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Metal‐ion‐induced expression of gene fragments from subseafloor micro‐organisms in the Kumano forearc basin, Nankai Trough

Byline: T. Wakamatsu,Y. Morono,T. Futagami, T. Terada, S. Nishikawa, T. Morisawa, K. Ohshita, F. Inagaki, M. Ashiuchi Keywords: subseafloor; gene expression; metal ion; sediment; substrate-induced gene expression; uncharacterized gene Abstract Aims Using substrate-induced gene-expression (SIGEX) scr... Full description

Journal Title: Journal of Applied Microbiology November 2018, Vol.125(5), pp.1396-1407
Main Author: Wakamatsu, T.
Other Authors: Morono, Y. , Futagami, T. , Terada, T. , Nishikawa, S. , Morisawa, T. , Ohshita, K. , Inagaki, F. , Ashiuchi, M.
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ID: ISSN: 1364-5072 ; E-ISSN: 1365-2672 ; DOI: 10.1111/jam.14061
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recordid: wj10.1111/jam.14061
title: Metal‐ion‐induced expression of gene fragments from subseafloor micro‐organisms in the Kumano forearc basin, Nankai Trough
format: Article
creator:
  • Wakamatsu, T.
  • Morono, Y.
  • Futagami, T.
  • Terada, T.
  • Nishikawa, S.
  • Morisawa, T.
  • Ohshita, K.
  • Inagaki, F.
  • Ashiuchi, M.
subjects:
  • Subseafloor
  • Gene Expression
  • Metal Ion
  • Sediment
  • Substrate‐Induced Gene Expression
  • Uncharacterized Gene
ispartof: Journal of Applied Microbiology, November 2018, Vol.125(5), pp.1396-1407
description: Byline: T. Wakamatsu,Y. Morono,T. Futagami, T. Terada, S. Nishikawa, T. Morisawa, K. Ohshita, F. Inagaki, M. Ashiuchi Keywords: subseafloor; gene expression; metal ion; sediment; substrate-induced gene expression; uncharacterized gene Abstract Aims Using substrate-induced gene-expression (SIGEX) screening on subseafloor sediment samples from the Nankai Trough, Japan, we identified gene fragments showing an induction response to metal ions. Methods and Results Environmental DNA libraries in Escherichia coli host cells were tested by the addition of metal ions (Ni.sub.2+, Co.sub.2+, Ga.sub.3+ or Mo.sub.6+), followed by cell sorting of clones exhibiting green fluorescence upon co-expression of green fluorescence protein downstream of the inserted gene fragments. One clone displayed Ni.sub.2+-specific induction, three clones displayed Ga.sub.3+-specific induction and three clones displayed an induction response to multiple metal ions. DNA sequence analysis showed that a variety of genes showed induction responses in the screened clones. Conclusions Using the SIGEX approach, we retrieved gene fragments with no previously identified response to metal ions that exhibited metal-ion-induced expression. This method has the potential to promote exploration of gene function through gene-induction response. Significance and Impact of the Study We successfully linked gene-induction response with sequence information for gene fragments of previously unknown function. The SIGEX-based approach exhibited the potential to identify genetic function in unknown gene pools from the deep subseafloor biosphere, as well as novel genetic components for future biotechnological applications. Article Note: These authors contributed equally to this work.
language:
source:
identifier: ISSN: 1364-5072 ; E-ISSN: 1365-2672 ; DOI: 10.1111/jam.14061
fulltext: fulltext
issn:
  • 1364-5072
  • 13645072
  • 1365-2672
  • 13652672
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titleMetal‐ion‐induced expression of gene fragments from subseafloor micro‐organisms in the Kumano forearc basin, Nankai Trough
creatorWakamatsu, T. ; Morono, Y. ; Futagami, T. ; Terada, T. ; Nishikawa, S. ; Morisawa, T. ; Ohshita, K. ; Inagaki, F. ; Ashiuchi, M.
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subjectSubseafloor ; Gene Expression ; Metal Ion ; Sediment ; Substrate‐Induced Gene Expression ; Uncharacterized Gene
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descriptionByline: T. Wakamatsu,Y. Morono,T. Futagami, T. Terada, S. Nishikawa, T. Morisawa, K. Ohshita, F. Inagaki, M. Ashiuchi Keywords: subseafloor; gene expression; metal ion; sediment; substrate-induced gene expression; uncharacterized gene Abstract Aims Using substrate-induced gene-expression (SIGEX) screening on subseafloor sediment samples from the Nankai Trough, Japan, we identified gene fragments showing an induction response to metal ions. Methods and Results Environmental DNA libraries in Escherichia coli host cells were tested by the addition of metal ions (Ni.sub.2+, Co.sub.2+, Ga.sub.3+ or Mo.sub.6+), followed by cell sorting of clones exhibiting green fluorescence upon co-expression of green fluorescence protein downstream of the inserted gene fragments. One clone displayed Ni.sub.2+-specific induction, three clones displayed Ga.sub.3+-specific induction and three clones displayed an induction response to multiple metal ions. DNA sequence analysis showed that a variety of genes showed induction responses in the screened clones. Conclusions Using the SIGEX approach, we retrieved gene fragments with no previously identified response to metal ions that exhibited metal-ion-induced expression. This method has the potential to promote exploration of gene function through gene-induction response. Significance and Impact of the Study We successfully linked gene-induction response with sequence information for gene fragments of previously unknown function. The SIGEX-based approach exhibited the potential to identify genetic function in unknown gene pools from the deep subseafloor biosphere, as well as novel genetic components for future biotechnological applications. Article Note: These authors contributed equally to this work.
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