This work is supported by the Youth Innovation Promotion Association CAS (2021084) and the Key Deployment Project Support Fund of the Three-Year Action Plan of the Institute of Microbiology, Chinese Academy of Sciences.

1. Preparation of N. benthamiana plants
<ol>
	<li>Place seedling blocks in a tray, add 1 L of water and soak for approximately 2 h until fully saturated.</li>
	<li>Evenly sprinkle wild-type N. benthamiana seeds on the seedling blocks, cover with a lid, and germinate for 1 week. Grow N. benthamiana in a greenhouse with 18 h photoperiod, 24 &#176;C, 45% relative humidity, and fertilize every 2 weeks.</li>
	<li>Once the seeds have sprouted, use tweezers to gently remove a seedling, taking care not to cause damage to its roots. Dig a small pit in the center of a new tray, place the seedling in it, and cover the roots lightly with soil. Cover with a lid and continue to grow.</li>
	<li>Grow till the seedlings have three leaves, with the lid on. Remove the lid when the 4th true leaf emerges.</li>
	<li>Allow plants to continue growing for two more weeks before agroinfiltration.</li>
</ol>
2. Construction of the recombinant GFP-His
<ol>
	<li>Perform N. benthamiana codon optimization and synthesis of GFP and PR1a (MGFVLFSQLPSFLLVSTLLLFLVISHSCRAG) based on the gene sequences.</li>
	<li>Carry out double digestion of pCAMBIA1300 vector using Xba I and Sac I enzymes (see Table of Materials).</li>
	<li>Perform amplification of PR1a using upstream primers (TTGGAGAGAACACGGGGGACTCTAGAATGGGATT 
	TGTTCTCTTTTC) and downstream primers (TCCTCG 
	CCCTTGCTCACCATGTCGACCCCGGCACGGCAAGA 
	GTGGG), amplification of GFP using upstream primers (CCCACTCTTGCCGTGCCGGGGTCGACATGGTGAG 
	CAAGGGCGAGGA) and downstream primers (GGGGAAATTCGAGCTCTCAGTGGTGATGGTGGTG 
	GTGAGATCTTCCGGACTTGT).</li>
	<li>Using homologous recombination, clone PR1a, and GFP into the pCAMBIA1300 plant expression vector. After transferring into E. coli, select single clones and send them to the company for sequencing. Comparison of sequencing results and the right plasmid is the recombinant plasmid pCAMBIA1300-PR1a-GFP-His, referred to as p35s-PR1a-GFP-His.</li>
</ol>
3. Production of GFP-His in N. benthamiana
<ol>
	<li>Add 1 &#181;L of GFP plasmid into 50 &#181;L of Agrobacterium receptor cells GV3101, mix gently and add to the electrode cup, remove after electrocution on the electroshocker.</li>
	<li>Spread transformed Agrobacterium tumefaciens on an LB solid medium plate containing 50 &#181;g/mL kanamycin (Kan) and 50 &#181;g/mL rifampicin (Rif). Incubate inverted at 28 &#176;C for 48 h. The pCAMBIA1300 vector is kan-resistant, and Agrobacterium is rif-resistant; only the correct Agrobacterium can grow on plates with kan and rif. The monoclonal clones were the positive transformants, named A. tumefaciens GV3101-p35s-PR1a-GFP-His (AtGPG).</li>
	<li>Use a sterilized toothpick to pick up an appropriate amount of AtGPG and inoculate it into 4 mL of liquid LB with Kan and Rif. Culture at 28 &#176;C, 220-300 rpm for 24 h.</li>
	<li>Subculture bacteria 1:50 into fresh LB (50 &#181;g/mL Kan, 10 mM 2-(N-Morpholino) ethanesulfonic acid (MES), 20 &#181;M acetosyringone (AS)) and incubate at 28 &#176;C, 220-300 rpm for 10-12 h.</li>
	<li>Harvest bacteria by centrifugation at 1500 x g for 10 min and resuspend the pellet with 1 mL of MMA (10 mM MgCl2, 10 mM MES pH 5.6, 100 &#181;M AS).</li>
	<li>Measure and adjust the optical density (OD) of AtGPG to OD600=0.8 using MMA. Incubate the bacteria for another 2-4 h at room temperature. Draw up the bacterial solution with a needleless syringe, press it against the back of the leaves lightly, and give pressure to penetrate the solution into the leaves. Inject only the middle 3-4 leaves per plant.</li>
	<li>Continue to grow N. benthamiana in the greenhouse for 3-4 days before harvesting leaves for protein extraction.</li>
</ol>
4. Observing subcellular localization of GFP
<ol>
	<li>After 48 h of agroinfiltration, select a flat leaf and use a 6 mm hole punch to clamp the blade for punching.</li>
	<li>Drip 30% sucrose solution onto a glass slide, place the leaf sample with the back facing upwards and cover it with a cover glass.</li>
	<li>Set the excitation wavelength to 488 nm and detect the green fluorescence at 490-550 nm after magnification of 400x. Take the first photo once the slide is prepared and another one 10 min later.</li>
</ol>
5. Extracting GFP from plant
<ol>
	<li>AWF extraction
	<ol>
		<li>Collect the intact fresh N. benthamiana leaves expressing recombinant GFP at 3 days post agroinfiltration. Treat the leaf gently and maintain leaf integrity to avoid intracellular protein efflux. Use collected leaves for the next step immediately to avoid protein degradation.</li>
		<li>Rinse leaf blade with pre-cooled sterilized ddH2O to remove debris.</li>
		<li>Weigh fresh leaves and submerge 20 g leaves (abaxial side down) in 100 mL of pre-cooled 100 mM phosphate buffer (PB 100 mM Na2HPO4 and 100 mM NaH2PO4 were separately configured and mixed at a ratio of 2.2:1 pH 7.0) in a 200 mL wide-mouth beaker. Cover leaves with 100 mesh nylon fine mesh yarn (see Table of Materials) and a plastic plate. 
		NOTE: Pre-cooling prevents protein degradation. Buffer volumes can be adjusted based on the experimental scale. Ensure all leaves are immersed.</li>
		<li>Place the beaker into a vacuum pump. Apply 0.8 MPa vacuum for 1 min, then quickly restore to atmospheric pressure.</li>
		<li>Remove leaves from the buffer and gently blot dry with absorbent paper. Roll up leaves, wrap with mesh yarn, and place 5 g of leaves into each 50 mL centrifuge tube. To collect AWF, position rolled leaves tip-side up in tubes with mesh yarn fastened by the tube caps.</li>
		<li>Centrifuge at 4 &#176;C, 500 x g for 5 min. Remove leaves and collect the AWF at the bottom of the tube using a pipette. About 5 mL of AWF can be obtained from each tube. 
		NOTE: In order to minimize interference from intracellular proteins and to extract the maximum amount of AWF proteins, the extraction can be repeated 2x-3x, but not more than 3x.</li>
	</ol>
	</li>
	<li>Total soluble protein extraction
	<ol>
		<li>Grind 20 g leaves into fine powder in liquid nitrogen. Add extraction buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 10% glycerol, 1% Triton X-100, 0.034% &#946;-mercaptoethanol (see Table of Materials)) at a 1: 2 ratio.</li>
		<li>Shake homogenate in a vertical mixer for 30 min at 4 &#176;C. Centrifuge homogenate at 13,000 x g for 15 min at 4 &#176;C.</li>
		<li>Transfer the supernatant to a new tube and repeat centrifugation for 15 min. Transfer the cleared supernatant to another tube.</li>
		<li>Filter the supernatant through a 0.22 &#181;m filter (see Table of Materials) to obtain total soluble protein extract.</li>
	</ol>
	</li>
</ol>
&#160;&#160;
6. Purification of GFP-His with nickel (Ni) affinity chromatography
NOTE: Perform all steps at 4 &#176;C.
<ol>
	<li>Add Ni sepharose excel resin (see Table of Materials) to a tube in a 1:1000 ratio relative to the protein extract volume from step 5.1.6. Resin volume equals 1/1000th of the protein extract volume.</li>
	<li>Wash Ni resin 3x with 10x resin volume of ddH2O and PB (pH 7.0) separately in turn and remove the supernatant.</li>
	<li>Incubate protein extract with Ni resin for 2 h to allow full binding. Centrifuge at 500 x g for 5 min to remove unbound proteins in the supernatant. Wash 3x with 20x resin volume of PB. Centrifuge at 500 x g for 5 min and remove the supernatant.</li>
	<li>Elute GFP-His by adding 10x resin volume of 250 mM imidazole (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 10% glycerol, 250 mM imidazole) and collect the supernatant.</li>
</ol>
7. Coomassie blue staining of proteins
<ol>
	<li>Add 10 &#181;L of 5x SDS loading buffer to 40 &#181;L of protein samples, boil for 10 min, then run on 15% SDS-PAGE at 110 V for 60 min.</li>
	<li>Stain protein gels with Coomassie blue solution (0.1% R-250, 25% isopropanol, 10% Glacial acetic acid) for 2 h.</li>
	<li>Pour off the solution and wash with decolorizing solution for 2 h. Observe the gel; proteins on the gel will be colored blue.</li>
</ol>
8. Western blotting of proteins
<ol>
	<li>Add 10 &#181;L of 5x SDS loading buffer to 40 &#181;L of protein samples, boil for 10 min, then run on 15% SDS-PAGE at 110 V for 60 min.</li>
	<li>Transfer proteins to a 0.45 &#181;m nitrocellulose membrane at 280 mA. Block the membrane with 5% skimmed milk for 1 h.</li>
	<li>Dilute the anti-His-tag antibodies at 1:5000 and incubate the membrane with the antibodies for 1 h. Use the tris-buffered saline and tween 20 (TBST) to wash the membrane 4x for 5 min.</li>
	<li>Dilute the anti-mouse antibodies at 1:10000 and incubate the membrane with the antibodies for 1 h. Use TBST to wash the membrane 4x for 5 min.</li>
	<li>Mix the developer (see Table of Materials) in the ratio of 1:1. Add 400 &#181;L to the membrane and allow to react for 1 min. Take photographs after 1 min exposure with a visualizer.</li>
</ol>
9. Protein concentration assay
<ol>
	<li>Add 5 &#181;L of protein to 1 mL of Bradford 1x dye reagent and react for 5 min.</li>
	<li>Determine the OD595 value after zeroing and calculate the protein concentration from the standard curve.</li>
</ol>
10. Protein quantification&#160;31
<ol>
	<li>Perform Western blotting of protein samples together with standards.</li>
	<li>Perform quantification of GFP by ratio to standards using ImageJ 1.5.0 greyscale analysis.</li>
</ol>
&#160;&#160;

Efficient Extraction and Purification of GFP-His from N. benthamiana Leaves

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The authors declare no conflict of interest.

Using plants to produce therapeutic proteins has expanded quickly in recent years1,2,3,4,5,6. Protein-encoding genes are cloned into expression vectors and delivered into plant tissues via agroinfiltration. After production by plant cells, proteins are purified for downstream applications. Typically, recombinant proteins are ...

Nowadays, various plant-produced recombinant therapeutic proteins are under study, including antibodies, vaccines, bioactive proteins, enzymes, and small polypeptides1,2,3,4,5,6. Plants are becoming an increasingly utilized platform for producing therapeutic proteins due to their safety, low cost, and ability to rapidly scale production7,8. Protein expression and modification in plant systems, along with protein purification, are critical factors determining the productivity of plant bioreactors9,10. Enhancing plant productivity and obtaining high-purity target proteins are core challenges facing plant-based production systems11,12.
The subcellular localization and modification of recombinant proteins depends on the specific signal peptide encoded at the N-terminus, which targets the protein to its final organelle destination during gene expression. Recombinant proteins are designed to localize to the apoplast, endoplasmic reticulum (ER), chloroplast, vacuole, or cytoplasm, based on their unique properties13. For antigens and antibodies, secreted proteins are preferred. Before secretion, proteins progress through ER and Golgi for correct folding and post-translational modifications14,15,16.
After production in plants, recombinant proteins must be purified from plant extracts. Typically, proteins are purified from total soluble plant extracts, which contain abundant intracellular proteins, misfolded and unmodified products, and cytochromes17. To remove impurities, plant extracts undergo extensive fractionation, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-specific affinity chromatography, phytate precipitation, polyethylene glycol precipitation, and adjustment of temperature and pH18,19. Such impurity-removal steps are laborious and can compromise protein quality.
The plant cell compartment beyond the plasma membrane is defined as the apoplast, encompassing the cell wall, intercellular spaces, and xylem20. The aqueous phase is commonly called apoplast washing fluid (AWF). AWF contains molecules secreted by cells to regulate numerous biological progresses like transport, cell wall metabolism, and stress responses21,22. In contrast to TSP, the molecular constituents of AWF are less complex. Extracting recombinant proteins from AWF may avoid contamination by intracellular proteins, misfolded products, and cytoplasmic remnants. Briefly, extraction lipid enters leaves through the stomata under negative pressure, and the AWF is collected by gentle centrifugation23. While isolation of AWF is widely employed to study the biological progress inside apoplast24,25,26,27, it has not been exploited in plant-based production systems.
Improving plant productivity and obtaining high purity target proteins are central challenges for plant production systems28. Typically, proteins are purified from total soluble plant extracts containing large amounts of intracellular proteins, misfolded and unmodified products, and cytochromes29, which require great costs for subsequent purification30. The use of AWF protein extraction methods for the extraction of exogenous recombinant proteins secreted into apoplast can effectively improve the homogeneity of recombinant proteins and reduce the cost of protein purification. Here, we use a signal peptide PR1a to enable exogenous protein secretion into the apoplast space and introduce a detailed method for recombinant protein purification from the AWF of N. benthamiana.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>100 mesh nylon fine mesh yarn</td>
			<td>Guangzhou Huayu Trading limited company</td>
			<td>hy-230724-2</td>
			<td>For AWF protein extraction</td>
		</tr>
		<tr>
			<td>50 ml centrifuge tubes</td>
			<td>Vazyme</td>
			<td>TCF00150</td>
			<td>For centrifuge</td>
		</tr>
		<tr>
			<td>ClonExpress II one step cloning kit</td>
			<td>Vazyme</td>
			<td>C112-02</td>
			<td>For clone</td>
		</tr>
		<tr>
			<td>FastDigest Sac1</td>
			<td>NEB</td>
			<td>R3156S</td>
			<td>For clone</td>
		</tr>
		<tr>
			<td>FastDigest XbaI</td>
			<td>NEB</td>
			<td>FD0685</td>
			<td>For clone</td>
		</tr>
		<tr>
			<td>ImageJ 1.5.0</td>
			<td>/</td>
			<td>/</td>
			<td>For greyscale analysis</td>
		</tr>
		<tr>
			<td>Large filter</td>
			<td>Thermo Fisher</td>
			<td>NEST</td>
			<td>For filtering</td>
		</tr>
		<tr>
			<td>Laser scanning confocal microscopy</td>
			<td>Leica SP8</td>
			<td></td>
			<td>For subcellular localization</td>
		</tr>
		<tr>
			<td>Ni sepharose excel</td>
			<td>Cytiva</td>
			<td>10339806</td>
			<td>For protein purification</td>
		</tr>
		<tr>
			<td>Precast protein plus gel</td>
			<td>YEASEN</td>
			<td>36246ES10</td>
			<td>For SDS-PAGE</td>
		</tr>
		<tr>
			<td>Small filter</td>
			<td>Nalgene</td>
			<td>1660045</td>
			<td>For filtering</td>
		</tr>
		<tr>
			<td>SuperSignal West Femto Substrate Trial Kit</td>
			<td>Thermo Fisher</td>
			<td>34076</td>
			<td>For western blotting</td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>SCR</td>
			<td>30188928</td>
			<td>To configure the extraction buffer</td>
		</tr>
		<tr>
			<td>Type rotaryvang vacuum pump</td>
			<td>Zhejiang taizhouqiujing vacuum pump limited company</td>
			<td>2XZ-2</td>
			<td>For vacuum infiltration</td>
		</tr>
		<tr>
			<td>Vertical mixer</td>
			<td>Haimen Qilinbel Instrument Manufacturing limited company</td>
			<td>BE-1200</td>
			<td>For mixing</td>
		</tr>
		<tr>
			<td>&#946;-mercaptoethanol</td>
			<td>SIGMA</td>
			<td>BCBK8223V</td>
			<td>To configure the extraction buffer</td>
		</tr>
	</tbody>
</table>

apoplast-extraction based method to improve the purity of plant produced recombinant protein  

Plants are a newly developing eukaryotic expression system being explored to produce therapeutic proteins. Purification of recombinant proteins from plants is one of the most critical steps in the production process. Typically, proteins were purified from total soluble proteins (TSP), and the presence of miscellaneous intracellular proteins and cytochromes poses challenges for subsequent protein purification steps. Moreover, most therapeutic proteins like antigens and antibodies are secreted to obtain proper glycosylation, and the presence of incompletely modified proteins leads to inconsistent antigen or antibody structures. This work introduces a more effective method to obtain highly purified recombinant proteins from the plant apoplastic space. The recombinant Green fluorescent protein (GFP) is engineered to be secreted into the apoplast of Nicotiana benthamiana and is then extracted using an infiltration-centrifugation method. The GFP-His from the extracted apoplast is then purified by nickel affinity chromatography. In contrast to the traditional methods from TSP, purification from the apoplast produces highly purified recombinant proteins. This represents an important technological improvement for plant production systems.

GFP-His is targeted for secretion into the apoplastic space of N. benthamiana 
GFP was cloned into the pCAMBIA1300 plasmid with an N-terminal PR1a signal peptide for secretion and a C-terminal His-tag for purification, generating p35s-PR1a-GFP-His (Figure 1A). The recombinant protein was transiently expressed in N. benthamiana and a 30 kDa band was detected by western blot using anti-His antibody at 3 days post agroinfiltration <strong...

Author Spotlight: Optimizing Apoplast Protein Extraction for Efficient Recovery of Recombinant Proteins from Plant Cells

The purification of recombinant proteins from plant systems is usually challenged by plant proteins. This work provides a method to effectively extract and purify a secreted recombinant protein from the apoplast of Nicotiana benthamiana.

Apoplast-Extraction Based Method to Improve the Purity of Plant Produced Recombinant Protein  

Plants are a newly developing eukaryotic expression system being explored to produce therapeutic proteins. Purification of recombinant proteins from ...

We investigated how to extract recombinant proteins from plant cells more efficiently. We answered the question of whether the apoplast protein extraction method is feasible when applied to the recombinant proteins. This extraction method extracts proteins secreted into the apoplast, so they have homogeneity.There is no need for cell disruption, which reduce the interference from intracellular proteins and the subsequent purification costs. We will focus on how to increase the secretion of recombinant proteins in the apoplast space to further improve the efficiency of the apoplast protein extraction method.

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757 Views.  Shandong First Medical University. We investigated how to extract recombinant proteins from plant cells more efficiently. We answered the question of whether the apoplast protein extraction method is feasible when applied to the recombinant proteins. This extraction method extracts proteins secreted into the apoplast, so they have homogeneity.There is no need for cell disruption, which reduce the interference from intracellular proteins and the subsequent purification costs. We will focus on how to increase the secretio...

Video: Author Spotlight: Optimizing Apoplast Protein Extraction for Efficient Recovery of Recombinant Proteins from Plant Cells

A Method For Production of Recombinant mCD1d Protein in Insect Cells.

CD1 proteins constitute a third class of antigen-presenting molecules. They are cell surface glycoproteins, expressed as approximately 50-kDa glycosylated heavy chains that are noncovalently associated with beta2-microglobulin. They bind lipids rather than peptides. Although their structure confirms the similarity of CD1 proteins to MHC class I and class II antigen presenting molecules, the mCD1d groove is relatively narrow, deep, and highly hydrophobic and it has two binding pockets instead of the several shallow pockets described for the classical MHC-encoded antigen-presenting molecules. Based upon their amino acid sequences, such a hydrobphobic groove provides an ideal environment for the binding of lipid antigens. The Natural Killer T (NKT) cells use their TCR to recognize glycolipids bound to or presented by CD1d. T cells reactive to lipids presented by CD1 have been involved in the protection against autoimmune and infectious diseases and in tumor rejection. Thus, the ability to identify, purify , and track the response of CD1-reactive NKT cell is of great importance . The generation of tetramers of alpha Galactosyl ceramide (a-Galcer) with CD1d has significant insight into the biology of NKT cells. Tetramers constructed from other CD1 molecules have also been generated and these new reagents have greatly expanded the knowledge of the functions of lipid-reactive T cells, with potential use in monitoring the response to lipid-based vaccines and in the diagnosis of autoimmune diseases and other treatments.

A Method to prepare Insect cells and infect them with baculovirus for the the purpose of production of recombinant mCD1d proteinand generating mCD1d tetramers.

CD1 proteins constitute a third class of antigen-presenting molecules. They are cell surface glycoproteins, expressed as approximately 50-kDa glycosylated ...

Using the GELFREE 8100 Fractionation System for Molecular Weight-Based Fractionation with Liquid Phase Recovery

The GELFREE 8100 Fractionation System is a novel protein fractionation system designed to maximize protein recovery during molecular weight based fractionation. The system is comprised of single-use, 8-sample capacity cartridges and a benchtop GELFREE Fractionation Instrument. During separation, a constant voltage is applied between the anode and cathode reservoirs, and each protein mixture is electrophoretically driven from a loading chamber into a specially designed gel column gel. Proteins are concentrated into a tight band in a stacking gel, and separated based on their respective electrophoretic mobilities in a resolving gel. As proteins elute from the column, they are trapped and concentrated in liquid phase in the collection chamber, free of the gel. The instrument is then paused at specific time intervals, and fractions are collected using a pipette. This process is repeated until all desired fractions have been collected. If fewer than 8 samples are run on a cartridge, any unused chambers can be used in subsequent separations.
This novel technology facilitates the quick and simple separation of up to 8 complex protein mixtures simultaneously, and offers several advantages when compared to previously available fractionation methods. This system is capable of fractionating up to 1mg of total protein per channel, for a total of 8mg per cartridge. Intact proteins over a broad mass range are separated on the basis of molecular weight, retaining important physiochemical properties of the analyte. The liquid phase entrapment provides for high recovery while eliminating the need for band or spot cutting, making the fractionation process highly reproducible1.

The accompanying video describes the use of the GELFREE 8100 Fractionation System, which partitions complex protein samples on the basis of molecular weight and recovers the fractions in liquid phase. The video describes how the technology works, how it is used, and provides resultant data, with polyacrylamide gel electrophoresis analysis of fractionated bovine liver homogenate.

The GELFREE 8100 Fractionation System is a novel protein fractionation system designed to maximize protein recovery during molecular weight based ...

A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica

Wild-type I. cylindrica (cogongrass) is one of the top ten worst invasive plants in the world, negatively impacting agricultural and natural resources in 73 different countries throughout Africa, Asia, Europe, New Zealand, Oceania and the Americas1-2. Cogongrass forms rapidly-spreading, monodominant stands that displace a large variety of native plant species and in turn threaten the native animals that depend on the displaced native plant species for forage and shelter. To add to the problem, an ornamental variety [I. cylindrica var. koenigii (Retzius)] is widely marketed under the names of Imperata cylindrica 'Rubra', Red Baron, and Japanese blood grass (JBG). This variety is putatively sterile and noninvasive and is considered a desirable ornamental for its red-colored leaves. However, under the correct conditions, JBG can produce viable seed (Carol Holko, 2009 personal communication) and can revert to a green invasive form that is often indistinguishable from cogongrass as it takes on the distinguishing characteristics of the wild-type invasive variety4 (Figure 1). This makes identification using morphology a difficult task even for well-trained plant taxonomists. Reversion of JBG to an aggressive green phenotype is also not a rare occurrence. Using sequence comparisons of coding and variable regions in both nuclear and chloroplast DNA, we have confirmed that JBG has reverted to the green invasive within the states of Maryland, South Carolina, and Missouri. JBG has been sold and planted in just about every state in the continental U.S. where there is not an active cogongrass infestation. The extent of the revert problem in not well understood because reverted plants are undocumented and often destroyed.
Application of this molecular protocol provides a method to identify JBG reverts and can help keep these varieties from co-occurring and possibly hybridizing. Cogongrass is an obligate outcrosser and, when crossed with a different genotype, can produce viable wind-dispersed seeds that spread cogongrass over wide distances5-7. JBG has a slightly different genotype than cogongrass and may be able to form viable hybrids with cogongrass. To add to the problem, JBG is more cold and shade tolerant than cogongrass8-10, and gene flow between these two varieties is likely to generate hybrids that are more aggressive, shade tolerant, and cold hardy than wild-type cogongrass. While wild-type cogongrass currently infests over 490 million hectares worldwide, in the Southeast U.S. it infests over 500,000 hectares and is capable of occupying most of the U.S. as it rapidly spreads northward due to its broad niche and geographic potential3,7,11. The potential of a genetic crossing is a serious concern for the USDA-APHIS Federal Noxious Week Program. Currently, the USDA-APHIS prohibits JBG in states where there are major cogongrass infestations (e.g., Florida, Alabama, Mississippi). However, preventing the two varieties from combining can prove more difficult as cogongrass and JBG expand their distributions. Furthermore, the distribution of the JBG revert is currently unknown and without the ability to identify these varieties through morphology, some cogongrass infestations may be the result of JBG reverts. Unfortunately, current molecular methods of identification typically rely on AFLP (Amplified Fragment Length Polymorphisms) and DNA sequencing, both of which are time consuming and costly. Here, we present the first cost-effective and reliable PCR-based molecular genotyping method to accurately distinguish between cogongrass and JBG revert.

A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica

We provide a cost-effective and rapid molecular genotyping protocol that employs variety-specific PCR primers that target DNA sequence differences within the chloroplast trnL-F spacer region to differentiate between varieties of Imperata cylindrica (cogongrass) that cannot be distinguished by morphology alone. These varieties include the federally listed noxious weed, cogongrass and closely-related, wide-spread ornamental variety, I. cylindrica var. koenigii (Japanese blood grass).

Wild-type I. cylindrica (cogongrass) is one of the top ten worst invasive plants in the world, negatively impacting agricultural and natural resources in ...

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

Protein-protein interactions are fundamental for many biological processes in the cell. Therefore, their characterization plays an important role in current research and a plethora of methods for their investigation is available1. Protein-protein interactions often are highly dynamic and may depend on subcellular localization, post-translational modifications and the local protein environment2. Therefore, they should be investigated in their natural environment, for which co-immunoprecipitation approaches are the method of choice3. Co-precipitated interaction partners are identified either by immunoblotting in a targeted approach, or by mass spectrometry (LC-MS/MS) in an untargeted way. The latter strategy often is adversely affected by a large number of false positive discoveries, mainly derived from the high sensitivity of modern mass spectrometers that confidently detect traces of unspecifically precipitating proteins. A recent approach to overcome this problem is based on the idea that reduced amounts of specific interaction partners will co-precipitate with a given target protein whose cellular concentration is reduced by RNAi, while the amounts of unspecifically precipitating proteins should be unaffected. This approach, termed QUICK for QUantitative Immunoprecipitation Combined with Knockdown4, employs Stable Isotope Labeling of Amino acids in Cell culture (SILAC)5 and MS to quantify the amounts of proteins immunoprecipitated from wild-type and knock-down strains. Proteins found in a 1:1 ratio can be considered as contaminants, those enriched in precipitates from the wild type as specific interaction partners of the target protein. Although innovative, QUICK bears some limitations: first, SILAC is cost-intensive and limited to organisms that ideally are auxotrophic for arginine and/or lysine. Moreover, when heavy arginine is fed, arginine-to-proline interconversion results in additional mass shifts for each proline in a peptide and slightly dilutes heavy with light arginine, which makes quantification more tedious and less accurate5,6. Second, QUICK requires that antibodies are titrated such that they do not become saturated with target protein in extracts from knock-down mutants.
Here we introduce a modified QUICK protocol which overcomes the abovementioned limitations of QUICK by replacing SILAC for 15N metabolic labeling and by replacing RNAi-mediated knock-down for affinity modulation of protein-protein interactions. We demonstrate the applicability of this protocol using the unicellular green alga Chlamydomonas reinhardtii as model organism and the chloroplast HSP70B chaperone as target protein7 (Figure 1). HSP70s are known to interact with specific co-chaperones and substrates only in the ADP state8. We exploit this property as a means to verify the specific interaction of HSP70B with its nucleotide exchange factor CGE19.

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

We present a variation of the QUICK (QUantitative Immunoprecipitation Combined with Knockdown) approach that was introduced previously to distinguish between true and false protein-protein interactions. Our approach is based on 15N metabolic labeling, the modulation of affinities of protein-protein interactions by the presence/absence of ATP, immunoprecipitation, and quantitative mass spectrometry.

Protein-protein interactions are fundamental for many biological processes in the cell. Therefore, their characterization plays an important role in ...

Identification of Post-translational Modifications of Plant Protein Complexes

Plants adapt quickly to changing environments due to elaborate perception and signaling systems. During pathogen attack, plants rapidly respond to infection via the recruitment and activation of immune complexes. Activation of immune complexes is associated with post-translational modifications (PTMs) of proteins, such as phosphorylation, glycosylation, or ubiquitination. Understanding how these PTMs are choreographed will lead to a better understanding of how resistance is achieved.
Here we describe a protein purification method for nucleotide-binding leucine-rich repeat (NB-LRR)-interacting proteins and the subsequent identification of their post-translational modifications (PTMs). With small modifications, the protocol can be applied for the purification of other plant protein complexes. The method is based on the expression of an epitope-tagged version of the protein of interest, which is subsequently partially purified by immunoprecipitation and subjected to mass spectrometry for identification of interacting proteins and PTMs.
This protocol demonstrates that: i). Dynamic changes in PTMs such as phosphorylation can be detected by mass spectrometry; ii). It is important to have sufficient quantities of the protein of interest, and this can compensate for the lack of purity of the immunoprecipitate; iii). In order to detect PTMs of a protein of interest, this protein has to be immunoprecipitated to get a sufficient quantity of protein.

We describe here a protocol for the purification and characterization of plant protein complexes. We demonstrate that by immunoprecipitating a single protein within a complex, so we can identify its post-translational modifications and its interacting partners.

Plants adapt quickly to changing environments due to elaborate perception and signaling systems. During pathogen attack, plants rapidly respond to ...

High Throughput Quantitative Expression Screening and Purification Applied to Recombinant Disulfide-rich Venom Proteins Produced in E. coli

Escherichia coli (E. coli) is the most widely used expression system for the production of recombinant proteins for structural and functional studies. However, purifying proteins is sometimes challenging since many proteins are expressed in an insoluble form. When working with difficult or multiple targets it is therefore recommended to use high throughput (HTP) protein expression screening on a small scale (1-4&#160;ml cultures) to quickly identify conditions for soluble expression. To cope with the various structural genomics programs of the lab, a quantitative (within a range of 0.1-100 mg/L culture of recombinant protein) and HTP protein expression screening protocol was implemented and validated on thousands of proteins. The protocols were automated with the use of a liquid handling robot but can also be performed manually without specialized equipment.
Disulfide-rich venom proteins are gaining increasing recognition for their potential as therapeutic drug leads. They can be highly potent and selective, but their complex disulfide bond networks make them challenging to produce. As a member of the FP7 European Venomics project (<a href="http://www.venomics.eu">www.venomics.eu</a>), our challenge is to develop successful production strategies with the aim of producing thousands of novel venom proteins for functional characterization. Aided by the redox properties of disulfide bond isomerase DsbC, we adapted our HTP production pipeline for the expression of oxidized, functional venom peptides in the E. coli cytoplasm. The protocols are also applicable to the production of diverse disulfide-rich proteins. Here we demonstrate our pipeline applied to the production of animal venom proteins. With the protocols described herein it is likely that soluble disulfide-rich proteins will be obtained in as little as a week. Even from a small scale, there is the potential to use the purified proteins for validating the oxidation state by mass spectrometry, for characterization in pilot studies, or for sensitive micro-assays.

High Throughput Quantitative Expression Screening and Purification Applied to Recombinant Disulfide-rich Venom Proteins Produced in E. coli

A protocol for the quantitative, high throughput expression screening and analytical purification of fusion proteins from small-scale Escherichia coli cultures is described and applied to the expression of disulfide-rich animal venom protein targets.

Escherichia coli (E. coli) is the most widely used expression system for the production of recombinant proteins for structural and functional studies. ...

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and the inherent instability of many membrane proteins once solubilized in detergents. A protocol is described that combines ligation independent cloning of membrane proteins as GFP fusions with expression in Escherichia coli detected by GFP fluorescence. This enables the construction and expression screening of multiple membrane protein/variants to identify candidates suitable for further investment of time and effort. The GFP reporter is used in a primary screen of expression by visualizing GFP fluorescence following SDS polyacrylamide gel electrophoresis (SDS-PAGE). Membrane proteins that show both a high expression level with minimum degradation as indicated by the absence of free GFP, are selected for a secondary screen. These constructs are scaled and a total membrane fraction prepared and solubilized in four different detergents. Following ultracentrifugation to remove detergent-insoluble material, lysates are analyzed by fluorescence detection size exclusion chromatography (FSEC). Monitoring the size exclusion profile by GFP fluorescence provides information about the mono-dispersity and integrity of the membrane proteins in different detergents. Protein: detergent combinations that elute with a symmetrical peak with little or no free GFP and minimum aggregation are candidates for subsequent purification. Using the above methodology, the heterologous expression in E. coli of SED (shape, elongation, division, and sporulation) proteins from 47 different species of bacteria was analyzed. These proteins typically have ten transmembrane domains and are essential for cell division. The results show that the production of the SEDs orthologues in E. coli was highly variable with respect to the expression levels and integrity of the GFP fusion proteins. The experiment identified a subset for further investigation.

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

A streamlined approach to screening for the expression of recombinant membrane proteins in Escherichia coli based on fusion to green fluorescent protein is presented.

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and ...

A Comparative Analysis of Recombinant Protein Expression in Different Biofactories: Bacteria, Insect Cells and Plant Systems

Plant-based systems are considered a valuable platform for the production of recombinant proteins as a result of their well-documented potential for the flexible, low-cost production of high-quality, bioactive products.
In this study, we compared the expression of a target human recombinant protein in traditional fermenter-based cell cultures (bacterial and insect) with plant-based expression systems, both transient and stable.
For each platform, we described the set-up, optimization and length of the production process, the final product quality and the yields and we evaluated provisional production costs, specific for the selected target recombinant protein.
Overall, our results indicate that bacteria are unsuitable for the production of the target protein due to its accumulation within insoluble inclusion bodies. On the other hand, plant-based systems are versatile platforms that allow the production of the selected protein at lower-costs than Baculovirus/insect cell system. In particular, stable transgenic lines displayed the highest-yield of the final product and transient expressing plants the fastest process development. However, not all recombinant proteins may benefit from plant-based systems but the best production platform should be determined empirically with a case-by-case approach, as described here.

In this study the expression of a target human recombinant protein in different production platforms was compared. We focused on traditional fermenter-based cultures and on plants, describing the set-up of each system and highlighting, on the basis of the reported results, the inherent limits and advantages for each platform.

Plant-based systems are considered a valuable platform for the production of recombinant proteins as a result of their well-documented potential for the ...

Standardized Method for High-throughput Sterilization of Arabidopsis Seeds

Arabidopsis thaliana (Arabidopsis) seedlings often need to be grown on sterile media. This requires prior seed sterilization to prevent the growth of microbial contaminants present on the seed surface. Currently, Arabidopsis seeds are sterilized using two distinct sterilization techniques in conditions that differ slightly between labs and have not been standardized, often resulting in only partially effective sterilization or in excessive seed mortality. Most of these methods are also not easily scalable to a large number of seed lines of diverse genotypes. As technologies for high-throughput analysis of Arabidopsis continue to proliferate, standardized techniques for sterilizing large numbers of seeds of different genotypes are becoming essential for conducting these types of experiments. The response of a number of Arabidopsis lines to two different sterilization techniques was evaluated based on seed germination rate and the level of seed contamination with microbes and other pathogens. The treatments included different concentrations of sterilizing agents and times of exposure, combined to determine optimal conditions for Arabidopsis seed sterilization. Optimized protocols have been developed for two different sterilization methods: bleach (liquid-phase) and chlorine (Cl2) gas (vapor-phase), both resulting in high seed germination rates and minimal microbial contamination. The utility of these protocols was illustrated through the testing of both wild type and mutant seeds with a range of germination potentials. Our results show that seeds can be effectively sterilized using either method without excessive seed mortality, although detrimental effects of sterilization were observed for seeds with lower than optimal germination potential. In addition, an equation was developed to enable researchers to apply the standardized chlorine gas sterilization conditions to airtight containers of different sizes. The protocols described here allow easy, efficient, and inexpensive seed sterilization for a large number of Arabidopsis lines.

The objective of this study was to determine the effects of bleach and chlorine gas sterilization on seed germination of a range of Arabidopsis genotypes grown on sterile media. Optimized sterilization protocols have been developed to prevent the growth of microbial contaminants while providing satisfactory seed survival.

Arabidopsis thaliana (Arabidopsis) seedlings often need to be grown on sterile media. This requires prior seed sterilization to prevent the growth of ...

Two-layered Membrane Sandwich Method for Laodelphax striatellus Saliva Collection

Rice stripe virus (RSV), which causes significant economic loss of agriculture in East Asia, entirely depends on insect vectors for its effective transmission among host rice. Laodelphax striatellus (small brown planthopper, SBPH) is the primary insect vector that horizontally transmits RSV while sucking sap from the phloem. Saliva plays a significant role in insects' feeding behavior. A convenient method that will be useful for research on insects' saliva with piercing-sucking feeding behavior is described here. In this method, insects were allowed to feed on an artificial diet sandwiched between two stretched paraffin film layers. The diet containing the saliva was collected each day, filtered, and concentrated for further analysis. Finally, the quality of collected saliva was examined by protein staining and immunoblotting. This method was exemplified by detecting the presence of RSV and a mucin-like protein in the saliva of SBPH. These artificial feeding and saliva collection method will lay a foundation for further research on factors in insect saliva related to feeding behavior and virus transmission.

Two-layered Membrane Sandwich Method for Laodelphax striatellus Saliva Collection

The present protocol describes a method to collect sufficient saliva from piercing-sucking insects using an artificial medium. This is a convenient method for collecting insect saliva and studying salivary function on insect feeding behavior and vector-borne virus transmission.