First reference map for Phanerochaete chrysosporium proteome

Yıldırım, Volkan
In this study, the soluble protein fraction of P. chrysosporium grown under standard conditions was analyzed by using 2D-PAGE approach and a 2-D reference map was constructed. 910 spots could be separated and detected on Coomassie-stained 2-D gels by the help of Delta2D image analysis software. 720 spots could be cut from the master gel and were subjected to MALDI-TOF MS analysis followed by MASCOT search. A total of 517 spots out of 720 were assigned to specific accession numbers from the P. chrysosporium genome database. Further analysis of the data revealed 314 different gene products (distinct ORFs). The theoretical pI and MW values were plotted against the experimental migration distances. Results indicated the existence of 124 protein spots whose horizontal migration differed significantly from the expected migration according to the calculated pI values and 52 spots with an apparent molecular weight that is significantly different from their theoretical molecular weight. While protein modification could be predicted by these analyses, the main support was the presence of multiple spots of the same gene product. As much as 118 ORFs yielded multiple spots on the master gel, corresponding to 37.5% of the all distinct ORFs identified in this work. The relative abundance of each of the 517 identified polypeptides was calculated in terms of spot intensity. The majority of the most abundant proteins were found to be housekeeping ones. When the relative distribution of the proteins into four main functional categories was taken into consideration, أMetabolismؤ appeared the most important category with a share of 50.6% among identified proteins. However, among the functional classes, أPosttranslational modifications, protein turnover, chaperonesؤ which is listed under the main category أCellular Processing and Signallingؤ was represented by the highest number (104) of


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Pilavtepe, Mutlu; Alpas, Hami; Department of Food Engineering (2007)
The main objective of this study was to determine the pressure induced inactivation mechanism of pressure-resistant Escherichia coli O157:H7 933 and Staphylococcus aureus 485 in a low acid food. Firstly, inactivation curves of pathogens were obtained at 200 to 400 MPa at 40ºC in peptone water and carrot juice. First-order and Weibull models were fitted and Weibull model described the inactivation curves of both pathogens more accurately than first-order model, revealing that food systems could exhibit eithe...
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Pediococcus pentosaceus Pep1 is a vacuum-packaged Turkish sausage isolate which produces a potentially novel bacteriocin of the pediocin (anti-Listeria) family of peptides designated as pediocin P. Curing experiments and plasmid profile analysis indicated that both bacteriocin immunity and production determinants were linked and encoded by 9.0 MDa plasmid, pHD1.0. Attempts to transform purified plasmid pHD1.0 into recipient Escherichia coli JM109 cells by electroporation were successful but none of the E. c...
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Orman, Mehmet Ali; Çalık, Pınar; Department of Chemical Engineering (2007)
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Cephamycin C production by Streptomyces clavuligerus mutants impaired in regulation of aspartokinase
Zeyniyev, Araz; Özcengiz, Gülay; Department of Biotechnology (2006)
Aspartokinase is the first enzyme of the aspartate family amino acids biosynthetic pathway. Cephamycin C is a β-lactam antibiotic produced as a secondary metabolite via the enzymatic reactions in the lysine branch of this pathway in Streptomyces clavuligerus. The aspartokinase activity of S. clavuligerus is under concerted feedback inhibition by two of the end product amino acids, lysine plus threonine. It is also known that carbon flow through the lysine branch of the aspartate pathway is rate limiting ste...
Effects of warming and nutrients on the microbial food web in shallow lake mesocosms
Zingel, Priit; Cremona, Fabien; Noges, Tiina; Cao, Yu; Neif, Erika M.; Coppens, Jan; Iskin, Ugur; Lauridsen, Torben L.; Davidson, Thomas A.; Sondergaard, Martin; Beklioğlu, Meryem; Jeppesen, Erik (Elsevier BV, 2018-06-01)
We analysed changes in the abundance, biomass and cell size of the microbial food web community (bacteria, heterotrophic nanoflagellates, ciliates) at contrasting nutrient concentrations and temperatures during a simulated heat wave. We used 24 mesocosms mimicking shallow lakes in which two nutrient levels (unenriched and enriched by adding nitrogen and phosphorus) and three different temperature scenarios (ambient, IPCC A2 scenario and A2+%50) are simulated (4 replicates of each). Experiments using the mes...
Citation Formats
V. Yıldırım, “First reference map for Phanerochaete chrysosporium proteome,” M.S. - Master of Science, Middle East Technical University, 2006.