Ecological geneticsEcological geneticsЭкологическая генетика1811-09322411-9202Eco-Vector1348810.17816/ecogen17447-55Genetic basis of ecosystems evolutionГенетические основы эволюции экосистемResearch ArticleThe analysis of the polyamine oxidase genes in the methylotrophic yeast Komagataella phaffiiАнализ генов полиаминоксидаз у метилотрофных дрожжей Komagataella phaffiiIvanovaAlina V.ИвановаАлина Владиславовна
Russian Federation

4th year Student of the Department of Genetics and Biotechnology

студентка 4-го курса кафедры генетики и биотехнологии

alinalans@gmail.comSidorinAnton V.СидоринАнтон Витальевич
Russian Federation

Bachelor of Science (BSc) in the Genetics and Biotechnology Department

бакалавр кафедры генетики и биотехнологии

spacerocketpilot@gmail.comhttps://orcid.org/0000-0003-0837-04986603061322H-6895-20138281-8020SambukElena V.СамбукЕлена Викторовна
Russian Federation

Doctor of Science, Professor of the Department of Genetics and Biotechnology

д-р биол. наук, профессор кафедры генетики и биотехнологии

esambuk@mail.ruhttps://orcid.org/0000-0002-1744-3890553706588009335-1184RumyantsevAndrei M.РумянцевАндрей Михайлович
Russian Federation

PhD, Senior Researcher of the Department of Genetics and Biotechnology

канд. биол. наук, младший научный сотрудник кафедры генетики и биотехнологии

rumyantsev-am@mail.ruSt. Petersburg State UniversityФГБОУ ВО «Санкт-Петербургский государственный университет»021220191512201917447551706201902122019Copyright ©; 2019, Ivanova A.V., Sidorin A.V., Sambuk E.V., Rumyantsev A.M.Copyright ©; 2019, Иванова А.В., Сидорин А.В., Самбук Е.В., Румянцев А.М.2019Ivanova A.V., Sidorin A.V., Sambuk E.V., Rumyantsev A.M.Иванова А.В., Сидорин А.В., Самбук Е.В., Румянцев А.М.http://creativecommons.org/licenses/by/4.0https://journals.eco-vector.com/ecolgenet/article/view/13488

Polyamines are present in all living cells and regulate a wide range of biological processes. In Saccharomyces cerevisiae the polyamine oxidase Fms1p converts spermine to spermidine and 3-aminopropionaldehyde, which is necessary for the synthesis of pantothenic acid and hypusination. This paper shows that S. cerevisiae FMS1 gene orthologs are present in all major representatives of the Saccharomycotina subdivision, but their copy numbers are different. In the Komagataella phaffii (Pichia pastoris) yeast, two polyamine oxidase genes (KpFMS1 and KpFMS2) were identified, and the regulation of their promoters activity was studied.

Полиамины присутствуют во всех живых клетках и регулируют широкий спектр биологических процессов. У дрожжей Saccharomyces cerevisiae полиаминоксидаза Fms1p превращает спермин в спермидин и 3-аминопропаналь, что необходимо для синтеза пантотеновой кислоты и гипузинирования. В данной работе показано, что ортологи гена FMS1 дрожжей S. cerevisiae присутствуют у всех основных представителей подотдела Saccharomycotina, однако их копийность различна. У дрожжей Komagataella рhaffii (Pichia pastoris) идентифицированы два гена полиаминоксидаз (KpFMS1 и KpFMS2) и изучена регуляция активности их промоторов.

polyamine oxidasesmethylotrophic yeastKomagataella phaffiiPichia pastorisполиаминоксидазыметилотрофные дрожжиKomagataella phaffiiPichia pastorisRFBRРФФИThis work was supported by the RFBR grant No. 18-34-00750 mol_a.Работа выполнена при поддержке гранта РФФИ № 18-34-00750 мол_а.Wallace HM, Fraser AV, Hughes A. A perspective of polyamine metabolism. Biochem J. 2003;376(Pt 1):1-14. https://doi.org/10.1042/BJ20031327.Miller-Fleming L, Olin-Sandoval V, Campbell K, Ralser M. Remaining mysteries of molecular biology: the role of polyamines in the cell. J Mol Biol. 2015;427(21):3389-3406. https://doi.org/10.1016/j.jmb.2015.06.020.Wallace HM. Polyamines: specific metabolic regulators or multifunctional polycations? Biochem Soc Trans. 1998;26(4):569-571. https://doi.org/10.1042/bst0260569.White WH, Gunyuzlu PL, Toyn JH. Saccharomyces cerevisiae is capable of de novo pantothenic acid biosynthesis involving a novel pathway of beta-alanine production from spermine. J Biol Chem. 2001;276(14):10794-10800. https://doi.org/10.1074/jbc.M009804200.Chattopadhyay MK, Tabor CW, Tabor H. Spermidine but not spermine is essential for hypusine biosynthesis and growth in Saccharomyces cerevisiae: spermine is converted to spermidine in vivo by the FMS1-amine oxidase. Proc Natl Acad Sci USA. 2003;100(24):13869-74. https://doi.org/10.1073/pnas.1835918100.Polticelli F, Salvi D, Mariottini P, et al. Molecular evolution of the polyamine oxidase gene family in Metazoa. BMC Evol Biol. 2012;12:90. https://doi.org/10.1186/1471-2148-12-90.Reumann S, Ma C, Lemke S, Babujee L. AraPerox. A database of putative Arabidopsis proteins from plant peroxisomes. Plant Physiol. 2004;136(1):2587-2608. https://doi.org/10.1104/pp.104.043695.Valdes-Santiago L, Cervantes-Chavez JA, Leon-Ramirez CG, Ruiz-Herrera J. Polyamine metabolism in fungi with emphasis on phytopathogenic species. J Amino Acids. 2012;2012:837932. https://doi.org/10.1155/2012/837932.Landry J, Sternglanz R. Yeast Fms1 is a FAD-utilizing polyamine oxidase. Biochem Biophys Res Commun. 2003;303(3):771-776. https://doi.org/10.1016/s0006-291x(03)00416-9.Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol. 1990;215(3): 403-410. https://doi.org/10.1016/S0022-2836(05) 80360-2.Kumar S, Stecher G, Li M, et al. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547-1549. https://doi.org/10.1093/molbev/msy096.Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673-4680. https://doi.org/10.1093/nar/22.22.4673.Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol. 2008;25(7):1307-20. https://doi.org/10.1093/molbev/msn067.Rumjantsev AM, Bondareva OV, Padkina MV, Sambuk EV. Effect of nitrogen source and inorganic phosphate concentration on methanol utilization and PEX genes expression in Pichia pastoris. Scientific World Journal. 2014;2014:743615. https://doi.org/10.1155/2014/743615.Guthrie C, Fink GR. Guide to yeast genetics and molecular biology. Methods Enzymol. 1991;194: 1-863. https://doi.org/10.1016/s0076-6879(00)x 0276-5.Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983;166(4):557-580. https://doi.org/10.1016/s0022-2836(83)80284-8.Wu S, Letchworth GJ. High efficiency transformation by electroporation of Pichia pastoris pretreated with lithium acetate and dithiothreitol. Biotechniques. 2004;36(1):152-154. https://doi.org/10.2144/04361DD02.Остерман Л.А. Методы исследования белков и нуклеиновых кислот. Электрофорез и ультрацентрифугирование (практическое пособие). – М.: Наука, 1981. – 288 с. [Osterman LA. Metody issledovaniya belkov i nukleinovykh kislot. Elektroforez i ul’tratsentrifugirovaniye (prakticheskoye posobiye). Moscow: Nauka; 1981. 288 p. (In Russ).]Самсонова М.Г., Падкина М.В., Краснопевцева Н.Г. Генетико-биохимическое изучение кислых фосфатаз дрожжей Saccharomyces cerevisiae // Генетика. – 1975. – Т. 11. – № 9. – С. 104-115. [Samsonova MG, Padkina MV, Krasnopevtseva NG. Genetiko-biokhimicheskoye izucheniye kislykh fosfataz drozhzhey Saccharomyces cerevisiae. Genetika. 1975;11(9):104-115. (In Russ.)]Shen XX, Zhou X, Kominek J, et al. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3 (Bethesda). 2016;6(12):3927-3939. https://doi.org/10.1534/g3.116.034744.Notzel C, Lingner T, Klingenberg H, Thoms S. Identification of new fungal peroxisomal matrix proteins and revision of the PTS1 consensus. Traffic. 2016;17(10):1110-1124. https://doi.org/10.1111/tra.12426.Almagro Armenteros JJ, Sonderby CK, Sonderby SK, et al. DeepLoc: prediction of protein subcellular localization using deep learning. Bioinformatics. 2017;33(21):3387-3395. https://doi.org/10.1093/bioinformatics/btx431.Ellis SB, Brust PF, Koutz PJ, et al. Isolation of alcohol oxidase and two other methanol regulatable genes from the yeast Pichia pastoris. Mol Cell Biol. 1985;5(5):1111-21. https://doi.org/10.1128/mcb.5.5.1111.Tschopp JF, Brust PF, Cregg JM, et al. Expression of the lacZ gene from two methanol-regulated promoters in Pichia pastoris. Nucleic Acids Res. 1987;15(9):3859-76. https://doi.org/10.1093/nar/15.9.3859.Assis R, Bachtrog D. Neofunctionalization of young duplicate genes in Drosophila. Proc Natl Acad Sci. 2013;110(43):17409-17414. https://doi.org/10.1073/pnas.1313759110.He X, Zhang J. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics. 2005;169(2):1157-1164. https://doi.org/10.1534/genetics.104.037051.Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004;428(6983):617-624. https://doi.org/10.1038/nature02424.Lin-Cereghino GP, Godfrey L, de la Cruz BJ, et al. Mxr1p, a key regulator of the methanol utilization pathway and peroxisomal genes in Pichia pastoris. Mol Cell Biol. 2006;26(3):883-897. https://doi.org/10.1128/MCB.26.3.883-897.2006.Kranthi BV, Kumar R, Kumar NV, et al. Identification of key DNA elements involved in promoter recognition by Mxr1p, a master regulator of methanol utilization pathway in Pichia pastoris. Biochim Biophys Acta. 2009;1789(6-8):460-468. https://doi.org/10.1016/j.bbagrm.2009.05.004.Wang X, Cai M, Shi L, et al. PpNrg1 is a transcriptional repressor for glucose and glycerol repression of AOX1 promoter in methylotrophic yeast Pichia pastoris. Biotechnol Lett. 2016;38(2):291-298. https://doi.org/10.1007/s10529-015-1972-4.Wilkinson D, Váchová L, Hlaváček O, et al. Long noncoding RNAs in yeast cells and differentiated subpopulations of yeast colonies and biofilms. Oxid Med Cell Longev. 2018;2018:4950591. https://doi.org/10.1155/2018/4950591.