The ribosomal protein P0 of soybean (Glycine max L. Merr.) has antigenic cross-reactivity to soybean seed lectin

Soybean (Glycine max L. Merr.) mutants lacking the ability to produce the lectin normally found in soybean seeds (SBL) are designated Le-. A protein of higher molecular weight that cross-reacts with antibodies raised to SBL was found at nearly equivalent levels in roots, hypocotyls, and leaves, and at lower levels in cotyledons and dry seeds of both Le+ and Le- soybean cultivars. Earlier work suggested that this protein was a novel lectin. Clones isolated from a Le- soybean root cDNA library produced a cross-reacting protein of the same size in Escherichia coli. Sequence analysis of these clones revealed a high degree of similarity to the ribosomal protein P0. The cross-reacting protein co-purified with ribosomes, and a monoclonal antibody raised to purified brine shrimp P0 cross-reacted to the same protein. The protein showed no lectin activity in a hemagglutination assay, nor did it bind to an N-acetyl-D-galactosamine affinity column. On the basis of this evidence, we conclude that the SBL-cross-reacting protein is not a lectin but a homologue of the ribosomal protein P0. Consequently, Le- soybeans must produce a lectin that is dissimilar to SBL at both the DNA and amino acid levels and we suggest that it is this lectin which is involved in nodulation.     

Foreword: The structural biology of membrane proteins

Membrane protein-protein interactions are important for regulation, targeting, and activity of proteins in membranes but are difficult to detect and analyse. This review covers current approaches to studying membrane protein interactions. In addition to standard biochemical and genetic techniques, the classic yeast nuclear two-hybrid system has been highly successful in identification and characterization of soluble protein-protein interactions. However, classic yeast two-hybrid assays do not work for membrane proteins because such yeast-based interactions must occur in the nucleus. Here, we highlight recent advances in yeast systems for the detection and characterization of eukaryote membrane protein-protein interactions. We discuss these implications for drug screening and discovery.     

cDNA cloning and overexpression of acidic ribosomal phosphoprotein P1 gene (RPLP1) from the giant panda

RPLP1 is one of acidic ribosomal phosphoproteins encoded by RPLP1 gene, which plays an important role in the elongation step of protein synthesis. The cDNA of RPLP1 was cloned successfully for the first time from the Giant Panda (Ailuropoda melanoleuca) using RT-PCR technology, which was also sequenced, analyzed preliminarily and expressed in E.coli. The cDNA fragment cloned is 449bp in size, containing an open reading frame of 344bp encoding 114 amino acids. Alignment analysis indicated that the nucleotide sequence and the deduced amino acid sequence are highly conserved to other five species studied, including Homo sapiens, Mus musculus, Rattus norvegicus, Bos Taurus and Sus scrofa. The homologies for nucleotide sequences of Giant Panda PPLP1 to that of these species are 92.4%, 89.8%, 89.0%, 91.3% and 87.5%, while the homologies for amino acid sequences are 96.5%, 94.7%, 95.6%, 96.5% and 88.6%. Topology prediction showed there are three Casein kinase II phosphorylation sites and two N-myristoylation sites in the RPLP1 protein of the Giant Panda (Ailuropoda melanoleuca). The RPLP1 gene was overexpressed in E. coli and the result indicated that RPLP1 fusion with the N-terminally His-tagged form gave rise to the accumulation of an expected 18kDa polypeptide, which was in accordance with the predicted protein and could also be used to purify the protein and study its function.     

Identification of proteins that interact with a protein of interest: Applications of the yeast two-hybrid system

The yeast two-hybrid system is a molecular genetic test for protein interaction. Here we describe a step by step procedure to screen for proteins that interact with a protein of interest using the two-hybrid system. This process includes, construction and testing of the bait plasmid, screening a plasmid library for interacting fusion proteins, elimination of false positives and deletion analysis of true positives. This procedure is designed to allow investigators to identify proteins and their encoding cDNAs that have a biologically significant interaction with your protein of interest.     

Identification of TH1 as an interaction partner of A-Raf kinase

A-Raf is an important intermediate of the growth factor Ras-MAP kinase pathway. In a two-hybrid screen of human fetal liver cDNA library, TH1 was detected as a new interaction partner of A-Raf. TH1 is a highly conserved and widely expressed protein, which was recently cloned by Bonthron DT group. The binding between A-Raf and TH1 was specific, as no binding between TH1 and B-Raf or c-Raf was observed, and the amino-terminal 162 amino acids in the A-Raf regulatory domain were found to be sufficient for this interaction. This specific interaction may have played a critical role in the activation of A-Raf.     

沙眼衣原体CT-249基因编码蛋白为一包涵体膜蛋白

使用融合蛋白GST-CT249的抗体对假想蛋白CT249的特性进行研究。使用PCR方法从L2型沙眼衣原体的基因组中扩增编码CT249蛋白的开放读码区基因,限制性内切酶BamHⅠ和NotⅠ消化、T4连接酶连接导入pGEX-6p2载体,进一步把重组质粒pGEX-6p2-CT249转化到XL1-blue细菌,并诱导表达融合蛋白GST-CT249。在融合蛋白GST-CT249免疫小鼠制备抗体后,应用直接免疫荧光技术对衣原体感染细胞内的CT249基因表达的内源性蛋白进行初步定位。成功克隆出沙眼衣原体基因CT249,全长为351bp,并表达了融合蛋白GST-CT249,分子量为38.2kDa。制备了融合蛋白GST-CT249的抗体并初步定位假想蛋白CT249于沙眼衣原体包涵体膜蛋白上。总之,使用融合蛋白GST-CT249的抗体,鉴定假想蛋白CT249为一种新的沙眼衣原体包涵体膜蛋白。该发现将为进一步深入研究衣原体与宿主细胞间某些机制提供了有用的途径。     

Interaction map of the Trypanosoma cruzi ribosomal P protein complex (stalk) and the elongation factor 2

The large subunit of the eukaryotic ribosome possesses a long and protruding stalk formed by the ribosomal P proteins. This structure is involved in the translation step of protein synthesis through interaction with the elongation factor 2 (EF‐2). The Trypanosoma cruzi stalk complex is composed of four proteins of about 11 kDa, TcP1α, TcP1β, TcP2α, TcP2β and a fifth TcP0 of about 34 kDa. In a previous work, a yeast two‐hybrid (Y2H) protein–protein interaction map of T. cruzi ribosomal P proteins was generated. In order to gain new insight into the assembly of the stalk, a complete interaction map was generated by surface plasmon resonance (SPR) and the kinetics of each interaction was calculated. All previously detected interactions were confirmed and new interacting pairs were found, such as TcP1β–TcP2α and TcP1β–TcP2β. Moreover P2 but not P1 proteins were able to homo‐oligomerize. In addition, the region comprising amino acids 210–270 on TcP0 was identified as the region interacting with P1/P2 proteins, using Y2H and SPR. The interaction domains on TcP2β were also mapped by SPR identifying two distinct regions. The assembly order of the pentameric complex was assessed by SPR showing the existence of a hierarchy in the association of the different P proteins forming the stalk. Finally, the TcEF‐2 gene was identified, cloned, expressed and refolded. Using SPR analysis we showed that TcEF‐2 bound with similar affinity to the four P1/P2 ribosomal P proteins of T. cruzi but with reduced affinity to TcP0. Copyright © 2010 John Wiley & Sons, Ltd.     

Identification of novel putative-binding proteins for cellular prion protein and a specific interaction with the STIP1 homology and U-Box-containing protein 1

ABSTRACT

Prion diseases involve the conversion of the endogenous cellular prion protein, PrP^C, into a misfolded infectious isoform, PrP^Sc. Several functions have been attributed to PrP^C, and its role has also been investigated in the olfactory system. PrP^C is expressed in both the olfactory bulb (OB) and olfactory epithelium (OE) and the nasal cavity is an important route of transmission of diseases caused by prions. Moreover, Prnp^?/? mice showed impaired behavior in olfactory tests. Given the high PrP^C expression in OE and its putative role in olfaction, we screened a mouse OE cDNA library to identify novel PrP^C-binding partners. Ten different putative PrP^C ligands were identified, which were involved in functions such as cellular proliferation and apoptosis, cytoskeleton and vesicle transport, ubiquitination of proteins, stress response, and other physiological processes. In vitro binding assays confirmed the interaction of PrP^C with STIP1 homology and U-Box containing protein 1 (Stub1) and are reported here for the first time. Stub1 is a co-chaperone with ubiquitin E3-ligase activity, which is associated with neurodegenerative diseases characterized by protein misfolding and aggregation. Physiological and pathological implications of PrP^C-Stub1 interaction are under investigation. The PrP^C-binding proteins identified here are not exclusive to the OE, suggesting that these interactions may occur in other tissues and play general biological roles. These data corroborate the proposal that PrP^C is part of a multiprotein complex that modulates several cellular functions and provide a platform for further studies on the physiological and pathological roles of prion protein.     

神经元蛋白3.1结合蛋白的筛选与鉴定

哺乳动物肺组织发育的基本模式总体分为上皮分支的形态发生和分隔膜的形成两个部分．基因p311是克隆到的一个在分隔膜形成阶段特异表达的基因,可能在肺泡发育中起重要作用．为进一步探讨神经元蛋白3.1(P311)对肺发育过程的影响,构建了小鼠肺组织 cDNA文库,以融合Gal4 DNA结合结构域的重组P311蛋白为诱饵,利用酵母双杂交技术从文库中筛选P311结合蛋白．通过免疫共沉淀和双分子荧光互补等技术进一步验证, SPARC(secreted protein, acidic and rich in cysteine)被确定为P311 相互作用蛋白．进一步的研究发现,SPARC在肺组织中具有与P311相似的表达时序特征,双重免疫组织化学染色显示SPARC和P311在小鼠肺组织中共定位于肺泡上皮细胞和肌成纤维细胞中．提示P311可能通过与SPARC的相互作用影响肺泡发育．     

The unique N‐terminal insert in the ribosomal protein,phosphoprotein P0, of Tetrahymena thermophila: Bioinformatic evidence for an interaction with 26S rRNA

Phosphoprotein P0 (P0) is part of the stalk complex of the eukaryotic large ribosomal subunit necessary for recruiting elongation factors. While the P0 sequence is highly conserved, our group noted a 15–16 residue insert exclusive to the P0s of ciliated protists, including Tetrahymena thermophila. We hypothesized that this insert may have a function unique in ciliated protists, such as stalk regulation via phosphorylation of the insert. Almost no mention of this insert exists in the literature, and although the T. thermophila ribosome has been crystallized, there is limited structural data for Tetrahymena's P0 (TtP0) and its insert. To investigate the structure and function of the TtP0 insert, we performed in silico analyses. The TtP0 sequence was scanned with phosphorylation site prediction tools to detect the likelihood of phosphorylation in the insert. TtP0's sequence was also used to produce a homology model of the N‐terminal domain of TtP0, including the insert. When the insert was modeled in the context of the 26S rRNA, it associated with a region identified as expansion segment 7B (ES7B), suggesting a potential functional interaction between ES7B and the insert in T. thermophila. We were not able to obtain sufficient data to determine whether a similar relationship exists in other ciliated protists. This study lays the groundwork for future experimental studies to verify the presence of TtP0 insert/ES7 interactions in Tetrahymena, and to explore their functional significance during protein synthesis. Proteins 2015; 83:1078–1090. © 2015 Wiley Periodicals, Inc.     

小鼠P311蛋白与类赖氨酰氧化酶-1相互作用的鉴定

P311是利用抑制差减杂交技术从小鼠肺组织中筛选到的一个肺泡发育上游调节基因.它高水平表达于肺泡发育的相关阶段,而在慢性阻塞性肺病(chronic obstructive pulmonary disease,COPD)患者肺组织中表达水平大大下降.为深入探讨P311蛋白的作用机制,构建pGBKT7-P311诱饵表达载体,利用酵母双杂交技术,从小鼠肺组织cDNA文库中筛选出P311相互作用蛋白类赖氨酰氧化酶-1(lysyl oxidase-like 1,Loxl-1).并通过体内外免疫共沉淀及双分子荧光互补实验进行验证.为进一步研究P311蛋白的生物学功能提供新的思路。     

Binding of human ribosomal protein p40 and its truncated mutants to the small ribosomal subunit

Ribosomal protein SA (rpSA), or p40, is a structural element of the small subunit of the eukaryotic ribosome. The N-terminal and central parts of rpSA are homologous to prokaryotic S2, whereas its C-terminal part is specific to eukaryotes. Preparations of 40S ribosomal subunits isolated from full-term human placenta proved to be deficient in SA to a varying extent. To study the rpSA binding to human 40S subunits, recombinant rpSA and its mutant forms with N-and C-terminal deletions were synthesized. The full-size and N-truncated rpSA variants bound to 40S subunits, while deletion of the C-terminal domain completely abolished the binding.     

Design of improved membrane protein production experiments: quantitation of the host response

Eukaryotic membrane proteins cannot be produced in a reliable manner for structural analysis. Consequently, researchers still rely on trial-and-error approaches, which most often yield insufficient amounts. This means that membrane protein production is recognized by biologists as the primary bottleneck in contemporary structural genomics programs. Here, we describe a study to examine the reasons for successes and failures in recombinant membrane protein production in yeast, at the level of the host cell, by systematically quantifying cultures in high-performance bioreactors under tightly-defined growth regimes. Our data show that the most rapid growth conditions of those chosen are not the optimal production conditions. Furthermore, the growth phase at which the cells are harvested is critical: We show that it is crucial to grow cells under tightly-controlled conditions and to harvest them prior to glucose exhaustion, just before the diauxic shift. The differences in membrane protein yields that we observe under different culture conditions are not reflected in corresponding changes in mRNA levels of FPS1, but rather can be related to the differential expression of genes involved in membrane protein secretion and yeast cellular physiology.     

酵母双杂交筛选与GsCBRLK相互作用的蛋白质

GsCBRLK(calcium/calmodulin-binding receptor-like kinase from Glycine soja)在ABA及盐胁迫诱导的钙离子信号通路中起到关键的调节作用。为深入研究GsCBRLK蛋白的作用机制, 文章采用膜酵母双杂交系统, 以GsCBRLK为诱饵蛋白, 筛选与其相互作用的蛋白质。通过构建野生大豆盐胁迫条件下的cDNA文库、膜酵母双杂交系统筛选、复筛、回转验证、生物信息学分析以及酵母体内互作验证等手段, 最终获得2个(SNARE 和 14-3-3 蛋白)与GsCBRLK诱饵蛋白相互作用的蛋白质。