A bioinformatics approach to identifying tail-anchored proteins in the human genome

Intracellular proteins with a carboxy-terminal transmembrane domain and the amino-terminus oriented toward the cytosol are known as 'tail-anchored' proteins. Tail-anchored proteins have been of considerable interest because several important classes of proteins, including the vesicle-targeting/fusion proteins known as SNAREs and the apoptosis-related proteins of the Bcl-2 family, among others, utilize this unique membrane-anchoring motif. Here, we use a bioinformatic technique to develop a comprehensive list of potentially tail-anchored proteins in the human genome. Our final list contains 411 entries derived from 325 unique genes. We also analyzed both known and predicted tail-anchored proteins with respect to the amino acid composition of the transmembrane segments. This analysis revealed a distinctive composition of the membrane anchor in SNARE proteins.     

糖尿病伤口愈合的分子机制

伤口愈合不良是糖尿病的一个并发症,严重时可能导致截肢,已成为糖尿病患者住院率最高的疾病,但是其确切的分子机制尚不清楚。目前研究发现糖尿病发生时有多种分子和细胞功能受损,如生长因子、一氧化氮、活性氧分子、基质金属蛋白酶、m icroRNA、内皮祖细胞等,最终导致糖尿病伤口愈合不良。本文将就其近年研究的相关分子机制予以详述。     

Mutational neighbourhood and mutation supply rate constrain adaptation in Pseudomonas aeruginosa

Understanding adaptation by natural selection requires understanding the genetic factors that determine which beneficial mutations are available for selection. Here, using experimental evolution of rifampicin-resistant Pseudomonas aeruginosa, we show that different genotypes vary in their capacity for adaptation to the cost of antibiotic resistance. We then use sequence data to show that the beneficial mutations associated with fitness recovery were specific to particular genetic backgrounds, suggesting that genotypes had access to different sets of beneficial mutations. When we manipulated the supply rate of beneficial mutations, by altering effective population size during evolution, we found that it constrained adaptation in some selection lines by restricting access to rare beneficial mutations, but that the effect varied among the genotypes in our experiment. These results suggest that mutational neighbourhood varies even among genotypes that differ by a single amino acid change, and this determines their capacity for adaptation as well as the influence of population biology processes that alter mutation supply rate.     

Bicyclic peptidomimetic tetrahydrofuro[3,2-b]pyrrol-3-one and hexahydrofuro[3,2-b]pyridine-3-one based scaffolds: synthesis and cysteinyl proteinase inhibition

A stereoselective synthesis of (3aS,6aR)-tetrahydrofuro[3,2-b]pyrrol-3-ones and (3aS,7aR)-hexahydrofuro[3,2-b]pyridine-3-ones has been developed through Fmoc protected scaffolds 12 and 13. A key design element within these novel bicyclic scaffolds, in particular the 5,5-fused system, was the inherent stability of the cis-fused geometry in comparison to that of the corresponding trans-fused. Since the bridgehead stereocentre situated beta to the ketone was of a fixed and stable configuration, the fact that cis ring fusion is both kinetically and thermodynamically stable with respect to trans ring fusion provides chiral stability to the bridgehead stereocentre that is situated alpha to the ketone. To exemplify this principle, building blocks 12 and 13 were designed, prepared and utilised in a solid phase combinatorial synthesis of peptidomimetic inhibitors 10, 45a-e, 11 and 46. Both series were chirally stable with 5,5-series 10 and 45a-e exhibiting potent in vitro activity against a range of CAC1 cysteinyl proteinases. Compound 10, a potent and selective inhibitor of cathepsin K, possessed good primary DMPK properties along with promising activity in an in vitro cell-based human osteoclast assay of bone resorption.     

Weak functional coupling of the melanocortin-1 receptor expressed in human adipocytes

The melanocortin (MC) receptor type-1 (MC1-R) is the only one of the five MC receptor subtypes expressed in human adipose tissue explants, human mesenchymal stem cells (MSCs), and MSC-derived adipocytes. Following our recent expression studies (Obesity 2007, 15, 40-49), we now investigated the functional role of MC1-R in these tissues and cells to deduce the coupling state of MC1-R to intracellular output signals in human fat cells and tissue. Expression of MC1-R by undifferentiated and differentiated MSCs was quantified by real-time TaqMan PCR. Intracellular output signals (cAMP, lipolysis, secretion of IL-6, IL-10, and TNF-alpha), as well as effects on the metabolic rate and proliferation of human MSCs were analyzed by standard assays, exposing undifferentiated and differentiated MSCs and, in part, human adipose tissue explants to the potent MC1-R agonist, [Nle(4), D-Phe(7)]-alpha-MSH (NDP-MSH). This agonist induced a weak cAMP signal in MSC-derived adipocytes. However, it did not affect lipolysis in these cells or in adipose tissue explants, nor did it modulate cytokine release and mRNA expression of IL-6, IL-8, and TNF-alpha upon LPS stimulation. In undifferentiated MSCs, NDP-MSH did not alter the metabolic rate, but it showed a significant antiproliferative effect. Therefore, it appears that MC1-R-effector coupling in (differentiated) human adipocytes is too weak to induce a regulatory effect on lipolysis or inflammation; by contrast, MC1-R stimulation in undifferentiated MSCs induces an inhibitory signal on cell proliferation.     

Interaction of Hsp90 with the nascent form of the mutant epidermal growth factor receptor EGFRvIII

EGFRvIII is a mutant epidermal growth factor that promotes aggressive growth of glioblastomas. We made a plasmid that directed the expression of an EGFRvIII with three copies of the Flag epitope at its amino terminus. Flag-tagged EGFRvIII was expressed at the same levels as unmodified EGFRvIII, and showed the same subcellular localization. However, the Flag epitope could only be detected on EGFRvIII present in the endoplasmic reticulum; the epitope was covalently modified during trafficking of the receptor through the Golgi so that it was no longer recognized by anti-Flag antibody. This property was exploited to selectively purify nascent EGFRvIII from glioblastoma cells. Nascent EGFRvIII was found to copurify with a set of other proteins, identified by mass spectrometry as the two endoplasmic reticulum chaperones Grp94 and BiP, and the two cytosolic chaperones Hsc70 and Hsp90. The Hsp90-associated chaperone Cdc37 also co-purified with EGFRvIII, suggesting that Hsp90 binds EGFRvIII as a complex with this protein. Geldanamycin and radicicol, two chemically unrelated inhibitors of Hsp90, decreased the expression of EGFRvIII in glioblastoma cells. These studies show that nascent EGFRvIII in the endoplasmic reticulum associates with Hsp90 and Cdc37, and that the Hsp90 association is necessary to maintain expression of EGFRvIII.     

Methane emissions reduce the radiative cooling effect of a subtropical estuarine mangrove wetland by half

The role of coastal mangrove wetlands in sequestering atmospheric carbon dioxide (CO₂) and mitigating climate change has received increasing attention in recent years. While recent studies have shown that methane (CH₄) emissions can potentially offset the carbon burial rates in low‐salinity coastal wetlands, there is hitherto a paucity of direct and year‐round measurements of ecosystem‐scale CH₄ flux (F_CH4) from mangrove ecosystems. In this study, we examined the temporal variations and biophysical drivers of ecosystem‐scale F_CH4 in a subtropical estuarine mangrove wetland based on 3 years of eddy covariance measurements. Our results showed that daily mangrove F_CH4 reached a peak of over 0.1 g CH₄‐C m^?2 day^?1 during the summertime owing to a combination of high temperature and low salinity, while the wintertime F_CH4 was negligible. In this mangrove, the mean annual CH₄ emission was 11.7 ± 0.4 g CH₄‐C m^–2 year^?1 while the annual net ecosystem CO₂ exchange ranged between ?891 and ?690 g CO₂‐C m^?2 year^?1, indicating a net cooling effect on climate over decadal to centurial timescales. Meanwhile, we showed that mangrove F_CH4 could offset the negative radiative forcing caused by CO₂ uptake by 52% and 24% over a time horizon of 20 and 100 years, respectively, based on the corresponding sustained‐flux global warming potentials. Moreover, we found that 87% and 69% of the total variance of daily F_CH4 could be explained by the random forest machine learning algorithm and traditional linear regression model, respectively, with soil temperature and salinity being the most dominant controls. This study was the first of its kind to characterize ecosystem‐scale F_CH4 in a mangrove wetland with long‐term eddy covariance measurements. Our findings implied that future environmental changes such as climate warming and increasing river discharge might increase CH₄ emissions and hence reduce the net radiative cooling effect of estuarine mangrove forests.