2012 Vol. 3, No. 12

The BK channel: a vital link between cellular calcium and electrical signaling
Brad S. Rothberg
2012, 3(12): 883-892. doi: 10.1007/s13238-012-2076-8
Large-conductance Ca2+-activated K+ channels (BK channels) constitute an key physiological link between cellular Ca2+ signaling and electrical signaling at the plasma membrane. Thus these channels are critical to the control of action potential firing and neurotransmitter release in several types of neurons, as well as the dynamic control of smooth muscle tone in resistance arteries, airway, and bladder. Recent advances in our understanding of K+ channel structure and function have led to new insight toward the molecular mechanisms of opening and closing (gating) of these channels. Here we will focus on mechanisms of BK channel gating by Ca2+, transmembrane voltage, and auxiliary subunit proteins.
A versatile building block: the structures and functions of negative-sense single-stranded RNA virus nucleocapsid proteins
Yuna Sun, Yu Guo, Zhiyong Lou
2012, 3(12): 893-902. doi: 10.1007/s13238-012-2087-5
Nucleocapsid protein (NPs) of negative-sense singlestranded RNA (-ssRNA) viruses function in different stages of viral replication, transcription, and maturation. Structural investigations show that -ssRNA viruses that encode NPs preliminarily serve as structural building blocks that encapsidate and protect the viral genomic RNA and mediate the interaction between genomic RNA and RNA-dependent RNA polymerase. However, recent structural results have revealed other biological functions of -ssRNA viruses that extend our understanding of the versatile roles of virally encoded NPs.
MCP-1-induced protein-1, an immune regulator
Jiwei Xu, Sheng Fu, Wei Peng, Zihe Rao
2012, 3(12): 903-910. doi: 10.1007/s13238-012-2075-9
MCP-1-induced protein-1 (MCPIP1) is a newly identified protein that is crucial to immune regulation. Mice lacking MCPIP1 gene suffer from severe immune disorders, and most of them cannot survive longer than 12 weeks. Considerable progress has been made in revealing the mechanism underlying the immune regulatory function of MCPIP1. MCPIP1 can act as an RNase to promote the mRNA degradation of some inflammatory cytokines, such as IL-6 and IL-1. Pre-microRNAs are also confirmed to be the substrate of MCPIP1 RNase. The structure of MCPIP1 N-terminal conserved domain shows a PilT N-terminus-like RNase structure, further supporting the notion that MCPIP1 has RNase activity. MCPIP1 can also deubiquitinate TNF receptor-associated factor family proteins, which are known to mediate immune and inflammatory responses. In this review, we summarize recent progress on the immune regulatory role of MCPIP1 and discuss the mechanisms underlying its function.
Intersection of autophagy with pathways of antigen presentation
Natalie L. Patterson, Justine D. Mintern
2012, 3(12): 911-920. doi: 10.1007/s13238-012-2097-3
Traditionally, macroautophagy (autophagy) is viewed as a pathway of cell survival. Autophagy ensures the elimination of damaged or unwanted cytosolic components and provides a source of cellular nutrients during periods of stress. Interestingly, autophagy can also directly intersect with, and impact, other major pathways of cellular function. Here, we will review the contribution of autophagy to pathways of antigen presentation. The autophagy machinery acts to modulate both MHCI and MHCⅡ antigen presentation. As such autophagy is an important participant in pathways that elicit host cell immunity and the elimination of infectious pathogens.
An effective system for detecting protein-protein interaction based on in vivo cleavage by PPV NIa protease
Nuoyan zheng, Xiahe Huang, Bojiao Yin, Dan Wang, Qi Xie
2012, 3(12): 921-928. doi: 10.1007/s13238-012-2101-y
Detection of protein-protein interaction can provide valuable information for investigating the biological function of proteins. The current methods that applied in protein-protein interaction, such as co-immunoprecipitation and pull down etc., often cause plenty of working time due to the burdensome cloning and purification procedures. Here we established a system that characterization of protein-protein interaction was accomplished by co-expression and simply purification of target proteins from one expression cassette within E. coli system. We modified pET vector into co-expression vector pInvivo which encoded PPV NIa protease, two cleavage site F and two multiple cloning sites that flanking cleavage sites. The target proteins (for example:protein A and protein B) were inserted at multiple cloning sites and translated into polyprotein in the order of MBP tag-protein A-site F-PPV NIa protease-site F-protein B-His6 tag. PPV NIa protease carried out intracellular cleavage along expression, then led to the separation of polyprotein components, therefore, the interaction between protein A-protein B can be detected through one-step purification and analysis. Negative control for protein B was brought into this system for monitoring interaction specificity. We successfully employed this system to prove two cases of reported protien-protein interaction:RHA2a/ANAC and FTA/FTB. In conclusion, a convenient and efficient system has been successfully developed for detecting protein-protein interaction.
SNObase, a database for S-nitrosation modification
Xu Zhang, Bo Huang, Lunfeng Zhang, Yuying Zhang, Yingying Zhao, Xiaofei Guo, Xinhua Qiao, Chang Chen
2012, 3(12): 929-933. doi: 10.1007/s13238-012-2094-6
S-Nitros(yl)ation is a ubiquitous redox-based posttranslational modification of protein cysteine thiols by nitric oxide or its derivatives, which transduces the bioactivity of nitric oxide (NO) by regulation of protein conformation, activity, stability, localization and protein-protein interactions. These years, more and more S-nitrosated proteins were identified in physiological and pathological processes and the number is still growing. Here we developed a database named SNObase (http://www.nitrosation.org), which collected S-nitrosation targets extracted from literatures up to June 1st, 2012. SNObase contained 2561 instances, and provided information about S-nitrosation targets, sites, biological model, related diseases, trends of S-nitrosation level and effects of S-nitrosation on protein function. With SNObase, we did functional analysis for all the SNO targets:In the gene ontology (GO) biological process category, some processes were discovered to be related to S-nitrosation ("response to drug", "regulation of cell motion") besides the previously reported related processes. In the GO cellular component category, cytosol and mitochondrion were both enriched. From the KEGG pathway enrichment results, we found SNO targets were enriched in different diseases, which suggests possible significant roles of S-nitrosation in the progress of these diseases. This SNObase means to be a database with precise, comprehensive and easily accessible information, an environment to help researchers integrate data with comparison and relevancy analysis between different groups or works, and also an SNO knowledgebase offering feasibility for systemic and global analysis of S-nitrosation in interdisciplinary studies.
Compound screening platform using human induced pluripotent stem cells to identify small molecules that promote chondrogenesis
Sheng-Lian Yang, Erica Harnish, Thomas Leeuw, Uwe Dietz, Erika Batchelder, Paul S. Wright, Jane Peppard, Paul August, Cecile Volle-Challier, Francoise Bono, Jean-Marc Herbert, Juan Carlos Izpisua Belmonte
2012, 3(12): 934-942. doi: 10.1007/s13238-012-2107-5
Articular cartilage, which is mainly composed of collagen Ⅱ, enables smooth skeletal movement. Degeneration of collagen Ⅱ can be caused by various events, such as injury, but degeneration especially increases over the course of normal aging. Unfortunately, the body does not fully repair itself from this type of degeneration, resulting in impaired movement. Microfracture, an articular cartilage repair surgical technique, has been commonly used in the clinic to induce the repair of tissue at damage sites. Mesenchymal stem cells (MSC) have also been used as cell therapy to repair degenerated cartilage. However, the therapeutic outcomes of all these techniques vary in different patients depending on their age, health, lesion size and the extent of damage to the cartilage. The repairing tissues either form fibrocartilage or go into a hypertrophic stage, both of which do not reproduce the equivalent functionality of endogenous hyaline cartilage. One of the reasons for this is inefficient chondrogenesis by endogenous and exogenous MSC. Drugs that promote chondrogenesis could be used to induce self-repair of damaged cartilage as a non-invasive approach alone, or combined with other techniques to greatly assist the therapeutic outcomes. The recent development of human induced pluripotent stem cell (iPSCs), which are able to self-renew and differentiate into multiple cell types, provides a potentially valuable cell resource for drug screening in a "more relevant" cell type. Here we report a screening platform using human iPSCs in a multi-well plate format to identify compounds that could promote chondrogenesis.
Expression of YB-1 enhances production of murine leukemia virus vectors by stabilizing genomic viral RNA
Wei Li, Xinlu Wang, Guangxia Gao
2012, 3(12): 943-949. doi: 10.1007/s13238-012-2090-x
Murine leukemia virus (MLV)-based retroviral vectors is widely used for gene transfer and basic research, and production of high-titer retroviral vectors is very important. Here we report that expression of the Y-box binding protein 1 (YB-1) enhanced the production of infectious MLV vectors. YB-1 specifically increased the stability of viral genomic RNA in virus-producing cells, and thus increasing viral RNA levels in both producer cells and virion particles. The viral element responsive to YB-1 was mapped to the repeat sequence (R region) in MLV genomic RNA. These results identified YB-1 as a MLV mRNA stabilizer, which can be used for improving production of MLV vectors.
Research articles
Structural basis of heparan sulfate-specific degradation by heparinase Ⅲ
Wei Dong, Weiqin Lu, Wallace L. McKeehan, Yongde Luo, Sheng Ye
2012, 3(12): 950-961. doi: 10.1007/s13238-012-2056-z
Heparinase Ⅲ (HepⅢ) is a 73-kDa polysaccharide lyase (PL) that degrades the heparan sulfate (HS) polysaccharides at sulfate-rare regions, which are important co-factors for a vast array of functional distinct proteins including the well-characterized antithrombin and the FGF/FGFR signal transduction system. It functions in cleaving metazoan heparan sulfate (HS) and providing carbon, nitrogen and sulfate sources for host microorganisms. It has long been used to deduce the structure of HS and heparin motifs; however, the structure of its own is unknown. Here we report the crystal structure of the HepⅢ from Bacteroides thetaiotaomicron at a resolution of 1.6 Å. The overall architecture of HepⅢ belongs to the (α/α)5 toroid subclass with an N-terminal toroid-like domain and a C-terminal β-sandwich domain. Analysis of this high-resolution structure allows us to identify a potential HS substrate binding site in a tunnel between the two domains. A tetrasaccharide substrate bound model suggests an elimination mechanism in the HS degradation. Asn260 and His464 neutralize the carboxylic group, whereas Tyr314 serves both as a general base in C-5 proton abstraction, and a general acid in a proton donation to reconstitute the terminal hydroxyl group, respectively. The structure of HepⅢ and the proposed reaction model provide a molecular basis for its potential practical utilization and the mechanism of its eliminative degradation for HS polysaccarides.