Bu çalışma, Gençlik İnovasyonu Teşvik Derneği CAS (2021084) ve Çin Bilimler Akademisi Mikrobiyoloji Enstitüsü Üç Yıllık Eylem Planının Anahtar Dağıtım Projesi Destek Fonu tarafından desteklenmektedir.

1. N. benthamiana bitkilerinin hazırlanması
<ol><li>Fide bloklarını bir tepsiye koyun, 1 L su ekleyin ve tamamen dolana kadar yaklaşık 2 saat bekletin.</li>
	<li>Fide bloklarının üzerine eşit şekilde yabani tip N. benthamiana tohumlarını serpin, bir kapakla örtün ve 1 hafta boyunca çimleyin. N. benthamiana'yı 18 saat fotoperiyodu, 24 °C, %45 bağıl nemi olan bir serada yetiştirin ve her 2 haftada bir gübreleyin.</li>
	<li>Tohumlar filizlendikten sonra, köklerine zarar vermemeye dikkat ederek bir fideyi nazikçe çıkarmak için cımbız kullanın. Yeni bir tepsinin ortasına küçük bir çukur kazın, fideyi içine yerleştirin ve kökleri hafifçe toprakla örtün. Bir kapakla örtün ve büyümeye devam edin.</li>
	<li>Fidelerin kapağı kapalı olarak üç yaprağı olana kadar büyütün. 4. gerçek yaprak çıktığında kapağı çıkarın.</li>
	<li>Agroinfiltrasyondan önce bitkilerin iki hafta daha büyümeye devam etmesine izin verin.</li>
</ol>2. Rekombinant GFP-His'in inşası
<ol><li>Gen dizilerine dayalı olarak GFP ve PR1a'nın (MGFVLFSQLPSFLLVSTLLLFLVISHSCRAG) N . benthamiana kodon optimizasyonunu ve sentezini gerçekleştirin.</li>
	<li>Xba I ve Sac I enzimlerini kullanarak pCAMBIA1300 vektörünün çift sindirimini gerçekleştirin (bkz. Malzeme Tablosu).</li>
	<li>Yukarı akış primerleri kullanarak PR1a'nın amplifikasyonunu gerçekleştirin (TTGGAGAGAACACGGGGGACTCTAGAATGGGATT TGTTCTCTTTTC) ve aşağı akış primerleri (TCCTCG CCCTTGCTCACCATGTCGACCCCGGCACGGCAAGA GTGGG), yukarı akış primerleri (CCCACTCTTGCCGTGCCGGGGTCGACATGGTGAG kullanılarak GFP'nin amplifikasyonu CAAGGGCGAGGA) ve aşağı akış primerleri (GGGGAAATTCGAGCTCTCAGTGGTGATGGTGGTG GTGAGATCTTCCGGACTTGT).</li>
	<li>Homolog rekombinasyon kullanarak, PR1a ve GFP'yi pCAMBIA1300 bitki ekspresyon vektörüne klonlayın. E. coli'ye aktardıktan sonra, tek klonları seçin ve sıralama için şirkete gönderin. Dizileme sonuçlarının ve sağ plazmitin karşılaştırılması, p35s-PR1a-GFP-His olarak adlandırılan rekombinant plazmid pCAMBIA1300-PR1a-GFP-His'tir.</li>
</ol>3. N. benthamiana'da GFP-His üretimi 
<ol><li>50 μL Agrobacterium reseptör hücresi GV3101'e 1 μL GFP plazmidi ekleyin, hafifçe karıştırın ve elektrot kabına ekleyin, elektroşok makinesinde elektrik çarpmasından sonra çıkarın.</li>
	<li>Dönüştürülmüş Agrobacterium tumefaciens'i 50 μg/mL kanamisin (Kan) ve 50 μg/mL rifampisin (Rif) içeren bir LB katı orta plaka üzerine yayın. 28 ° C'de 48 saat ters çevrilmiş olarak inkübe edin. pCAMBIA1300 vektörü kana dirençlidir ve Agrobacterium rif'e dirençlidir; sadece doğru Agrobacterium, kan ve rif içeren plakalarda büyüyebilir. Monoklonal klonlar, A. tumefaciens GV3101-p35s-PR1a-GFP-His (AtGPG) olarak adlandırılan pozitif dönüştürücülerdi.</li>
	<li>Uygun miktarda AtGPG almak için sterilize edilmiş bir kürdan kullanın ve Kan ve Rif ile 4 mL sıvı LB'ye aşılayın. 28 °C'de, 24 saat boyunca 220-300 rpm'de kültür.</li>
	<li>Bakterileri 1:50 taze LB (50 μg/mL Kan, 10 mM 2-(N-Morpholino) etansülfonik asit (MES), 20 μM asetosiringon (AS)) içine subkültür yapın ve 28 ° C'de, 220-300 rpm'de 10-12 saat inkübe edin.</li>
	<li>Bakterileri 10 dakika boyunca 1500 x g'da santrifüjleme ile hasat edin ve peleti 1 mL MMA (10 mM MgCl2, 10 mM MES pH 5.6, 100 μM AS) ile yeniden süspanse edin.</li>
	<li>MMA kullanarak AtGPG'nin optik yoğunluğunu (OD) OD600=0.8 olarak ölçün ve ayarlayın. Bakterileri oda sıcaklığında 2-4 saat daha inkübe edin. Bakteri çözeltisini iğnesiz bir şırınga ile çekin, yaprakların arkasına hafifçe bastırın ve çözeltiyi yapraklara nüfuz etmesi için baskı yapın. Bitki başına sadece ortadaki 3-4 yaprağı enjekte edin.</li>
	<li>Protein ekstraksiyonu için yaprakları hasat etmeden önce 3-4 gün boyunca serada N. benthamiana yetiştirmeye devam edin.</li>
</ol>4. GFP'nin hücre altı lokalizasyonunun gözlemlenmesi
<ol><li>48 saatlik agroinfiltrasyondan sonra, düz bir yaprak seçin ve delme için bıçağı sıkıştırmak için 6 mm'lik bir delgeç kullanın.</li>
	<li>%30 sükroz solüsyonunu bir cam lam üzerine damlatın, yaprak örneğini arkası yukarı bakacak şekilde yerleştirin ve üzerini bir kapak camı ile örtün.</li>
	<li>Uyarma dalga boyunu 488 nm'ye ayarlayın ve 400x büyütmeden sonra 490-550 nm'de yeşil floresansı tespit edin. Slayt hazırlandıktan sonra ilk fotoğrafı çekin ve 10 dakika sonra başka bir fotoğraf çekin.</li>
</ol>5. Bitkiden GFP'nin çıkarılması
<ol><li>AWF çıkarma<ol><li>Agroinfiltrasyondan 3 gün sonra rekombinant GFP'yi ifade eden bozulmamış taze N. benthamiana yapraklarını toplayın. Hücre içi protein akışını önlemek için yaprağa nazikçe davranın ve yaprak bütünlüğünü koruyun. Protein bozulmasını önlemek için toplanan yaprakları hemen bir sonraki adım için kullanın.</li>
		<li>Kalıntıları temizlemek için yaprak bıçağı önceden soğutulmuş sterilize edilmiş ddH2O ile durulayın.</li>
		<li>Taze yaprakları tartın ve 20 g yaprağı (abaksiyal tarafı aşağı) 100 mL önceden soğutulmuş 100 mM fosfat tamponuna batırın (PB 100 mM Na2HPO4 ve 100 mM NaH2PO4 ayrı ayrı yapılandırıldı ve 2.2: 1 pH 7.0 oranında karıştırıldı) 200 mL geniş ağızlı bir beherde. Yaprakları 100 gözenekli naylon ince örgü iplik ( Malzeme Tablosuna bakınız) ve plastik bir plaka ile örtün. NOT: Ön soğutma, protein bozulmasını önler. Tampon hacimleri deneysel ölçeğe göre ayarlanabilir. Tüm yaprakların suya daldırıldığından emin olun.</li>
		<li>Beheri bir vakum pompasına yerleştirin. 1 dakika boyunca 0,8 MPa vakum uygulayın, ardından hızlı bir şekilde atmosfer basıncına geri dönün.</li>
		<li>Yaprakları tampondan çıkarın ve emici kağıtla nazikçe kurulayın. Yaprakları sarın, örgü iplikle sarın ve her 50 mL'lik santrifüj tüpüne 5 g yaprak yerleştirin. AWF'yi toplamak için, haddelenmiş yaprakları, tüp kapakları tarafından tutturulmuş ağ ipliği ile tüplere uç tarafı yukarı bakacak şekilde yerleştirin.</li>
		<li>4 °C'de, 500 x g'da 5 dakika santrifüjleyin. Yaprakları çıkarın ve AWF'yi bir pipet kullanarak tüpün altında toplayın. Her tüpten yaklaşık 5 mL AWF elde edilebilir. NOT: Hücre içi proteinlerden kaynaklanan paraziti en aza indirmek ve maksimum miktarda AWF proteinini çıkarmak için, ekstraksiyon 2x-3x tekrarlanabilir, ancak 3x'ten fazla olamaz.</li>
	</ol></li>
	<li>Toplam çözünür protein ekstraksiyonu<ol><li>20 g yaprağı sıvı nitrojen içinde ince toz haline getirin. 1: 2 oranında ekstraksiyon tamponu (50 mM Tris-HCl pH 7.4, 150 mM NaCl,% 10 gliserol,% 1 Triton X-100,% 0.034 β-merkaptoetanol (Malzeme Tablosuna bakınız)) ekleyin.</li>
		<li>Homojenatı dikey bir karıştırıcıda 4 °C'de 30 dakika çalkalayın. 13.000 x g'da 4 °C'de 15 dakika santrifüjleyin.</li>
		<li>Süpernatanı yeni bir tüpe aktarın ve santrifüjlemeyi 15 dakika boyunca tekrarlayın. Temizlenmiş süpernatanı başka bir tüpe aktarın.</li>
		<li>Toplam çözünür protein ekstraktı elde etmek için süpernatanı 0.22 μm'lik bir filtreden süzün ( Malzeme Tablosuna bakınız).</li>
	</ol></li>
</ol>  
6. GFP-His'in nikel (Ni) afinite kromatografisi ile saflaştırılması
NOT: Tüm adımları 4 °C'de gerçekleştirin.
<ol><li>Adım 5.1.6'daki protein özü hacmine göre 1:1000 oranında bir tüpe Ni sefaroz excel reçinesi ( Malzeme Tablosuna bakınız) ekleyin. Reçine hacmi, protein özühacminin 1 /1000'ine eşittir.</li>
	<li>Ni reçinesi 3x'i 10x reçine hacmi ddH,2O ve PB (pH 7.0) ile sırayla yıkayın ve süpernatanı çıkarın.</li>
	<li>Tam bağlanmayı sağlamak için protein ekstraktını Ni reçinesi ile 2 saat inkübe edin. Süpernatanttaki bağlanmamış proteinleri çıkarmak için 5 dakika boyunca 500 x g'da santrifüjleyin. 3x'i 20x reçine hacmi PB ile yıkayın. 5 dakika boyunca 500 x g'da santrifüjleyin ve süpernatanı çıkarın.</li>
	<li>10x reçine hacmine 250 mM imidazol (50 mM Tris-HCl pH 7.4, 150 mM NaCl, %10 gliserol, 250 mM imidazol) ekleyerek GFP-His'i elute edin ve süpernatanı toplayın.</li>
</ol>7. Proteinlerin Coomassie mavisi boyanması
<ol><li>40 μL protein örneğine 10 μL 5x SDS yükleme tamponu ekleyin, 10 dakika kaynatın, ardından 60 dakika boyunca 110 V'ta %15 SDS-PAGE üzerinde çalıştırın.</li>
	<li>Protein jellerini Coomassie blue çözeltisi (% 0.1 R-250,% 25 izopropanol,% 10 Buzlu asetik asit) ile 2 saat boyunca boyayın.</li>
	<li>Solüsyonu dökün ve 2 saat renk giderici solüsyonla yıkayın. Jeli gözlemleyin; Jel üzerindeki proteinler mavi renkte olacaktır.</li>
</ol>8. Proteinlerin batı lekelenmesi
<ol><li>40 μL protein örneğine 10 μL 5x SDS yükleme tamponu ekleyin, 10 dakika kaynatın, ardından 60 dakika boyunca 110 V'ta %15 SDS-PAGE üzerinde çalıştırın.</li>
	<li>Proteinleri 280 mA'da 0.45 μm nitroselüloz membrana aktarın. Membranı 1 saat% 5 yağsız sütle bloke edin.</li>
	<li>Anti-His-tag antikorlarını 1:5000'de seyreltin ve zarı antikorlarla 1 saat inkübe edin. Membranı 4x'i 5 dakika boyunca yıkamak için tris-tamponlu salin ve tween 20 (TBST) kullanın.</li>
	<li>Anti-fare antikorlarını 1:10000'de seyreltin ve zarı antikorlarla 1 saat inkübe edin. Membranı 4x'i 5 dakika yıkamak için TBST kullanın.</li>
	<li>Geliştiriciyi ( Malzeme Tablosuna bakın) 1:1 oranında karıştırın. Membrana 400 μL ekleyin ve 1 dakika reaksiyona girmesine izin verin. Bir görselleştirici ile 1 dakika maruz kaldıktan sonra fotoğraf çekin.</li>
</ol>9. Protein konsantrasyonu tahlili
<ol><li>1 mL Bradford 1x boya reaktifine 5 μL protein ekleyin ve 5 dakika reaksiyona sokun.</li>
	<li>Sıfırlamadan sonra OD595 değerini belirleyin ve standart eğriden protein konsantrasyonunu hesaplayın.</li>
</ol>10. Protein miktar tayini 31
<ol><li>Protein örneklerinin standartlarla birlikte Western blotlamasını gerçekleştirin.</li>
	<li>ImageJ 1.5.0 gri tonlama analizini kullanarak GFP'nin standartlara oranına göre nicelleştirilmesini gerçekleştirin.</li>
</ol>

N. benthamiana Yapraklarından GFP-His'in Verimli Ekstraksiyonu ve Saflaştırılması

<ol>
	<li>Zahmanova, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Green+biologics:+Harnessing+the+power+of+plants+to+produce+pharmaceuticals.">Green biologics: Harnessing the power of plants to produce pharmaceuticals.</a> Int J Mol Sci. 24 (24), 1757 (2023).</li><li>PREVAIL II Writing Group. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+randomized,+controlled+trial+of+ZMapp+for+Ebola+virus+infection.">A randomized, controlled trial of ZMapp for Ebola virus infection.</a> N Engl J Med. 375 (15), 1448-1456 (2016).</li><li>Ma, J. K. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulatory+approval+and+a+first-in-human+phase+I+clinical+trial+of+a+monoclonal+antibody+produced+in+transgenic+tobacco+plants.">Regulatory approval and a first-in-human phase I clinical trial of a monoclonal antibody produced in transgenic tobacco plants.</a> Plant Biotechnol J. 13 (8), 1106-1120 (2015).</li><li>Shanmugaraj, B., Rattanapisit, K., Manopwisedjaroen, S., Thitithanyanont, A., Phoolcharoen, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monoclonal+antibodies+B38+and+H4+produced+in+Nicotiana+benthamiana+neutralize+SARS-CoV-2+in+vitro.">Monoclonal antibodies B38 and H4 produced in Nicotiana benthamiana neutralize SARS-CoV-2 in vitro.</a> Front Plant Sci. 11, 589995 (2020).</li><li>Takeyama, N., Kiyono, H., Yuki, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plant-based+vaccines+for+animals+and+humans:+Recent+advances+in+technology+and+clinical+trials.">Plant-based vaccines for animals and humans: Recent advances in technology and clinical trials.</a> Ther Adv Vaccines. 3 (5-6), 139-154 (2015).</li><li>Ward, B. J., S&#233;guin, A., Couillard, J., Tr&#233;panier, S., Landry, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phase+III:+Randomized+observer-blind+trial+to+evaluate+lot-to-lot+consistency+of+a+new+plant-derived+quadrivalent+virus+like+particle+influenza+vaccine+in+adults+18-49+years+of+age.">Phase III: Randomized observer-blind trial to evaluate lot-to-lot consistency of a new plant-derived quadrivalent virus like particle influenza vaccine in adults 18-49 years of age.</a> Vaccine. 39 (10), 1528-1533 (2021).</li><li>Siriwattananon, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plant-produced+receptor-binding+domain+of+SARS-CoV-2+elicits+potent+neutralizing+responses+in+mice+and+non-human+primates.">Plant-produced receptor-binding domain of SARS-CoV-2 elicits potent neutralizing responses in mice and non-human primates.</a> Front Plant Sci. 12, 682953 (2021).</li><li>Leblanc, Z., Waterhouse, P., Bally, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plant-based+vaccines:+The+way+ahead.">Plant-based vaccines: The way ahead.</a> Viruses. 13 (1), 5 (2020).</li><li>Sethi, L., Kumari, K., Dey, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Engineering+of+plants+for+efficient+production+of+therapeutics.">Engineering of plants for efficient production of therapeutics.</a> Mol Biotechnol. 63 (12), 1125-1137 (2021).</li><li>Webster, D. E., Thomas, M. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Post-translational+modification+of+plant-made+foreign+proteins;+glycosylation+and+beyond.">Post-translational modification of plant-made foreign proteins; glycosylation and beyond.</a> Biotechnol Adv. 30 (2), 410-418 (2012).</li><li>Streatfield, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Approaches+to+achieve+high-level+heterologous+protein+production+in+plants.">Approaches to achieve high-level heterologous protein production in plants.</a> Plant Biotechnol J. 5 (1), 2-15 (2007).</li><li>Nandi, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Process+development+and+economic+evaluation+of+recombinant+human+lactoferrin+expressed+in+rice+grain.">Process development and economic evaluation of recombinant human lactoferrin expressed in rice grain.</a> Transgenic Res. 14 (3), 237-249 (2005).</li><li>Ullrich, K. K., Hiss, M., Rensing, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Means+to+optimize+protein+expression+in+transgenic+plants.">Means to optimize protein expression in transgenic plants.</a> Curr Opin Biotechnol. 32, 61-67 (2015).</li><li>Su, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plant-made+vaccines+against+viral+diseases+in+humans+and+farm+animals.">Plant-made vaccines against viral diseases in humans and farm animals.</a> Front Plant Sci. 14, 1170815 (2023).</li><li>Agrawal, G. K., Jwa, N. S., Lebrun, M. H., Job, D., Rakwal, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plant+secretome:+Unlocking+secrets+of+the+secreted+proteins.">Plant secretome: Unlocking secrets of the secreted proteins.</a> Proteomics. 10 (4), 799-827 (2010).</li><li>Kim, T., Gondr&#233;-Lewis, M. C., Arnaoutova, I., Loh, Y. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dense-core+secretory+granule+biogenesis.">Dense-core secretory granule biogenesis.</a> Physiology. 21, 124-133 (2006).</li><li>Menkhaus, T. J., Bai, Y., Zhang, C., Nikolov, Z. L., Glatz, C. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Considerations+for+the+recovery+of+recombinant+proteins+from+plants.">Considerations for the recovery of recombinant proteins from plants.</a> Biotechnol Prog. 20 (4), 1001-1014 (2004).</li><li>Kim, S. T., Cho, K. S., Jang, Y. S., Kang, K. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two-dimensional+electrophoretic+analysis+of+rice+proteins+by+polyethylene+glycol+fractionation+for+protein+arrays.">Two-dimensional electrophoretic analysis of rice proteins by polyethylene glycol fractionation for protein arrays.</a> Electrophoresis. 22 (10), 2103-2109 (2001).</li><li>Xi, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polyethylene+glycol+fractionation+improved+detection+of+low-abundant+proteins+by+two-dimensional+electrophoresis+analysis+of+plant+proteome.">Polyethylene glycol fractionation improved detection of low-abundant proteins by two-dimensional electrophoresis analysis of plant proteome.</a> Phytochemistry. 67 (21), 2341-2348 (2006).</li><li>Dani, V., Simon, W. J., Duranti, M., Croy, R. R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Changes+in+the+tobacco+leaf+apoplast+proteome+in+response+to+salt+stress.">Changes in the tobacco leaf apoplast proteome in response to salt stress.</a> Proteomics. 5 (3), 737-745 (2005).</li><li>Delaunois, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Uncovering+plant-pathogen+crosstalk+through+apoplastic+proteomic+studies.">Uncovering plant-pathogen crosstalk through apoplastic proteomic studies.</a> Front Plant Sci. 5, 249 (2014).</li><li>Andreasson, E., Abreha, K. B., Resj&#246;, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+apoplast.">Isolation of apoplast.</a> Methods Mol. Biol. 1511, 233-240 (2017).</li><li>Lohaus, G., Pennewiss, K., Sattelmacher, B., Hussmann, M., Hermann, M. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Is+the+infiltration-centrifugation+technique+appropriate+for+the+isolation+of+apoplastic+fluid?+A+critical+evaluation+with+different+plant+species.">Is the infiltration-centrifugation technique appropriate for the isolation of apoplastic fluid? A critical evaluation with different plant species.</a> Physiol Plant. 111 (4), 457-465 (2001).</li><li>Nouchi, I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overcoming+the+difficulties+in+collecting+apoplastic+fluid+from+rice+leaves+by+the+infiltration-centrifugation+method.">Overcoming the difficulties in collecting apoplastic fluid from rice leaves by the infiltration-centrifugation method.</a> Plant Cell Physiol. 53 (9), 1659-1668 (2012).</li><li>Rumyantseva, N. I., Valieva, A. I., Kostyukova, Y. A., Ageeva, M. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effect+of+leaf+plasticity+on+the+isolation+of+apoplastic+fluid+from+leaves+of+tartary+buckwheat+plants+grown+in+vivo+and+in+vitro.">The effect of leaf plasticity on the isolation of apoplastic fluid from leaves of tartary buckwheat plants grown in vivo and in vitro.</a> Plants. 12 (23), 4048 (2023).</li><li>Ekanayake, G., Gohmann, R., Mackey, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+method+for+quantitation+of+apoplast+hydration+in+Arabidopsis+leaves+reveals+water-soaking+activity+of+effectors+of+Pseudomonas+syringae+during+biotrophy.">A method for quantitation of apoplast hydration in Arabidopsis leaves reveals water-soaking activity of effectors of Pseudomonas syringae during biotrophy.</a> Sci Rep. 12 (1), 18363 (2022).</li><li>Preston, G. M., Fones, H. N., Mccraw, S., Rico, A., O'leary, B. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+infiltration-centrifugation+technique+for+extraction+of+apoplastic+fluid+from+plant+leaves+using+phaseolus+vulgaris+as+an+example.">The infiltration-centrifugation technique for extraction of apoplastic fluid from plant leaves using phaseolus vulgaris as an example.</a> J Vis Exp. (94), e52113 (2014).</li><li>Nandi, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Process+development+and+economic+evaluation+of+recombinant+human+lactoferrin+expressed+in+rice+grain.">Process development and economic evaluation of recombinant human lactoferrin expressed in rice grain.</a> Transgenic Res. 14 (3), 237-249 (2005).</li><li>Menkhaus, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Considerations+for+the+recovery+of+recombinant+proteins+from+plants.">Considerations for the recovery of recombinant proteins from plants.</a> Biotechnol Prog. 20 (4), 1001-1014 (2004).</li><li>Streatfield, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Approaches+to+achieve+high-level+heterologous+protein+production+in+plants.">Approaches to achieve high-level heterologous protein production in plants.</a> Plant Biotechnol J. 5 (1), 2-15 (2007).</li><li>Yamamoto, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improvement+of+the+transient+expression+system+for+production+of+recombinant+proteins+in+plants.">Improvement of the transient expression system for production of recombinant proteins in plants.</a> Sci Rep. 8 (1), 4755 (2018).</li><li>Zhao, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wheat+Apoplast-localized+lipid+transfer+protein+TaLTP3+enhances+defense+responses+against+Puccinia+triticina.">Wheat Apoplast-localized lipid transfer protein TaLTP3 enhances defense responses against Puccinia triticina.</a> Front Plant Sci. 12, 771806 (2021).</li><li>Venkataraman, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recent+advances+in+expression+and+purification+strategies+for+plant+made+vaccines.">Recent advances in expression and purification strategies for plant made vaccines.</a> Front Plant Sci. 14, 1273958 (2023).</li><li>Witzel, K., Shahzad, M., Matros, A., Mock, H. P., M&#252;hling, K. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparative+evaluation+of+extraction+methods+for+apoplastic+proteins+from+maize+leaves.">Comparative evaluation of extraction methods for apoplastic proteins from maize leaves.</a> Plant Meth. 7, 48 (2011).</li></ol>

Yazarlar herhangi bir çıkar çatışması beyan etmemektedir.

Terapötik proteinler üretmek için bitkilerin kullanılması son yıllarda hızla genişledi 1,2,3,4,5,6. Protein kodlayan genler, ekspresyon vektörlerine klonlanır ve agroinfiltrasyon yoluyla bitki dokularına verilir. Bitki hücreleri tarafından üretildikten sonra, proteinler sonraki uygulamalar için saflaştırılı...

Günümüzde, antikorlar, aşılar, biyoaktif proteinler, enzimler ve küçük polipeptitler 1,2,3,4,5,6 dahil olmak üzere bitki tarafından üretilen çeşitli rekombinant terapötik proteinler incelenmektedir. Bitkiler, güvenlikleri, düşük maliyetleri ve üretimi hızlı bir şekilde ölçeklendirme yetenekleri nedeniyle terapötik proteinler üretmek için giderek daha fazla kullanılan bir platform haline gelmektedir 7,8. Bitki sistemlerinde protein ekspresyonu ve modifikasyonu, protein saflaştırması ile birlikte, bitki biyoreaktörlerininverimliliğini belirleyen kritik faktörlerdir 9,10. Bitki verimliliğini artırmak ve yüksek saflıkta hedef proteinler elde etmek, bitki bazlı üretim sistemlerinin karşılaştığı temel zorluklardır11,12.
Rekombinant proteinlerin hücre altı lokalizasyonu ve modifikasyonu, gen ekspresyonu sırasında proteini nihai organel hedefine hedefleyen N-terminalinde kodlanan spesifik sinyal peptidine bağlıdır. Rekombinant proteinler, benzersiz özelliklerine bağlı olarak apoplast, endoplazmik retikulum (ER), kloroplast, vakuol veya sitoplazmaya lokalize olacak şekilde tasarlanmıştır13. Antijenler ve antikorlar için salgılanan proteinler tercih edilir. Sekresyondan önce, proteinler doğru katlanma ve translasyon sonrası modifikasyonlar için ER ve Golgi boyunca ilerler 14,15,16.
Bitkilerde üretimden sonra, rekombinant proteinler bitki özlerinden saflaştırılmalıdır. Tipik olarak proteinler, bol miktarda hücre içi proteinler, yanlış katlanmış ve modifiye edilmemiş ürünler ve sitokromlar17 içeren toplam çözünür bitki özlerinden saflaştırılır. Safsızlıkları gidermek için bitki özleri, ribuloz-1,5-bifosfat karboksilaz/oksijenaz (RuBisCO) spesifik afinite kromatografisi, fitat çökeltme, polietilen glikol çökeltme ve sıcaklık ve pH 18,19'un ayarlanması dahil olmak üzere kapsamlı fraksiyonlamaya tabi tutulur. Bu tür safsızlık giderme adımları zahmetlidir ve protein kalitesini tehlikeye atabilir.
Plazma zarının ötesindeki bitki hücresi bölmesi, hücre duvarını, hücreler arası boşlukları ve ksilem20'yi kapsayan aplast olarak tanımlanır. Sulu faz genellikle apoplast yıkama sıvısı (AWF) olarak adlandırılır. AWF, taşıma, hücre duvarı metabolizması ve stres tepkileri gibi çok sayıda biyolojik ilerlemeyi düzenlemek için hücreler tarafından salgılanan molekülleri içerir21,22. TSP'nin aksine, AWF'nin moleküler bileşenleri daha az karmaşıktır. AWF'den rekombinant proteinlerin çıkarılması, hücre içi proteinler, yanlış katlanmış ürünler ve sitoplazmik kalıntılar tarafından kontaminasyonu önleyebilir. Kısaca, ekstraksiyon lipidi yapraklara negatif basınç altında stomalardan girer ve AWF nazik santrifüjleme23 ile toplanır. AWF'nin izolasyonu, apoplast24,25,26,27 içindeki biyolojik ilerlemeyi incelemek için yaygın olarak kullanılırken, bitki bazlı üretim sistemlerinde kullanılmamıştır.
Bitki verimliliğinin artırılması ve yüksek saflıkta hedef proteinlerin elde edilmesi, bitki üretim sistemleri için temel zorluklardır28. Tipik olarak, proteinler, büyük miktarlarda hücre içi proteinler, yanlış katlanmış ve modifiye edilmemiş ürünler ve sonraki saflaştırma için büyük maliyetler gerektirensitokromlar 29 içeren toplam çözünür bitki özlerindensaflaştırılır 30. Apoplast içine salgılanan eksojen rekombinant proteinlerin ekstraksiyonu için AWF protein ekstraksiyon yöntemlerinin kullanılması, rekombinant proteinlerin homojenliğini etkili bir şekilde artırabilir ve protein saflaştırma maliyetini azaltabilir. Burada, apoplast boşluğuna eksojen protein salgılanmasını sağlamak için bir sinyal peptidi PR1a kullanıyoruz ve N. benthamiana'nın AWF'sinden rekombinant protein saflaştırması için ayrıntılı bir yöntem sunuyoruz.

<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  

Bitkiler, terapötik proteinler üretmek için araştırılan yeni gelişen bir ökaryotik ekspresyon sistemidir. Bitkilerden rekombinant proteinlerin saflaştırılması, üretim sürecindeki en kritik adımlardan biridir. Tipik olarak, proteinler toplam çözünür proteinlerden (TSP) saflaştırıldı ve çeşitli hücre içi proteinlerin ve sitokromların varlığı, sonraki protein saflaştırma adımları için zorluklar doğurur. Ayrıca, antijenler ve antikorlar gibi terapötik proteinlerin çoğu, uygun glikozilasyon elde etmek için salgılanır ve tam olarak değiştirilmemiş proteinlerin varlığı, tutarsız antijen veya antikor yapılarına yol açar. Bu çalışma, bitki apoplastik alanından yüksek oranda saflaştırılmış rekombinant proteinler elde etmek için daha etkili bir yöntem sunmaktadır. Rekombinant Yeşil floresan proteini (GFP), Nicotiana benthamiana'nın apoplastına salgılanmak üzere tasarlanmıştır ve daha sonra bir infiltrasyon-santrifüjleme yöntemi kullanılarak ekstrakte edilir. Ekstrakte edilen apoplasttan elde edilen GFP-His daha sonra nikel afinite kromatografisi ile saflaştırılır. TSP'nin geleneksel yöntemlerinin aksine, apoplasttan saflaştırma, yüksek oranda saflaştırılmış rekombinant proteinler üretir. Bu, bitki üretim sistemleri için önemli bir teknolojik gelişmeyi temsil eder.

GFP-His, N. benthamiana'nın apoplastik alanına salgılanması hedefleniyor GFP, sekresyon için bir N-terminal PR1a sinyal peptidi ve saflaştırma için bir C-terminal His-tag ile pCAMBIA1300 plazmidine klonlandı ve p35s-PR1a-GFP-His üretildi (Şekil 1A). Rekombinant protein N . benthamiana'da geçici olarak eksprese edildi ve agroinfiltrasyondan 3 gün sonra anti-His antikoru kullanılarak western blot ile 30 kDa bandı tespit edil...

Yazar Spotlight: Bitki Hücrelerinden Rekombinant Proteinlerin Verimli Bir Şekilde Geri Kazanılması için Apoplast Protein Ekstraksiyonunun Optimize Edilmesi

Bitki sistemlerinden rekombinant proteinlerin saflaştırılması genellikle bitki proteinleri tarafından sorgulanır. Bu çalışma, Nicotiana benthamiana'nın apoplastından salgılanan bir rekombinant proteini etkili bir şekilde ekstrakte etmek ve saflaştırmak için bir yöntem sağlar.

Bitki Tarafından Üretilen Rekombinant Proteinin Saflığını Artırmak için Apoplast-Ekstraksiyon Bazlı Yöntem  

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

apoplast-extraction-based-method-to-improve-purity-plant-produced

Research

JoVE Journal

Biology

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

844 Görüntüleme.  Shandong First Medical University. Rekombinant proteinlerin bitki hücrelerinden daha verimli bir şekilde nasıl çıkarılacağını araştırdık. Apoplast protein ekstraksiyon yönteminin rekombinant proteinlere uygulandığında uygulanabilir olup olmadığı sorusunu yanıtladık. Bu ekstraksiyon yöntemi, apoplasta salgılanan proteinleri çıkarır, böylece homojenliğe sahip olurlar.Hücre içi proteinlerden kaynaklanan etkileşimi ve müteakip saflaştırma maliyetlerini azal...

Video: Yazar Spotlight: Bitki Hücrelerinden Rekombinant Proteinlerin Verimli Bir Şekilde Geri Kazanılması için Apoplast Protein Ekstraksiyonunun Optimize Edilmesi

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.

Rekombinant mCD1d Böcek Hücrelerde Protein Üretimi İçin Bir Yöntem.

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

Biyoloji

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.

Sıvı Faz Kurtarma Moleküler Ağırlık Tabanlı Fraksiyonu GELFREE 8100 Fraksiyonu Sisteminin Kullanılması

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-tip ve Süs Çeşitler arasında ayırt A PCR tabanlı Genotiplendirme Yöntemi Imperata cylindrica</em

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.

Dayanarak protein-protein etkileşimleri ve kimliği için bir protokol<sup&gt; 15</sup&gt; K Metabolik Etiketleme, immünopresipitasyon, Kantitatif Kütle Spektrometrisi ve Affinity Modülasyon

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.

Plant protein kompleksleri, çevirim sonrası değişikliklerin belirlenmesi

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.

Üretilen Rekombinant Disülfid zengin Venom Proteinler Uygulanan Yüksek Randımanlı Sayısal Anlatım Tarama ve Arıtma<em&gt; E. coli</em

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.

Membran proteinlerinin Yeşil floresan proteini temelli Ekspresyon elemesinde<em&gt; Escherichia coli</em

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.

Bakteriler, Böcek Hücreleri ve Bitki Sistemleri: Rekombinant Protein Farklı Biofactories İfade Karşılaştırmalı Analizi

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.

Yüksek işlem hacmi sterilizasyon Arabidopsis tohum için standart yöntem

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.