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The Role of Proteases in Plant Development
Umeå University, Faculty of Science and Technology, Chemistry.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution.

Systematic comparative analysis of the available sequenced genomes of two model organisms led to the identification of an increasing number of protease genes, giving insights about protein sequences that are conserved in the different species, and thus are likely to have common functions in them and the acquisition of new genes, elucidate issues concerning non-functionalization, neofunctionalization and subfunctionalization.

The involvement of proteases in senescence and PCD was investigated. While PCD in woody tissues shows the importance of vacuole proteases in the process, the senescence in leaves demonstrate to be a slower and more ordered mechanism starting in the chloroplast where the proteases there localized become important.

The light-harvesting complex of Photosystem II is very susceptible to protease attack during leaf senescence. We were able to show that a metallo-protease belonging to the FtsH family is involved on the process in vitro. Arabidopsis knockout mutants confirmed the function of FtsH6 in vivo.

Place, publisher, year, edition, pages
Umeå: Kemi , 2007. , 45 p.
Keyword [en]
Comparative genomics, protease, PCD, leaf senescence, FtsH, Arabidopsis, Populus
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:umu:diva-1386ISBN: 978-91-7264-422-9 (print)OAI: oai:DiVA.org:umu-1386DiVA: diva2:140837
Public defence
2007-10-26, KB3B1, KBC-huset, Linnaeus V. 6, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2007-10-05 Created: 2007-10-05 Last updated: 2009-09-08Bibliographically approved
List of papers
1. A genomic approach to investigate developmental cell death in woody tissues of Populus trees
Open this publication in new window or tab >>A genomic approach to investigate developmental cell death in woody tissues of Populus trees
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2005 (English)In: Genome Biology, ISSN 1465-6906, Vol. 6, no 4, R34:1-14 p.Article in journal (Refereed) Published
Abstract [en]

Background

Poplar (Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag (EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers.

Results

One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences.

Conclusions

In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers.

Identifiers
urn:nbn:se:umu:diva-13063 (URN)doi:10.1186/gb-2005-6-4-r34 (DOI)
Note
Även med namnet Courtois-Moreau, Charleen, Laetitia samt Moreau-Courtois, Charleen L.Available from: 2007-05-23 Created: 2007-05-23 Last updated: 2015-04-29Bibliographically approved
2. AtFtsH6 is involved in the degradation of the light-harvesting complex II during high-light acclimation and senescence
Open this publication in new window or tab >>AtFtsH6 is involved in the degradation of the light-harvesting complex II during high-light acclimation and senescence
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2005 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 1091-6490, Vol. 102, no 39, 13699-704 p.Article in journal (Refereed) Published
Abstract [en]

Degradation of the most abundant membrane protein on earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under various environmental conditions, e.g., light stress, to prevent photochemical damage to the reaction center. We identified the LHC II degrading protease in Arabidopsis thaliana as a Zn2+-dependent metalloprotease, activated by the removal of unknown extrinsic factors, similar to the proteolytic activity directed against Lhcb3 in barley. By using a reversed genetic approach, the chloroplast-targeted protease FtsH6 was identified as being responsible for the degradation. T-DNA KO A. thaliana mutants, lacking ftsH6, were unable to degrade either Lhcb3 during dark-induced senescence or Lhcb1 and Lhcb3 during highlight acclimation. The A. thaliana ftsH6 gene has a clear orthologue in the genome of Populus trichocarpa. It is likely that FtsH6 is a general LHC II protease and that FtsH6-dependent LHC II proteolysis is a feature of all higher plants.

Keyword
membrane protein, photosynthesis, protease
Identifiers
urn:nbn:se:umu:diva-13068 (URN)doi:10.1073/pnas.0503472102 (DOI)
Available from: 2008-03-31 Created: 2008-03-31 Last updated: 2015-04-29Bibliographically approved
3. Degradation of the main Photosystem II light-harvesting complex
Open this publication in new window or tab >>Degradation of the main Photosystem II light-harvesting complex
2005 (English)In: Photochemical and Photobiological Sciences, ISSN 1474-905X, Vol. 4, 1065-1071 p.Article in journal (Refereed) Published
Abstract [en]

Many factors trigger the degradation of proteins, including changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Despite the importance for viability, still very little is known about protein degradation and its regulation. The degradation of the most abundant membrane protein on Earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under different environmental conditions, e.g. light stress, to prevent photochemical damage of the reaction center. However, despite major effort to identify the protease/proteases involved in the degradation of the apoproteins of LHC II the molecular details of this important process remain obscure. LHC II belongs to the family of chlorophyll a/b binding proteins (CAB proteins) and is located in the thylakoid membrane of the plant chloroplast. The results of biochemical experiments to isolate and characterize the protease degrading LHC II are summarized here and compared to our own recent finding indicating that a metalloprotease of the FtsH family is involved in this process.

Identifiers
urn:nbn:se:umu:diva-14500 (URN)doi:10.1039/b506625e (DOI)
Available from: 2007-06-05 Created: 2007-06-05 Last updated: 2009-09-08Bibliographically approved
4. Protease gene families in Populus and Arabidopsis
Open this publication in new window or tab >>Protease gene families in Populus and Arabidopsis
2006 (English)In: BMC Plant Biology, ISSN 1471-2229, Vol. 6, no 30, 1-24 p.Article in journal (Refereed) Published
Abstract [en]

Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution. RESULTS: We have performed a comparative analysis of protease genes in the two sequenced dicot genomes, Arabidopsis thaliana and Populus trichocarpa by using genes coding for proteases in the MEROPS database 1 for Arabidopsis to identify homologous sequences in Populus. A multigene-based phylogenetic analysis was performed. Most protease families were found to be larger in Populus than in Arabidopsis, reflecting recent genome duplication. Detailed studies on e.g. the DegP, Clp, FtsH, Lon, rhomboid and papain-Like protease families showed the pattern of gene family expansion and gene loss was complex. We finally show that different Populus tissues express unique suites of protease genes and that the mRNA levels of different classes of proteases change along a developmental gradient. CONCLUSION: Recent gene family expansion and contractions have made the Arabidopsis and Populus complements of proteases different and this, together with expression patterns, gives indications about the roles of the individual gene products or groups of proteases.

Identifiers
urn:nbn:se:umu:diva-10870 (URN)doi:10.1186/1471-2229-6-30 (DOI)17181860 (PubMedID)
Available from: 2008-04-03 Created: 2008-04-03 Last updated: 2015-04-29Bibliographically approved
5. ATP-dependent proteases in the chloroplast
Open this publication in new window or tab >>ATP-dependent proteases in the chloroplast
2008 (English)In: ATP-dependent Proteases in the Plant Chloroplast / [ed] Eva Kutejová, Kerala, India: Research Signpost , 2008, 145-176 p.Chapter in book (Refereed)
Abstract [en]

Systematic comparative analysis of the available sequenced genomes of model organisms has led to the identification of an increasing number of protease genes. ATP-dependent proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated to several essential physiological pathways. FtsH-, Clp-, and Lon-like proteases, all derived from bacterial ancestors, also have been identified in the plant chloroplast, where they form multi-subunit complexes consisting of different gene products. Recent studies in model organisms like the annual plant Arabidopsis thaliana or the photosynthetic cyanobacterium Synechocystis sp. PCC 6803 have identified substrates and functions of these isomers. Although only a limited number of proteases has been identified by biochemical methods, novel protease homologous that are targeted to plastids have been predicted. This review covers the current knowledge on ATP-dependent proteases in the chloroplast.

Place, publisher, year, edition, pages
Kerala, India: Research Signpost, 2008
National Category
Chemical Sciences
Identifiers
urn:nbn:se:umu:diva-11494 (URN)978-81-308-0282-4 (ISBN)
Note
Introduction - ATP-dependent proteases constitute a unique proteolytic system. Although proteolysis is an exergonic process, these proteases require energy derived from ATP hydrolysis in order to function. This energy requirement is closely related to their structures and mechanisms of action. Their proteolytic active sites are usually sequestered in barrel-like structures that prevent uncontrolled proteolysis. These ring shaped proteolytic domains, or proteolytic sub-complexes, are connected to and cooperate with structurally similar ATPase domains or ATPase sub-complexes. Substrates bind to these ATPase domains or ATPase sub-complexes and the energy released by ATP hydrolysis is used to unfold and translocate the substrate into the proteolytic cavity and to activate the proteases themselves. ATP-dependent proteases are present in all prokaryotic and eukaryotic cells. In eukaryotic cells, they are localized in the cytosol and in the nucleus (proteasome) as well as in the organelles: mitochondria, chloroplasts and peroxisomes (Lon, Clp proteases, FtsH, HslUV). They are responsible for the degradation of damaged or misassembled proteins and of non-assembled protein subunits that might be harmful to the cells. ATP-dependent proteases also help control the concentration of several regulatory proteins. In prokaryotes, they are involved in stress response, pathogenicity, cell signaling and development. In eukaryotes, they are important for the proper functioning of organelles and for the immune and stress responses. Deficiencies in ATP-dependent proteases are connected with such severe disorders as dystrophies, neurodegenerative diseases and cancer and are thought to affect aging as well. ATP-dependent proteases are thus important for the biogenesis and homeostasis of living organisms. In this book, we focus on a particular group of ATP-dependent proteases (Lon, Clp proteases, FtsH and HslUV) that function in both prokaryotes and in the organelles of eukaryotes. We discuss the biological, biochemical, structural and evolutionary aspects of this important group of proteases. We do not describe the structure and function of the proteasomes, since they represent highly complex systems and would require a separate volume. We hope you enjoy reading our book!Available from: 2009-01-13 Created: 2009-01-13 Last updated: 2011-12-01Bibliographically approved

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