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The complexity of vesicle transport factors in plants examined by orthology search

Paul, Puneet; Simm, Stefan; Mirus, Oliver; Scharf, Klaus-Dieter...

PloS One 9 (5), e97745.
DOI: 10.1371/journal.pone.0097745


Open Access Peer Reviewed
 

Vesicle transport is a central process to ensure protein and lipid distribution in eukaryotic cells. The current knowledge on the molecular components and mechanisms of this process is majorly based on studies in Saccharomyces cerevisiae and Arabidopsis thaliana, which revealed 240 different proteinaceous factors either experimentally proven or predicted to be involved in vesicle transport. In here, we performed an orthologue search using two different algorithms to identify the components of the secretory pathway in yeast and 14 plant genomes by using the ’core-set’ of 240 factors as bait. We identified 4021 orthologues and (co-)orthologues in the discussed plant species accounting for components of COP-II, COP-I, Clathrin Coated Vesicles, Retromers and ESCRTs, Rab GTPases, Tethering factors and SNAREs. In plants, we observed a significantly higher number of (co-)orthologues than yeast, while only 8 tethering factors from yeast seem to be absent in the analyzed plant genomes. To link the identified (co-)orthologues to vesicle transport, the domain architecture of the proteins from yeast, genetic model plant A. thaliana and agriculturally relevant crop Solanum lycopersicum has been inspected. For the orthologous groups containing (co-)orthologues from yeast, A. thaliana and S. lycopersicum, we observed the same domain architecture for 79% (416/527) of the (co-)orthologues, which documents a very high conservation of this process. Further, publically available tissue-specific expression profiles for a subset of (co-)orthologues found in A. thaliana and S. lycopersicum suggest that some (co-)orthologues are involved in tissue-specific functions. Inspection of localization of the (co-)orthologues based on available proteome data or localization predictions lead to the assignment of plastid- as well as mitochondrial localized (co-)orthologues of vesicle transport factors and the relevance of this is discussed.

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Neuroscience and the Importance of a Neurobioethics: A Reflection upon Fritz Jahr

Giordano, J.; Benedikter, R.; Kohls, Niko (2013)

In A. Muzur & H. M. Sass (Eds.), Fritz Jahr and the Foundations of Global Bioethics - The Future of Integrative Bioethics (Vol. 37, pp. 267 - 280). Münster: Lit. Vol. 37, 267-280.


Spiritual Needs in Patients Suffering from Fibromyalgia

Offenbaecher, M.; Kohls, Niko; Toussaint, L.; Sigl, C.; Winkelmann, A.; Hieblinger, R....

Evidence-based Complementary and Alternative Medicine, 2013, 13. .


Peer Reviewed

Achtsamkeit und achtsamkeitsbasierte Interventionen

Kohls, Niko (2013)

In J. Galuska (Ed.), Bewusstsein: Grundlagen Anwendungen und Entwicklung (pp. 83 - 93). Berlin: MWV., 83-93.


3ENCULT Monument Information System: The “Raumbuch”-principle extended to energy issues

Haas, Franziska; Exner, Dagmar; Troi, Alexandra; Franzen, Christoph; Frey, Wolfgang (2013)

Proceedings of the 2013 Digital Heritage International Congress (DigitalHeritage), 781–781.
DOI: 10.1109/DigitalHeritage.2013.6743847


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Kontrakturprävention in der Langzeitpflege von Menschen im fortgeschrittenen Alter - Stand der Forschung und Bedeutung für die Praxis.

Herold-Majumdar, A.; Rieß, J.; Daubner, A.; Randzio, O; Kohls, Niko; Müller, M....

Gesundheit zwischen Wirtschaft und Demographie. Gemeinsamer Kongress der Deutschen Gesellschaft für Sozialmedizin und Prävention und der Deutschen Gesellschaft für Medizinische Soziologie, 19.9.2013, 358-359.


Peer Reviewed

Achtsamkeit in Organisationen: Vom Stressmanagement über das achtsame Interagieren und Führen zur bewussten Gestaltung von Veränderungsprozessen

Kohls, Niko; Berzlanovich, A.; Sauer, S. (2013)

In W. Kersten & J. Wittmann (Eds.), Kompetenz, Interdisziplinarität und Komplexität in der Betriebswirtschaftslehre (pp. 163-177). Wiesbaden: Springer , 163-177.


Optimierte Varianten- und Anforderungsabdeckung im Test

Cmyrev , A. ; Reißing, Ralf (2013)

Informatik 2013, 11. Workshop Automotive Software Engineering, September 2013, Koblenz. .


Peer Reviewed

Treatment with D3 Removes Amyloid Deposits, Reduces Inflammation, and Improves Cognition in Old AβPP/PS1 Double Transgenic Mice

van Groen, Thomas; Kadish, Inga; Funke, Susanne A.; Bartnik , Dirk ...

J Alzheimers Dis. 2013; 34(3): 609–620. , 34 | 609-620.
DOI: 10.3233/JAD-121792


Open Access Peer Reviewed
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Neuroethical address of neuroscience and technology to support and foster integration of complementary approaches within healthcare systems: A paradigmatic thesis

Hadley, T.; Kohls, Niko; Plischke , Herbert ; Giordano, J. (2013)

Int Neuroethics Soc Abstr..


Peer Reviewed

The Book – Finding Nazi Loot. Boston Review

Andert, K.; Kohls, Niko (2013)

07/08, 36 – 40., 36-40.


Contractures with special reference in elderly: definition and risk factors – a systematic review with practical implications

Offenbächer, M.; Sauer, S.; Rieß, J.; Müller, M.; Grill, E.; Daubner, A.; Randzio, O...

Disability and Rehabilitation, 36(7), 529-538., 529-538.


Peer Reviewed

Freiheitsentziehende Maßnahmen – Eine spezielle Form von Gewalt in der Pflege

Berzlanovich, A.; Kirsch, S.; Kohls, Niko (2013)

PflegeLeben, 1, 6 – 10..


Freiheit oder Sicherheit? – Verantwortungsvoller Umgang mit freiheitsentziehenden Maßnahmen in der Pflege

Berzlanovich, A.; Kirsch, S.; Kohls, Niko (2013)

Pflege in Bayern 2013; 26:8-10..


Human Adequate Lighting in Optimal Healing Environments – Measuring Non-visual Light Effects of a LED Light Source According to German Draft Pre-standard DIN SPEC 5031-100:2012, Berlin, Heidelberg.

Plischke , Herbert ; Schierz, C.; Paulick, P.; Kohls, Niko (2013)

Measuring Non-visual Light Effects of a LED Light Source According to German Draft Pre-standard DIN SPEC 5031-100:2012, Berlin, Heidelberg..


Neuroethical Address of Neuroscience and Technology to Support and Foster Integration of Complementary Approaches Within Healthcare Systems: A Paradigmatic Thesis; Abstr Intl Neuroethics Society; 2013.

Hadley, T.; Kohls, Niko; Plischke , Herbert ; Giordano, J. (2013)

A Paradigmatic Thesis; Abstr Intl Neuroethics Society; 2013.


Peer Reviewed

Die Rückgabe eines Buches des protestantischen Gelehrten Wilhelm Wundt aus dem Besitz des enteigneten jüdischen Apothekers Leopold Scheyer an seine Erben - Teil II.

Andert, K.; Kohls, Niko (2013)

Bibliotheksdienst, 47(5), 308 - 314.


Rasch-Analyse des Freiburger Fragebogens zur Achtsamkeit

Sauer, S.; Strobl, C.; Walach, H.; Kohls, Niko (2013)

Diagnostica, 59(2), 86-99..


Peer Reviewed

Exceptional experiences, mindfulness, spiritual practice, and mental distress

Kohls, Niko; Silver, C. F.; Hood, R. W.; Walach, H. (2013)

8th annual congress of the International Society for Complementary Medicine Research (ISCMR), London, 11-13.3.2013 .


Peer Reviewed

The protein translocation systems in plants - composition and variability on the example of Solanum lycopersicum

Paul, Puneet; Simm, Stefan; Blaumeiser, Andreas; Scharf, Klaus-Dieter...

BMC genomics 14, 189.
DOI: 10.1186/1471-2164-14-189


Open Access Peer Reviewed
 

BACKGROUND: Protein translocation across membranes is a central process in all cells. In the past decades the molecular composition of the translocation systems in the membranes of the endoplasmic reticulum, peroxisomes, mitochondria and chloroplasts have been established based on the analysis of model organisms. Today, these results have to be transferred to other plant species. We bioinformatically determined the inventory of putative translocation factors in tomato (Solanum lycopersicum) by orthologue search and domain architecture analyses. In addition, we investigated the diversity of such systems by comparing our findings to the model organisms Saccharomyces cerevisiae, Arabidopsis thaliana and 12 other plant species. RESULTS: The literature search end up in a total of 130 translocation components in yeast and A. thaliana, which are either experimentally confirmed or homologous to experimentally confirmed factors. From our bioinformatic analysis (PGAP and OrthoMCL), we identified (co-)orthologues in plants, which in combination yielded 148 and 143 orthologues in A. thaliana and S. lycopersicum, respectively. Interestingly, we traced 82% overlap in findings from both approaches though we did not find any orthologues for 27% of the factors by either procedure. In turn, 29% of the factors displayed the presence of more than one (co-)orthologue in tomato. Moreover, our analysis revealed that the genomic composition of the translocation machineries in the bryophyte Physcomitrella patens resemble more to higher plants than to single celled green algae. The monocots (Z. mays and O. sativa) follow more or less a similar conservation pattern for encoding the translocon components. In contrast, a diverse pattern was observed in different eudicots. CONCLUSIONS: The orthologue search shows in most cases a clear conservation of components of the translocation pathways/machineries. Only the Get-dependent integration of tail-anchored proteins seems to be distinct. Further, the complexity of the translocation pathway in terms of existing orthologues seems to vary among plant species. This might be the consequence of palaeoploidisation during evolution in plants; lineage specific whole genome duplications in Arabidopsis thaliana and triplications in Solanum lycopersicum.

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monika.schnabel[at]hs-coburg.de