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Proteomic analysis of Arabidopsis thaliana
Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

A complete proteome analysis of the chloroplast stroma, using 2D-PAGE, from spinach and Arabidopsis was performed. To improve the identification of proteins a computer program named SPECLUST was used. In SPECLUST, peak masses that are similar in many spots cluster together because they originate from the same protein with different locations on the gel. Within this program peaks in a cluster can be investigated in detail by peaks-in-common, and the unidentified masses that differ between spots in a cluster could be caused by protein modifications, which was analysed further by MS/MS.

The thylakoid is an internal membrane system in the chloroplast where protein complexes involved in photosynthesis are housed. Enclosed in the thylakoid membrane is the chloroplast lumen, with a proteome estimated to contain 80-200 different proteins. Because the chloroplast lumen is close to the photosynthesis machinery in the plant, one can expect that the lumen proteome will change depending on if the plant is dark or light adapted. DIGE analysis of lumen proteins found that 15 lumen proteins show increased relative abundance in light-adapted plants. In addition co-expression analysis of lumen protein genes suggests that the lumen protein genes are uniformly transcriptionally regulated, not only by light but in a general manner.

Plastocyanin is one of the proteins involved in the electron transfer in photosynthesis. Two homologous plastocyanin isoforms are encoded by the genes PETE1 and PETE2 in the nuclear genome of Arabidopsis, where PETE2 is the more abundant isoform. Knockout mutants of each of the plastocyanin isoforms shows that a 90% reduction of plastocyanin levels affects rates of photosynthesis and growth only slightly. A corresponding over-expression of plastocyanin in each of the two knockout mutants results in essentially wild-type photosynthetic performance. Reduced plastocyanin levels make the plant sensitive to Cu stress and therefore plastocyanin plays a major role as a Cu sink.

A by-product of photosynthesis is hydrogen peroxide, which may be harmful for the plant. The discovery that an abundant protein found in the chloroplast lumen, TL29, shared sequence homology to Ascorbate Peroxidase (APX) was therefore of interest. We have evidence that TL29 is not an APX protein; it lacks the heme-binding active site and shows no activity. TL29 is located in the grana region and is electrostaticaly attached to the thylakoid membrane. It has four isoforms, with different pIs, both in the native and denatured form. It has no interaction with ascorbate, when compared to raAPX1. TL29 has two cysteine residues and one of them seems to have redox-regulated function, proposing that it may interact with other proteins close to PSII.

Place, publisher, year, edition, pages
Umeå: Kemi , 2008. , p. 38
Keywords [en]
Proteomic, speclust, post-translational modification, DIGE, plastocyanin, TL29, APX, thylakoid lumen, chloroplast stroma
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:umu:diva-1820ISBN: 978-91-7264-630-8 (print)OAI: oai:DiVA.org:umu-1820DiVA, id: diva2:142115
Public defence
2008-10-03, KB3B1 (stora hörsalen), KBChuset, Umeå Universitet, 901 87, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2008-09-12 Created: 2008-09-12 Last updated: 2011-12-21Bibliographically approved
List of papers
1. Clustering of MS spectra as a rationale to resolve protein variants by detecting modified peptides within clusters
Open this publication in new window or tab >>Clustering of MS spectra as a rationale to resolve protein variants by detecting modified peptides within clusters
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(English)Manuscript (preprint) (Other academic)
Identifiers
urn:nbn:se:umu:diva-3426 (URN)
Available from: 2008-09-12 Created: 2008-09-12 Last updated: 2022-03-17
2. Proteomic and transcriptomic analysis of the thylakoid lumen of Arabidopsis thaliana – light induced changes in protein expression and uniform regulation of transcription
Open this publication in new window or tab >>Proteomic and transcriptomic analysis of the thylakoid lumen of Arabidopsis thaliana – light induced changes in protein expression and uniform regulation of transcription
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Manuscript (Other academic)
Identifiers
urn:nbn:se:umu:diva-3427 (URN)
Available from: 2008-09-12 Created: 2008-09-12 Last updated: 2010-01-13Bibliographically approved
3. Mutants, overexpressors, and interactors of Arabidopsis Plastocyanin Isoforms: Revised roles of Plastocyanin in photosynthetic electron flow and Thylakoid redox state
Open this publication in new window or tab >>Mutants, overexpressors, and interactors of Arabidopsis Plastocyanin Isoforms: Revised roles of Plastocyanin in photosynthetic electron flow and Thylakoid redox state
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2009 (English)In: Molecular Plant, ISSN 1674-2052, EISSN 1752-9867, Vol. 2, no 2, p. 236-248Article in journal (Refereed) Published
Abstract [en]

Two homologous plastocyanin isoforms are encoded by the genes PETE1 and PETE2 in the nuclear genome of Arabidopsis thaliana. The PETE2 transcript is expressed at considerably higher levels and the PETE2 protein is the more abundant isoform. Null mutations in the PETE genes resulted in plants, designated pete1 and pete2, with decreased plastocyanin contents. However, despite reducing plastocyanin levels by over 90%, a pete2 null mutation on its own affects rates of photosynthesis and growth only slightly, whereas pete1 knockout plants, with about 60-80% of the wild-type plastocyanin level, did not show any alteration. Hence, plastocyanin concentration is not limiting for photosynthetic electron flow under optimal growth conditions, perhaps implying other possible physiological roles for the protein. Indeed, plastocyanin has been proposed previously to cooperate with cytochrome c6A (Cyt c6A) in thylakoid redox reactions, but we find no evidence for a physical interaction between the two proteins, using interaction assays in yeast. We observed homodimerization of Cyt c6A in yeast interaction assays, but also Cyt c6A homodimers failed to interact with plastocyanin. Moreover, phenotypic analysis of atc6-1 pete1 and atc6-1 pete2 double mutants, each lacking Cyt c6A and one of the two plastocyanin-encoding genes, failed to reveal any genetic interaction. Overexpression of either PETE1 or PETE2 in the pete1 pete2 double knockout mutant background results in essentially wild-type photosynthetic performance, excluding the possibility that the two plastocyanin isoforms could have distinct functions in thylakoid electron flow.

Place, publisher, year, edition, pages
Oxford University Press, 2009
National Category
Biological Sciences
Identifiers
urn:nbn:se:umu:diva-11109 (URN)10.1093/mp/ssn041 (DOI)2-s2.0-65249171514 (Scopus ID)
Available from: 2008-11-17 Created: 2008-11-17 Last updated: 2023-03-23Bibliographically approved
4. The TL29 Protein is a Redox Regulated Extrinsic Protein of Photosystem II and not an Ascorbate Peroxidase
Open this publication in new window or tab >>The TL29 Protein is a Redox Regulated Extrinsic Protein of Photosystem II and not an Ascorbate Peroxidase
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(English)Manuscript (preprint) (Other academic)
Identifiers
urn:nbn:se:umu:diva-3429 (URN)
Available from: 2008-09-12 Created: 2008-09-12 Last updated: 2022-06-28

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