Metabolic coupling in the co-cultured fungal-yeast suite of Trametes ljubarskyi and Rhodotorula mucilaginosa leads to hypersecretion of laccase isozymes

Trametes ljubarskyi produces multiple laccase isozymes under various physicochemical conditions. During co-cultivation condition Rhodotorula mucilaginosa showed inter-specific interactions with T. ljubarskyi and hypersecretion of laccases; however, the underlying molecular mechanism is less-known. The analysis of proteomics data of co-cultivated cultures revealed the mechanism of metabolic coupling during fungal-yeast interactions. The results suggested high score GO terms related to stimulus-response, protein binding, membrane components, transport channels, oxidoreductases, and antioxidants. The SEM studies confirmed the cellular communication and their inter-specific interactions. This study allows us to deepen and refine our understanding of fungal-yeast symbiotic interaction; further, it also establishes a mutual relation by metabolic coupling for 10-fold higher laccase isozyme secretion (6532 U/ml). The purified laccase isozymes showed acidic pH optima (pH 3–4), higher thermo-stability (60 °C), and broad enzyme kinetics (K_m) values. Our study also provides an in-depth understanding of laccase isozymes and their potential to degrade synthetic dyes, which may help the fungi to survive in an adverse environment.     

The 20th anniversary of proteomics and some of its origins

The term “proteome” was first introduced into the scientific literature in July 1995. Almost 20 years ago attempts to characterize the “total protein complement able to be encoded by a given genome” only became possible due to privileged access to what were then the world's most complete sets of genomic data. Today, proteomics has become an important pillar in the fields of disease diagnosis and drug research and development, while also playing a critical role in the much larger field of Healthcare Analytics and Biomarker Discovery and Detection. It is important to note that this industry originated mostly from building blocks in analytical science that predated the term “proteomics” by many decades. However, proteomics, as a discipline, has allowed protein scientists to more favorably compete in the face of highly fashionable Big Science and, more specifically, genomics.     

Proteome profile of functional mitochondria from human skeletal muscle using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS

Mitochondria can be isolated from skeletal muscle in a manner that preserves tightly coupled bioenergetic function in vitro. The purpose of this study was to characterize the composition of such preparations using a proteomics approach. Mitochondria isolated from human vastus lateralis biopsies were functional as evidenced by their response to carbohydrate and fat-derived fuels. Using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS, 823 unique proteins were detected, and 487 of these were assigned to the mitochondrion, including the newly characterized SIRT5, MitoNEET and RDH13. Proteins detected included 9 of the 13 mitochondrial DNA-encoded proteins and 86 of 104 electron transport chain (ETC) and ETC-related proteins. In addition, 59 of 78 proteins of the 55S mitoribosome, several TIM and TOM proteins and cell death proteins were present. This study presents an efficient method for future qualitative assessments of proteins from functional isolated mitochondria from small samples of healthy and diseased skeletal muscle.     

HUPO World Congress Publication Committee Meeting August 2008, Amsterdam,The Netherlands

The plenary session of the Publications Committee of the Human Proteome Organisation at the 7^th annual HUPO world congress examined the relationship between journals, proteomics standardization initiatives, such as the work of the HUPO‐PSI, and the public domain data repositories. Delegates from industry, academia and the publishing houses discussed how best to bring these bodies closer to together and facilitate the publication process for the bench scientist.     

Comparative studies of four protein preparation methods for proteomic study of the dinoflagellate Alexandrium sp. using two-dimensional electrophoresis

Alexandrium is a wide-spread genus of dinoflagellate causing harmful algal blooms and paralytic shellfish poisoning around the world. Proteomics has been introduced to the study of Alexandrium, but the protein preparation method is still unsatisfactory with respect to protein spot number, separation and resolution, and this has limited the application of a proteomic approach to the study of dinoflagellates. In this study we compared four protein preparation methods for the two-dimensional electrophoresis (2DE) analysis of A. tamarense: (1) urea/Triton X-100 buffer extraction with trichloroacetic acid (TCA)/acetone precipitation; (2) direct precipitation with TCA/acetone; (3) 40 mM Tris (hydroxymethyl) aminomethane (Tris) buffer extraction; and (4) 50 mM Tris/5% glycerol buffer extraction. The results showed that, among the four protein preparation methods, the method combining the urea/Triton X-100 buffer extraction and TCA/acetone precipitation allowed detection of the highest number and quality of protein spots with a clear background. Although the direct TCA/acetone precipitation method also detected a high number of protein spots with a clear background, the spot number, separation and intensity were not as good as those obtained from the urea/Triton X-100 buffer extraction with TCA/acetone precipitation method. The 40 mM Tris buffer and 50 mM Tris/5% glycerol buffer methods allowed the detection of fewer protein spots and a pH range only from 4 to 7. Subsequently, the urea/Triton X-100 buffer extraction with TCA/acetone precipitation method was successfully applied to profiling protein expression in A. catenella under light stress conditions and the differential expression proteins were identified using MALDI TOF–TOF mass spectrometry. The method developed here appears to be promising for further proteomic studies of this organism and related species.     

蛋白质组学的研究方法

近年来,蛋白质组学的研究在生物医学领域正逐步深入,研究方法也正逐步完善。本文综述了蛋白质组学的几种研究方法,指出了各种方法的优点及局限性,并且对蛋白质组学的研究方法和前景进行了展望。     

急性早幼粒细胞白血病维甲酸耐药性的双向电泳分析

目的:研究急性早幼粒细胞白血病(APL)对全反式维甲酸(ATRA)治疗敏感和耐药患者的外周血淋巴细胞在蛋白质组水平上的差异。方法:采用双向凝胶电泳(2-DE)对敏感和耐药患者的外周血淋巴细胞进行蛋白质组差异分析。结果:ATRA敏感和耐药患者外周血淋巴细胞的2-DE平均蛋白质点分别为(746±57)和(617±41),敏感与耐药患者的2-DE相比,有16个蛋白点表达明显上调,22个明显下调。另有4个蛋白点(Mr/pI:24.6kD/8.05,32.3kD/5.17,22.3kD/6.51,25.1kD/7.09)在敏感患者中特异表达,5个蛋白点(Mr/pI:21.9kD/5.45,23.4kD/6.27,22.9kD/6.65,23.9kD/7.39,24.7kD/7.65)在耐药患者中特异表达。结论:结果提示这些差异表达的蛋白质可能与APL对ATRA耐药的机制有关,该研究有助于揭示APL对ATRA耐药机理和发现新的临床分子标志物。