Herbisit dayanıklılığını anlamak: Domates ve patatesteki AHAS (asetohidroksiasit sentetaz) genlerinin biyoinformatik analizleri

Abstract

Enzimlerin mutasyon bölgelerinin belirlenmesi herbisitlere dayanıklı bitkilerin yetiştirilmesi ve yabancı ot kontrol uygulamalarının başarısı için önemlidir. Bu çalışma domates (SlAHAS) ve patatesteki (StAHAS) asetohidroksiasit sentetaz (AHAS, EC 2.2.1.6) enzimlerine herbisit dayanıklılığını sağlayacak mutasyon bölgelerinin biyoinformatik yöntemlerle belirlenmesi amacıyla yapılmıştır. AHAS proteinleri evrimsel olarak yüksek oranda korunmasına rağmen bu proteinlerin uzunlukları farklılık göstermektedir. SlAHAS’ta Lys541 ve Val542 amino asitleri (aa) enzim aktivitesi için önem taşımaktadır ve Lys541 Ala, Phe, Arg, ve Val aa ile yer değiştirebilirken; Ile sadece Val542 ile yer değiştirebilir aa olarak bulunmuştur. Benzer şekilde StAHAS’ta Ile124, Met266 ve Leu272 stabilizasyonu sağlayacı aa olarak bulunmuştur. Lys ve Arg, Ile124 ile değişebilir aa olarak saptanırken; Leu, Met266 ile ve Ala, Pro ve Ser ise Leu272 ile enzim stabilizayonunu sağlayıcı yer değiştirebilir aa olarak bulunmuştur. SlAHAS’taki kenetlenme analizlerine göre klorosülfüron (CS) için Ser387, Arg235 ve His341; imazakin (IQ) içinse Phe11, Ala40 ve His341 en yüksek bağlanma sonuçlarını vermiştir. StAHAS’ta ise Lys232, Asn123 ve Arg53’ün CS ile bağlandığı; Lys405, Lys489 ve Arg268 ise IQ ile bağlanabilecek aa’ler olduğu tespit edilmiştir. His341 ve Gln478’in CS ve IQ ile SlAHAS’ta; Val61 ve Arg366’nın ise StAHAS’ta sırasıyla her iki ligand ile bağ yapabildiği görülmüştür. Bunun yanısıra Arg366 SlAHAS’ta IQ ligantının bağlanabileceği aa olarak bulunmuştur.

Keywords

• Asetohidroksiasit sentetaz,Asetolaktat sentetaz,Herbisit dayanıklılığı,Mutasyon

Insights into herbicide resistance: Bioinformatics analyses of AHAS (acetohydroxyacid synthase) genes in tomato and potato

Abstract

The identification of enzymes’ mutable sites is important to the development of herbicide resistant crops and for weed control practices. The objective of this study was to provide insights into mutable residues causing resistance to the acetohydroxyacid synthase enzyme (AHAS, EC 2.2.1.6) inhibitor herbicides in the tomato (SlAHAS) and potato (StAHAS) through bioinformatics approaches. The results showed AHAS proteins investigated in this study were highly conserved but differed in length. Mutation analyses showed that Lys541 and Val542 in SlAHAS were mutable sites for preservation of the enzyme activity. While Ala, Phe, Arg, and Val residues were found to be substitutable with Lys541, Ile was exchangeable for Val542. Similarly, Ile124, Met266, and Leu272 in StAHAS were identified as protein stabilizing residues. In this respect, Lys and Arg were substitutable residues for Ile124, whereas Leu was for Met266 and Ala, Pro and Ser were suitable residues for Leu272 regarding enzyme stabilization. The docking analyses displayed that the best binding affinities were obtained for Ser387, Arg235, and His341 for chlorosulfuron (CS) and Phe11, Ala40, and His341 have the highest binding score for imazaquin (IQ) in SlAHAS. As for StAHAS, Lys232, Asn123, and Arg53 residues were found to bind with CS whereas Lys405, Lys489, and Arg268 amino acids were identified as sites where IQ bound. His341 and Gln478 were binding residues for both CS and IQ in SlAHAS whereas both ligands were found to bind with Val61 and Arg366 in StAHAS. Arg366 was identified as a binding site in SlAHAS for IQ as well.

Keywords

• Acetohydroxyacid synthase,Acetolactate synthase,Herbicide resistance,Mutation

References

1. Adamczewski K, Maysiak K (2012) The mechanism of resistance to ALS-inhibiting herbicides in biotypes of wind bent grass (Apera spica-venti L.) with cross and multiple resistance. Polish Journal of Agronomy 10: 3–8.
2. Bailey TL, Mikael Bode´n B, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research 37: 202–208.
3. Bendl J, Stourac J, Sebestova E, Vavra O, Musil M, Brezovsky J, Damborsky J (2016) HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. Nucleic Acids Research 44(W1): W479-W487.
4. Bernasconi P, Woodworth AR, Rosen BA, Subramanian MV, Siehl DL (1995) A naturally occurring point mutation confers broad range tolerance to herbicides that target acetolactate synthase. The Journal of Biological Chemistry 270(29): 17381-17385.
5. Brosnan JT, Vargas JJ, Breeden GK, Grier L, Aponte RA, Tresch S, Laforest M (2016) A new amino acid substitution (Ala-205-Phe) in acetolactate synthase (ALS) confers broad spectrum resistance to ALS-inhibiting herbicides. Planta 243: 149–159.
6. Busi R, Vila-Ajub MM, Beckie HJ, Gaines TA, Goggin DE, Kaundun SS, Lacoste M, Neve P, Nissen SJ, Norsworthy JK, Renton M, Shaner DL, Tranel PJ, Wright T, Yu Q, Powles SB (2013) Herbicide-resistant weeds: from research and knowledge to future needs. Evolutionary Applications 6(8): 1218–1221.
7. Duggleby RG, Pang SS (2000) Acetohydroxyacid synthase. Journal of Biochemistry and Molecular Biology 33(1): 1–36.
8. Duggleby RG, McCourt JA, Guddat LW (2008) Structure and mechanism of inhibition of plant acetohydroxyacid synthase. Plant Physiology and Biochemistry 46: 309-24.

9. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research. Database Issue 44: D279-D285.
10. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel, RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The Proteomics Protocols Handbook, Louisville: Humana, pp. 571–607.
11. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Rokhsar DS (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 40: 1178–1186.
12. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
13. Hawkins CF, Borges A, Perham RN (1989) A common structural motif in thiamin pyrophosphate-binding enzymes. Federation of European Biochemical Societies 255(l): 77-82.
14. Jimenez F, Rojano-Delgado AM, Fernandez PT, Rodriguez-Suarez CR, Atienza SG, De Parado R (2016) Physiological, biochemical and molecular characterization of an induced mutation conferring imidazolinone resistance in wheat. Physiologia Plantarum 158: 2-10.
15. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.
16. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols 10(6): 845–858.
17. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33: 1870-1874.
18. Lee H, Rustgi S, Kumar N, Burke I, Yenis JP, Gill KS, von Wettstein D, Ulrich SE (2011) Single nucleotide mutation in the barley acetohydroxy acid synthase (AHAS) gene confers resistance to imidazolinone herbicides. Proceedings of National Academy of Sciences of the United States of America 108(21): 890-13.
19. Li M, Yu Q, Han H, Vila-Aiub M, Powles SB (2013) ALS herbicide resistance mutations in Raphanus raphanistrum: evaluation of pleiotropic effects on vegetative growth and ALS activity. Pest Management Science 69: 689–695.
20. McCourt JA, Pang SS, Guddat LW, Duggleby RG (2005) Elucidating the specificity of binding of sulfonylurea herbicides to acetohydroxyacid synthase. Biochemistry 44(7): 2330-8.
21. McCourt JA, Pang SS, King-Scott J, Guddat LW, Duggleby RG (2006) Herbicide-binding sites revealed in the structure of plant acetohydroxyacid synthase. Proceedings of the National Academy of Sciences of the United States (PNAS) 103(3): 569-573.
22. Menegat A, Bailly GC, Aponte R, Heinrich GMT, Sievernich B, Gerhards R (2016) Acetohydroxyacid synthase (AHAS) amino acid substitution Asp376Glu in Lolium perenne: effect on herbicide efficacy and plant growth. Journal of Plant Diseases and Production 123: 145–153.
23. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell, DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. Journal of Computational Chemistry 30: 2785–2791.
24. Nguyen MN, Tan KP, Madhusudhan, MS (2011) CLICK-topology-independent comparison of biomolecular 3D structures. Nucleic Acids Research 39: W24-W28.
25. Pandolfo CE, Presotto A, Moreno F, Dossou I, Migasso JP, Sakima E, Cantamutto M (2016) Broad resistance to acetohydroxyacid-synthase-inhibiting herbicides in feral radish (Raphanus sativus L.) populations from Argentina. Pest Management Science 72(2): 354-61.
26. Pang SS, Duggleby RG, Guddat LW (2002) Crystal structure of yeast acetohydroxyacid synthase: A target for herbicidal inhibitors. Journal of Molecular Biology 317: 249-262.
27. Pang SS, Guddat, LW, Duggleby RG (2003) Molecular basis of sulfonylurea herbicide inhibition of acetohydroxyacid synthase. Journal of Molecular Biology 278: 7639–7644.
28. Parthiban V, Gromiha MM, Schomburg D (2006) CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Research 34: W239-42.
29. Piao Z, Wang W, Wei Y, Zonta F, Wan C, Bai J, Wu S, Wang X, Fang J (2017) Characterization of an acetohydroxy acid synthase mutant conferring tolerance to imidazolinone herbicides in rice (Oryza sativa). Planta 247(3): 693-703.
30. Sanner MF (1999) Python: a programming language for software integration and development. Journal of Molecular Graphics and Modelling 17(1): 57-61.
31. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus TL, Dupuis M, Montgomery JA (1993) General atomic and molecular electronic structure system. Journal of Computational Chemistry 14: 1347-1363.
32. Shimizu M, Kawai K, Kaku K, Shimizu T, Kobayashi S (2011) Application of mutated acetolactate synthase genes for herbicide resistance to crop improvement. Herbicides, Theory and Applications, Prof. Marcelo Larramendy (Ed.), ISBN: 978-953-307-975-2, InTech.
33. Singh BK, Lumanglas A, Wang BS (1991) Production of a monocot-specific monoclonal antibody against acetohydroxyacid synthase and its use in the purification and characterization of the enzyme. Proceedings National Academy of Sciences of United States of America (PNAS) 88(11): 4572-4576.
34. Spratt BG, Greenwood BM (2000) Prevention of pneumococcal disease by vaccination: does serotype replacement matter? Lancet 356: 1210-1211.
35. Stidham MA (1991) Herbicides that inhibit acetohydroxyacid synthase. Weed Science 39(3): 428-34.
36. Thompson C, Tar’an B (2014) Genetic characterization of the acetohydroxyacid synthase (AHAS) gene responsible for resistance to imidazolinone in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 127: 1583–1591.
37. Tranel PJ, Wright TR (2002) Resistance of weeds to ALS-inhibiting herbicides: what have we learned? Weed Science 50: 700–712.
38. Vila-Aiub, MM, Neve P, Powles SB (2009) Fitness costs associated with evolved herbicide resistance alleles in plants. New Physiologist 184(4): 751-67.
39. Willard L, Ranjan A, Zhang H, Monzavi, H, Boyko RF, Sykes BD, Wishart DS (2003) VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Research 31(13): 3316–3319.
40. Yaqoob U, Kaul T, Nawchoo IA (2016) In-silico analysis, structural modelling and phylogenetic analysis of acetohydroxyacid synthase gene of Oryza sativa. Medicinal and Aromatic Plants (Los Angel) 5: 272.
41. Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins 64: 643–651.
42. Yu Q, Han H, Vila-Aiub, MM, Powles SB (2010) AHAS herbicide resistance endowing mutations: effect on AHAS functionality and plant growth. Journal of Experimental Botany 61(14): 3925–3934.
43. Yu Q, Powles SB (2014) Resistance to AHAS inhibitor herbicides: current understanding. Pest Managemant Science 70(9): 1340-50.
44. Zhang Y, Xu Y, Wang S, Li X, Zheng M (2017a) Resistance mutations of Pro197, Asp376 and Trp574 in the acetohydroxyacid synthase (AHAS) affect pigments, growths, and competitiveness of Descurainia sophia L.. Scientific Reports 7, 16380.
45. Zhang L, Li W, Guo W, Wu C, Wang H, Liu W, Wang J (2017b) Herbicides cross resistance of a tribenuron-methyl resistant Capsella bursa-pastoris (L.) Medik. population in wheat field. Chilean Journal of Agricultural Research 77(1): 65-70.