Elastic membrane heterogeneity of living cells revealed by stiff nanoscale membrane domains

Many approaches have been developed to characterize the heterogeneity of membranes in living cells. In this study, the elastic properties of specific membrane domains in living cells are characterized by atomic force microscopy. Our data reveal the existence of heterogeneous nanometric scale domains with specific biophysical properties. We focused on glycosylphosphatidylinositol (GPI)-anchored proteins, which play an important role in membrane trafficking and cell signaling under both physiological and pathological conditions and which are known to partition preferentially into cholesterol-rich microdomains. We demonstrate that these GPI-anchored proteins reside within domains that are stiffer than the surrounding membrane. In contrast, membrane domains containing the transferrin receptor, which does not associate with cholesterol-rich regions, manifest no such feature. The heightened stiffness of GPI domains is consistent with existing data relating to the specific condensation of lipids and the slow diffusion rates of lipids and proteins therein. Our quantitative data may forge the way to unveiling the links that exist between membrane stiffness, molecular diffusion, and signaling activation.     

毛竹GRF转录因子家族的全基因组鉴定与分析

利用生物信息学方法,于毛竹(Phyllostachys edulis (Carr.) Lehaie)全基因组中鉴定获得18个GRF转录因子,并对其理化特性、保守结构域、系统发育关系、mi R396靶位点以及基因表达模式进行了分析。结果表明,18个Pe GRF蛋白长度为170～551 aa,分子量为18.5～58.8 k D;这些Pe GRF蛋白均具有QLQ和WRC结构域,部分Pe GRF含有FFD和TQL保守结构域。对毛竹、拟南芥(Arabidopsis thaliana (L.) Heynh)和水稻(Oryza sativa L.)的系统进化分析结果显示,毛竹18个GRF可分为3个亚类,且单子叶植物毛竹和水稻的GRF转录因子亲缘关系更近。mi R396靶位点预测分析结果发现,在13个Pe GRF基因序列的编码区存在毛竹mi R396结合位点; Pe GRF基因表达模式分析结果显示,Pe GRF主要在毛竹的竹笋中表达。     

Interactions via intrinsically disordered regions: what kind of motifs?

Proteins containing intrinsically disordered (ID) regions are widespread in eukaryotic organisms and are mostly utilized in regulatory processes. ID regions can mediate binary interactions of proteins or promote organization of large assemblies. Post-translational modifications of ID regions often serve as decision points in signaling pathways. Why Nature distinguished ID proteins in molecular recognition functions? In a simple view, binding of ID regions is accompanied by a large entropic penalty as compared to folded proteins. Even in complexes however, ID regions can preserve their conformational freedom, thereby recruit further partners and perform various functions. What sort of benefits ID regions offer for molecular interactions and which properties are exploited in the corresponding complexes? Here, we review models explaining the recognition mechanisms of ID proteins. Motif-based interactions are central to all proposed scenarios, including prestructured elements, anchoring sites and linear motifs. We aim to extract consensus features of the models, which could be used to predict ID-binding sites for a variety of partners.     

A decade and a half of protein intrinsic disorder: Biology still waits for physics

The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically “freeze” while their “pictures are taken.” However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs.     

转录调控因子WRKY 超级家族: 起源、结构和功能*

WRKY 蛋白质是一个植物特有的超级转录调控因子家族, 在拟南芥和水稻基因组中分别拥有至少74 个和97 个成员。最古老的WRKY 转录调控因子拥有2 个高度保守的WRKY 结构域, 可能起源于15~ 20 亿年前的真核生物。虽然所有WRKY 蛋白质主要通过特异地结合靶基因启动子区域的W 盒序列而调控其表达, 但各家族成员基因的生物学功能存在着各自的特异性。本文详细总结了WRKY 蛋白质在调控植物发育和逆境诱导反应的信号转导途径建立等方面的分子生物学功能。