Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization,Evolution and Expression of the Nitrogen Fixation Genes

We provide here a comparative genome analysis of 31 strains within the genus Paenibacillus including 11 new genomic sequences of N₂-fixing strains. The heterogeneity of the 31 genomes (15 N₂-fixing and 16 non-N₂-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N₂-fixing strains. The nif cluster is under control of a σ⁷⁰-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe–S] cluster is highly conserved in N₂-fixing and non-N₂-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N₂-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N₂-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N₂-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes. This study not only reveals the organization and distribution of nitrogen fixation genes in Paenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.     

Thermostability enhancement of polyethylene terephthalate degrading PETase using self- and nonself-ligating protein scaffolding approaches

Polyethylene terephthalate (PET) hydrolase enzymes show promise for enzymatic PET degradation and green recycling of single-use PET vessels representing a major source of global pollution. Their full potential can be unlocked with enzyme engineering to render activities on recalcitrant PET substrates commensurate with cost-effective recycling at scale. Thermostability is a highly desirable property in industrial enzymes, often imparting increased robustness and significantly reducing quantities required. To date, most engineered PET hydrolases show improved thermostability over their parental enzymes. Here, we report engineered thermostable variants of Ideonella sakaiensis PET hydrolase enzyme (IsPETase) developed using two scaffolding strategies. The first employed SpyCatcher-SpyTag technology to covalently cyclize IsPETase, resulting in increased thermostability that was concomitant with reduced turnover of PET substrates compared to native IsPETase. The second approach using a GFP-nanobody fusion protein (vGFP) as a scaffold yielded a construct with a melting temperature of 80°C. This was further increased to 85°C when a thermostable PETase variant (FAST PETase) was scaffolded into vGFP, the highest reported so far for an engineered PET hydrolase derived from IsPETase. Thermostability enhancement using the vGFP scaffold did not compromise activity on PET compared to IsPETase. These contrasting results highlight potential topological and dynamic constraints imposed by scaffold choice as determinants of enzyme activity.     

互花米草人工植被生态效益和经济效益的初步研究

前言在我国海涂中被日潮淹没的中、低潮带,天然生长的高等植物种类比较贫乏,分布面积也较小,许多中低潮带海滩为光滩裸地。为了绿化海滩、保护海滩,提高海滩生态系统的初级生产力,我国在1963年和1978年分别从英国     

目标?鄄诱饵库搜索策略在蛋白质组质谱鉴定和质控中的应用及研究进展

基于串联质谱的蛋白质组研究会产生海量的质谱数据,这些数据通常使用数据库搜索引擎进行鉴定分析,并根据肽段谱图匹配(PSM)反推真实的样品蛋白质．对于高通量蛋白质组数据的处理,其鉴定结果的可信是后续分析应用的前提,因此对鉴定结果的质量控制尤为重要,而基于目标-诱饵库(target-decoy)搜索策略的质量控制是目前应用最为广泛的方法．本文首先介绍了基于目标-诱饵库搜索策略搜库和质量控制的实施流程,然后综述了基于目标-诱饵库搜索策略的质量控制工具,并提出了目标-诱饵库搜索策略的不足及改善方法,最后对目标-诱饵库搜索策略进行了总结与展望．     

利用锌特异性探针HL~1示踪植物细胞外Zn~(2+)的分布

以拟南芥(Arabidopsis thaliana)和谷子(Setaria italic)为研究材料,利用锌特异性探针HL1,使用荧光分光光度仪、等温滴定热量测定仪(ITC200)和倒置荧光显微镜等仪器探究了该化学探针的特性以及植物细胞外游离Zn~(2+)的分布。结果表明,当HL1与不同元素溶液混合时,只与Zn~(2+)特异性结合,在紫外光(UV)激发下,发射出波长为500 nm的蓝色荧光;生成物的平衡解离常数KD=7.02×10–4 mol·L–1,具有很好的稳定性。拟南芥叶片中的Zn~(2+)分布于细胞间隙及叶表皮毛的外周和表层,且叶表皮毛的荧光强度具有明显的浓度依赖性;谷子叶片中的Zn~(2+)分布在细胞间隙以及维管组织。拟南芥根中的Zn~(2+)分布于根的伸长区,且荧光强度也明显地表现出与浓度相关。由此推断,根伸长区与Zn~(2+)运输有关,叶的维管组织是植物细胞外运输Zn~(2+)的主要途径,细胞间隙和叶表皮毛是植物储存Zn~(2+)的主要区域。HL1适用于检测细胞外Zn~(2+)的分布。     

大豆C3HC4型RING锌指蛋白基因GmRZFP1克隆与表达分析

锌指蛋白在调节植物防卫基因表达和抗性反应上起关键作用。目前,对大豆中C3HC4型RING锌指蛋白基因的研究不多。本研究利用核蛋白筛选系统(NTT)筛选大豆(铁丰8号)干旱处理5h的cDNA文库,获得一个RING锌指蛋白基因。该基因全长927bp,编码308个氨基酸,含有C3HC4-type RING锌指结构域,命名为GmRZFP1。系统进化树分析显示,Gm-RZFP1属于C3HC4-type锌指亚家族。Real-time PCR结果表明,GmRZFP1基因受干旱、高盐、高温、低温、乙烯和ABA等胁迫诱导表达,表明该蛋白涉及多种胁迫相关的信号传导途径。亚细胞定位结果表明,163hGFP-GmRZFP1融合蛋白定位于细胞核中。本研究结果有助于研究该类基因在大豆逆境应答反应中的作用,阐明大豆抗逆分子机制。     

Observation on the initial inoculum source and dissemination of Entomophthorales-caused epizootics in populations of cereal aphids

A total number of 1092 migratory alates were trapped from air in wheat grown area of Yuanyang County, Henan Province from early April through May 2002 in order to confirm the source and dissemination of entomophthoralean inocula to cause epizootics of cereal aphids. Those included 415 Sitobion avenae, 642 Rhopalosiphum padi, 22 Metopolophium dirhodum, and 13 Schizaphis graminum. The trapped alates were daily collected and individually reared for 7 days on wheat plants in laboratory. Of those 341 alates died of fungal infection, taking 31.2% in the trapped alates. These included 224 S. avenae, 106 R. padi, 8 M. dirhodum, and 3 S. graminum. Deaths of all infected alates occurred during the first 5 days and 78.9% of the deaths occurred within the first 3 days. Individual examination under microscope proved that all deaths were attributed to entomophthoralean fungi. Of those Pandora neoaphidis accounted for 84.6%, Conidiobolus obscurus for 9.9%, and Entomophthora planchoniana for 5.5%. Four alate deaths die     

棘托竹荪挥发油化学成分及抑菌作用的研究*

利用水蒸汽蒸馏法提取棘托竹荪的挥发油,得油率为0.45%。.应用气相色谱—质谱联用系统首次对其挥发油的化学成分进行研究。以FFAP柱分离出36个峰,用质谱法鉴定出28个成分,其主要成分为13-甲基-环氧十四烷-2-酮 (23.53%)、亚油酸(17.56%)、芹子烯(12.37%)、棕榈酸(8.20%)、9-十六碳烯酸(7.84%)、(-)-Lepidozenal(7.82%)等, 占总挥发油的97.76%。对挥发油进行抑菌试验,其结果为:桔黄青霉、啤酒酵母最敏感, 黑根霉、黑曲霉次之,白色假丝酵母、金色葡萄球菌,大肠杆菌稍差。     

Photosynthetic traits of Sphagnum and feather moss species in undrained,drained and rewetted boreal spruce swamp forests

In restored peatlands, recovery of carbon assimilation by peat‐forming plants is a prerequisite for the recovery of ecosystem functioning. Restoration by rewetting may affect moss photosynthesis and respiration directly and/or through species successional turnover. To quantify the importance of the direct effects and the effects mediated by species change in boreal spruce swamp forests, we used a dual approach: (i) we measured successional changes in moss communities at 36 sites (nine undrained, nine drained, 18 rewetted) and (ii) photosynthetic properties of the dominant Sphagnum and feather mosses at nine of these sites (three undrained, three drained, three rewetted). Drainage and rewetting affected moss carbon assimilation mainly through species successional turnover. The species differed along a light‐adaptation gradient, which separated shade‐adapted feather mosses from Sphagnum mosses and Sphagnum girgensohnii from other Sphagna, and a productivity and moisture gradient, which separated Sphagnum riparium and Sphagnum girgensohnii from the less productive S. angustifolium, S. magellanicum and S. russowii. Undrained and drained sites harbored conservative, low‐production species: hummock‐Sphagna and feather mosses, respectively. Ditch creation and rewetting produced niches for species with opportunistic strategies and high carbon assimilation. The direct effects also caused higher photosynthetic productivity in ditches and in rewetted sites than in undrained and drained main sites.