Concordant gene regulation related to perturbations of three GDP-mannose-related genes

Anssi Törmä, Juha-Pekka Pitkänen, Laura Huopaniemi, Pirkko Mattila, Risto Renkonen (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

Abstract

Glycosylation of proteins is one of the most crucial post-translational modifications. In order to access system-level and state-dependent data related to the regulation of glycosylation events, we cultivated yeast cell strains each harboring a selected conditional knockdown construct for a gene (either SEC53, VRG4 or DPM1) related to GDP-mannose synthesis or its utilization in glycan biosynthesis. In order to carry this out efficiently, we developed automated sampling from bioreactor cultivations, a collection of in silico workflows for data analysis as well as their integration into a large data warehouse. Using the above-mentioned approaches, we could show that conditional knocking down of transcripts related to GDP-mannose synthesis or transportation led to altered levels of over 300 transcripts. These transcripts and their corresponding proteins were characterized by their gene ontology (GO) annotations, and their putative transcriptional regulation was analyzed. Furthermore, novel pathways were generated indicating interactions between GO categories with common proteins, putative transcriptional regulators of such induced GO categories, and the large protein–protein interaction network among the proteins whose transcripts indicated altered expression levels. When these results are always added to an ever-expanding data warehouse as annotations, they will incrementally increase the knowledge of biological systems.
Original languageEnglish
Pages (from-to)63-72
Number of pages10
JournalFEMS Yeast Research
Volume9
Issue number1
DOIs
Publication statusPublished - 2009
MoE publication typeA1 Journal article-refereed

Fingerprint

Guanosine Diphosphate Mannose
Gene Ontology
Glycosylation
Genes
Protein Interaction Maps
Molecular Sequence Annotation
Workflow
Bioreactors
Post Translational Protein Processing
Computer Simulation
Polysaccharides
Proteins
Yeasts

Keywords

  • gene regulation
  • conditional knockdown
  • perturbation
  • gdp-mannose
  • yeast

Cite this

Törmä, Anssi ; Pitkänen, Juha-Pekka ; Huopaniemi, Laura ; Mattila, Pirkko ; Renkonen, Risto. / Concordant gene regulation related to perturbations of three GDP-mannose-related genes. In: FEMS Yeast Research. 2009 ; Vol. 9, No. 1. pp. 63-72.
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abstract = "Glycosylation of proteins is one of the most crucial post-translational modifications. In order to access system-level and state-dependent data related to the regulation of glycosylation events, we cultivated yeast cell strains each harboring a selected conditional knockdown construct for a gene (either SEC53, VRG4 or DPM1) related to GDP-mannose synthesis or its utilization in glycan biosynthesis. In order to carry this out efficiently, we developed automated sampling from bioreactor cultivations, a collection of in silico workflows for data analysis as well as their integration into a large data warehouse. Using the above-mentioned approaches, we could show that conditional knocking down of transcripts related to GDP-mannose synthesis or transportation led to altered levels of over 300 transcripts. These transcripts and their corresponding proteins were characterized by their gene ontology (GO) annotations, and their putative transcriptional regulation was analyzed. Furthermore, novel pathways were generated indicating interactions between GO categories with common proteins, putative transcriptional regulators of such induced GO categories, and the large protein–protein interaction network among the proteins whose transcripts indicated altered expression levels. When these results are always added to an ever-expanding data warehouse as annotations, they will incrementally increase the knowledge of biological systems.",
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Törmä, A, Pitkänen, J-P, Huopaniemi, L, Mattila, P & Renkonen, R 2009, 'Concordant gene regulation related to perturbations of three GDP-mannose-related genes', FEMS Yeast Research, vol. 9, no. 1, pp. 63-72. https://doi.org/10.1111/j.1567-1364.2008.00461.x

Concordant gene regulation related to perturbations of three GDP-mannose-related genes. / Törmä, Anssi; Pitkänen, Juha-Pekka; Huopaniemi, Laura; Mattila, Pirkko; Renkonen, Risto (Corresponding Author).

In: FEMS Yeast Research, Vol. 9, No. 1, 2009, p. 63-72.

Research output: Contribution to journalArticleScientificpeer-review

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AU - Pitkänen, Juha-Pekka

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AU - Renkonen, Risto

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