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The chloroplast lumen proteome of Arabidopsis thaliana
Södertörn University, School of Life Sciences. Karolinska Institutet.
2006 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In plants, the chloroplast organelles host the photosynthetic machinery, which catalyzes the conversion of light energy to chemical energy used for synthesis of carbohydrates. Inside the chloroplast, the lumen compartment forms an integral part of the thylakoid network that performs the light reactions of photosynthesis. Despite intensive research within the field of photosynthesis, the lumen located proteins were relatively unexplored. To get insight into the lumen proteins and their roles in photosynthesis this thesis aimed at characterising the chloroplast lumen proteome. A 2-dimensional protein map of the lumen proteome of Arabidopsis thaliana revealed a high protein content within this chloroplast compartment. Thirty-eight proteins were experimentally identified demonstrating that the chloroplast lumen contains it own specific proteome. Comparison of the Arabidopsis chloroplast lumen proteome with the spinach lumen proteome showed good correlation and demonstrated that Arabidopsis can serve as a model for characterising the lumen proteins. An in silico determination of the chloroplast lumen proteome from the Arabidopsis genome sequence data showed that the experimentally identified proteins are good representatives of the proteome. Combining the in silico proteome with the experimental proteome, the chloroplast lumen estimates to contain at least 80 different proteins. The putative ascorbate peroxidase TL29 detected in the thylakoid lumen was biochemically characterised. The protein associated to the PSII-enriched grana membrane fraction by electrostatic forces and accumulated upon high light illumination. Functional analysis showed that the TL29 protein is not a peroxidase but was able to bind ascorbate and may be involved in regulating the ascorbate levels in the chloroplast lumen. The dynamics of the lumen proteome were studied during the cold acclimation process. The lumen proteome was relatively insensitive to cold stress but important changes to the proteome were observed in the long-term developmental response to cold. These included changes in abundance of the different isoforms of the extrinsic PSII subunits, the PSII assembly factor Hcf136 and immunophilins. In comparison, the stroma proteome responded at an earlier stage in the acclimation process. Changes to the stroma proteome involved proteins related to photosynthesis, other plastid metabolism, hormone biosynthesis, and stress & signal transduction.

Place, publisher, year, edition, pages
Stockholm: Karolinska instiutet , 2006. , 55 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:sh:diva-31996ISBN: 91-7140-654-9 (print)OAI: oai:DiVA.org:sh-31996DiVA: diva2:1072799
Public defence
2006-05-24, MA648, Alfred Nobels allé 7, Huddinge, 10:00 (English)
Opponent
Supervisors
Available from: 2017-02-08 Created: 2017-02-08 Last updated: 2017-02-08Bibliographically approved
List of papers
1. A peroxidase homologue and novel plastocyanin located by proteomics to the Arabidopsis chloroplast thylakoid lumen
Open this publication in new window or tab >>A peroxidase homologue and novel plastocyanin located by proteomics to the Arabidopsis chloroplast thylakoid lumen
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2000 (English)In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 480, no 2-3, 271-276 p.Article in journal (Refereed) Published
Abstract [en]

A study by two-dimensional electrophoresis showed that the soluble, lumenal fraction of Arabidopsis thaliana thylakoids can be resolved into 300 protein spots. After subtraction of low-intensity spots and accounting for low-level stromal contamination, the number of more abundant, lumenal proteins was estimated to be between 30 and 60. Two of these proteins have been identified: a novel plastocyanin that also was the predominant component of the total plastocyanin pool, and a putative ascorbate peroxidase. Import studies shamed that these proteins are routed to the thylakoid lumen by the Sec- and delta pH-dependent translocation pathways, respectively, In addition, novel isoforms of PsbO and PsbQ were identified.

National Category
Biochemistry and Molecular Biology Cell Biology
Identifiers
urn:nbn:se:sh:diva-15738 (URN)10.1016/S0014-5793(00)01890-1 (DOI)000089209900041 ()11034343 (PubMedID)2-s2.0-0034284577 (Scopus ID)
Available from: 2012-03-07 Created: 2012-03-07 Last updated: 2017-02-08Bibliographically approved
2. Proteome map of the chloroplast lumen of Arabidopsis thaliana
Open this publication in new window or tab >>Proteome map of the chloroplast lumen of Arabidopsis thaliana
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2002 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 277, no 10, 8354-8365 p.Article in journal (Refereed) Published
Abstract [en]

The thylakoid membrane of the chloroplast is the center of oxygenic photosynthesis. To better understand the function of the luminal compartment within the thylakoid network, we have carried out a systematic characterization of the luminal thylakoid proteins from the model organism Arabidopsis thaliana. Our data show that the thylakoid lumen has its own specific proteome, of which 36 proteins were identified. Besides a large group of peptidyl-prolyl cis-trans isomerases and pro. teases, a family of novel PsbP domain proteins was found. An analysis of the luminal signal peptides showed that 19 of 36 luminal precursors were marked by a twin-arginine motif for import via the Tat pathway. To compare the model organism Arabidopsis with another typical higher plant, we investigated the proteome from the thylakoid lumen of spinach and found that the luminal proteins from both plants corresponded well. As a complement to our experimental investigation, we made a theoretical prediction of the luminal proteins from the whole Arabidopsis genome and estimated that the thylakoid lumen of the chloroplast contains similar to80 proteins.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-15812 (URN)10.1074/jbc.M108575200 (DOI)000174268000094 ()11719511 (PubMedID)2-s2.0-0037040944 (Scopus ID)
Available from: 2012-03-08 Created: 2012-03-07 Last updated: 2017-02-08Bibliographically approved
3. The TL29 protein a proposed ascorbate regulator in the thylakoid lumen of Arabidopsis thaliana
Open this publication in new window or tab >>The TL29 protein a proposed ascorbate regulator in the thylakoid lumen of Arabidopsis thaliana
(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-31995 (URN)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2017-02-08 Created: 2017-02-08 Last updated: 2017-02-08Bibliographically approved
4. The chloroplast lumen and stromal proteomes of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature
Open this publication in new window or tab >>The chloroplast lumen and stromal proteomes of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature
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2006 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 47, no 5, 720-734 p.Article in journal (Refereed) Published
Abstract [en]

Cold acclimation and over-wintering by herbaceous plants are energetically expensive and are dependent on functional plastid metabolism. To understand how the stroma and the lumen proteomes adapt to low temperatures, we have taken a proteomic approach (difference gel electrophoresis) to identify proteins that changed in abundance in Arabidopsis chloroplasts during cold shock (1 day), and short- (10 days) and long-term (40 days) acclimation to 5 degrees C. We show that cold shock (1 day) results in minimal change in the plastid proteomes, while short-term (10 days) acclimation results in major changes in the stromal but few changes in the lumen proteome. Long-term acclimation (40 days) results in modulation of the proteomes of both compartments, with new proteins appearing in the lumen and further modulations in protein abundance occurring in the stroma. We identify 43 differentially displayed proteins that participate in photosynthesis, other plastid metabolic functions, hormone biosynthesis and stress sensing and signal transduction. These findings not only provide new insights into the cold response and acclimation of Arabidopsis, but also demonstrate the importance of studying changes in protein abundance within the relevant cellular compartment.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-14282 (URN)10.1111/j.1365-313X.2006.02821.x (DOI)000239700000006 ()16923014 (PubMedID)2-s2.0-33747046042 (Scopus ID)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2011-12-21 Created: 2011-12-20 Last updated: 2017-02-08Bibliographically approved

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