrane Proteins. Chemistry. 18(31):9485-90.
• Hawkins et al. (2021). Membrane protein extraction and purification using partially-esterified SMA polymers. Biochim Biophys Acta Biomembr. 1863(12):183758.
• Hesketh et al. (2020). Styrene maleic-acid lipid particles (SMALPs) into detergent or amphipols: An exchange protocol for membrane protein characterisation. Biochim Biophys Acta Biomembr. 1862(5):183192. 

• Xu et al. (2020). A simplified method to isolate rice mitochondria. Plant Methods volume 16, Article number: 149.
• Rurek et al. (2018). Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes. Int J Mol Sci. 16;19(3):877. 
• Boussardon  et al. (2020). Tissue-Specific Isolation of Arabidopsis/plant Mitochondria - IMTACT (Isolation of Mitochondria TAgged in specific Cell Types). The Plant Journal 103:459-473
• Boussardon C and Keech O (2022). "Cell Type-Specific Isolation of Mitochondria in Arabidopsis." Methods Mol Biol 2363: 13-23

• Sikorskaite et al. (2013). Protocol: Optimised methodology for isolation of nuclei from leaves of species in the Solanaceae and Rosaceae families. Plant Methods volume 9, Article number: 31.

• Niu et al. (2018). Protein Extraction Methods Shape Much of the Extracted Proteomes. Front Plant Sci. 12:9:802. 

https://plantmethods.biomedcentral.com/

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