Two-dimensional mass spectra generated from the analysis of 15N-labeled and unlabeled peptides for efficient protein identification and de novo peptide sequencing

Protein identification has been greatly facilitated by database searches against protein sequences derived from product ion spectra of peptides. This approach is primarily based on the use of fragment ion mass information contained in a MS/MS spectrum. Unambiguous protein identification from a spectrum with low sequence coverage or poor spectral quality can be a major challenge. We present a two-dimensional (2D) mass spectrometric method in which the numbers of nitrogen atoms in the molecular ion and the fragment ions are used to provide additional discriminating power for much improved protein identification and de novo peptide sequencing. The nitrogen number is determined by analyzing the mass difference of corresponding peak pairs in overlaid spectra of (15)N-labeled and unlabeled peptides. These peptides are produced by enzymatic or chemical cleavage of proteins from cells grown in (15)N-enriched and normal media, respectively. It is demonstrated that, using 2D information, i.e., m/z and its associated nitrogen number, this method can, not only confirm protein identification results generated by MS/MS database searching, but also identify peptides that are not possible to identify by database searching alone. Examples are presented of analyzing Escherichia coli K12 extracts that yielded relatively poor MS/MS spectra, presumably from the digests of low abundance proteins, which can still give positive protein identification using this method. Additionally, this 2D MS method can facilitate spectral interpretation for de novo peptide sequencing and identification of posttranslational or other chemical modifications. We envision that this method should be particularly useful for proteome expression profiling of organelles or cells that can be grown in (15)N-enriched media.     

北祁连山东段早石炭世棘鱼类、辐鳍鱼类和软骨鱼类--北祁连山东段石炭纪鱼类序列研究之一

对甘肃靖远一带和内蒙古自治区黑山地区早石炭世前黑山组、臭牛沟组和靖远组中三亚纲鱼类微体化石进行了形态学和古组织学研究。这些化石涉及 7个目或亚目 ,含 4属 4种 ,其中有 2新种。文中记述的属均为全球广布的属。建立了 3个早石炭世鱼类组合 ,这是我国早石炭世第一个鱼类组合序列。辐鳍鱼类和软骨鱼类中 2个目的化石均为我国早石炭世鱼类的首次记录     

牛磺酸对失血性休克再灌注肺损伤的防护作用及其机制探讨

目的:探讨失血性休克再灌注肺损伤与一氧化氮的关系及牛磺酸对其的影响.方法:健康家兔24只随机分为三组:对照组、单纯休克组、牛磺酸治疗组.采用失血性休克再灌注后肺损伤模型.测定肺组织及血浆中一氧化氮合酶(NOS)活性、一氧化氮代谢产物(NO2-/NO3-)含量、超氧化物歧化酶(SOD)活性、丙二醛(MDA)含量、肺湿重/肺干重、肺水含量、肺通透指数(LPI)、肺泡灌洗液(PALF)中蛋白含量等指标的变化,并常规留取肺标本进行病理形态观察.结果:①再灌注3 h时肺组织及血浆中SOD活性显著下降,而上述其它指标均显著升高,与对照组相比差异有显著性(均P<0.01).②血浆、肺组织中NO2-/NO3-含量与MDA含量均呈正相关,且肺组织中NO2-/NO3-含量和肺损伤指标呈显著正相关.③牛磺酸(40 mg*kg-1,iv)可减轻上述指标的变化.结论:NO在休克再灌注肺损伤中起重要作用,牛磺酸可减少NO的生成、增强自由基的清除从而使肺组织损伤减轻.     

Soluble expression and characterization of a GFP-fused pea actin isoform（PEAc1）

A pea actin isoform PEAcl with green fluorescent protein (GFP) fusion to its C-terminus and His-tag to its Nterminus, was expressed in prokaryotic cells in soluble form, and highly purified with Ni-Chelating Sepharose^TM Fast Flow column. The purified fusion protein (PEAcl-GFP) efficiently inhibited DNase I activities before polymerization,and activated the myosin Mg-ATPase activities after polymerization. The PEAcl-GFP also polymerized into green fluorescent filamentous structures with a critical concentration of 0.75μM. These filamentous structures were labeled by TRITC-phalloidin, a specific agent for staining actin microfilaments, and identified as having 9 nm diameters by negative staining. These results indicated that PEAc 1 preserved the essential characteristics of actin even with His-tag and GFP fusion, suggesting a promising potential to use GFP fusion protein in obtainning soluble plant actin isoform to analyze its physical and biochemical properties in vitro. The PEAcl-GFP was also expressed in tobacco BY2 cells,which offers a new pathway for further studying its distribution and function in vivo.     

Characterization of a novel toxin-antitoxin module, VapBC, encoded by Leptospira interrogans chromosome

Comparative genomic analysis of the coding sequences (CDSs) of Leptospira interrogans revealed a pair of closely linked genes homologous to the vapBC loci of many other bacteria with respect to both deduced amino acid sequencesand operon organizations. Expression of single vapC gene in Escherichia coli resulted in inhibition of bacterial growth,whereas co-expression of vapBC restored the growth effectively. This phenotype is typical for three other character-ized toxin-antitoxin systems of bacteria, i.e., mazEF[1], reIBE[2] and chplK[3]. The VapC proteins of bacteria and a thermophilic archeae, Solfolobus tokodaii, form a structurally distinguished group of toxin different from the other known toxins of bacteria. Phylogenetic analysis of both toxins and antitoxins of all categories indicated that althought oxins were evolved from divergent sources and may or may not follow their speciation paths (as indicated by their 16s RNA seouences）, co-evolution with their antitoxins was obvious.     

FRAGILE FIBER3, an Arabidopsis gene encoding a type II inositol polyphosphate 5-phosphatase, is required for secondary wall synthesis and actin organization in fiber cells

Type II inositol polyphosphate 5-phosphatases (5PTases) in yeast and animals have been known to regulate the level of phosphoinositides and thereby influence various cellular activities, such as vesicle trafficking and actin organization. In plants, little is known about the phosphatases involved in hydrolysis of phosphoinositides, and roles of type II 5PTases in plant cellular functions have not yet been characterized. In this study, we demonstrate that the FRAGILE FIBER3 (FRA3) gene of Arabidopsis thaliana, which encodes a type II 5PTase, plays an essential role in the secondary wall synthesis in fiber cells and xylem vessels. The fra3 mutations caused a dramatic reduction in secondary wall thickness and a concomitant decrease in stem strength. These phenotypes were associated with an alteration in actin organization in fiber cells. Consistent with the defective fiber and vessel phenotypes, the FRA3 gene was found to be highly expressed in fiber cells and vascular tissues in stems. The FRA3 protein is composed of two domains, an N-terminal localized WD-repeat domain and a C-terminal localized 5PTase catalytic domain. In vitro activity assay demonstrated that recombinant FRA3 exhibited phosphatase activity toward PtdIns(4,5)P2, PtdIns(3,4,5)P3, and Ins(1,4,5)P3, with the highest substrate affinity toward PtdIns(4,5)P2. The fra3 missense mutation, which caused an amino acid substitution in the conserved motif II of the 5PTase catalytic domain, completely abolished the FRA3 phosphatase activity. Moreover, the endogenous levels of PtdIns(4,5)2 and Ins(1,4,5)P3 were found to be elevated in fra3 stems. Together, our findings suggest that the FRA3 type II 5PTase is involved in phosphoinositide metabolism and influences secondary wall synthesis and actin organization.