Mô hình cấu trúc và sự điều chỉnh môi trường của arginine decarboxylase trong Synechocystis sp. PCC 6803

Archiv für Mikrobiologie - Tập 184 - Trang 397-406 - 2005
Saowarath Jantaro1,2, Heidi Kidron3, Delphine Chesnel3, Aran Incharoensakdi2, Paula Mulo1, Tiina Salminen3, Pirkko Mäenpää1
1Department of Biology, Laboratory of Plant Physiology and Molecular Biology, University of Turku, Turku, Finland
2Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
3Department of Biochemistry and Pharmacy, Åbo Akademi University, Turku, Finland

Tóm tắt

Arginine decarboxylase (ADC) là enzyme đầu tiên trong con đường thay thế để tổng hợp putrescine trong con đường sinh tổng hợp polyamine ở vi khuẩn và thực vật. Trong nghiên cứu này, chúng tôi đã tập trung vào tác động của các loại stress ngắn hạn khác nhau đối với lượng bản sao và hoạt tính cụ thể của ADC Synechocystis sp. PCC 6803. Kết quả của chúng tôi cho thấy sự tích lũy bản sao trong trạng thái ổn định và hoạt động enzyme không liên quan đến nhau theo cách đơn giản, vì chỉ có quá trình quang heterotrophy và sự kết hợp giữa stress muối và stress ánh sáng mạnh tác động đến cả hai tham số một cách tương tự. Sự thay đổi trong sự tích lũy mRNA ADC trong trạng thái ổn định dưới các điều kiện stress ngắn hạn khác mà chúng tôi đã nghiên cứu chỉ có tác động nhỏ đến hoạt tính enzyme, cho thấy sự điều chỉnh sau phiên mã. Dựa trên mô hình cấu trúc, ADCs của Synechocystis có một miền dư thuyết, có thể tham gia vào việc điều chỉnh sau phiên mã hoạt động của ADC trong Synechocystis. Ngoài ra, hai liên kết disulfide đối xứng giữa các tiểu đơn vị dường như ổn định cấu trúc dimer của ADCs. Có hai gen mã hóa cho ADC và agmatinase, một enzyme khác trong con đường polyamine, trong bộ gen của Synechocystis, trong khi các gen mã hóa cho ornithine decarboxylase và một số enzyme khác trong con đường polyamine chưa được xác định thông qua các tìm kiếm tính đồng nhất.

Từ khóa

#argine decarboxylase #Synechocystis #enzyme #stress ngắn hạn #điều chỉnh sau phiên mã #mô hình cấu trúc

Tài liệu tham khảo

Almrud JJ, Oliveira MA, Kern AD, Grishin NV, Phillips MA, Hackert ML (2000) Crystal structure of human ornithine decarboxylase at 2.1. A resolution: structural insights to antizyme binding. J Mol Biol 295:7–16 Bagni N (1989) Polyamines in plant growth and development. In: Bachrach U, Heimer YM (eds) The physiology of polyamines, 2nd edn. CRC Press, Boca Raton, pp 107–120 Bagni N, Tassoni A (2001) Biosynthesis, oxidation and conjugation of aliphatic polyamines in plants. Amino Acids 20:301–317 Balbo PB, Patel CN, Sell KG, Adcock RS, Neelakantan S, Crooks PA, Oliveira MA (2003) Spectrophotometric and steady-state kinetic analysis of the biosynthetic arginine decarboxylase of Yersinia pestis utilizing arginine analogues as inhibitors and alternative substrates. Biochemistry 42:15189–15196 Barton GJ (1993) ALSCRIPT a tool to format multiple sequence alignments. Protein Eng 1:37–40 Bell E, Malmberg RL (1990) Analysis of cDNA encoding arginine decarboxylase from oat reveals similarity to the Escherichia coli arginine decarboxylase and evidence of protein processing. Mol Gen Genet 224:431–436 Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795 Bouchereau A, Aziz A, Larher F, Martin-Tanguy JM (1999) Polyamines and environmental challenges: recent development. Plant Sci 140:103–125 Bradford MM (1976) A rapid sensitive method for the quantization of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254 Chattopadhyay MK, Gupta S, Sengupta DN, Ghosh B (1997) Expression of arginine decarboxylase in seedlings of indica rice (Oryza sativa L.) cultivars as affected by salinity stress. Plant Mol Biol 34:477–483 Coleman CS, Hu G, Pegg AE (2004) Putrescine biosynthesis in mammalian tissues. Biochem J 379:849–855 Galloway GL, Malmberg RL, Price RA (1998) Phylogenetic utility of the nuclear gene arginine decarboxylase: an example from Brassicaceae. Mol Biol Evol 15:1312–1320 Gibon Y, Blaesing OE, Hannemann J, Carillo P, Höhne M, Hendriks JHM, Palacios N, Cross J, Selbig J, Stitt M (2004) A robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness. Plant Cell 16:3304–3325 Gill RT, Katsoulakis E, Schmitt W, Taroncher-Oldenburg G, Misra J, Stephanopoulos G (2002) Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp. Strain PCC 6803. J Bacteriol 184:3671–3681 Gokulan K, Rupp B, Pavelka MS Jr, Jacobs WR Jr, Sacchettini JC (2003) Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis. J Biol Chem 278:18588–18596 Hanfrey C, Sommer S, Mayer MJ, Burtin D, Michael AJ (2001) Arabidopsis polyamine biosynthesis: absence of ornithine decarboxylase and the mechanism of arginine decarboxylase activity. Plant J 27:551–560 Hao YJ, Kitashiba H, Honda C, Nada K, Moriguchi T (2005) Expression of arginine decarboxylase and ornithine decarboxylase genes in apple cells and stressed shoots. J Exp Bot 56:1105–1115 He L, Nada K, Kasukabe Y, Tachibana S (2002) Enhanced susceptibility of photosynthesis to low-temperature photoinhibition due to interruption of chill-induced increase of S-adenosylmethionine decarboxylase activity in leaves of spinach (Spinacia oleracea L.). Plant Cell Physiol 43:196–206 Hofmann K, Stoffel W (1993) TMbase—a database of membrane spanning proteins segments. Biol Chem Hoppe Seyler 374:166 Hihara Y, Kamei A, Kanehisa M, Kaplan A, Ikeuchi M (2001) DNA microarray analysis of cyanobacterial gene expression during acclimation to light. Plant Cell 13:793–806 Horyn O, Luhovvy B, Lazarow A, Daikhin Y, Nissim I, Yudkoff M, Nissim I (2005) Biosynthesis of agmatine in isolated mitochondria and perfused rat liver: studies with 15N-labeled arginine. Biochem J 388:419–425. DOI: 10.1042/BJ20041260 Illingworth C, Mayer MJ, Elliott K, Hanfrey C, Walton NJ, Michael AJ (2003) The diverse bacterial origins of the Arabidopsis polyamine biosynthetic pathway. FEBS Lett 549:26–30 Jackson LK, Brooks HB, Osterman AL, Goldsmith EJ, Phillips MA (2000) Altering the reaction specificity of eukaryotic ornithine decarboxylase. Biochemistry 39:11247–11257 Jansonius JN (1998) Structure, evolution and action of of vitamin B6-dependent enzymes. Curr Opin Struct Biol 8:759–769 Jantaro S, Mäenpää P, Mulo P, Incharoensakdi A (2003) Content and biosynthesis of polyamines in salt and osmotically stresses cells of Synechocystis sp. PCC 6803. FEMS Microbiol Lett 228:129–135 Johnson MS, Lehtonen JV (2000) Comparison of protein three-dimensional structures. In: Higgins D, Taylor W (eds) Bioinformatics: sequence, structure and databanks. Oxford University Press, Oxford UK, pp 15–50 Johnson MS, Overington JP (1993) A structural basis for the comparison of sequences: an evaluation of scoring methodologies. J Mol Biol 233:716–738 Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, Kimura T, Hosouchi T, Matsuno A, Muraki A, Nakazaki N, Naruo K, Okumura S, Shimpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC 6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109–136 Kanesaki Y, Suzuki I, Allakhverdiev SI, Mikami K, Murata N (2002) Salt stress and hyperosmotic stress regulate the expression of different sets of genes in Synechocystis sp. PCC 6803. Biochem Biophys Res Co 290:339–348 Kasinathan V, Wingler A (2004) Effect of reduced arginine decarboxylase activity on salt tolerance and on polyamine formation during salt stress in Arabidopsis thaliana. Physiol Plant 121:101–107 Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946–950 Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291 Lehtonen JV, Still DJ, Rantanen VV, Ekholm J, Björklund D, Iftikhar Z, Huhtala M, Repo S, Jussila A, Jaakkola J, Pentikäinen O, Nyrönen T, Salminen T, Gyllenberg M, Johnson MS (2004) BODIL: a molecular modeling environment for structure–function analysis and drug design. J Comp Aided Mol Des 18:401–419 Malmberg RL, Smith KE, Bell E, Cellino ML (1992) Arginine Decarboxylase of oats is clipped from a precursor into two polypeptides found in the soluble enzyme. Plant Physiol 100:146–152 Malmberg RL, Cellino ML (1994) Arginine decarboxylase of oats is activated by enzymatic cleavage into two polypeptides. J Biol Chem 269:2703–2706 Merritt EA, Bacon DJ (1997) Raster3D: photorealistic molecular graphics. Methods Enzymol 277:505–524 Minocha R, Long S, Maki H, Minocha SC (1999) Assays for the activities of polyamine biosynthetic enzymes using intact tissues. Plant Physiol Biochem 37:597–603 Mohamed A, Jansson C (1989) Influence of light on accumulation of photosynthesis-specific transcripts in the cyanobacterium Synechocystis 6803. Plant Mol Biol 13:693–700 Mullineaux CW (2001) How do cyanobacteria sense and respond to light? Mol Microbiol 41:965–971 Muro-Pastor MI, Reyes JC, Florencio FJ (2001) Cyanobacteria perceive nitrogen status by sensing intracellular 2-oxoglutarate levels. J Biol Chem 276:38320–38328 Patel CN, Adcock RS, Sell KG, Oliveira MA (2004) Crystallization, X-ray diffraction and oligomeric characterization of arginine decarboxylase from Yersinia pestis, a key polyamine biosynthetic enzyme. Acta Cryst D 60:2396–2398 Primikirios NI, Roubelakis-Angelakis KA (1999) Cloning and expression of an arginine decarboxylase cDNA from Vitis viniferea L. cell-suspension cultures. Planta 208:574–582 Quintero MJ, Muro-Pastor AM, Herrero A, Flores E (2000) Arginine catabolism in the cyanobacterium Synechocystis sp. Strain PCC 6803 involves the urea cycle and arginase pathway. J Bacteriol 182:1008–1015 Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK (2002) Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor. Structure 10:1499–1508 Rost B (1996) PHD: predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol 266:525–539 Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815 Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17:355–362 Tassoni A, Fornalé S, Bagni N (2003) Putative ornithine decarboxylase activity in Arabidopsis thaliana: inhibition and intracellular localization. Plant Physiol Biochem 41:871–875 Urano K, Yoshiba Y, Nanjo T, Ito T, Yamaguchi-Shinozaki K, Shinozaki K (2004) Arabidopsis stress-inducible gene for arginine decarboxylase AtADC2 is required for accumulation of putrescine in salt tolerance. Biochem Biophys Res Co 313:369–375 Watson MB, Malmberg RL (1996) Regulation of Arabidopsis thaliana L. Heynh arginine decarboxylase by potassium-deficiency stress. Plant Physiol 111:1077–1083 Williams GKJ (1988) Construction of specific mutations in photosystem II photosynthetic reaction center by genetic engineering methods in Synechocystis 6803. Methods Enzymol 167:766–778