Identification of a human trans-3-hydroxy-L-proline dehydratase, the first characterized member of a novel family of proline racemase-like enzymes

A family of eukaryotic proline racemase-like genes has recently been identified. Several members of this family have been well characterized and are known to catalyze the racemization of free proline or trans-4-hydroxyproline. However, the majority of eukaryotic proline racemase-like proteins, including a human protein called C14orf149, lack a specific cysteine residue that is known to be critical for racemase activity. Instead, these proteins invariably contain a threonine residue at this position. The function of these enzymes has remained unresolved until now. In this study, we demonstrate that three enzymes of this type, including human C14orf149, catalyze the dehydration of trans-3-hydroxy-L-proline to Δ(1)-pyrroline-2-carboxylate (Pyr2C). These are the first enzymes of this subclass of proline racemase-like genes for which the enzymatic activity has been resolved. C14orf149 is also the first human enzyme that acts on trans-3-hydroxy-L-proline. Interestingly, a mutant enzyme in which the threonine in the active site is mutated back into cysteine regained 3-hydroxyproline epimerase activity. This result suggests that the enzymatic activity of these enzymes is dictated by a single residue. Presumably, human C14orf149 serves to degrade trans-3-hydroxy-L-proline from the diet and originating from the degradation of proteins that contain this amino acid, such as collagen IV, which is an important structural component of basement membrane.     

Systems biology of evolution: the involvement of metal ions

This article outlines a novel way of looking at the relevance of metal ions in organisms to the whole of life as part of an ecosystem bringing together the environment and cellular life. It does so by examining the evolution of the environment due to the “waste”, mainly oxygen, from cell metabolism which back reacts with the cells themselves. The oxygen generates a progressive change in the metal ions in the environment. The resultant change is buffered by ferrous iron and sulfide and is therefore slow so that there is a gradual adaptation of life to utilisation of elements in a time sequence. In order to appreciate this, systems (biological) evolution, it is necessary to describe the very nature of a thermodynamic flow system of which life is an example.     

Bioinformatic Characterization of P-Type ATPases Encoded Within the Fully Sequenced Genomes of 26 Eukaryotes

P-type ATPases play essential roles in numerous processes, which in humans include nerve impulse propagation, relaxation of muscle fibers, secretion and absorption in the kidney, acidification of the stomach and nutrient absorption in the intestine. Published evidence suggests that uncharacterized families of P-type ATPases with novel specificities exist. In this study, the fully sequenced genomes of 26 eukaryotes, including animals, plants, fungi and unicellular eukaryotes, were analyzed for P-type ATPases. We report the organismal distributions, phylogenetic relationships, probable topologies and conserved motifs of nine functionally characterized families and 13 uncharacterized families of these enzyme transporters. We have classified these proteins according to the conventions of the functional and phylogenetic IUBMB-approved transporter classification system (, Saier et al. in Nucleic Acids Res 34:181–186, 2006; Nucleic Acids Res 37:274–278, 2009). Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Novel fluorescent dyes based on oligopropylamines for the in vivo staining of eukaryotic unicellular algae

Weakly basic fluorescent dyes are used to visualize organelles within live cells due to their affinity to acidic subcellular organelles. In particular, they are used to stain the silica deposited in the silica deposition vesicles (SDVs) of diatoms during the course of their frustule synthesis. This study involved the synthesis of fluorescent dyes derived from oligopropylamines, compounds similar to those found in diatoms. The dyes were obtained by reacting oligopropylamines with 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole. The reaction was realized using methylated oligopropylamines with two or three nitrogen atoms and yielded two novel fluorescent dyes: NBD-N2 and NBD-N3. The dyes appeared to be highly efficient in the in vivo staining of growing siliceous frustules of diatoms at concentrations at least 10 times lower than those required for staining with HCK-123. NBD-N3 also efficiently stained other subcellular vesicles of eukaryotic unicellular algae. NBD-N2 stained only growing diatom frustules, whereas NBD-N3 also stained various subcellular organelles of different eukaryotic unicellular algae. NBD-N2 and NBD-N3 were not removed from stained diatom frustules by drastic treatments with H₂SO₄ and H₂O₂. Fluorescent silica can also be obtained by its chemical precipitation in the presence of NBD-N2 and NBD-N3.     

信号肽及其在蛋白质表达中的应用

分子生物学研究已进入后基因组时代,其中心任务是更多地关注基因组表达的蛋白质的结构和功能。由于基因功能最终通过其表达产物——蛋白质来实现,因此,要了解基因组全部功能活动,最终也必须回到蛋白质上。另外,在菌株、培养和发酵等逐渐成熟的条件下,构建高效的表达载体以提高外源蛋白质的表达量是降低工业化生产成本的关键。随着研究的深入,发现信号肽对蛋白质的定位有着非常重要的作用,使得信号肽的研究不仅具有重要的理论意义,而且也具有潜在的应用价值。就信号肽的结构和功能,信号肽的捕获方法及其在原核表达系统和真核表达系统中表达外源蛋白质的应用做一些介绍。     

论山西中元古代晚期汝阳群微体化石组合

我国北方18-19亿年前的串岭沟组中获得的大球形疑源类,迄今,被认为是可信的最古老真核化石记录。自上世纪80年代以来,东秦岭北坡的中元古代晚期汝阳群陆续发现了丰富的球形光面疑源类,具刺疑源类,丝状微体化石和一些有疑问的动物遗迹。很显然,在中元古代晚期真核生物曾有重大辐射。     

杆状病毒表面展示系统的研究进展

杆状病毒表面展示系统是近几年发展起来的一种新的真核展示系统 ,通过在病毒衣壳蛋白gp6 4插入外源肽、二者融合表达或与特异性的锚定部位结合 ,在病毒表面进行融合表达而筛选出目的活性肽或蛋白。可用来展示需糖基化、二硫键异构化等翻译后修饰才表现功能活性的复杂真核蛋白及构建多肽文库、抗体库等。本文简述了该技术的原理、研究进展、应用及发展前景等。可以预见 ,杆状病毒表面展示技术的发展必将对生命科学及相关领域的发展产生深远的影响     

真核基因PolyA信号的人工神经网络识别研究

本文采用神经网络方法对真核基因的PolyA信号进行识别．文中选择了人类、牛、猪、猫、山羊、兔、绵羊、大鼠、小鼠、小马、鸡、仓鼠共12种真核生物的270个基因组作为研究对象，训练组包括230个基因，预测组包括40个基因．结果表明，结合PolyA上游的碱基顺序特异性（紧挨PolyA的上游地GC），可以从神经网络识别的大量可能PolyA信号中得到正确PolyA信号．     

Cryopreservation of marine thraustochytrids (Labyrinthulomycetes)

In this research, the viability of three marine thraustochytrid isolates (fungoid protists) (WSG05, W15 and WH3) were investigated after freezing in liquid nitrogen. Five cryopreservative combinations containing horse serum, glycerol and dimethylsulfide (Me₂SO) were used. The thraustochytrids were assessed directly after removal from liquid nitrogen and cell concentration measured for 10 days post-thawing. Results indicated that a combination of horse serum and Me₂SO were the most effective cryoprotectants for each of the strains tested. Glycerol was only successful in producing growth in one of the strains once thawed.The protocols developed and tested in this study may have further application for cryopreserving other isolates in this class.