原核生物蛋白质基因组学研究进展

随着基因组测序技术的不断发展,大量微生物基因组序列可以在短时间内得以准确鉴定。为了进一步探究基因组的结构与功能,基于序列特征与同源特征的基因组注释算法广泛应用于新测序物种。然而受基因组测序质量以及算法本身准确性偏低等问题的影响,现有的基因组注释存在着相当比例的假基因以及注释错误,尤其是蛋白质N端的注释错误。为了弥补基因组注释的不足,以基因芯片或RNA-seq为核心的转录组测序技术和以串联质谱为核心的蛋白质组测序技术可以高通量地对基因的转录和翻译产物进行精确测定,进而实现预测基因结构的实验验证。然而,原核生物细胞中存在的大量非编码RNA给转录组测序技术引入了污染数据,限制了其对基因组注释的应用。相对而言,以串联质谱技术为核心的蛋白质组学测序可以在短时间内鉴定到生物体内大量的蛋白质,实现注释基因的验证甚至校准。已成为基因组注释和重注释的重要依据,并因而衍生了"蛋白质基因组学"的新研究方向。文中首先介绍传统的基于序列预测和同源比对的基因组注释算法,指出其中存在的不足。在此基础上,结合转录组学与蛋白质组学的技术特点,分析蛋白质组学对于原核生物基因组注释的优势,总结现阶段大规模蛋白质基因组学研究的进展情况。最后从信息学角度指出当前蛋白质组数据进行基因组重注释存在的问题与相应的解决方案,进而探讨未来蛋白质基因组学的发展方向。     

植物蛋白激酶研究进展

近年来,在分子生物学技术不断完善和在酵母与动物蛋白激酶研究的基础上,植物蛋白激酶的研究已取得了很大的进展。就近十年来国内外学者对植物蛋白激酶的发现,家族分类,磷酸化过程及其生理功能等方面的研究进行综述。最后分析了存在的问题并对今后的研究提出了展望。     

有丝分裂激酶Aurora B的研究进展

真核生物细胞通过有丝分裂将遗传物质均等地分配到两个子细胞中,从而维持基因组的稳定性。有丝分裂的每一环节都需要精准而细致的调控,这依赖于一系列调节机制,尤其需要多个相关激酶的共同协调。Aurora B是一个关键的有丝分裂调控激酶,伴随有丝分裂的进行,其先后在染色体臂、内着丝粒、中央纺锤体、中体上动态分布。与其高度时空动态性相一致的是,Aurora B在有丝分裂的多个环节,如姐妹染色体粘连、动粒微管连接、纺锤体检验点和胞质分裂过程中都发挥着一系列重要功能。本文将概述近年来Aurora B激酶功能与调控方面的研究进展。     

原核生物蛋白O-糖基化的研究进展

自从在原核生物中发现蛋白糖基化之后,越来越多的O-糖基化机制在不同种属的细菌中被发现。本文根据对O-寡糖基转移酶(O-oligosaccharide transferase,OTase)的依赖与否,将原核生物的O-糖基化分为OTase非依赖型和OTase依赖型,并分别对这两种糖基化机制进行了详细阐述。通过对不同的O-糖基化机制的深入了解,为以后更好地利用这些途径来合成工程化的目标糖蛋白奠定基础。     

原核生物中小RNA的功能及研究进展

在原核生物基因组中,除了tRNA、rRNA和mRNA这3种我们很熟悉的RNA以外,目前已经知道还含有许多编码非常规调控的RNA。这些RNA的长度为50～400核苷酸,通常由原核生物的基因间区编码,但并不翻译成蛋白质,因此被称为非编码小RNA（sRNA）,简称小RNA或非编码RNA。近年来,随着生物信息学和分子生物学技术的不断发展,在原核生物体内陆续发现了上百种sRNA分子,这些sRNA分子具有多样的生物学功能,作为一类新发现的基因表达调控子已经引起了高度的重视。     

粘着斑激酶

粘着斑激酶（ｆｏｃａｌ ａｄｈｅｓｉｏｎ ｋｉｎａｓｅ,ＦＡＫ）是蛋白酪氨酸激酶,属于非受体蛋白酪氨酸激酶,分布在细胞粘着斑部位。ＦＡＫ位于神经肽,整合素和癌基因作用的聚合点,可发生酪氨酸磷酸化,它参与调节细胞发育,生长,存活,凋亡,粘附,骨架重组,转化,扩散和迁延等过程。     

原核生物中的类钙调蛋白

钙是重要的生命元素之一,真核生物中普遍存在介导钙信号的钙调蛋白已有深入的研究,证明钙调蛋白是细胞复杂调控系统中的一个重要成员,但是在原核生物中是否也存在类似的蛋白因子却一直说法不一.自80年代初在大肠杆菌(Escherichia coli)中首次发现类钙调蛋白(calmodulin-like-protein)以来,已在多种原核生物中陆续发现了类钙调蛋白的存在,证明其可能参与了原核生物的孢子形成,细胞分裂,生物固氮,异型胞形成和兰细菌光合作用等多种调控功能.文章综述了近年来这一领域的部分研究成果.     

原核生物染色体多复制起始点的研究进展

复制起始点是调控DNA复制启动的重要元件之一.近年来,研究人员已经在多种原核生物的染色体中预测或鉴定出了多个复制起始点,并通过合成生物学或基因组工程的手段成功构建了能够稳定遗传的具有多复制起始点染色体的菌株.然而现有的生物化学或细胞生物学的相关教材,有关原核生物复制起始点数目的 介绍尚未对这些最新研究进展进行更新和补充...     

ICNP与SeqCode：组学时代原核生物命名面临的机遇与挑战

自1936年细菌学家Buchanan负责起草专门的细菌命名法规以来,国际原核生物命名法规(International Code of Nomenclature of Prokaryotes, ICNP)在不断发展和完善过程中,积极促进了原核生物分类学及相关学科的发展。随着组学技术在原核生物多样性研究中的应用,越来越多未培养的细菌和古菌新类群被发现,却因为ICNP要求活的生物材料作为命名模式(nomenclatural type),而无法获得生效名称(validly published name)。2022年,原核生物命名法规从序列数据描述原核生物命名法(Code of Nomenclature of Prokaryotes Described from Sequence Data, SeqCode)正式发布,以补充ICNP在未培养微生物类群命名方面的不足。SeqCode不希望和ICNP产生较大分歧,并尽可能保留在将来和ICNP合并的可能性。然而,作为两种独立运行的命名法规,尚不明确SeqCode和ICNP并存会对学术界产生怎样的影响。本文系统介绍了ICNP和SeqCode各自的发展历程和主要内容,分析了二者的优势和局限性,并呼吁微生物学相关领域的学者共同关注原核生物命名法规并应用于实践,以期构建更加合理、有效的原核生物名称系统。     

工程原核生物和酵母菌中生产单克隆抗体和抗体片段研究进展 *

抗体药物和抗体片段药物在药物市场占据了重要的地位,主要通过哺乳动物细胞系统进行生产,操作复杂并且成本高。为了能够克服哺乳动物细胞系统生产抗体药物的弊端,越来越多的抗体及抗体片段在原核细胞及酵母菌中生产,但是产率往往不高并且没有糖基化。从基因转录和翻译的优化、分子伴侣的共表达和抑制蛋白水解降解等方面概述了在原核生物表达系统及酵母菌中提高单克隆抗体和抗体片段产量的研究进展,为未来利用原核生物和酵母菌实现工业化生产单克隆抗体及抗体片段奠定基础。     

Phosphorylation of Neurofilament Proteins in Isolated Goldfish Mauthner Axoplasm

Abstract: The six neurofilament proteins (NFPs) in the goldfish Mauthner axon (M-axon) have molecular sizes of 235, 145, 123, 105, 80, and 60 kDa. To determine if NFPs in the M-axon are phosphorylated, isolated Mauthner axoplasm (M-axoplasm) and a neurofilament-enriched extract (NFE) prepared from M-axoplasm were incubated with ³²P, which resulted in the radiolabeling of NFPs as determined by their detection on autoradiograms. Kinase inhibitors directed against cyclic AMP-dependent kinases (PKAs) or cofactor-independent kinases significantly reduced the in vitro phosphorylation of NFPs in NFE, whereas inhibitors directed against protein kinase C did not significantly reduce the in vitro phosphorylation of NFPs in NFE. Experiments using two kinase inhibitors directed against different kinases significantly reduced the in vitro phosphorylation of NFPs in NFE to a greater extent than the reduction produced using any single kinase inhibitor. These data suggest that NFPs in the M-axon are phosphorylated and that the in vitro (and perhaps the in vivo) phosphorylation of NFPs is mediated by PKA and/or cofactor-independent kinases that copurify with NFPs.     

Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution.Reviewing Editor: Dr. John Oakeshott     

Substrate specificity of N-acetylhexosamine kinase towards N-acetylgalactosamine derivatives

We report herein a bacterial N-acetylhexosamine kinase, NahK, with broad substrate specificity towards structurally modified GalNAc analogues, and the production of a GalNAc-1-phosphate library using this kinase.     

Thiamin biosynthesis in prokaryotes

Twelve genes involved in thiamin biosynthesis in prokaryotes have been identified and overexpressed. Of these, six are required for the thiazole biosynthesis (thiFSGH, thiI, and dxs), one is involved in the pyrimidine biosynthesis (thiC), one is required for the linking of the thiazole and the pyrimidine (thiE), and four are kinase genes (thiD, thiM, thiL, and pdxK). The specific reactions catalyzed by ThiEF, Dxs, ThiDM, ThiL, and PdxK have been reconstituted in vitro and ThiS thiocarboxylate has been identified as the sulfur source. The X-ray structures of thiamin phosphate synthase and 5-hydroxyethyl-4-methylthiazole kinase have been completed. The genes coding for the thiamin transport system (thiBPQ) have also been identified. Remaining problems include the cloning and characterization of thiK (thiamin kinase) and the gene(s) involved in the regulation of thiamin biosynthesis. The specific reactions catalyzed by ThiC (pyrimidine formation), and ThiGH and ThiI (thiazole formation) have not yet been identified. Received: 23 August 1998 / Accepted: 16 January 1999     

Regulation of Human Cytidine Triphosphate Synthetase 2 by Phosphorylation

Cytidine triphosphate synthetase (CTPS) is the rate-limiting enzyme in de novo CTP synthesis and is required for the formation of RNA, DNA, and phospholipids. This study determined the kinetic properties of the individual human CTPS isozymes (hCTPS1 and hCTPS2) and regulation through substrate concentration, oligomerization, and phosphorylation. Kinetic analysis demonstrated that both hCTPS1 and hCTPS2 were maximally active at physiological concentrations of ATP, GTP, and glutamine, whereas the K_m and IC₅₀ values for the substrate UTP and the product CTP, respectively, were close to their physiological concentrations, indicating that the intracellular concentrations of UTP and CTP may precisely regulate hCTPS activity. Low serum treatment increased hCTPS2 phosphorylation, and five probable phosphorylation sites were identified in the hCTPS2 C-terminal domain. Metabolic labeling of hCTPS2 with [³²P]H₃PO₄ demonstrated that Ser⁵⁶⁸ and Ser⁵⁷¹ were two major phosphorylation sites, and additional studies demonstrated that Ser⁵⁶⁸ was phosphorylated by casein kinase 1 both in vitro and in vivo. Interestingly, mutation of Ser⁵⁶⁸ (S568A) but not Ser⁵⁷¹ significantly increased hCTPS2 activity, demonstrating that Ser⁵⁶⁸ is a major inhibitory phosphorylation site. The S568A mutation had a greater effect on the glutamine than ammonia-dependent activity, indicating that phosphorylation of this site may influence the glutaminase domain of hCTPS2. Deletion of the C-terminal regulatory domain of hCTPS1 also greatly increased the V_max of this enzyme. In summary, this is the first study to characterize the kinetic properties of hCTPS1 and hCTPS2 and to identify Ser⁵⁶⁸ as a major site of CTPS2 regulation by phosphorylation.     

Recent advances in kinase signaling network profiling by mass spectrometry

Mass spectrometry-based phosphoproteomics is currently the leading methodology for the study of global kinase signaling. The scientific community is continuously releasing technological improvements for sensitive and fast identification of phosphopeptides, and their accurate quantification. To interpret large-scale phosphoproteomics data, numerous bioinformatic resources are available that help understanding kinase network functional role in biological systems upon perturbation. Some of these resources are databases of phosphorylation sites, protein kinases and phosphatases; others are bioinformatic algorithms to infer kinase activity, predict phosphosite functional relevance and visualize kinase signaling networks. In this review, we present the latest experimental and bioinformatic tools to profile protein kinase signaling networks and provide examples of their application in biomedicine.     

The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins

Recent phosphoproteomics studies of several bacterial species have firmly established protein phosphorylation on Ser/Thr/Tyr residues as a PTM in bacteria. In particular, our recent reports on the Ser/Thr/Tyr phosphoproteomes of bacterial model organisms Bacillus subtilis and Escherichia coli detected over 100 phosphorylation events in each of the bacterial species. Here we extend our analyses to Lactococcus lactis, a lactic acid bacterium widely employed by the food industry, in which protein phosphorylation at Ser/Thr/Tyr residues was barely studied at all. Despite the lack of almost any prior evidence of Ser/Thr/Tyr protein phosphorylation in L. lactis, we identified a phosphoproteome of a size comparable to that of E. coli and B. subtilis, with 73 phosphorylation sites distributed over 63 different proteins. The presence of several multiply phosphorylated proteins, as well as over-representation of phosphothreonines seems to be the distinguishing features of the L. lactis phosphoproteome. Evolutionary comparison and the conservation of phosphorylation sites in different bacterial organisms indicate that a majority of the detected phosphorylation sites are species-specific, and therefore have probably co-evolved with the adaptation of the bacterial species to their present-day ecological niches.     

A general strategy for studying multisite protein phosphorylation using label-free selected reaction monitoring mass spectrometry

The majority of eukaryotic proteins are phosphorylated in vivo, and phosphorylation may be the most common regulatory posttranslational modification. Many proteins are phosphorylated at numerous sites, often by multiple kinases, which may have different functional consequences. Understanding biological functions of phosphorylation events requires methods to detect and quantify individual sites within a substrate. Here we outline a general strategy that addresses this need and relies on the high sensitivity and specificity of selected reaction monitoring (SRM) mass spectrometry, making it potentially useful for studying in vivo phosphorylation without the need to isolate target proteins. Our approach uses label-free quantification for simplicity and general applicability, although it is equally compatible with stable isotope quantification methods. We demonstrate that label-free SRM-based quantification is comparable to conventional assays for measuring the kinetics of phosphatase and kinase reactions in vitro. We also demonstrate the capability of this method to simultaneously measure relative rates of phosphorylation and dephosphorylation of substrate mixtures, including individual sites on intact protein substrates in the context of a whole cell extract. This strategy should be particularly useful for characterizing the physiological substrate specificity of kinases and phosphatases and can be applied to studies of other protein modifications as well.     

Protein kinase C-related kinase targets nuclear localization signals in a subset of class IIa histone deacetylases

Class IIa histone deacetylases (HDACs) -4, -5, -7 and -9 undergo signal-dependent nuclear export upon phosphorylation of conserved serine residues that are targets for 14-3-3 binding. Little is known of other mechanisms for regulating the subcellular distribution of class IIa HDACs. Using a biochemical purification strategy, we identified protein kinase C-related kinase-2 (PRK2) as an HDAC5-interacting protein. PRK2 and the related kinase, PRK1, phosphorylate HDAC5 at a threonine residue (Thr-292) positioned within the nuclear localization signal (NLS) of the protein. HDAC7 and HDAC9 contain analogous sites that are phosphorylated by PRK, while HDAC4 harbors a non-phosphorylatable alanine residue at this position. We provide evidence to suggest that the unique phospho-acceptor cooperates with the 14-3-3 target sites to impair HDAC nuclear import.

Structured summary

MINT-7710106:HDAC5 (uniprotkb:Q9UQL6) physically interacts (MI:0915) with PRK2 (uniprotkb:Q16513) by pull down (MI:0096)