TY - JOUR A1 - Schubert, Dieter A1 - Schluckebier, Gerd A1 - Backmann, Jan A1 - Granzien, Joachim A1 - Kisker, Caroline A1 - Choe, Hui-Woog A1 - Hahn, Ulrich A1 - Pfeil, Wolfgang A1 - Saenger, Wolfram T1 - X-ray crystallographic and calorimetric studies of the effects of the mutation Trp59Tyr in ribonuclease T1 Y1 - 1994 ER - TY - JOUR A1 - Kalimuthu, Palraj A1 - Leimkühler, Silke A1 - Bernhardt, Paul V. T1 - Xanthine dehydrogenase electrocatalysis autocatalysis and novel activity JF - The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces & biophysical chemistry N2 - The enzyme xanthine dehydrogenase (XDH) from the purple photosynthetic bacterium Rhodobacter capsulatus catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid as part of purine metabolism. The native electron acceptor is NAD(+) but herein we show that uric acid in its 2-electron oxidized form is able to act as an artificial electron acceptor from XDH in an electrochemically driven catalytic system. Hypoxanthine oxidation is also observed with the novel production of uric acid in a series of two consecutive 2-electron oxidation reactions via xanthine. XDH exhibits native activity in terms of its pH optimum and inhibition by allopurinol. Y1 - 2011 U6 - https://doi.org/10.1021/jp111809f SN - 1520-6106 VL - 115 IS - 11 SP - 2655 EP - 2662 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Pacholsky, Dirk A1 - Vakeel, Padmanabhan A1 - Himmel, Mirko A1 - Lowe, T. A1 - Stradal, T. A1 - Rottner, K. A1 - Fürst, Dieter Oswald A1 - vanderVen, Peter F. M. T1 - Xin repeats define a novel actin-binding motif N2 - Xin is a protein that is expressed during early developmental stages of cardiac and skeletal muscles. Immunolocalization studies indicated a peripheral localization in embryonic mouse heart, where Xin localizes with beta- catenin and N-cadherin. In adult tissues, Xin is found primarily in the intercalated discs of cardiomyocytes and the myotendinous junctions of skeletal muscle cells, both specialized attachment sites of the myofibrillar ends to the sarcolemma. A large part of the Xin protein consists of unique 16 amino acid repeats with unknown function. We have investigated the characteristics of the Xin repeats by transfection experiments and actin-binding assays and ascertained that, upon expression in cultured cells, these repeats bind to and stabilize the actin-based cytoskeleton. In vitro co- sedimentation assays with skeletal muscle actin indicated that they not only directly bind actin filaments, but also have the capability of arranging microfilaments into networks that sediment upon low-speed centrifugation. Very similar repeats were also found in Xin-repeat protein 2' (XIRP2), a novel protein that seems to be expressed mainly in striated muscles. Human XIRP2 contains 28 Xin repeats with properties identical to those of Xin. We conclude that the Xin repeats define a novel, repetitive actin-binding motif present in at least two different muscle proteins. These Xin- repeat proteins therefore constitute the first two members of a novel family of actin-binding proteins Y1 - 2004 SN - 0021-9533 ER - TY - JOUR A1 - Redelberger, David A1 - Seduk, Farida A1 - Genest, Olivier A1 - Mejean, Vincent A1 - Leimkühler, Silke A1 - Iobbi-Nivol, Chantal T1 - YcdY Protein of Escherichia coli, an Atypical Member of the TorD Chaperone Family JF - Journal of bacteriology N2 - The TorD family of specific chaperones is divided into four subfamilies dedicated to molybdoenzyme biogenesis and a fifth one, exemplified by YcdY of Escherichia coli, for which no defined partner has been identified so far. We propose that YcdY is the chaperone of YcdX, a zinc protein involved in the swarming motility process of E. coli, since YcdY interacts with YcdX and increases its activity in vitro. Y1 - 2011 U6 - https://doi.org/10.1128/JB.05927-11 SN - 0021-9193 VL - 193 IS - 23 SP - 6512 EP - 6516 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Albrecht, Tanja A1 - Haebel, Sophie A1 - Koch, Anke A1 - Krause, Ulrike A1 - Eckermann, Nora A1 - Steup, Martin T1 - Yeast glycogenin (Glg2p) produced in Escherichia coli is simultaneously glucosylated at two vicinal tyrosin residues but results in a reduced bacterial glycogen accumulation N2 - Saccharomyces cerevisiae possesses two glycogenin isoforms (designated as Glg1p and Glg2p) that both contain a conserved tyrosine residue, Tyr232. However, Glg2p possesses an additional tyrosine residue, Tyr230 and therefore two potential autoglucosylation sites. Glucosylation of Glg2p was studied using both matrix-assisted laser desorption ionization and electrospray quadrupole time of flight mass spectrometry. Glg2p, carrying a C-terminal (His(6)) tag, was produced in Escherichia coli and purified. By tryptic digestion and reversed phase chromatography a peptide (residues 219-246 of the complete Glg2p sequence) was isolated that contained 4-25 glucosyl residues. Following incubation of Glg2p with UDPglucose, more than 36 glucosyl residues were covalently bound to this peptide. Using a combination of cyanogen bromide cleavage of the protein backbone, enzymatic hydrolysis of glycosidic bonds and reversed phase chromatography, mono- and diglucosylated peptides having the sequence PNYGYQSSPAM were generated. MS/MS spectra revealed that glucosyl residues were attached to both Tyr232 and Tyr230 within the same peptide. The formation of the highly glucosylated eukaryotic Glg2p did not favour the bacterial glycogen accumulation. Under various experimental conditions Glg2p-producing cells accumulated approximately 30% less glycogen than a control transformed with a Glg2p lacking plasmid. The size distribution of the glycogen and extractable activities of several glycogen-related enzymes were essentially unchanged. As revealed by high performance anion exchange chromatography, the intracellular maltooligosaccharide pattern of the bacterial cells expressing the functional eukaryotic transgene was significantly altered. Thus, the eukaryotic glycogenin appears to be incompatible with the bacterial initiation of glycogen biosynthesis Y1 - 2004 ER - TY - JOUR A1 - Lilie, Hauke A1 - Bär, Dorit A1 - Kettner, Karina A1 - Weininger, Ulrich A1 - Balbach, Jochen A1 - Naumann, Manfred A1 - Müller, Eva-Christina A1 - Otto, Albrecht A1 - Gast, Klaus A1 - Golbik, Ralph T1 - Yeast hexokinase isoenzyme ScHxk2 : stability of a two-domain protein with discontinuous domains N2 - The hexokinase isoenzyme 2 of Saccharomyces cerevisiae (ScHxk2) represents an archetype of a two-domain protein with the active site located in a cleft between the two domains. Binding of the substrate glucose results in a rigid body movement of the two domains leading to a cleft closure of the active site. Both domains of this enzyme are composed of discontinuous peptide sequences. This structural feature is reflected in the stability and folding of the ScHxk2 protein. Structural transitions induced by urea treatment resulted in the population of a thermodynamically stable folding intermediate, which, however, does not correspond to a molecule with one domain folded and the other unfolded. As demonstrated by different spectroscopic techniques, both domains are structurally affected by the partial denaturation. The intermediate possesses only 40% of the native secondary structural content and a substantial increase in the Stokes radius as judged by circular dichroism and dynamic light scattering analyses. One-dimensional 1H NMR data prove that all tryptophan residues are in a non-native environment in the intermediate, indicating substantial changes in the tertiary structure. Still, the intermediate possesses quite a high stability for a transition intermediate of about ;G = ;22 kJ mol;1. Y1 - 2011 UR - http://peds.oxfordjournals.org/content/24/1-2/79.long SN - 0269-2139 ER - TY - JOUR A1 - Lilie, Hauke A1 - Baer, Dorit A1 - Kettner, Karina A1 - Weininger, Ulrich A1 - Balbach, Jochen A1 - Naumann, Manfred A1 - Mueller, Eva-Christina A1 - Otto, Albrecht A1 - Gast, Klaus A1 - Golbik, Ralph A1 - Kriegel, Thomas T1 - Yeast hexokinase isoenzyme ScHxk2 stability of a two-domain protein with discontinuous domains JF - Protein engineering design & selection N2 - The hexokinase isoenzyme 2 of Saccharomyces cerevisiae (ScHxk2) represents an archetype of a two-domain protein with the active site located in a cleft between the two domains. Binding of the substrate glucose results in a rigid body movement of the two domains leading to a cleft closure of the active site. Both domains of this enzyme are composed of discontinuous peptide sequences. This structural feature is reflected in the stability and folding of the ScHxk2 protein. Structural transitions induced by urea treatment resulted in the population of a thermodynamically stable folding intermediate, which, however, does not correspond to a molecule with one domain folded and the other unfolded. As demonstrated by different spectroscopic techniques, both domains are structurally affected by the partial denaturation. The intermediate possesses only 40% of the native secondary structural content and a substantial increase in the Stokes radius as judged by circular dichroism and dynamic light scattering analyses. One-dimensional H-1 NMR data prove that all tryptophan residues are in a non-native environment in the intermediate, indicating substantial changes in the tertiary structure. Still, the intermediate possesses quite a high stability for a transition intermediate of about Delta G = -22 kJ mol(-1). KW - dynamic light scattering KW - NMR KW - ScHxk2 KW - stability KW - transition intermediate Y1 - 2011 U6 - https://doi.org/10.1093/protein/gzq098 SN - 1741-0126 VL - 24 IS - 1-2 SP - 79 EP - 87 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Mirhaj, M. A1 - Boit, Alice A1 - Razzak, M. A. A1 - Wahab, M. A. T1 - Yield performance comparison between cultures of rice cum prawn (Macrobrachium rosenbergii) and rice cum fish (Cyprinus carpio, Oreochromis niloticus) in North-Eastern Bangladesh JF - Aquaculture : an international journal devoted to research on the exploration and improvement of all aquatic food resources, both floristic and faunistic, from freshwater, brackish and marine environment, related directly or indirectly to human consumption N2 - Integrated and concurrent cultures in rice fields are a promising approach to sustainable farming as the demand for aquacultural and agricultural products continues to grow while land and water resources become increasingly scarce. Prawn farming mainly takes place in coastal regions in improved extensive to semi-intensive aquacultures but a trend to shift the industry to inland regions has been noticed. This inland study in Northern Bangladesh used different input regimes such as fertilizer and additional feed to compare the performance of prawn and fish in flooded paddy fields in regard to water quality measurements. Maximal net yields and body weight gain with minimized negative impact on water quality were found when initial body weights of prawn were optimized. Regarding yield factors in reference to the reduction of costs due to the avoidance of expensive fertilizer/feed and effort, prawn performed better than integrated fish cultures considering a higher market value of prawn with net yields of up to 97 +/- 55 kg ha(-1) for unfed and 151 +/- 61 kg ha(-1) for fed treatments. Rice yields of up to 4.7 +/- 0.1 t ha(-1) for unfed and 4.4 +/- 0.1 t ha(-1) were achieved for fed treatments. The findings suggest that for small scale farmers, prawn cum rice cultures are an economically profitable and comparatively easily manageable alternative to rice cum fish cultures. KW - Rice cum prawn culture KW - Macrobrachium rosenbergii KW - Sustainable aquaculture KW - Polyculture Y1 - 2013 U6 - https://doi.org/10.1016/j.aquaculture.2013.01.038 SN - 0044-8486 VL - 392 IS - 5 SP - 26 EP - 33 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Cui, Xiao A1 - Lv, Yang A1 - Chen, Miaolin A1 - Nikoloski, Zoran A1 - Twell, David A1 - Zhang, Dabing T1 - Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome JF - Molecular plant N2 - The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betran et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis' hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and antimicrobial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator' for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male' model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens. KW - pollen KW - evolution KW - young genes KW - transcriptome Y1 - 2015 U6 - https://doi.org/10.1016/j.molp.2014.12.008 SN - 1674-2052 SN - 1752-9867 VL - 8 IS - 6 SP - 935 EP - 945 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Grönke, Ottokar A1 - Klepel, Gert T1 - Zelle, Einzeller, Vielzeller Y1 - 2000 SN - 3-06-010768-8 ER -