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Farklı Biyolojik Organizmalarda Proteomik Uygulamalar

Year 2016, Volume: 73 Issue: 4, 405 - 418, 01.12.2016

Abstract

Marc Wilkins tarafından ilk defa 1994 yılında açıklanan proteomiks terimi bir organizma, doku veya hücrede herhangi bir zamanda bulunan proteinlerin tamamının, geniş çaplı protein ayırma ve tanımlama yöntemleri kullanılarak analiz edilmesi esasına dayanmaktadır. Proteom; belli bir zaman ve mekânda bir organizmanın sahip olduğu ve ifade ettiği bütün farklı proteinlerin tamamıdır. Proteomik; belli bir zamanda belli bir yerde bulunan tüm proteinlerin yapılarını, yerleşimlerini, miktarlarını, translasyon sonrası modifikasyonlarını, doku ve hücrelerdeki işlevlerini, diğer proteinlerle ve makro moleküllerle olan etkileşimlerini ifade eder. Farklı doku ve organların hücrelerinde bulunan DNA’lar birbirine benzese de proteinler birbirine benzememektedir. Bu nedenle özellikle çeşitli hastalıkların tanısında sadece genetik bilimi yeterli olmamakta, aynı zamanda proteomiks bilimine ihtiyaç da gün geçtikçe artmaktadır. Bu derleme kapsamında öncelikle farklı protein ekstraksiyon yöntemleri, iki boyutlu jel elektroforezi 2-DE ve kütle spektrometresi teknolojilerini içeren proteomik uygulamalar ele alındı. Daha sonra; farklı organizma veya doku kullanımı ile tıbbın farklı alanlarında proteomik yöntemler uygulanarak gerçekleştirilen çalışmalardan bahsedildi. Ayrıca, son yıllarda proteom analizi ile farklı biyolojik organizmaların biyotik veya abiyotik strese maruz kalınca verdiği yanıtın ve savunma mekanizmalarında kullanılan çalışmalar üzerine değerlendirmeler yapıldı.proteinlerin belirlenmesine yönelik

References

  • Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, et al. Progress with proteome projects: Why all proteins expressed by genome should be identified and how to do. Biotechnol Gen Engin Rev, 1995; 13: 19-50.
  • Wilkins MR, Gasteiger E, Gooley AA, Herbert BR, Molloy MP, Binz PA, et al. High through put mass spectro. Anadolu Uni J Sci Technol,1999; 6 (2): 135.
  • Özcengiz G. Proteomik: Post-genomik dönemin en güçlü teknolojisi. ODTÜ Haber, 2007; 15: 13-9.
  • Tang P, Liu JK, Chou SM, Hor LI, Chen WJ, Ching-Chen S. A proteomic analysis of Klebsiella oxytoca after exposure to succinonitrile. Process Biochem, 2008; 43: 753–7.
  • Srivastava AK, Bhargava P, Thapar R, Rai LC. Salinity-induced physiological and proteomic changes in Anabaena doliolum. Environ Experimen Bot, 2008; 64: 49–57.
  • Tran NP, Park JK, Hong SJ, Lee CG. Proteomics of protein associated with astaxsanthin accumilation in the green algae Haematococcus lacustris under the influence of sodium orthovanadate. Biotechnol Lett, 2009; 12: 1917-22.
  • Tran, NP., Park, JK., Lee, CG. Proteomics analysis of proteins in green alga Haematococcus lacustris (Chlorophyceae) expressed under combined stress of nitrogen starvation and high irradiance. Enzyme Microb Technol, 2009;45: 241–6.
  • Rustichelli C, Visioli G, KosteckaD, Vurro E, Sanita di Toppi L, Marmiroli N. Proteomic analysis in the lichen Psysica adscendens expose to cadmium stress. Environ Pollut, 2008; 156(3): 1121-7.
  • Zörb C, Yan F, Schubert S, Sümer A. Evidence of Na+ toxicity for the vegetative growth of maize (Zea mays L.) during the first phase of salt stress. Appl Bot Food Qual, 2004; 78: 135-9.
  • Ahsan N, Lee DG, Lee SH, Kang KY, Lee JJ, Kim PJ, et al. Excess copper induced physiological and proteomic changes in germinating rice seeds. Chemosphere, 2007a; 67: 1182–93.
  • Ahsan N, Lee SH, Lee DG, Lee H, Lee SW, Bahk JD, et al. Physiological and protein profiles alternation of germinating rice seedlings exposed to acute cadmium toxicity. Biologies, 2007b; 330: 735–46.
  • Leea DG, Ahsana N, Leea SH, Leeb JJ, Bahka JD, Kanga KY, et al. Chilling stress-induced proteomic changes in rice roots. Plant Physiol, 2009; 166: 1-11.
  • Natarajan SS, Xu C, Cregan P, Caperna TJ, Garrett MW, Devanand L. Utility of proteomics techniques for assessing protein expression. Regulat Toxicol Pharmacol, 2009; 54: 32–6.
  • Toorchi M, Yukawa K, Nouri MZ, Komatsu S. Proteomics approach for identifying osmotic- stress-related proteins in soybean roots. Peptides, 2009; 30: 2108–17.
  • Zhang J, Ma H, Chen S, Ji M, Perl A, Kovacs L, et al. Stress response proteins ‘differential expression in embryogenic callus of Vitis vinifera L. cv. Cabernet Sauvignon -A proteomic approach. Plant Sci, 2009; 2: 103-13.
  • Ahsan N, Lee DG, Kim KH, Alam I, Lee SH, Lee KW, et al. Analysis of arsenic stress induced differentially expressed proteins in rice leaves by two-dimensional gel electrophoresis coupled with mass spectrometry. Chemosphere, 2010; 78: 224–31.
  • Lee K, Bae DW, Kim SH, Han HJ, Liu X, Park HJ, et al. Comparative proteomic analysis of the short-term responses of rice roots and leaves to cadmium. Plant Physiol, 2010; 167: 161–8.
  • Monagasa M, Quintanilla-López JE, Gómez- Cordovésa C, Bartoloméa B, Lebrón-Aguilarc R. MALDI-TOF MS analysis of plant proanthocyanidins. Pharmac Biomed Anal, 2010; 51: 358–72.
  • Wen FP, Zhang ZH, Bai T, Xu Q, Pan YH. Proteomics reveals th effecets of giberellic acid (GA3) on salt-stressed rice (Oryza sativa L.) shoots. Pl Sci, 2010; 2: 170-5.
  • Fana W, Cuia W, Lia X, Chena S, Liua G, Shena S. Proteomics analysis of rice seedling responses to ovine saliva. Pl Physiol, 2011; 168: 500–9.
  • Hwang H, Cho MH, Hahn BS, Lim H, Kwon YK, Hahn TR, et al. Proteomic identification of rhythmic proteins in rice seedlings. Biochim Biophysica Acta, 2011; 1814: 470–9.
  • Zhao L, Sun YL, Cui SX, Chen M, Yang HM, Liu HM, et al. Cd-induced changes in leaf proteome of the hyper accumulator plant Phytolacca americana. Chemosphere, 2011; 1: 56-66.
  • Li J, Sun J, Yang Y, Guo S, Glick BR. Identification of hypoxic-responsive proteins in cucumber roots using a proteomic Approach Pl Physiol Biochem, 2012; 51: 74-80.
  • Ngara R, Ndimbab R, Borch-Jensenc J, Jensenc ON, Ndimbaa O. Identification and profiling of salinity stress-responsive proteins in Sorghum bicolor seedlings. Proteom, 2012; 75 (13): 4139- 50.
  • Sarhadi E, Bazargani MM, Sajise AG, Abdolahi S, Vispo NA, Arceta M,et al. Proteomic analysis of rice anthers under salt stres. Pl Physiol Biochem, 2012; 58: 280-7.
  • Wang L, Ma H, Song L, Shu Y, Gu W. Comparative proteomics analysis reveals the mechanism of pre-harvest seed deterioration of soybean under high temperature and humidity stres. Proteom, 2012; 7: 2109-27.
  • Zheng M, Wang Y, Liu K, Shu H, Zhou Z. Protein exspression changes during cotton fiber elongation in response to low temperature stres. Pl Physiol, 2012; 4: 399-409.
  • Rana B, Sreenivasulu Y. Protein changes during ethanol induced seed germination in Aconitum heterophyllum. Pl Sci, 2013; 198: 27-38.
  • Müller A, Langklotz S, Lupilova N, Kuhlmann K, Bandow JE, Leichert LI. Activation of Rida chaperone function by N-chlorination. Nature Commun, 2014; 17(5): 5804.
  • Doğanay A. Hydatidosisin Serodiagnozunda Kist Sıvısı Antijenlerinin SDS-PAGE ve Western Blotting Yöntemleri İle Karşılaştırmalı Analizi. Ankara Üniversitesi Bilimsel Araştırma Projesi, Proje no: 08-10-059. 2005.
  • Gülaçtı İ, Bulut H, Bolat Y. Sığır vebası virüsünün hemaglutinin proteinine karşı monoklonal antikorun üretimi ve karakterizasyonu. Fırat Üniv Sağ Bilim Vet Derg, 2005; 19(1): 1-5.
  • Koç E, Yılmaz M, Ersan Y, Alaş A. Hekzavalent Kromun Capoeta capoeta (Guldenstaedt 1773) ve Squalius cephalus (Linnaeus 1758) üzerine olan etkisinin histopatolojik ve elektroforetik yöntemlerle saptanması. Kafkas Üniv Vet Fak Derg, 2013; 19 (6): 979-84.
  • Ünübol-Aypak S, Uysal H. Koyun ve farelerde kist hidatik proteinlerinin karşılaştırmalı analizi ve antijenik proteinlerde glikoprotein varlığının değerlendirilmesi. Ank Üniv Vet Fak Derg, 2014; 61: 243-8.

Proteomic Applications of Different Biological Organizms

Year 2016, Volume: 73 Issue: 4, 405 - 418, 01.12.2016

Abstract

Proteomics described in 1994 for the first time by Marc Wilkins is based on the analysis all proteins present at any time in an organism, tissue or cell by using a largescale protein separation and identification methods. The proteome is all the different proteins that an organism possesses and expresses at a certain time and place. Proteomic expresses the structures of all proteins at a certain time and place, placements, quantities, the post-translational modifications, functions in tissues and cells, and the interactions of other proteins and macro molecules. DNAs in cells of different tissues and organs are similar, but proteins are dissimilar. Therefore, science of genetics is not sufficient for the diagnosis of various diseases. For this reason, there is increasing interest in the science of proteomics day by day. In this review, firstly, we evaluated different protein extraction methods, two-dimensional gel electrophoresis 2DE , and proteomic applications which include mass spectrometry MS techniques. Secondly, it is mentioned that the studies carried out by proteomics in different field of medicine through using of different organism or tissue. In addition, in recent years, the studies have been evaluated to determine the response of different organizmaların biyotik veya abiyotik strese maruz kalınca verdiği yanıtın ve savunma mekanizmalarında kullanılan çalışmalar üzerine değerlendirmeler yapıldı.proteinlerin belirlenmesine yönelik

References

  • Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, et al. Progress with proteome projects: Why all proteins expressed by genome should be identified and how to do. Biotechnol Gen Engin Rev, 1995; 13: 19-50.
  • Wilkins MR, Gasteiger E, Gooley AA, Herbert BR, Molloy MP, Binz PA, et al. High through put mass spectro. Anadolu Uni J Sci Technol,1999; 6 (2): 135.
  • Özcengiz G. Proteomik: Post-genomik dönemin en güçlü teknolojisi. ODTÜ Haber, 2007; 15: 13-9.
  • Tang P, Liu JK, Chou SM, Hor LI, Chen WJ, Ching-Chen S. A proteomic analysis of Klebsiella oxytoca after exposure to succinonitrile. Process Biochem, 2008; 43: 753–7.
  • Srivastava AK, Bhargava P, Thapar R, Rai LC. Salinity-induced physiological and proteomic changes in Anabaena doliolum. Environ Experimen Bot, 2008; 64: 49–57.
  • Tran NP, Park JK, Hong SJ, Lee CG. Proteomics of protein associated with astaxsanthin accumilation in the green algae Haematococcus lacustris under the influence of sodium orthovanadate. Biotechnol Lett, 2009; 12: 1917-22.
  • Tran, NP., Park, JK., Lee, CG. Proteomics analysis of proteins in green alga Haematococcus lacustris (Chlorophyceae) expressed under combined stress of nitrogen starvation and high irradiance. Enzyme Microb Technol, 2009;45: 241–6.
  • Rustichelli C, Visioli G, KosteckaD, Vurro E, Sanita di Toppi L, Marmiroli N. Proteomic analysis in the lichen Psysica adscendens expose to cadmium stress. Environ Pollut, 2008; 156(3): 1121-7.
  • Zörb C, Yan F, Schubert S, Sümer A. Evidence of Na+ toxicity for the vegetative growth of maize (Zea mays L.) during the first phase of salt stress. Appl Bot Food Qual, 2004; 78: 135-9.
  • Ahsan N, Lee DG, Lee SH, Kang KY, Lee JJ, Kim PJ, et al. Excess copper induced physiological and proteomic changes in germinating rice seeds. Chemosphere, 2007a; 67: 1182–93.
  • Ahsan N, Lee SH, Lee DG, Lee H, Lee SW, Bahk JD, et al. Physiological and protein profiles alternation of germinating rice seedlings exposed to acute cadmium toxicity. Biologies, 2007b; 330: 735–46.
  • Leea DG, Ahsana N, Leea SH, Leeb JJ, Bahka JD, Kanga KY, et al. Chilling stress-induced proteomic changes in rice roots. Plant Physiol, 2009; 166: 1-11.
  • Natarajan SS, Xu C, Cregan P, Caperna TJ, Garrett MW, Devanand L. Utility of proteomics techniques for assessing protein expression. Regulat Toxicol Pharmacol, 2009; 54: 32–6.
  • Toorchi M, Yukawa K, Nouri MZ, Komatsu S. Proteomics approach for identifying osmotic- stress-related proteins in soybean roots. Peptides, 2009; 30: 2108–17.
  • Zhang J, Ma H, Chen S, Ji M, Perl A, Kovacs L, et al. Stress response proteins ‘differential expression in embryogenic callus of Vitis vinifera L. cv. Cabernet Sauvignon -A proteomic approach. Plant Sci, 2009; 2: 103-13.
  • Ahsan N, Lee DG, Kim KH, Alam I, Lee SH, Lee KW, et al. Analysis of arsenic stress induced differentially expressed proteins in rice leaves by two-dimensional gel electrophoresis coupled with mass spectrometry. Chemosphere, 2010; 78: 224–31.
  • Lee K, Bae DW, Kim SH, Han HJ, Liu X, Park HJ, et al. Comparative proteomic analysis of the short-term responses of rice roots and leaves to cadmium. Plant Physiol, 2010; 167: 161–8.
  • Monagasa M, Quintanilla-López JE, Gómez- Cordovésa C, Bartoloméa B, Lebrón-Aguilarc R. MALDI-TOF MS analysis of plant proanthocyanidins. Pharmac Biomed Anal, 2010; 51: 358–72.
  • Wen FP, Zhang ZH, Bai T, Xu Q, Pan YH. Proteomics reveals th effecets of giberellic acid (GA3) on salt-stressed rice (Oryza sativa L.) shoots. Pl Sci, 2010; 2: 170-5.
  • Fana W, Cuia W, Lia X, Chena S, Liua G, Shena S. Proteomics analysis of rice seedling responses to ovine saliva. Pl Physiol, 2011; 168: 500–9.
  • Hwang H, Cho MH, Hahn BS, Lim H, Kwon YK, Hahn TR, et al. Proteomic identification of rhythmic proteins in rice seedlings. Biochim Biophysica Acta, 2011; 1814: 470–9.
  • Zhao L, Sun YL, Cui SX, Chen M, Yang HM, Liu HM, et al. Cd-induced changes in leaf proteome of the hyper accumulator plant Phytolacca americana. Chemosphere, 2011; 1: 56-66.
  • Li J, Sun J, Yang Y, Guo S, Glick BR. Identification of hypoxic-responsive proteins in cucumber roots using a proteomic Approach Pl Physiol Biochem, 2012; 51: 74-80.
  • Ngara R, Ndimbab R, Borch-Jensenc J, Jensenc ON, Ndimbaa O. Identification and profiling of salinity stress-responsive proteins in Sorghum bicolor seedlings. Proteom, 2012; 75 (13): 4139- 50.
  • Sarhadi E, Bazargani MM, Sajise AG, Abdolahi S, Vispo NA, Arceta M,et al. Proteomic analysis of rice anthers under salt stres. Pl Physiol Biochem, 2012; 58: 280-7.
  • Wang L, Ma H, Song L, Shu Y, Gu W. Comparative proteomics analysis reveals the mechanism of pre-harvest seed deterioration of soybean under high temperature and humidity stres. Proteom, 2012; 7: 2109-27.
  • Zheng M, Wang Y, Liu K, Shu H, Zhou Z. Protein exspression changes during cotton fiber elongation in response to low temperature stres. Pl Physiol, 2012; 4: 399-409.
  • Rana B, Sreenivasulu Y. Protein changes during ethanol induced seed germination in Aconitum heterophyllum. Pl Sci, 2013; 198: 27-38.
  • Müller A, Langklotz S, Lupilova N, Kuhlmann K, Bandow JE, Leichert LI. Activation of Rida chaperone function by N-chlorination. Nature Commun, 2014; 17(5): 5804.
  • Doğanay A. Hydatidosisin Serodiagnozunda Kist Sıvısı Antijenlerinin SDS-PAGE ve Western Blotting Yöntemleri İle Karşılaştırmalı Analizi. Ankara Üniversitesi Bilimsel Araştırma Projesi, Proje no: 08-10-059. 2005.
  • Gülaçtı İ, Bulut H, Bolat Y. Sığır vebası virüsünün hemaglutinin proteinine karşı monoklonal antikorun üretimi ve karakterizasyonu. Fırat Üniv Sağ Bilim Vet Derg, 2005; 19(1): 1-5.
  • Koç E, Yılmaz M, Ersan Y, Alaş A. Hekzavalent Kromun Capoeta capoeta (Guldenstaedt 1773) ve Squalius cephalus (Linnaeus 1758) üzerine olan etkisinin histopatolojik ve elektroforetik yöntemlerle saptanması. Kafkas Üniv Vet Fak Derg, 2013; 19 (6): 979-84.
  • Ünübol-Aypak S, Uysal H. Koyun ve farelerde kist hidatik proteinlerinin karşılaştırmalı analizi ve antijenik proteinlerde glikoprotein varlığının değerlendirilmesi. Ank Üniv Vet Fak Derg, 2014; 61: 243-8.
There are 33 citations in total.

Details

Primary Language Turkish
Journal Section Research Article
Authors

Sinem Özenoğlu This is me

Hatice Yıldızhan This is me

Duygu Özel-demiralp This is me

Demet Cansaran-duman This is me

Publication Date December 1, 2016
Published in Issue Year 2016 Volume: 73 Issue: 4

Cite

APA Özenoğlu, S., Yıldızhan, H., Özel-demiralp, D., Cansaran-duman, D. (2016). Farklı Biyolojik Organizmalarda Proteomik Uygulamalar. Türk Hijyen Ve Deneysel Biyoloji Dergisi, 73(4), 405-418.
AMA Özenoğlu S, Yıldızhan H, Özel-demiralp D, Cansaran-duman D. Farklı Biyolojik Organizmalarda Proteomik Uygulamalar. Turk Hij Den Biyol Derg. December 2016;73(4):405-418.
Chicago Özenoğlu, Sinem, Hatice Yıldızhan, Duygu Özel-demiralp, and Demet Cansaran-duman. “Farklı Biyolojik Organizmalarda Proteomik Uygulamalar”. Türk Hijyen Ve Deneysel Biyoloji Dergisi 73, no. 4 (December 2016): 405-18.
EndNote Özenoğlu S, Yıldızhan H, Özel-demiralp D, Cansaran-duman D (December 1, 2016) Farklı Biyolojik Organizmalarda Proteomik Uygulamalar. Türk Hijyen ve Deneysel Biyoloji Dergisi 73 4 405–418.
IEEE S. Özenoğlu, H. Yıldızhan, D. Özel-demiralp, and D. Cansaran-duman, “Farklı Biyolojik Organizmalarda Proteomik Uygulamalar”, Turk Hij Den Biyol Derg, vol. 73, no. 4, pp. 405–418, 2016.
ISNAD Özenoğlu, Sinem et al. “Farklı Biyolojik Organizmalarda Proteomik Uygulamalar”. Türk Hijyen ve Deneysel Biyoloji Dergisi 73/4 (December 2016), 405-418.
JAMA Özenoğlu S, Yıldızhan H, Özel-demiralp D, Cansaran-duman D. Farklı Biyolojik Organizmalarda Proteomik Uygulamalar. Turk Hij Den Biyol Derg. 2016;73:405–418.
MLA Özenoğlu, Sinem et al. “Farklı Biyolojik Organizmalarda Proteomik Uygulamalar”. Türk Hijyen Ve Deneysel Biyoloji Dergisi, vol. 73, no. 4, 2016, pp. 405-18.
Vancouver Özenoğlu S, Yıldızhan H, Özel-demiralp D, Cansaran-duman D. Farklı Biyolojik Organizmalarda Proteomik Uygulamalar. Turk Hij Den Biyol Derg. 2016;73(4):405-18.