مطالعه فیلوژنتیکی و ساختاری پلی‌آمین اکسیدازهای گیاهی

نوع مقاله: علمی پژوهشی

نویسندگان

1 دانشجو دکتری گروه علوم و زیست‌فناوری گیاهی، دانشکده علوم و فناوری زیستی، دانشگاه شهید بهشتی، تهران، ایران

2 استاد گروه علوم و زیست‌فناوری گیاهی، دانشکده علوم و فناوری زیستی، دانشگاه شهید بهشتی، تهران، ایران

چکیده

محتوای پلی‌آمین‌های درون سلولی نه تنها توسط بیوسنتز و انتقال بلکه توسط کاتابولیسم آن‌ها به وسیله پلی‌آمین اکسیدازهای (PAO) وابسته به فلاوین آدنین دی‌نوکلئوتید (FAD) تنظیم می‌شود. نتایج حاصل از مطالعات مختلف در مورد پروتئین‌‌های PAO در فرایندهای مختلف نموی و پاسخ به تنش‌های محیطی تأیید کننده اهمیت این پروتئین در زندگی گیاهی می‌باشد، با این حال مطالعه جامعی در مورد روابط فیلوژنتیکی و ساختاری PAOs گیاهی وجود ندارد. در این مطالعه آنالیزهای بیوانفورماتیکی به منظور درک بهتر روابط فیلوژنتیکی و ساختاری بر روی 58 توالی پروتئینی PAO از 15 گونه مختلف گیاهی انجام شد. کلاسترهای چندگانه با دو برابر شدگی ژنی هم در گونه‌های تک‌لپه‌ای و هم در گونه‌های دو لپه‌ای شناسایی شد. بر اساس موتیف‌های حفاظت شده به‌دست آمده توسط ابزارهای MEME و MAST، چهار موتیف در بیشتر گونه‌های گیاهی یکسان بودند. آنالیزهای ساختاری بر روی PAOs مربوط به Oryza sativa و Arabidopsis thaliana به عنوان نماینده گیاهان تک‌لپه‌ای و دو لپه‌ای که اطلاعات ساختاری آن‌ها در دسترس نبود، انجام شد. آنالیز ساختار دوم نشان داد که مارپیچ آلفا در میان عناصر ساختار دوم غالب بوده و پس از آن به‌ترتیب راندوم کویل، صفحات بتا و دور بتا برای تمامی توالی‌ها دارای بیشترین مقدار بود. پیش‌بینی ساختار سوم توسط سرور SWISS-MODEL انجام شد. ساختمان این توالی‌ها دارای دو دومین مشترک بود. این اولین مطالعه در مورد روابط فیلوژنتیکی و ساختاری PAOs گیاهی است و این نتایج ممکن است مبنای نظری برای مطالعات آتی در مورد جزئیات ساختمانی و عملکردی PAOs گیاهی فراهم کند.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Structural and functional studies of plant Polyamine Oxidase

نویسندگان [English]

  • Mohsen Hosseini 1
  • Abbas Saidi 2
1 Ph.D. Candidate, Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, G.C, Tehran, Iran.
2 Professor, Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, G.C, Tehran, Iran.
چکیده [English]

Intracellular polyamine contents are regulated not only by biosynthesis and transport but also by catabolism through FAD dependent polyamine oxidases (PAOs). The results of various studies on PAO proteins in developmental processes and response to environmental stresses confirm the importance of this protein in plant life; however, there is no comprehensive study of phylogenetic and structural relationships of plant PAOs. In the present study, to better understand phylogenetic and structural relationships of PAO proteins, bioinformatics analyses were performed on 58 PAO protein sequences of 15 different plant species. Multiple clusters with gene duplications were identified in both dicot and monocot-species. According to the conserved motifs obtained by MEME and MAST tools, four motifs were similar in most plant species. As there is no structural information available on PAOs, structural analyses were carried out on PAOs from Oryza sativa and Arabidopsis thaliana as representative of monocot and dicot plants, respectively. Secondary structure analysis revealed that alpha helix dominated among secondary structure elements followed by random coils, extended strand and beta turns for all sequences. Tertiary structures were predicted with SWISS-MODEL server. The best templates with high similarity that their structure determined by experimental methods were selected. To our knowledge, this is the first report of phylogenetic and structural relationships of plant PAOs. Our results may provide a theoretical basis for future studies of functional and structural details of plants PAOs.

کلیدواژه‌ها [English]

  • Bioinformatics analysis
  • Phylogenetic
  • Polyamine
  • Polyamine oxidases
Agudelo-Romero P, Bortolloti C, Pais MS, Tiburcio AF, Fortes M (2013) Study of polyamines during grape ripening indicate an important role of polyamine catabolism. Plant Physiology and Biochemistry 67: 105-119.

Ahou A, Martignago D, Alabdallah O, Tavazza R, Stano P, Macone A, Angelini R (2014) A plant spermine oxidase/dehydrogenase regulated by the proteasome and polyamines. Journal of experimental botany 65: 1585-1603.

Bailey TL, Boden M, Buske F.A, 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(suppl_2), pp. W202-W208.

Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T, (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic acids research, 42(W1), pp. W252-W258.

Binda C, Mattevi A, Edmondson DE (2002). Structure-function relationships in flavoenzyme-dependent amine oxidations: a comparison of polyamine oxidase and monoamine oxidase. Journal of biological chemistry.

Cervelli M, Caro OD, Penta AD, Angelini R, Federico R, Vitale A, Mariottini P 2004. A novel C‐terminal sequence from barley polyamine oxidase is a vacuolar sorting signal. The Plant Journal, 40(3), pp.410-418.

Darabi M, Seddigh S, Abarshahr M (2017) Structural, functional, and phylogenetic studies of cytochrome P450 (CYP) enzyme in seed plants by bioinformatics tools. Caryologia 70: 62-76.

Freitas VS, de Souza Miranda R, Costa JH, de Oliveira DF, de Oliveira Paula S, de Castro Miguel E, Gomes-Filho E (2018) Ethylene triggers salt tolerance in maize genotypes by modulating polyamine catabolism enzymes associated with H2O2 production. Environmental and Experimental Botany 145: 75-86.

Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003). ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic acids research, 31(13), pp.3784-3788.

Geourjon C, Deleage G (1995) SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics 11: 681-684.

Jasso-Robles FI, Jiménez-Bremont JF, Becerra-Flora A, Juárez-Montiel M, Gonzalez ME, Pieckenstain FL, Rodríguez-Kessler M (2016) Inhibition of polyamine oxidase activity affects tumor development during the maize-Ustilago maydis interaction. Plant Physiology and Biochemistry 102: 115-124.

Kamada-Nobusada T, Hayashi M, Fukazawa M, Sakakibara H, Nishimura M (2008) A putative peroxisomal polyamine oxidase, AtPAO4, is involved in polyamine catabolism in Arabidopsis thaliana. Plant and Cell Physiology 49: 1272-1282.

Kaur G, Guruprasad K, Temple BR, Shirvanyants DG, Dokholyan NV, Pati PK (2018) Structural complexity and functional diversity of plant NADPH oxidases. Amino acids 50: 79-94.

Krogh A, Larsson B, Von Heijne G, Sonnhammer EL (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of molecular biology, 305(3), pp.567-580.

Kusano T, Kim DW, Liu T, Berberich T (2015) Polyamine catabolism in plants. In Polyamines Springer, Tokyo 77-88

Labadorf A, Link A, Rogers MF, Thomas J, Reddy AS, Ben-Hur A (2010). Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC genomics, 11(1), p.114.

Liu T, Wook Kim D, Niitsu M, Berberich T, Kusano T (2014) POLYAMINE OXIDASE 1 from rice (Oryza sativa) is a functional ortholog of Arabidopsis POLYAMINE OXIDASE 5. Plant Signaling & Behavior 9: e29773.

Mahdizade VA, Nassaj Hosseini SM, Safaie N, Saidi A (2013) Practical Guide of NCBI. Agricultural Extension and Education Publishers (In Farsi).

Misumi O, Yoshida Y, Nishida K, Fujiwara T, Sakajiri T, Hirooka S, Nishimura Y, Kuroiwa T (2008). Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana. Journal of plant research, 121(1), pp.3-17.

Mo H, Wang X, Zhang Y, Zhang G, Zhang J, Ma Z (2015) Cotton polyamine oxidase is required for spermine and camalexin signalling in the defence response to Verticillium dahliae. The Plant Journal 83: 962-975

Moschou PN, Sanmartin M, Andriopoulou AH, Rojo E, Sanchez-Serrano JJ, Roubelakis-Angelakis K (2008) Bridging the gap between plant and mammalian polyamine catabolism: a novel peroxisomal polyamine oxidase responsible for a full back-conversion pathway in Arabidopsis. Plant Physiology 147: 1845-1857.

Ono Y, Kim DW, Watanabe K, Sasaki A, Niitsu M, Berberich T, Takahashi Y (2012) Constitutively and highly expressed Oryza sativa polyamine oxidases localize in peroxisomes and catalyze polyamine back conversion. Amino acids 42: 867-876.

Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature methods 8: 785.

Saidi, A, Hajibarat Z (2018). In silico analysis of floral mads-box gene in brachypodium distachyon. Bionature, 366-375.

Saidi A, Hajibarat Z (2019). Characterization of cis-elements in hormonal stress-responsive genes in Oryza sativa. AsPac J. Mol. Biol. Biotechnol. 27(95-102).

Samasil K, de Carvalho LL, Mäenpää P, Salminen TA, Incharoensakdi A (2017) Biochemical characterization and homology modeling of polyamine oxidase from cyanobacterium Synechocystis sp. PCC 6803. Plant Physiology and Biochemistry 119: 159-169.

Seddigh S, Darabi M (2014) Comprehensive analysis of beta-galactosidase protein in plants based on Arabidopsis thaliana. Turkish Journal of Biology 38: 140-150.

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Thompson JD (2011) Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(1), 539.

Sippl MJ (1993) Recognition of errors in three‐dimensional structures of proteins. Proteins: Structure, Function, and Bioinformatics 17: 355-362.

Small I, Peeters N, Legeai F, Lurin C (2004). Predotar: a tool for rapidly screening proteomes for N‐terminal targeting sequences. Proteomics, 4(6), pp.1581-1590.

Tavladoraki P, Rossi MN, Saccuti G, Perez-Amador MA, Polticelli F, Angelini R, Federico R (2006) Heterologous expression and biochemical characterization of a polyamine oxidase from Arabidopsis involved in polyamine back conversion. Plant Physiology 141: 1519-1532.

Wang P, Cheng T, Wu S, Zhao F, Wang G, Yang L, Lu M, Chen J, Shi J (2014) Phylogeny and molecular evolution analysis of PIN-FORMED 1 in angiosperm. PloS one 9: p.e89289.

Wang W, Liu JH (2015) Genome-wide identification and expression analysis of the polyamine oxidase gene family in sweet orange (Citrus sinensis). Gene 555: 421-429.

Wiederstein M, Sippl MJ (2007). ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(suppl_2), pp.W407-W410.

Yu, CS, Chen, YC, Lu CH, Hwang JK (2006). Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics, 64(3), pp.643-651.