Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs

Abstract The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom T...

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Autores principales:	Tore Brembu, Matilde Skogen Chauton, Per Winge, Atle M. Bones, Olav Vadstein
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/074634b090a640fd8550de6aad0461d5
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spelling	oai:doaj.org-article:074634b090a640fd8550de6aad0461d52021-12-02T15:05:47ZDynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs10.1038/s41598-017-04921-02045-2322https://doaj.org/article/074634b090a640fd8550de6aad0461d52017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-04921-0https://doaj.org/toc/2045-2322Abstract The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. Ten new proteins with silaffin-like motifs, two kinases and a novel family of putatively frustule-associated transmembrane proteins induced by Si shift-up with a possible role in frustule biosynthesis were identified. A separate cluster analysis performed on all significantly regulated silaffin-like proteins (SFLPs), as well as silaffin-like motifs, resulted in the classification of silaffins, cingulins and SFLPs into distinct clusters. A majority of the genes in the Si-responsive clusters are highly divergent, but positive selection does not seem to be the driver behind this variability. This study provides a high-resolution map over transcriptional responses to changes in Si availability in T. pseudonana. Hallmark Si-responsive genes are identified, characteristic motifs and domains are classified, and taxonomic and evolutionary implications outlined and discussed.Tore BrembuMatilde Skogen ChautonPer WingeAtle M. BonesOlav VadsteinNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tore Brembu Matilde Skogen Chauton Per Winge Atle M. Bones Olav Vadstein Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs
description	Abstract The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. Ten new proteins with silaffin-like motifs, two kinases and a novel family of putatively frustule-associated transmembrane proteins induced by Si shift-up with a possible role in frustule biosynthesis were identified. A separate cluster analysis performed on all significantly regulated silaffin-like proteins (SFLPs), as well as silaffin-like motifs, resulted in the classification of silaffins, cingulins and SFLPs into distinct clusters. A majority of the genes in the Si-responsive clusters are highly divergent, but positive selection does not seem to be the driver behind this variability. This study provides a high-resolution map over transcriptional responses to changes in Si availability in T. pseudonana. Hallmark Si-responsive genes are identified, characteristic motifs and domains are classified, and taxonomic and evolutionary implications outlined and discussed.
format	article
author	Tore Brembu Matilde Skogen Chauton Per Winge Atle M. Bones Olav Vadstein
author_facet	Tore Brembu Matilde Skogen Chauton Per Winge Atle M. Bones Olav Vadstein
author_sort	Tore Brembu
title	Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs
title_short	Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs
title_full	Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs
title_fullStr	Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs
title_full_unstemmed	Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs
title_sort	dynamic responses to silicon in thalasiossira pseudonana - identification, characterisation and classification of signature genes and their corresponding protein motifs
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/074634b090a640fd8550de6aad0461d5
work_keys_str_mv	AT torebrembu dynamicresponsestosiliconinthalasiossirapseudonanaidentificationcharacterisationandclassificationofsignaturegenesandtheircorrespondingproteinmotifs AT matildeskogenchauton dynamicresponsestosiliconinthalasiossirapseudonanaidentificationcharacterisationandclassificationofsignaturegenesandtheircorrespondingproteinmotifs AT perwinge dynamicresponsestosiliconinthalasiossirapseudonanaidentificationcharacterisationandclassificationofsignaturegenesandtheircorrespondingproteinmotifs AT atlembones dynamicresponsestosiliconinthalasiossirapseudonanaidentificationcharacterisationandclassificationofsignaturegenesandtheircorrespondingproteinmotifs AT olavvadstein dynamicresponsestosiliconinthalasiossirapseudonanaidentificationcharacterisationandclassificationofsignaturegenesandtheircorrespondingproteinmotifs
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Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs

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