RAB31 marks and controls an ESCRT-independent exosome pathway

Exosomes are generated within the multivesicular endosomes (MVEs) as intraluminal vesicles (ILVs) and secreted during the fusion of MVEs with the cell membrane. The mechanisms of exosome biogenesis remain poorly explored. Here we identify that RAB31 marks and controls an ESCRT-independent exosome pathway. Active RAB31, phosphorylated by epidermal growth factor receptor (EGFR), engages flotillin proteins in lipid raft microdomains to drive EGFR entry into MVEs to form ILVs, which is independent of the ESCRT (endosomal sorting complex required for transport) machinery. Active RAB31 interacts with the SPFH domain and drives ILV formation via the Flotillin domain of flotillin proteins. Meanwhile, RAB31 recruits GTPase-activating protein TBC1D2B to inactivate RAB7, thereby preventing the fusion of MVEs with lysosomes and enabling the secretion of ILVs as exosomes. These findings establish that RAB31 has dual functions in the biogenesis of exosomes: driving ILVs formation and suppressing MVEs degradation, providing an exquisite framework to better understand exosome biogenesis.Subject terms: Small GTPases, Endosomes, Multivesicular bodies, Lysosomes, ESCRT     

Tumor suppressor PALB2 maintains redox and mitochondrial homeostasis in the brain and cooperates with ATG7/autophagy to suppress neurodegeneration

The PALB2 tumor suppressor plays key roles in DNA repair and has been implicated in redox homeostasis. Autophagy maintains mitochondrial quality, mitigates oxidative stress and suppresses neurodegeneration. Here we show that Palb2 deletion in the mouse brain leads to mild motor deficits and that co-deletion of Palb2 with the essential autophagy gene Atg7 accelerates and exacerbates neurodegeneration induced by ATG7 loss. Palb2 deletion leads to elevated DNA damage, oxidative stress and mitochondrial markers, especially in Purkinje cells, and co-deletion of Palb2 and Atg7 results in accelerated Purkinje cell loss. Further analyses suggest that the accelerated Purkinje cell loss and severe neurodegeneration in the double deletion mice are due to excessive oxidative stress and mitochondrial dysfunction, rather than DNA damage, and partially dependent on p53 activity. Our studies uncover a role of PALB2 in mitochondrial homeostasis and a cooperation between PALB2 and ATG7/autophagy in maintaining redox and mitochondrial homeostasis essential for neuronal survival.     

枯草杆菌蛋白酶嗜热性改造单突变效果评判方法研究

对蛋白质进行嗜热性改造是蛋白质工程的主要问题之一,残基突变方法被广泛运用于其中。本文以枯草杆菌蛋白酶（SUBTILISIN BPN＇）为研究对象,旨在建立评判嗜热性改造效果的方法,选取了有可靠实验资料的9个突变点,运用分子动力学模拟方法,在四种不同模拟条件下,对其中的6个突变体和1个野生型蛋白进行了多种参量的对比分析,提取4个特征有效参量,建立了蛋白酶嗜热性改造单突变效果评判方法;利用该方法对其它3个突变效果进行评判,评判结果与实验资料完全吻合,证明该方法可用于枯草杆菌蛋白酶嗜热性改造单突变效果的评判。     

SCOP数据库蛋白质折叠类型的自动分类分析

蛋白质折叠规律研究是生命科学领域重要的前沿课题之一,蛋白质折叠类型分类是折叠规律研究的基础。本研究以SCOP数据库的蛋白质折叠类型分类为基础、以Astral SCOPe 2.05数据库中相似性小于40%的α、β、α+β及α/β类所属的折叠类型为研究对象,完成了989种蛋白质折叠类型的模板构建并形成模板数据库;基于折叠类型设计模板建立了蛋白质折叠类型分类方法,实现了SCOP数据库蛋白质折叠类型的自动化分类。家族模板自洽性检验与独立性检验所得的敏感性、特异性以及MCC的平均值分别为:95.00%、99.99%、0.94与90.00%、99.97%、0.92,折叠类型模板自洽性检验与独立性检验所得的敏感性、特异性以及MCC的平均值分别为:93.71%、99.97%、0.91与86.00%、99.93%、0.87。结果表明:模板设计合理,可有效用于对已知结构的蛋白质进行分类。     

基于设计模板的BRD-like折叠类型综合分类方法

蛋白质折叠规律研究是生命科学重大前沿课题,折叠类型分类是蛋白质折叠研究的基础。构建BRD-like折叠类型模板数据库,建立了基于多模板的综合分类方法,并用于该折叠类型的分类。对实验集的12 117个样本进行检验,结果的敏感性、特异性分别为0.923和0.997,MCC值为0.72;对独立检验集2 260个样本的检验,结果发现:敏感性、特异性分别为0.941和0.998,MCC值为0.86.结果表明:基于多模板的综合分类方法可用于蛋白质折叠类型分类。     

Phylogenetic analysis of the fecal flora of the wild pygmy loris

The bacterial diversity in fecal samples from the wild pygmy loris was examined with a 16S rDNA clone library and restriction fragment length polymorphism analysis. The clones were classified as Firmicutes (43.1%), Proteobacteria (34.5%), Actinobacteria (5.2%), and Bacteroidetes (17.2%). The 58 different kinds of 16S rDNA sequences were classified into 16 genera and 20 uncultured bacteria. According to phylogenetic analysis, the major genera within the Proteobacteria was Pseudomonas, comprising 13.79% of the analyzed clone sequences. Many of the isolated rDNA sequences did not correspond to known microorganisms, but had high homology to uncultured clones found in human feces. Am. J. Primatol. 72:699–706, 2010. © 2010 Wiley‐Liss, Inc.     

Comparison of pulmonary vascular response to endogenous nitric oxide inhibition in sheep and pigs living at 2,300 m

To compare the role of nitric oxide in an adaptive process to chronic hypoxia, we examined the effects of endogenous nitric oxide synthase inhibition on pulmonary vascular tone in conscious sheep and pigs living at high altitude. Unanesthetized male sheep (n=6) and pigs (n=5), born and residing in the highlands of Qinghai Province, China (2,300–3,000 m a.s.l.) were studied at that altitude. Pulmonary artery pressure (P_pa), pulmonary artery wedge pressure (P_cwp), and cardiac output (CO) were measured. Pulmonary vascular resistance (PVR) was calculated as (P_pa—P_cwp)/CO. Using a climatic chamber, hemodynamic measurements during exposures to atmospheric pressures corresponding to altitudes of 0, 2,300, and 4,500 m a.s.l. were performed with and without NO inhibition, using N^w-nitro-l-argine (NLA; 20 mg kg^–1), a potent stereospecific competitive inhibitor of nitric oxide synthase. P_pa and PVR at baseline (2,300 m) and during hypoxic exposure (4,500 m) were significantly higher in pigs than in sheep. After NLA administration, P_pa increased and CO decreased in both animals, resulting in significantly increased PVR at baseline and during hypoxic exposure. However, there were no significant differences in the percent increase in basal or hypoxic PVR after NLA administration between sheep and pigs. We conclude that augmented endogenous NO production could contribute to the regulation of pulmonary vascular tone at high altitude in sheep and pigs. However, it is unlikely that NO is responsible for the different pulmonary vascular tones between sheep and pigs at basal condition at moderately high altitude.Communicated by G. Heldmaier     

Casparian strips in needles of Pinus bungeana: isolation and chemical characterization

By using cell wall degrading enzymes, Casparian strips were for the first time isolated from Pinus bungeana needle endodermis. They appeared as a fine network, similar to those isolated from roots. Fourier transform infrared spectroscopic analysis provided evidence that the Casparian strips were impregnated with lignin, suberin, cellulose and cell wall proteins.     

The ATP binding cassette transporter A1 contributes to the secretion of interleukin 1beta from macrophages but not from monocytes

Deficiency of ABCA1 causes high density lipoprotein deficiency and macrophage foam cell formation in Tangier disease. ABCA1 was also postulated to mediate the secretion of IL-1beta from monocytes and macrophages. We investigated the contribution of ABCA1 to IL-1beta secretion from human monocytes and macrophages of normal donors and Tangier disease patients. Neither an anti-ABCA1 antisense oligonucleotide nor ABCA1 deficiency interfered with LPS-induced secretion of IL-1beta from full blood or freshly isolated monocytes. By contrast, anti-ABCA1 antisense oligonucleotides decreased the LPS-induced secretion of IL-beta from macrophages by 30-50%. The secretion of the precursor pro-IL-1beta and TNFalpha was not inhibited. Compared to normal macrophages, LPS-stimulated Tangier disease macrophages secreted less IL-1beta relative to TNFalpha. Also the spontaneous secretion of IL-1beta by Tangier macrophages was lower than by control cells. We conclude that IL-1beta is secreted from monocytes by an ABCA1-independent pathway and from macrophages by ABCA1-dependent and -independent pathways.     

Phosphorylation of 338SSYY341 regulates specific interaction between Raf-1 and MEK1

The present study characterizes the interaction between the Raf-1 kinase domain and MEK1 and examines whether the magnitude of their interaction correlates to the ability of Raf to phosphorylate MEK1. Here we show that the minimal domain required for the Raf kinase activity starts from tryptophan 342. Maximal binding of the Raf kinase domain to MEK1 and its kinase activity are achieved upon phosphorylation of the region (338)SSYY(341) in response to 4beta-12-O-tetradecanoylphorbol-13-acetate (TPA), or mutation of Y340Y341 to aspartic acids. Conversely, the TPA-stimulated MEK binding and kinase activity are diminished when this region is deleted or Ser(338) and Ser(339) are mutated to alanines. We also show that the integrity of the Raf ATP-binding site is necessary for the interaction between Raf-1 and MEK1. Furthermore, two MEK-binding sites are identified; the first is localized between amino acids 325 and 349, and the second is within the region between amino acids 350 and 648. Separately, the binding of each site to MEK1 is weak, but in a cis context, they give rise to a much stronger association, which can be further stimulated by TPA. Finally, we find that tryptophan 342, which is conserved among the Raf family and other protein kinases, is essential for the Ser(338) phosphorylation of the full-length Raf and its binding to MEK1. Taken together, our results indicate that the phosphorylation of Ser(338) and Tyr(341) on Raf exerts an important effect on reconfiguring the two MEK-binding sites. As a result, these two sites coordinate to form a high affinity MEK-binding epitope, leading to a marked increase in Raf kinase activity.