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  Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family

Rautengarten, C., Steinhauser, D., Buessis, D., Stintzi, A., Schaller, A., Kopka, J., et al. (2005). Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family. PLoS Computational Biology, 1(4), e40. doi:10.1371/journal.pcbi.0010040.

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Rautengarten, C.1, Author
Steinhauser, D.2, 3, Author              
Buessis, D.4, Author              
Stintzi, A.1, Author
Schaller, A.1, Author
Kopka, J.5, Author              
Altmann, T.4, Author              
Affiliations:
1External Organizations, ou_persistent22              
2Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753340              
3Systems Metabolomics, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, Am Mühlenberg 1, 14476 Potsdam-Golm, DE, ou_1797285              
4Developmental Physiology and Genomics, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753313              
5Applied Metabolome Analysis, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753338              

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Free keywords: Animals Arabidopsis/*enzymology/*genetics Chromosomes, Plant/genetics Computational Biology Gene Duplication Gene Expression Regulation, Plant *Models, Genetic Mutation Oligonucleotide Array Sequence Analysis Phylogeny Substrate Specificity Subtilisins/classification/*genetics/*metabolism Transcription, Genetic/genetics
 Abstract: The gene family of subtilisin-like serine proteases (subtilases) in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens confirmed 144 T-DNA insertion lines with knockouts for 55 out of the 56 subtilases. Apart from SDD1, none of the confirmed homozygous mutants revealed any obvious visible phenotypic alteration during growth under standard conditions. Apart from this specific case, forward genetics gave us no hints about the function of the individual 54 non-characterized subtilase genes. Therefore, the main objective of our work was to overcome the shortcomings of the forward genetic approach and to infer alternative experimental approaches by using an integrative bioinformatics and biological approach. Computational analyses based on transcriptional co-expression and co-response pattern revealed at least two expression networks, suggesting that functional redundancy may exist among subtilases with limited similarity. Furthermore, two hubs were identified, which may be involved in signalling or may represent higher-order regulatory factors involved in responses to environmental cues. A particular enrichment of co-regulated genes with metabolic functions was observed for four subtilases possibly representing late responsive elements of environmental stress. The kexin homologs show stronger associations with genes of transcriptional regulation context. Based on the analyses presented here and in accordance with previously characterized subtilases, we propose three main functions of subtilases: involvement in (i) control of development, (ii) protein turnover, and (iii) action as downstream components of signalling cascades. Supplemental material is available in the Plant Subtilase Database (PSDB) (http://csbdb.mpimp-golm.mpg.de/psdb.html), as well as from the CSB.DB (http://csbdb.mpimp-golm.mpg.de).

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Language(s): eng - English
 Dates: 2005-09-302005
 Publication Status: Published in print
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Title: PLoS Computational Biology
Source Genre: Journal
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Publ. Info: San Francisco, CA : Public Library of Science
Pages: - Volume / Issue: 1 (4) Sequence Number: - Start / End Page: e40 Identifier: ISSN: 1553-734X
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000017180_1