Gene Expression Differences between Noccaea caerulescens Ecotypes Help to Identify Candidate Genes for Metal Phytoremediation

P. Halimaa; Y.F. Lin; V.H. Ahonen; D. Blande; S. Clemens; A. Gyenesei; E. Haikio; S.O. Karenlampi; A. Laiho; M.G. Aarts; J.P. Pursiheimo; H. Schat; H. Schmidt; M.H. Tuomainen; A.I. Tervahauta

doi:10.1021/es4042995

Gene Expression Differences between Noccaea caerulescens Ecotypes Help to Identify Candidate Genes for Metal Phytoremediation

P. Halimaa, Y.F. Lin, V.H. Ahonen, D. Blande, S. Clemens, A. Gyenesei, E. Haikio, S.O. Karenlampi, A. Laiho, M.G. Aarts, J.P. Pursiheimo, H. Schat, H. Schmidt, M.H. Tuomainen, A.I. Tervahauta

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Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

Populations of Noccaea caerulescens show tremendous differences in their capacity to hyperaccumulate and hypertolerate metals. To explore the differences that could contribute to these traits, we undertook SOLiD high-throughput sequencing of the root transcriptomes of three phenotypically well-characterized N. caerulescens accessions, i.e., Ganges, La Calamine, and Monte Prinzera. Genes with possible contribution to zinc, cadmium, and nickel hyperaccumulation and hypertolerance were predicted. The most significant differences between the accessions were related to metal ion (di-, trivalent inorganic cation) transmembrane transporter activity, iron and calcium ion binding, (inorganic) anion transmembrane transporter activity, and antioxidant activity. Analysis of correlation between the expression profile of each gene and the metal-related characteristics of the accessions disclosed both previously characterized (HMA4, HMA3) and new candidate genes (e.g., for nickel IRT1, ZIP10, and PDF2.3) as possible contributors to the hyperaccumulation/tolerance phenotype. A number of unknown Noccaea-specific transcripts also showed correlation with Zn

Original language	English
Journal	Environmental Science and Technology
DOIs	https://doi.org/10.1021/es4042995
Publication status	Published - 2014

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Halimaa, P., Lin, Y. F., Ahonen, V. H., Blande, D., Clemens, S., Gyenesei, A., Haikio, E., Karenlampi, S. O., Laiho, A., Aarts, M. G., Pursiheimo, J. P., Schat, H., Schmidt, H., Tuomainen, M. H., & Tervahauta, A. I. (2014). Gene Expression Differences between Noccaea caerulescens Ecotypes Help to Identify Candidate Genes for Metal Phytoremediation. Environmental Science and Technology. https://doi.org/10.1021/es4042995

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title = "Gene Expression Differences between Noccaea caerulescens Ecotypes Help to Identify Candidate Genes for Metal Phytoremediation",

abstract = "Populations of Noccaea caerulescens show tremendous differences in their capacity to hyperaccumulate and hypertolerate metals. To explore the differences that could contribute to these traits, we undertook SOLiD high-throughput sequencing of the root transcriptomes of three phenotypically well-characterized N. caerulescens accessions, i.e., Ganges, La Calamine, and Monte Prinzera. Genes with possible contribution to zinc, cadmium, and nickel hyperaccumulation and hypertolerance were predicted. The most significant differences between the accessions were related to metal ion (di-, trivalent inorganic cation) transmembrane transporter activity, iron and calcium ion binding, (inorganic) anion transmembrane transporter activity, and antioxidant activity. Analysis of correlation between the expression profile of each gene and the metal-related characteristics of the accessions disclosed both previously characterized (HMA4, HMA3) and new candidate genes (e.g., for nickel IRT1, ZIP10, and PDF2.3) as possible contributors to the hyperaccumulation/tolerance phenotype. A number of unknown Noccaea-specific transcripts also showed correlation with Zn",

author = "P. Halimaa and Y.F. Lin and V.H. Ahonen and D. Blande and S. Clemens and A. Gyenesei and E. Haikio and S.O. Karenlampi and A. Laiho and M.G. Aarts and J.P. Pursiheimo and H. Schat and H. Schmidt and M.H. Tuomainen and A.I. Tervahauta",

year = "2014",

doi = "10.1021/es4042995",

language = "English",

journal = "Environmental Science and Technology",

issn = "0013-936X",

publisher = "American Chemical Society",

}

Halimaa, P, Lin, YF, Ahonen, VH, Blande, D, Clemens, S, Gyenesei, A, Haikio, E, Karenlampi, SO, Laiho, A, Aarts, MG, Pursiheimo, JP, Schat, H, Schmidt, H, Tuomainen, MH & Tervahauta, AI 2014, 'Gene Expression Differences between Noccaea caerulescens Ecotypes Help to Identify Candidate Genes for Metal Phytoremediation', Environmental Science and Technology. https://doi.org/10.1021/es4042995

TY - JOUR

T1 - Gene Expression Differences between Noccaea caerulescens Ecotypes Help to Identify Candidate Genes for Metal Phytoremediation

AU - Halimaa, P.

AU - Lin, Y.F.

AU - Ahonen, V.H.

AU - Blande, D.

AU - Clemens, S.

AU - Gyenesei, A.

AU - Haikio, E.

AU - Karenlampi, S.O.

AU - Laiho, A.

AU - Aarts, M.G.

AU - Pursiheimo, J.P.

AU - Schat, H.

AU - Schmidt, H.

AU - Tuomainen, M.H.

AU - Tervahauta, A.I.

PY - 2014

Y1 - 2014

N2 - Populations of Noccaea caerulescens show tremendous differences in their capacity to hyperaccumulate and hypertolerate metals. To explore the differences that could contribute to these traits, we undertook SOLiD high-throughput sequencing of the root transcriptomes of three phenotypically well-characterized N. caerulescens accessions, i.e., Ganges, La Calamine, and Monte Prinzera. Genes with possible contribution to zinc, cadmium, and nickel hyperaccumulation and hypertolerance were predicted. The most significant differences between the accessions were related to metal ion (di-, trivalent inorganic cation) transmembrane transporter activity, iron and calcium ion binding, (inorganic) anion transmembrane transporter activity, and antioxidant activity. Analysis of correlation between the expression profile of each gene and the metal-related characteristics of the accessions disclosed both previously characterized (HMA4, HMA3) and new candidate genes (e.g., for nickel IRT1, ZIP10, and PDF2.3) as possible contributors to the hyperaccumulation/tolerance phenotype. A number of unknown Noccaea-specific transcripts also showed correlation with Zn

AB - Populations of Noccaea caerulescens show tremendous differences in their capacity to hyperaccumulate and hypertolerate metals. To explore the differences that could contribute to these traits, we undertook SOLiD high-throughput sequencing of the root transcriptomes of three phenotypically well-characterized N. caerulescens accessions, i.e., Ganges, La Calamine, and Monte Prinzera. Genes with possible contribution to zinc, cadmium, and nickel hyperaccumulation and hypertolerance were predicted. The most significant differences between the accessions were related to metal ion (di-, trivalent inorganic cation) transmembrane transporter activity, iron and calcium ion binding, (inorganic) anion transmembrane transporter activity, and antioxidant activity. Analysis of correlation between the expression profile of each gene and the metal-related characteristics of the accessions disclosed both previously characterized (HMA4, HMA3) and new candidate genes (e.g., for nickel IRT1, ZIP10, and PDF2.3) as possible contributors to the hyperaccumulation/tolerance phenotype. A number of unknown Noccaea-specific transcripts also showed correlation with Zn

U2 - 10.1021/es4042995

DO - 10.1021/es4042995

M3 - Article

SN - 0013-936X

JO - Environmental Science and Technology

JF - Environmental Science and Technology

ER -

Gene Expression Differences between Noccaea caerulescens Ecotypes Help to Identify Candidate Genes for Metal Phytoremediation

Abstract

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