Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes

Zhao XQ, Aizawa T, Schneider J, Wang C, Shen RF, Sunairi M (2013)
MicrobiologyOpen 2(2): 308-317.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Zhao, Xue Qiang; Aizawa, Tomoko; Schneider, JessicaUniBi; Wang, Chao; Shen, Ren Fang; Sunairi, Michio
Abstract / Bemerkung
The complete mitochondrial genome of Rhodotorula taiwanensis RS1, an aluminum-tolerant Basidiomycota fungus, was determined and compared with the known mitochondrial genomes of 12 Basidiomycota species. The mitochondrial genome of R. taiwanensis RS1 is a circular DNA molecule of 40,392 bp and encodes the typical 15 mitochondrial proteins, 23 tRNAs, and small and large rRNAs as well as 10 intronic open reading frames. These genes are apparently transcribed in two directions and do not show syntenies in gene order with other investigated Basidiomycota species. The average G+C content (41%) of the mitochondrial genome of R. taiwanensis RS1 is the highest among the Basidiomycota species. Two introns were detected in the sequence of the atp9 gene of R. taiwanensis RS1, but not in that of other Basidiomycota species. Rhodotorula taiwanensis is the first species of the genus Rhodotorula whose full mitochondrial genome has been sequenced; and the data presented here supply valuable information for understanding the evolution of fungal mitochondrial genomes and researching the mechanism of aluminum tolerance in microorganisms.
Erscheinungsjahr
2013
Zeitschriftentitel
MicrobiologyOpen
Band
2
Ausgabe
2
Seite(n)
308-317
ISSN
2045-8827
Page URI
https://pub.uni-bielefeld.de/record/2558914

Zitieren

Zhao XQ, Aizawa T, Schneider J, Wang C, Shen RF, Sunairi M. Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes. MicrobiologyOpen. 2013;2(2):308-317.
Zhao, X. Q., Aizawa, T., Schneider, J., Wang, C., Shen, R. F., & Sunairi, M. (2013). Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes. MicrobiologyOpen, 2(2), 308-317. doi:10.1002/mbo3.74
Zhao, Xue Qiang, Aizawa, Tomoko, Schneider, Jessica, Wang, Chao, Shen, Ren Fang, and Sunairi, Michio. 2013. “Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes”. MicrobiologyOpen 2 (2): 308-317.
Zhao, X. Q., Aizawa, T., Schneider, J., Wang, C., Shen, R. F., and Sunairi, M. (2013). Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes. MicrobiologyOpen 2, 308-317.
Zhao, X.Q., et al., 2013. Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes. MicrobiologyOpen, 2(2), p 308-317.
X.Q. Zhao, et al., “Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes”, MicrobiologyOpen, vol. 2, 2013, pp. 308-317.
Zhao, X.Q., Aizawa, T., Schneider, J., Wang, C., Shen, R.F., Sunairi, M.: Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes. MicrobiologyOpen. 2, 308-317 (2013).
Zhao, Xue Qiang, Aizawa, Tomoko, Schneider, Jessica, Wang, Chao, Shen, Ren Fang, and Sunairi, Michio. “Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes”. MicrobiologyOpen 2.2 (2013): 308-317.

9 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Aluminum-Nitrogen Interactions in the Soil-Plant System.
Zhao XQ, Shen RF., Front Plant Sci 9(), 2018
PMID: 29967630
Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.
Tkavc R, Matrosova VY, Grichenko OE, Gostinčar C, Volpe RP, Klimenkova P, Gaidamakova EK, Zhou CE, Stewart BJ, Lyman MG, Malfatti SA, Rubinfeld B, Courtot M, Singh J, Dalgard CL, Hamilton T, Frey KG, Gunde-Cimerman N, Dugan L, Daly MJ., Front Microbiol 8(), 2017
PMID: 29375494
Complete mitochondrial genome of the Verticillium-wilt causing plant pathogen Verticillium nonalfalfae.
Jelen V, de Jonge R, Van de Peer Y, Javornik B, Jakše J., PLoS One 11(2), 2016
PMID: 26839950
A potential contribution of the less negatively charged cell wall to the high aluminum tolerance of Rhodotorula taiwanensis RS1.
Hu ZM, Zhao XQ, Bao XM, Wang C, Wang W, Zheng L, Lan P, Shen RF., Yeast 33(11), 2016
PMID: 27497064
Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis.
Hegedusova E, Brejova B, Tomaska L, Sipiczki M, Nosek J., Curr Genet 60(1), 2014
PMID: 24071901
High Rhodotorula sequences in skin transcriptome of patients with diffuse systemic sclerosis.
Arron ST, Dimon MT, Li Z, Johnson ME, Wood TA, Feeney L, Angeles JG, Lafyatis R, Whitfield ML., J Invest Dermatol 134(8), 2014
PMID: 24608988
Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes.
Himmelstrand K, Olson A, Brandström Durling M, Karlsson M, Stenlid J., Curr Genet 60(4), 2014
PMID: 25011705

42 References

Daten bereitgestellt von Europe PubMed Central.

GenomeView: a next-generation genome browser.
Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y., Nucleic Acids Res. 40(2), 2011
PMID: 22102585
Tandem repeats finder: a program to analyze DNA sequences.
Benson G., Nucleic Acids Res. 27(2), 1999
PMID: 9862982
Molecular phylogenetics of the genus Rhodotorula and related basidiomycetous yeasts inferred from the mitochondrial cytochrome b gene.
Biswas SK, Yokoyama K, Nishimura K, Miyaji M., Int. J. Syst. Evol. Microbiol. 51(Pt 3), 2001
PMID: 11411687
A novel motif for identifying rps3 homologs in fungal mitochondrial genomes.
Bullerwell CE, Burger G, Lang BF., Trends Biochem. Sci. 25(8), 2000
PMID: 10916154
Basidiomycetous yeasts: current status
Choudhary DK, Johri BN., 2009
The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao.
Costa GG, Cabrera OG, Tiburcio RA, Medrano FJ, Carazzolle MF, Thomazella DP, Schuster SC, Carlson JE, Guiltinan MJ, Bailey BA, Mieczkowski P, Pereira GA, Meinhardt LW., Fungal Biol 116(5), 2012
PMID: 22559916
Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis.
Fell JW, Boekhout T, Fonseca A, Scorzetti G, Statzell-Tallman A., Int. J. Syst. Evol. Microbiol. 50 Pt 3(), 2000
PMID: 10843082
Confidence limits on phylogenies: an approach using the bootstrap
Felsenstein J., 1985
The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid.
Formighieri EF, Tiburcio RA, Armas ED, Medrano FJ, Shimo H, Carels N, Goes-Neto A, Cotomacci C, Carazzolle MF, Sardinha-Pinto N, Thomazella DP, Rincones J, Digiampietri L, Carraro DM, Azeredo-Espin AM, Reis SF, Deckmann AC, Gramacho K, Goncalves MS, Moura Neto JP, Barbosa LV, Meinhardt LW, Cascardo JC, Pereira GA., Mycol. Res. 112(Pt 10), 2008
PMID: 18786820
Rfam: updates to the RNA families database.
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18953034
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
The CGView Server: a comparative genomics tool for circular genomes.
Grant JR, Stothard P., Nucleic Acids Res. 36(Web Server issue), 2008
PMID: 18411202
Approaches to Fungal Genome Annotation.
Haas BJ, Zeng Q, Pearson MD, Cuomo CA, Wortman JR., Mycology 2(3), 2011
PMID: 22059117
BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
Hall TA., 1999
The mitochondrial genome of the wood-degrading basidiomycete Trametes cingulata.
Haridas S, Gantt JS., FEMS Microbiol. Lett. 308(1), 2010
PMID: 20455947
Rhodotorula taiwanensis sp. nov., a novel yeast species from a plant in Taiwan.
Huang CH, Lee FL, Tien CJ, Hsieh PW., Antonie Van Leeuwenhoek 99(2), 2010
PMID: 20680683
Mitochondrial genome variation and the origin of modern humans.
Ingman M, Kaessmann H, Paabo S, Gyllensten U., Nature 408(6813), 2000
PMID: 11130070
The rapid generation of mutation data matrices from protein sequences.
Jones DT, Taylor WR, Thornton JM., Comput. Appl. Biosci. 8(3), 1992
PMID: 1633570
Preparation of pH 3.0 agar plate, enumeration of acid-tolerant, and Al-resistant microorganisms in acid soils
Kanazawa S, Kunito T., 1996
Isolation and characterization of acid- and Al-tolerant microorganisms.
Kawai F, Zhang D, Sugimoto M., FEMS Microbiol. Lett. 189(2), 2000
PMID: 10930728
How do crop plants tolerate acid soils? Mechanisms of aluminum tolerance and phosphorous efficiency.
Kochian LV, Hoekenga OA, Pineros MA., Annu Rev Plant Biol 55(), 2004
PMID: 15377228
Genera Burkholderia and Lipomyces are predominant aluminum-resistant microorganisms isolated from acidic forest soils using cycloheximide-amended growth media
Kunito T, Owaki M, Ihyo Y, Sumi H, Toda H, Fukuda D., 2012
Methods for isolation, phenotypic characterization and maintenance of yeasts
Kurtzman CP, Fell JW, Boekhout T, Robert V., 2011
Aluminum toxicity and astrocyte dysfunction: a metabolic link to neurological disorders.
Lemire J, Appanna VD., J. Inorg. Biochem. 105(11), 2011
PMID: 22099161
The Pfam protein families database.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22127870
Rhodotorula Harrison (1928)
Sampaio JP., 2011
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs.
Schattner P, Brooks AN, Lowe TM., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980563
RAPYD--rapid annotation platform for yeast data.
Schneider J, Blom J, Jaenicke S, Linke B, Brinkrolf K, Neuweger H, Tauch A, Goesmann A., J. Biotechnol. 155(1), 2010
PMID: 21040748
Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions.
Scorzetti G, Fell JW, Fonseca A, Statzell-Tallman A., FEMS Yeast Res. 2(4), 2002
PMID: 12702266
Automated generation of heuristics for biological sequence comparison.
Slater GS, Birney E., BMC Bioinformatics 6(), 2005
PMID: 15713233
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S., Mol. Biol. Evol. 28(10), 2011
PMID: 21546353
The crucial role of mitochondrial regulation in adaptive aluminium resistance in Rhodotorula glutinis.
Tani A, Inoue C, Tanaka Y, Yamamoto Y, Kondo H, Hiradate S, Kimbara K, Kawai F., Microbiology (Reading, Engl.) 154(Pt 11), 2008
PMID: 18957597
Evolution of linear chromosomes and multipartite genomes in yeast mitochondria.
Valach M, Farkas Z, Fricova D, Kovac J, Brejova B, Vinar T, Pfeiffer I, Kucsera J, Tomaska L, Lang BF, Nosek J., Nucleic Acids Res. 39(10), 2011
PMID: 21266473
The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom).
Wang Y, Zeng F, Hon CC, Zhang Y, Leung FC., FEMS Microbiol. Lett. 280(1), 2008
PMID: 18248422
High aluminum tolerance of Rhodotorula sp. RS1 is associated with thickening of the cell wall rather than chelation of aluminum ions
Wang C, Zhao XQ, Aizawa T, Sunairi M, Shen RF., 2013
Aluminum toxicity is associated with mitochondrial dysfunction and the production of reactive oxygen species in plant cells.
Yamamoto Y, Kobayashi Y, Devi SR, Rikiishi S, Matsumoto H., Plant Physiol. 128(1), 2002
PMID: 11788753
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