@article{Alings2014, abstract = {Chemical modifications of transfer RNA (tRNA) molecules are evolutionarily well conserved and critical for translation and tRNA structure. Little is known how these nucleoside modifications respond to physiological stress. Using mass spectrometry and complementary methods, we defined tRNA modification levels in six yeast species in response to elevated temperatures. We show that 2-thiolation of uridine at position 34 (s2U34) is impaired at temperatures exceeding 30°C in the commonly used Saccharomyces cerevisiae laboratory strains S288C and W303, and in Saccharomyces bayanus. Upon stress relief, thiolation levels recover and we find no evidence that modified tRNA or s2U34 nucleosides are actively removed. Our results suggest that loss of 2-thiolation follows accumulation of newly synthesized tRNA that lack s2U34 modification due to temperature sensitivity of the URM1 pathway in S. cerevisiae and S. bayanus. Furthermore, our analysis of the tRNA modification pattern in selected yeast species revealed two alternative phenotypes. Most strains moderately increase their tRNA modification levels in response to heat, possibly constituting a common adaptation to high temperatures. However, an overall reduction of nucleoside modifications was observed exclusively in S288C. This surprising finding emphasizes the importance of studies that utilize the power of evolutionary biology, and highlights the need for future systematic studies on tRNA modifications in additional model organisms.}, author = {Alings, Fiona and Sarin, L. Peter and Fufezan, Christian and Drexler, Hannes C. A. and Leidel, Sebastian A.}, doi = {10.1261/rna.048199.114}, journal = {RNA}, month = {dec}, pages = {202-212}, title = {An evolutionary approach uncovers a diverse response of tRNA 2-thiolation to elevated temperatures in yeast}, url = {http://rnajournal.cshlp.org/content/21/2/202.full.pdf}, volume = {21}, year = {2014} } @article{Bald2012, author = {Bald, Till and Barth, Johannes and Niehues, Anna and Specht, Michael and Hippler, Michael and Fufezan, Christian}, doi = {10.1093/bioinformatics/bts066}, journal = {Bioinformatics}, month = {feb}, pages = {1052-1053}, title = {PymzML-Python module for high-throughput bioinformatics on mass spectrometry data}, url = {https://academic.oup.com/bioinformatics/article-pdf/28/7/1052/552144/bts066.pdf}, volume = {28}, year = {2012} } @article{Barth2014, abstract = {Light and oxygen are factors that are very much entangled in the reactive oxygen species (ROS) stress response network in plants, algae and cyanobacteria. The first obligatory step in understanding the ROS network is to separate these responses. In this study, a LC-MS/MS based quantitative proteomic approach was used to dissect the responses of Chlamydomonas reinhardtii to ROS, light and oxygen employing an interlinked experimental setup. Application of novel bioinformatics tools allow high quality retention time alignment to be performed on all LC-MS/MS runs increasing confidence in protein quantification, overall sequence coverage and coverage of all treatments measured. Finally advanced hierarchical clustering yielded 30 communities of co-regulated proteins permitting separation of ROS related effects from pure light effects (induction and repression). A community termed redoxII was identified that shows additive effects of light and oxygen with light as the first obligatory step. Another community termed 4-down was identified that shows repression as an effect of light but only in the absence of oxygen indicating ROS regulation, for example, possibly via product feedback inhibition because no ROS damage is occurring. In summary the data demonstrate the importance of separating light, O2 and ROS responses to define marker genes for ROS responses. As revealed in this study, an excellent candidate is DHAR with strong ROS dependent induction profiles.}, author = {Barth, Johannes and Bergner, Sonja Verena and Jaeger, Daniel and Niehues, Anna and Schulze, Stefan and Scholz, Martin and Fufezan, Christian}, doi = {10.1074/mcp.m113.032771}, journal = {Molecular and Cellular Proteomics}, month = {jan}, pages = {969-989}, title = {The Interplay of Light and Oxygen in the Reactive Oxygen Stress Response of Chlamydomonas reinhardtii Dissected by Quantitative Mass Spectrometry*}, url = {http://www.mcponline.org/content/13/4/969.full.pdf}, volume = {13}, year = {2014} } @article{Bergner2015, abstract = {Abstract In plants and algae, the serine/threonine kinase STN7/STT7, orthologous protein kinases in Chlamydomonas reinhardtii and Arabidopsis (Arabidopsis thaliana), respectively, is an important regulator in acclimation to changing light environments. In this work, we assessed STT7-dependent protein phosphorylation under high light in C. reinhardtii, known to fully induce the expression of LIGHT-HARVESTING COMPLEX STRESS-RELATED PROTEIN3 (LHCSR3) and a nonphotochemical quenching mechanism, in relationship to anoxia where the activity of cyclic electron flow is stimulated. Our quantitative proteomics data revealed numerous unique STT7 protein substrates and STT7-dependent protein phosphorylation variations that were reliant on the environmental condition. These results indicate that STT7-dependent phosphorylation is modulated by the environment and point to an intricate chloroplast phosphorylation network responding in a highly sensitive and dynamic manner to environmental cues and alterations in kinase function. Functionally, the absence of the STT7 kinase triggered changes in protein expression and photoinhibition of photosystem I (PSI) and resulted in the remodeling of photosynthetic complexes. This remodeling initiated a pronounced association of LHCSR3 with PSI-LIGHT HARVESTING COMPLEX I (LHCI)-ferredoxin-NADPH oxidoreductase supercomplexes. Lack of STT7 kinase strongly diminished PSII-LHCII supercomplexes, while PSII core complex phosphorylation and accumulation were significantly enhanced. In conclusion, our study provides strong evidence that the regulation of protein phosphorylation is critical for driving successful acclimation to high light and anoxic growth environments and gives new insights into acclimation strategies to these environmental conditions.}, author = {Bergner, Sonja Verena and Scholz, Martin and Trompelt, Kerstin and Barth, Johannes and Gäbelein, Philipp and Steinbeck, Janina and Xue, Huidan and Clowez, Sophie and Fucile, Geoffrey and Goldschmidt-Clermont, Michel and Fufezan, Christian and Hippler, Michael}, doi = {10.1104/pp.15.00072}, journal = {Plant Physiology}, month = {apr}, pages = {615-634}, title = {STATE TRANSITION7-Dependent Phosphorylation Is Modulated by Changing Environmental Conditions, and Its Absence Triggers Remodeling of Photosynthetic Protein Complexes}, url = {http://www.plantphysiol.org/content/plantphysiol/168/2/615.full.pdf}, volume = {168}, year = {2015} } @article{Fufezan2009, author = {Fufezan, Christian and Specht, Michael}, doi = {10.1186/1471-2105-10-258}, journal = {BMC Bioinformatics}, month = {jan}, title = {p3d – Python module for structural bioinformatics}, url = {http://dx.doi.org/10.1186/1471-2105-10-258}, volume = {10}, year = {2009} } @article{Fufezan2010, abstract = {Nonbonding interactions are essential for protein stability and maintenance of secondary structure. Their strength, however, is not always experimentally accessible. One example is the stability of collagen, which is in part due to Buergi-Duntiz or n --> pi* interactions between the peptide backbone atoms [DeRider et al., J Am Chem Soc 2002;124:2497-2505]. Here, the overall frequency of n --> pi* interactions in proteins has been investigated. The analysis of a nonredundant set of protein structures showed that 45.1% of all residues have a backbone conformation favoring a n --> pi* nucleophilic attack between the carbonyl oxygen of residue i - 1 and the carbonyl carbon of residue i. These residues form a substantial fraction of right- and left-handed alpha helices, 3(10) helices, pi helices, and hydrogen bonded turns. Simulations showed that there are only four regions in Ramachandran space that favor backbone n(i-1) --> pi(i) (*) interactions and these Phi, Psi combinations are observed with high frequencies in the nonredundant protein structure set. Analysis of carbonyl carbon displacements out of the peptide plane in ultra-high resolution protein structures indeed reveals the presence of the Buergi-Dunitz trajectory. The Buergi-Dunitz interaction thus appears to play an important and general role in protein structure stability that has not hitherto been fully explored.}, author = {Fufezan, Christian}, doi = {10.1002/prot.22800}, journal = {Proteins: Structure, Function, and Bioinformatics}, month = {jun}, pages = {2831-2838}, title = {The role of Buergi-Dunitz interactions in the structural stability of proteins}, url = {https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fprot.22800}, volume = {78}, year = {2010} } @article{Fufezan2012, abstract = {Plants are often exposed to saturating light conditions, which can lead to oxidative stress. The carotenoid zeaxanthin, synthesized from violaxanthin by Violaxanthin De-Epoxidase (VDE) plays a major role in the protection from excess illumination. VDE activation is triggered by a pH reduction in the thylakoids lumen occurring under saturating light. In this work the mechanism of the VDE activation was investigated on a molecular level using multi conformer continuum electrostatic calculations, site directed mutagenesis and molecular dynamics. The pK(a) values of residues of the inactive VDE were determined to identify target residues that could be implicated in the activation. Five such target residues were investigated closer by site directed mutagenesis, whereas variants in four residues (D98, D117, H168 and D206) caused a reduction in enzymatic activity indicating a role in the activation of VDE while D86 mutants did not show any alteration. The analysis of the VDE sequence showed that the four putative activation residues are all conserved in plants but not in diatoms, explaining why VDE in these algae is already activated at higher pH. Molecular dynamics showed that the VDE structure was coherent at pH 7 with a low amount of water penetrating the hydrophobic barrel. Simulations carried out with the candidate residues locked into their protonated state showed instead an increased amount of water penetrating the barrel and the rupture of the H121-Y214 hydrogen bond at the end of the barrel, which is essential for VDE activation. These results suggest that VDE activation relies on a robust and redundant network, in which the four residues identified in this study play a major role.}, author = {Fufezan, Christian and Simionato, Diana and Morosinotto, Tomas}, doi = {10.1371/journal.pone.0035669}, journal = {PLoS ONE}, month = {apr}, pages = {e35669}, title = {Identification of Key Residues for pH Dependent Activation of Violaxanthin De-Epoxidase from Arabidopsis thaliana}, url = {http://dx.doi.org/10.1371/journal.pone.0035669}, volume = {7}, year = {2012} } @article{Hochmal2016, abstract = {AbstractCalcium (Ca2+) and redox signalling play important roles in acclimation processes from archaea to eukaryotic organisms. Herein we characterized a unique protein from Chlamydomonas reinhardtii that has the competence to integrate Ca2+- and redox-related signalling. This protein, designated as calredoxin (CRX), combines four Ca2+-binding EF-hands and a thioredoxin (TRX) domain. A crystal structure of CRX, at 1.6 Å resolution, revealed an unusual calmodulin-fold of the Ca2+-binding EF-hands, which is functionally linked via an inter-domain communication path with the enzymatically active TRX domain. CRX is chloroplast-localized and interacted with a chloroplast 2-Cys peroxiredoxin (PRX1). Ca2+-binding to CRX is critical for its TRX activity and for efficient binding and reduction of PRX1. Thereby, CRX represents a new class of Ca2+-dependent ‘sensor-responder’ proteins. Genetically engineered Chlamydomonas strains with strongly diminished amounts of CRX revealed altered photosynthetic electron transfer and were affected in oxidative stress response underpinning a function of CRX in stress acclimation.}, author = {Hochmal, Ana Karina and Zinzius, Karen and Charoenwattanasatien, Ratana and Gäbelein, Philipp and Mutoh, Risa and Tanaka, Hideaki and Schulze, Stefan and Liu, Gai and Scholz, Martin and Nordhues, André and Offenborn, Jan Niklas and Petroutsos, Dimitris and Finazzi, Giovanni and Fufezan, Christian and Huang, Kaiyao and Kurisu, Genji and Hippler, Michael}, doi = {10.1038/ncomms11847}, journal = {Nature Communications}, month = {jun}, title = {Calredoxin represents a novel type of calcium-dependent sensor-responder connected to redox regulation in the chloroplast}, url = {http://dx.doi.org/10.1038/ncomms11847}, volume = {7}, year = {2016} } @article{Höhner2013, abstract = {Iron is a crucial cofactor in numerous redox-active proteins operating in bioenergetic pathways including respiration and photosynthesis. Cellular iron management is essential to sustain sufficient energy production and minimize oxidative stress. To produce energy for cell growth, the green alga Chlamydomonas reinhardtii possesses the metabolic flexibility to use light and/or carbon sources such as acetate. To investigate the interplay between the iron-deficiency response and growth requirements under distinct trophic conditions, we took a quantitative proteomics approach coupled to innovative hierarchical clustering using different “distance-linkage combinations” and random noise injection. Protein co-expression analyses of the combined data sets revealed insights into cellular responses governing acclimation to iron deprivation and regulation associated with photosynthesis dependent growth. Photoautotrophic growth requirements as well as the iron deficiency induced specific metabolic enzymes and stress related proteins, and yet differences in the set of induced enzymes, proteases, and redox-related polypeptides were evident, implying the establishment of distinct response networks under the different conditions. Moreover, our data clearly support the notion that the iron deficiency response includes a hierarchy for iron allocation within organelles in C. reinhardtii. Importantly, deletion of a bifunctional alcohol and acetaldehyde dehydrogenase (ADH1), which is induced under low iron based on the proteomic data, attenuates the remodeling of the photosynthetic machinery in response to iron deficiency, and at the same time stimulates expression of stress-related proteins such as NDA2, LHCSR3, and PGRL1. This finding provides evidence that the coordinated regulation of bioenergetics pathways and iron deficiency response is sensitive to the cellular and chloroplast metabolic and/or redox status, consistent with systems approach data.}, author = {Höhner, Ricarda and Barth, Johannes and Magneschi, Leonardo and Jaeger, Daniel and Niehues, Anna and Bald, Till and Grossman, Arthur and Fufezan, Christian and Hippler, Michael}, doi = {10.1074/mcp.m113.029991}, journal = {Molecular and Cellular Proteomics}, month = {jul}, pages = {2774-2790}, title = {The Metabolic Status Drives Acclimation of Iron Deficiency Responses in Chlamydomonas reinhardtii as Revealed by Proteomics Based Hierarchical Clustering and Reverse Genetics*}, url = {https://doi.org/10.1074/mcp.m113.029991}, volume = {12}, year = {2013} } @article{Jaeger2013, author = {Jaeger, Daniel and Barth, Johannes and Niehues, Anna and Fufezan, Christian}, doi = {10.1093/bioinformatics/btt626}, journal = {Bioinformatics}, month = {oct}, pages = {896-898}, title = {PyGCluster, a novel hierarchical clustering approach}, url = {https://academic.oup.com/bioinformatics/article-pdf/30/6/896/17346028/btt626.pdf}, volume = {30}, year = {2013} } @article{Kuhlgert2012, author = {Kuhlgert, Sebastian and Drepper, Friedel and Fufezan, Christian and Sommer, Frederik and Hippler, Michael}, doi = {10.1021/bi300898j}, journal = {Biochemistry}, month = {aug}, pages = {7297-7303}, title = {Residues PsaB Asp612 and PsaB Glu613 of Photosystem I Confer pH-Dependent Binding of Plastocyanin and Cytochromec6}, url = {https://oadoi.org/10.1021/bi300898j}, volume = {51}, year = {2012} } @article{Kukuczka2014, abstract = {Abstract To investigate the functional importance of Proton Gradient Regulation5-Like1 (PGRL1) for photosynthetic performances in the moss Physcomitrella patens, we generated a pgrl1 knockout mutant. Functional analysis revealed diminished nonphotochemical quenching (NPQ) as well as decreased capacity for cyclic electron flow (CEF) in pgrl1. Under anoxia, where CEF is induced, quantitative proteomics evidenced severe down-regulation of photosystems but up-regulation of the chloroplast NADH dehydrogenase complex, plastocyanin, and Ca2+ sensors in the mutant, indicating that the absence of PGRL1 triggered a mechanism compensatory for diminished CEF. On the other hand, proteins required for NPQ, such as light-harvesting complex stress-related protein1 (LHCSR1), violaxanthin de-epoxidase, and PSII subunit S, remained stable. To further investigate the interrelation between CEF and NPQ, we generated a pgrl1 npq4 double mutant in the green alga Chlamydomonas reinhardtii lacking both PGRL1 and LHCSR3 expression. Phenotypic comparative analyses of this double mutant, together with the single knockout strains and with the P. patens pgrl1, demonstrated that PGRL1 is crucial for acclimation to high light and anoxia in both organisms. Moreover, the data generated for the C. reinhardtii double mutant clearly showed a complementary role of PGRL1 and LHCSR3 in managing high light stress response. We conclude that both proteins are needed for photoprotection and for survival under low oxygen, underpinning a tight link between CEF and NPQ in oxygenic photosynthesis. Given the complementarity of the energy-dependent component of NPQ (qE) and PGRL1-mediated CEF, we suggest that PGRL1 is a capacitor linked to the evolution of the PSII subunit S-dependent qE in terrestrial plants.}, author = {Kukuczka, Bernadeta and Magneschi, Leonardo and Petroutsos, Dimitris and Steinbeck, Janina and Bald, Till and Powikrowska, Marta and Fufezan, Christian and Finazzi, Giovanni and Hippler, Michael}, doi = {10.1104/pp.114.240648}, journal = {Plant Physiology}, month = {jun}, pages = {1604-1617}, title = {Proton Gradient Regulation5-Like1-Mediated Cyclic Electron Flow Is Crucial for Acclimation to Anoxia and Complementary to Nonphotochemical Quenching in Stress Adaptation.}, url = {http://www.plantphysiol.org/content/165/4/1604.full.pdf}, volume = {165}, year = {2014} } @article{Kösters2018, abstract = {Abstract Motivation In the new release of pymzML (v2.0), we have optimized the speed of this established tool for mass spectrometry data analysis to adapt to increasing amounts of data in mass spectrometry. Thus, we integrated faster libraries for numerical calculations, improved data retrieving algorithms and have optimized the source code. Importantly, to adapt to rapidly growing file sizes, we developed a generalizable compression scheme for very fast random access and applied this concept to mzML files to retrieve spectral data. Results pymzML performs at par with established C programs when it comes to processing times. However, it offers the versatility of a scripting language, while adding unprecedented fast random access to compressed files. Additionally, we designed our compression scheme in such a general way that it can be applied to any field where fast random access to large data blocks in compressed files is desired. Availability and implementation pymzML is freely available on https://github.com/pymzML/pymzML under GPL license. pymzML requires Python3.4+ and optionally numpy. Documentation available on http://pymzml.readthedocs.io. }, author = {Kösters, M. and Leufken, J. and Schulze, S. and Sugimoto, K. and Klein, J. and Zahedi, R. P. and Hippler, M. and Leidel, S. A. and Fufezan, C.}, doi = {10.1093/bioinformatics/bty046}, journal = {Bioinformatics}, month = {jan}, pages = {2513-2514}, title = {pymzML v2.0: introducing a highly compressed and seekable gzip format}, url = {https://oadoi.org/10.1093/bioinformatics/bty046}, volume = {34}, year = {2018} } @article{Mathieu-Rivet2013, abstract = {Chlamydomonas reinhardtii is a green unicellular eukaryotic model organism for studying relevant biological and biotechnological questions. The availability of genomic resources and the growing interest in C. reinhardtii as an emerging cell factory for the industrial production of biopharmaceuticals require an in-depth analysis of protein N-glycosylation in this organism. Accordingly, we used a comprehensive approach including genomic, glycomic, and glycoproteomic techniques to unravel the N-glycosylation pathway of C. reinhardtii. Using mass-spectrometry-based approaches, we found that both endogenous soluble and membrane-bound proteins carry predominantly oligomannosides ranging from Man-2 to Man-5. In addition, minor complex N-linked glycans were identified as being composed of partially 6-O-methylated Man-3 to Man-5 carrying one or two xylose residues. These findings were supported by results from a glycoproteomic approach that led to the identification of 86 glycoproteins. Here, a combination of in-source collision-induced dissodiation (CID) for glycan fragmentation followed by mass tag-triggered CID for peptide sequencing and PNGase F treatment of glycopeptides in the presence of (18)O-labeled water in conjunction with CID mass spectrometric analyses were employed. In conclusion, our data support the notion that the biosynthesis and maturation of N-linked glycans in the endoplasmic reticulum and Golgi apparatus occur via a GnT I-independent pathway yielding novel complex N-linked glycans that maturate differently from their counterparts in land plants.}, author = {Mathieu-Rivet, Elodie and Scholz, Martin and Arias, Carolina and Dardelle, Flavien and Schulze, Stefan and Le Mauff, François and Mauff, François Le and Teo, Gavin and Hochmal, Ana Karina and Blanco-Rivero, Amaya and Loutelier-Bourhis, Corinne and Kiefer-Meyer, Marie-Christine and Fufezan, Christian and Burel, Carole and Lerouge, Patrice and Martinez, Flor and Bardor, Muriel and Hippler, Michael}, doi = {10.1074/mcp.m113.028191}, journal = {Molecular and Cellular Proteomics}, month = {aug}, pages = {3160-3183}, title = {Exploring the N-glycosylation Pathway in Chlamydomonas reinhardtii Unravels Novel Complex Structures*}, url = {http://www.mcponline.org/content/12/11/3160.full.pdf}, volume = {12}, year = {2013} } @article{Negron2009, abstract = {Helical bundles which bind heme and porphyrin cofactors have been popular targets for cofactor-containing de novo protein design. By analyzing a highly nonredundant subset of the protein databank we have determined a rotamer distribution for helical histidines bound to heme cofactors. Analysis of the entire nonredundant database for helical sequence preferences near the ligand histidine demonstrated little preference for amino acid side chain identity, size, or charge. Analysis of the database subdivided by ligand histidine rotamer, however, reveals strong preferences in each case, and computational modeling illuminates the structural basis for some of these findings. The majority of the rotamer distribution matches that predicted by molecular simulation of a single porphyrin-bound histidine residue placed in the center of an all-alanine helix, and the deviations explain two prominent features of natural heme protein binding sites: heme distortion in the case of the cytochromes C in the m166 histidine rotamer, and a highly prevalent glycine residue in the t73 histidine rotamer. These preferences permit derivation of helical consensus sequence templates which predict optimal side chain-cofactor packing interactions for each rotamer. These findings thus promise to guide future design endeavors not only in the creation of higher affinity heme and porphyrin binding sites, but also in the direction of bound cofactor geometry.}, author = {Negron, Christopher and Fufezan, Christian and Koder, Ronald L.}, doi = {10.1002/prot.22143}, journal = {Proteins: Structure, Function, and Bioinformatics}, month = {feb}, pages = {400-416}, title = {Geometric Constraints for Porphyrin Binding in Helical Protein Binding Sites}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18636480}, volume = {74}, year = {2009} } @article{Perez-Riverol2016, abstract = {Bioinformatics is a broad discipline in which one common denominator is the need to produce and/or use software that can be applied to biological data in different contexts. To enable and ensure the replicability and traceability of scientific claims, it is essential that the scientific publication, the corresponding datasets, and the data analysis are made publicly available. All software used for the analysis should be either carefully documented (e.g., for commercial software) or, better yet, openly shared and directly accessible to others. The rise of openly available software and source code alongside concomitant collaborative development is facilitated by the existence of several code repository services such as SourceForge, Bitbucket, GitLab, and GitHub, among others. These resources are also essential for collaborative software projects because they enable the organization and sharing of programming tasks between different remote contributors. Here, we introduce the main features of GitHub, a popular webbased platform that offers a free and integrated environment for hosting the source code, documentation, and project-related web content for open-source projects. GitHub also offers paid plans for private repositories (see Box 1) for individuals and businesses as well as free plans including private repositories for research and educational use. ; Wellcome Trust (London, England) (Grant WT101477MA) ; Biotechnology and Biological Sciences Research Council (Great Britain) (Grants BB/K01997X/1, BB/I00095X/1, BB/L024225/1 and BB/L002817/1) ; Germany. Federal Ministry of Education and Research (Grant FKZ031 A 534A) ; National Institutes of Health (U.S.) (Grants R01-GM-094231 and R01-EB-017205 ) ; Engineering and Physical Sciences Research Council (Grant EP/M022641/1) ; National Science Foundation (U.S.) (Grant 1252893) ; Novo Nordisk Foundation}, author = {Perez-Riverol, Yasset and da Veiga Leprevost, Felipe and Gatto, Laurent and Wang, Rui and Sachsenberg, Timo and Uszkoreit, Julian and Leprevost, Felipe da Veiga and Fufezan, Christian and Ternent, Tobias and Eglen, Stephen J. and Katz, Daniel S. S. and Pollard, Tom Joseph and Konovalov, Alexander and Flight, Robert M. and Blin, Kai and Vizcaíno, Juan Antonio}, doi = {10.1371/journal.pcbi.1004947}, journal = {PLoS Computational Biology}, month = {apr}, pages = {e1004947}, title = {Ten Simple Rules for Taking Advantage of git and GitHub}, url = {https://doi.org/10.1371/journal.pcbi.1004947}, volume = {12}, year = {2016} } @article{Saga2010, abstract = {Plants are able to deal with variable environmental condi- tions; when exposed to strong illumination, they safely dissipate excess energy as heat and increase their capacity for scavenging reacting oxygen species. Both these protection mechanisms involve activation of the xanthophyll cycle, in which the carote- noid violaxanthin is converted to zeaxanthin by violaxanthin de-epoxidase, using ascorbate as the source of reducing power. In this work, following determination of the three-dimensional structure of the violaxanthin de-epoxidase catalytic domain, we identified the putative binding sites for violaxanthin and ascor- bate by in silico docking. Amino acid residues lying in close con- tact with the two substrates were analyzed for their involvement in the catalytic mechanism. Experimental results supported the proposed substrate-binding sites and point to two residues, Asp-177 and Tyr-198, which are suggested to participate in the catalytic mechanism, based on complete loss of activity in mutant proteins. The role of other residues and the mechanistic similarity to aspartic proteases and epoxide hydrolases are discussed.}, author = {Saga, Giorgia and Giorgetti, Alejandro and Fufezan, Christian and Giacometti, Giorgio M. and Bassi, Roberto and Morosinotto, Tomas}, doi = {10.1074/jbc.m110.115097}, journal = {Journal of Biological Chemistry}, month = {may}, pages = {23763-23770}, title = {Mutation Analysis of Violaxanthin De-epoxidase Identifies Substrate-binding Sites and Residues Involved in Catalysis*}, url = {http://www.jbc.org/content/285/31/23763.full.pdf}, volume = {285}, year = {2010} } @article{Schulze2014, abstract = {The scaffold protein Vac14 acts in a complex with the lipid kinase PIKfyve and its counteracting phosphatase FIG4, regulating the interconversion of phosphatidylinositol-3-phosphate (PI3P) to phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2). Dysfunctional Vac14 mutants, deficiency of one of the Vac14 complex components or inhibition of PIKfyve enzymatic activity result in the formation of large vacuoles in cells. How these vacuoles are generated and which processes are involved is only poorly understood. Here we show that ectopic overexpression of wildtype Vac14 as well as of the PIKfyve-binding deficient Vac14 L156R mutant causes vacuoles. Vac14-dependent vacuoles and PIKfyve inhibitor-dependent vacuoles resulted in elevated levels of late endosomal, lysosomal and autophagy-associated proteins. However, only late endosomal marker proteins are bound to the membrane of these enlarged vacuoles. To decipher the linkage between the Vac14 complex and regulators of the endolysosomal pathway, a protein affinity approach combined with the multidimensional protein identification technology (MudPIT) was conducted and unraveled novel molecular links. We found and verified the interaction of Rab9 and the Rab7 GAP TBC1D15 with Vac14. The identified Rab-related interaction partners support the theory that regulation of vesicular transport processes as well as phosphatidylinositol modifying enzymes are tightly interconnected.}, author = {Schulze, Ulf and Vollenbroeker, Beate and Vollenbröker, Beate and Braun, Daniela A. and Van Le, Truc and Granado, Daniel and Kremerskothen, Joachim and Fränzel, Benjamin and Fraenzel, Benjamin and Klosowski, Rafael Michael and Barth, Johannes and Fufezan, Christian and Wolters, Dirk A. and Pavenstaedt, Hermann and Pavenstadt, Hermann and Pavenstädt, Hermann and Weide, Thomas}, doi = {10.1074/mcp.m113.034108}, journal = {Molecular and Cellular Proteomics}, month = {feb}, pages = {1397-1411}, title = {The Vac14-interaction Network Is Linked to Regulators of the Endolysosomal and Autophagic Pathway*}, url = {https://doi.org/10.1074/mcp.m113.034108}, volume = {13}, year = {2014} } @article{Specht2011, abstract = {We present Proteomatic, an operating system independent and user-friendly platform that enables the construction and execution of MS/MS data evaluation pipelines using free and commercial software. Required external programs such as for peptide identification are downloaded automatically in the case of free software. Due to a strict separation of functionality and presentation, and support for multiple scripting languages, new processing steps can be added easily. Availability and Implementation: Proteomatic is implemented in C++/Qt, scripts are implemented in Ruby, Python and PHP. All source code is released under the LGPL. Source code and installers for Windows, Mac OS X, and Linux are freely available at http://www.proteomatic.org. CONTACT: michael.specht@uni-muenster.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, author = {Specht, Michael and Kuhlgert, Sebastian and Fufezan, Christian and Hippler, Michael}, doi = {10.1093/bioinformatics/btr081}, journal = {Bioinformatics}, month = {feb}, pages = {1183-1184}, title = {Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows}, url = {https://academic.oup.com/bioinformatics/article-pdf/27/8/1183/17101061/btr081.pdf}, volume = {27}, year = {2011} } @article{Terashima2012, abstract = { Cyclic photosynthetic electron flow (CEF) is crucial to photosynthesis because it participates in the control of chloroplast energy and redox metabolism, and it is particularly induced under adverse environmental conditions. Here we report that down-regulation of the chloroplast localized Ca 2+ sensor (CAS) protein by an RNAi approach in Chlamydomonas reinhardtii results in strong inhibition of CEF under anoxia. Importantly, this inhibition is rescued by an increase in the extracellular Ca 2+ concentration, inferring that CEF is Ca 2+ -dependent. Furthermore, we identified a protein, anaerobic response 1 (ANR1), that is also required for effective acclimation to anaerobiosis. Depletion of ANR1 by artificial microRNA expression mimics the CAS-depletion phenotype, and under anaerobic conditions the two proteins coexist within a large active photosystem I-cytochrome b 6 /f complex. Moreover, we provide evidence that CAS and ANR1 interact with each other as well as with PGR5-Like 1 (PGRL1) in vivo. Overall our data establish a Ca 2+ -dependent regulation of CEF via the combined function of ANR1, CAS, and PGRL1, associated with each other in a multiprotein complex. }, author = {Terashima, Mia and Petroutsos, Dimitris and Hüdig, Meike and Tolstygina, Irina and Trompelt, Kerstin and Gäbelein, Philipp and Fufezan, Christian and Kudla, Jörg and Weinl, Stefan and Finazzi, Giovanni and Hippler, Michael}, doi = {10.1073/pnas.1207118109}, journal = {Proceedings of the National Academy of Sciences}, month = {oct}, pages = {17717-17722}, title = {Calcium-dependent regulation of cyclic photosynthetic electron transfer by a CAS, ANR1, and PGRL1 complex}, url = {https://doi.org/10.1073/pnas.1207118109}, volume = {109}, year = {2012} }