非洲猪瘟病毒的非必需基因：真的可有可无吗？

非洲猪瘟(African swine fever,ASF)是由非洲猪瘟病毒(African swine fever virus,ASFV)引起的一种出血性、致死性的猪烈性传染病。ASF在全球广泛传播,给养猪业造成重大的经济损失。ASFV基因组庞大,可编码150多种蛋白,一些非必需基因编码的蛋白与调控病毒毒力、复制和免疫逃逸等相关。通过删除ASFV毒力相关的非必需基因所构建的减毒株是当前比较有前景的疫苗,然而其安全性有待提高。系统地鉴定ASFV非必需基因及其功能,不仅有助于ASF基因缺失疫苗的研发,也有益于ASFV致病机制研究。本文对目前已鉴定的ASFV非必需基因及其功能研究进行了总结分析,着重讨论了影响ASFV毒力、调控病毒复制、参与免疫逃逸的非必需基因及其编码蛋白的功能,旨在加深对ASFV病原学的认识,为新的ASFV非必需基因的鉴定和功能研究提供参考。     

铜绿假单胞菌必需基因的研究进展

铜绿假单胞菌为专性需氧非发酵革兰氏阴性杆菌,是医院感染的常见条件致病菌之一,可引起呼吸道、泌尿道、烧伤创面和菌血症等严重感染。铜绿假单胞菌耐药形势日益严峻,给临床治疗带来困难。必需基因是生长过程中必不可少的看家基因,对铜绿假单胞菌必需基因进行深入研究,不仅有助于了解细菌的生长、毒力等基本特性,也有助于筛选新的抗菌药物靶标。本文针对铜绿假单胞菌及其必需基因进行综述,首先介绍了铜绿假单胞菌的基本生理特性及目前耐药趋势,又归纳了必需基因的研究方法,最后对铜绿假单胞菌必需基因的研究进展进行总结。     

细菌必需基因、最小基因组和合成细胞

单细胞原核生物是原始的细胞生命形式,确定细菌必需基因和最小基因组对理解生命的本质、细胞生命的起源和进化有非常重要的意义。文中简要介绍近年来有关细菌的必需基因、最小基因组和合成细胞的研究方法、理论和进展。还特别介绍人工建立最小细菌基因组的策略以及应用前景。     

杆状病毒lef基因家族及其功能

病毒基因结构与功能和表达调控的研究是分子生物学领域的热点之一。其核心内容是揭示病毒基因组的复制机理以及早期基因对晚期基因的调控机制。昆虫杆状病毒基因的表达是级联式调控,按其表达的时序可分为极早期基因、早期基因、晚期基因和极晚期基因。早期基因主要为病毒基因组DNA复制、晚期基因的表达提供必需的蛋白因子。     

硒代谢网络与硒蛋白质组的生物信息学研究进展

硒是大多数生物所必需的微量元素,对维持氧化还原稳态平衡具有重要作用,并与许多重大疾病有着密切联系。一直以来,关于硒的研究工作主要集中于硒代谢机制和硒蛋白功能。近年来快速增长的各类组学数据为硒相关的生物信息学研究工作提供了重要条件与机遇。主要介绍了当前利用生物信息学的理论和方法研究硒的代谢通路、功能和进化等领域的最新进展。通过这些研究,一方面发现了大量新的硒蛋白基因,并确定了众多物种的硒蛋白质组;另一方面揭示了新的硒代谢通路及相关新基因,完善了硒代谢网络。在此基础上,通过比较基因组学分析,深入探讨了硒代谢通路、不同硒蛋白家族乃至硒蛋白质组的分布与进化规律,以期为进一步认识硒研究领域中的重要问题和未来的发展方向提供支持。     

HCMV增殖机制研究进展

人类巨细胞病毒(human cytomegalovirus,HCMV)感染在人群中广泛存在,病毒在感染细胞内增殖会对宿主细胞进行多水平调节和干扰,从而导致各种宏观疾病。本文对HCMV复制周期的基因表达时序、HCMV-DNA复制相关蛋白质及其编码基因、HCMV-DNA复制特点和HCMV必需基因、非必需基因及抑制基因等进行综述。     

Tup1突变对转录抑制局部网络中基因表达的非线性影响

研究基因网络的非线性行为特征是研制基因网络技术的基础。Tup1基因是酵母中作用最为广泛的转录抑制因子之一,利用酵母生物信息学数据库中蛋白相互作用关系,构建一个以Tup1为中心,4个层次741个基因的局部基因网络。统计分析六张Tup1不同突变的基因表达芯片数据,将局部基因网络中的全部基因按照3个网络特征进行统计分析：必需、非必需基因、网络层次和网络节点,并研究这些特征与基因表达之间的关系。初步发现基因表达变化的强度与节点数目成一定的反比关系,必需基因的平均变化程度较非必需基因为低,且由Tup1突变引发的其他基因的表达变化在以Tup1为中心的局部基因网络中近层次网络变化程度较大,远层次网络变化程度较低。     

一种温敏复制缺陷T载体的构建及在鸡白痢沙门氏菌基因敲除中的应用

基因敲除是基因功能研究的重要手段,载体是基因敲除的工具和核心。为获得有效的基因敲除载体以快速构建基因突变株及鉴定相应基因的必需性,在已有温敏复制缺陷pIDM1质粒的基础上,于EcoRⅠ和PstⅠ位点间插入串联的XcmⅠ酶切位点接头,构建了pIDM-T质粒;该质粒经XcmⅠ酶切可获得末端突出T的线性化pIDM-T载体。在验证了pIDM-T质粒复制的温敏特性基础上,应用构建的T载体克隆鸡白痢沙门氏菌CVCC527菌株的eno和ybdr两个基因,鉴定获得pIDM-T_eno和pIDM-T_ybdr两个重组质粒;将重组质粒转化527菌株,经IPC(Integration rate per cell)值计算,鉴定eno为必需基因,ybdr为非必需基因。挑取非必需ybdr基因527菌株重组菌(SalΔybdr),经PCR和测序,确认突变菌株重组位点的正确性。pIDM-T载体可快速克隆PCR产物,用于沙门氏菌的基因敲除及必需性鉴定,为沙门氏菌基因功能研究提供了一种有效快速的手段。     

酿酒酵母细胞基因组中与转录因子Rim101亚细胞定位相关的磷酸酶和激酶基因的筛选

Rim101是一个具有锌指结构的转录因子,在调控酿酒酵母细胞耐受碱性和高盐环境、钙离子稳态、细胞分裂以及硒毒性方面起作用。前人研究结果显示,细胞周期依赖性激酶基因PHO85的缺失,导致Rim101蛋白在细胞核内积累。为了探索Rim101亚细胞定位的新调节因子,通过荧光显微镜技术对酿酒酵母细胞基因组中编码磷酸酶的73个非必需基因缺失株和编码激酶的139个非必需基因缺失株进行了筛选,发现编码磷脂酰肌醇磷酸(Ptd Ins P)的磷酸酶Sac1调控Rim101的亚细胞定位。     

利用基因组比对方法寻找大肠杆菌DH1基因组中的非必需序列

目的:寻找大肠杆菌DH1基因组中的非必需序列。方法:采用基因组比对的方法,通过软件MAUVE分别对大肠杆菌DH1与miniMG1655、miniW3110进行基因组比对,筛选得到大肠杆菌DH1基因组中的候选非必需序列,进而以基因必需性评分的方法确定非必需序列。结果与结论:通过基因组比对及基因必需性评分的方法,确定了大肠杆菌DH1基因组中64个非必需序列区域,占全基因组的26.3%。非必需序列区域的确定,为后续构建基因组减小的大肠杆菌miniDH1提供了基础。     

Current status of theoretical studies on essential genes in microbes

Essential genes are indispensable for the survival of an organism in optimal conditions. Recently, study on essential gene is becoming a hot topic of microbiology, genomics, and bioinformatics. This paper described the experiments that determined essential genes in some microbes and the theoretical researches on essential genes were reviewed. The major content contained comparison of essential genes and non-essential genes based on information on evolutionary conservation and sequence composition, and in silico prediction of essential genes, and analysis of the chromosomal distributions of essential genes. Finally, related progresses were concluded and the open problems were pointed out.     

Metabolic network analysis revealed distinct routes of deletion effects between essential and non-essential genes

Interest in essential genes has arisen recently given their importance in antimicrobial drug development. Although knockouts of essential genes are commonly known to cause lethal phenotypes, there is insufficient understanding on the intermediate changes followed by genetic perturbation and to what extent essential genes correlate to other genes. Here, we characterized the gene knockout effects by using a list of affected genes, termed as 'damage lists'. These damage lists were identified through a refined cascading failure approach that was based on a previous topological flux balance analysis. Using an Escherichia coli metabolic network, we incorporated essentiality information into damage lists and revealed that the knockout of an essential gene mainly affects a large range of other essential genes whereas knockout of a non-essential gene only interrupts other non-essential genes. Also, genes sharing common damage lists tend to have the same essentiality. We extracted 72 core functional modules from the common damage lists of essential genes and demonstrated their ability to halt essential metabolites production. Overall, our network analysis revealed that essential and non-essential genes propagated their deletion effects via distinct routes, conferring mechanistic explanation to the observed lethality phenotypes of essential genes.     

Analysis and identification of essential genes in humans using topological properties and biological information

Genes that are indispensable for survival are termed essential genes. The analysis and identification of essential genes are very important for understanding the minimal requirements of cellular survival and for practical purposes. Proteins do not exert their function in isolation of one another but rather interact together in PPI networks. A global analysis of protein interaction networks provides an effective way to elucidate the relationships between proteins. With the recent large-scale identifications of essential genes and the production of large amounts of PPIs in humans, we are able to investigate the topological properties and biological properties of essential genes. However, until recently, no one has ever investigated human essential genes using topological and biological properties. In this study, for the first time, 28 topological properties and 22 biological properties were used to investigate the characteristics of essential and non-essential genes in humans. Most of the properties were statistically discriminative between essential and non-essential genes. The F-score was used to estimate the essentiality of each property. The GO-enrichment analysis was performed to investigate the functions of the essential and non-essential genes. Finally, based on the topological features and the biological characteristics, a machine-learning classifier was constructed to predict the essential genes. The results of the jackknife test and 10-fold cross validation test are encouraging, indicating that our classifier is an effective human essential gene discovery method.     

Role of essential genes in mitochondrial morphogenesis in Saccharomyces cerevisiae

Mitochondria are essential organelles of eukaryotic cells. Inheritance and maintenance of mitochondrial structure depend on cytoskeleton-mediated organelle transport and continuous membrane fusion and fission events. However, in Saccharomyces cerevisiae most of the known components involved in these processes are encoded by genes that are not essential for viability. Here we asked which essential genes are required for mitochondrial distribution and morphology. To address this question, we performed a systematic screen of a yeast strain collection harboring essential genes under control of a regulatable promoter. This library contains 768 yeast mutants and covers approximately two thirds of all essential yeast genes. A total of 119 essential genes were found to be required for maintenance of mitochondrial morphology. Among these, genes were highly enriched that encode proteins involved in ergosterol biosynthesis, mitochondrial protein import, actin-dependent transport processes, vesicular trafficking, and ubiquitin/26S proteasome-dependent protein degradation. We conclude that these cellular pathways play an important role in mitochondrial morphogenesis and inheritance.     

Large-scale identification of essential Salmonella genes by trapping lethal insertions

A novel screening approach based on insertion-duplication mutagenesis (IDM) was established to efficiently screen for essential genes of Salmonella enterica serovar Typhimurium under laboratory conditions. Small, randomly generated genomic fragments were cloned into a conditionally replicating vector, and the resulting library of single Salmonella clones was grown under permissive conditions. Upon switching to non-permissive temperature, discrimination between lethal and non-lethal insertions following homologous recombination allowed the trapping of genes with essential functions. Further characterization of a total of 498 fragments resulting in such lethal knockout revealed 145 known essential genes and 112 functionally characterized or hypothetical genes not yet shown to encode essential genes, among them three Salmonella-specific genes. The essentiality was demonstrated for a prioritised set of 15 putative indispensable genes by creating conditional lethal phenotypes. The results of this large-scale screening indicate that in rich media, the class of Salmonella genes indispensable for growth is composed of approximately 490 genes.     

Genetic analysis and complementation by germ-line transformation of lethal mutations in the unc-22 IV region of Caenorhabditis elegans

Summary The subject of this study is the organization of essential genes in the 2 map-unit unc-22 IV region of the Caenorhabditis elegans genome. With the goal of achieving mutational saturation of essential genes in this region, 6491 chromosomes mutagenized with ethyl methanesulfonate (EMS) were screened for the presence of lethal mutations in the unc-22 region. The genetic analysis of 21 lethal mutations in the unc-22 region resulted in the identification of 6 new essential genes, making a total of 36 characterized to date. A minimum of 49 essential genes are estimated to lie in this region. A set of seven formaldehyde-induced deficiencies of unc-22 and surrounding loci were isolated to facilitate the positioning of essential genes on the genetic and physical maps. In order to study essential genes at the molecular level, our approach was to rescue lethal mutations by the injection of genomic DNA in the form of cosmid clones into the germ-line of balanced heterozygotes carrying a lethal mutation. The cosmid clones containing let-56 and let-653 were identified by this method.     

Lethal mutations defining 112 complementation groups in a 4.5 Mb sequenced region of Caenorhabditis elegans chromosome III

The central gene cluster of chromosome III was one of the first regions to be sequenced by the Caenorhabditis elegans genome project. We have performed an essential gene analysis on the left part of this cluster, in the region around dpy-17III balanced by the duplication sDp3. We isolated 151 essential gene mutations and characterized them with regard to their arrest stages. To facilitate positioning of these mutations, we generated six new deficiencies that, together with preexisting chromosomal rearrangements, subdivide the region into 14 zones. The 151 mutations were mapped into these zones. They define 112 genes, of which 110 were previously unidentified. Thirteen of the zones have been anchored to the physical sequence by polymerase chain reaction deficiency mapping. Of the 112 essential genes mapped, 105 are within these 13 zones. They span 4.2?Mb of nucleotide sequence. From the nucleotide sequence data, 920 genes are predicted. From a Poisson distribution of our mutations, we predict that 234 of the genes will be essential genes. Thus, the 105 genes constitute 45% of the estimated number of essential genes in the physically defined zones and between 2 and 5% of all essential genes in C. elegans.     

Lethal mutations defining 112 complementation groups in a 4.5?Mb sequenced region of Caenorhabditis elegans chromosome III

The central gene cluster of chromosome III was one of the first regions to be sequenced by the Caenorhabditis elegans genome project. We have performed an essential gene analysis on the left part of this cluster, in the region around dpy-17III balanced by the duplication sDp3. We isolated 151 essential gene mutations and characterized them with regard to their arrest stages. To facilitate positioning of these mutations, we generated six new deficiencies that, together with preexisting chromosomal rearrangements, subdivide the region into 14 zones. The 151 mutations were mapped into these zones. They define 112 genes, of which 110 were previously unidentified. Thirteen of the zones have been anchored to the physical sequence by polymerase chain reaction deficiency mapping. Of the 112 essential genes mapped, 105 are within these 13 zones. They span 4.2 Mb of nucleotide sequence. From the nucleotide sequence data, 920 genes are predicted. From a Poisson distribution of our mutations, we predict that 234 of the genes will be essential genes. Thus, the 105 genes constitute 45% of the estimated number of essential genes in the physically defined zones and between 2 and 5% of all essential genes in C. elegans. Received: 23 April 1998 / Accepted: 18 August 1998     

Comparative analysis of essential genes and nonessential genes in Escherichia coli K12

Genes can be classified as essential or nonessential based on their indispensability for a living organism. Previous researches have suggested that essential genes evolve more slowly than nonessential genes and the impact of gene dispensability on a gene’s evolutionary rate is not as strong as expected. However, findings have not been consistent and evidence is controversial regarding the relationship between the gene indispensability and the rate of gene evolution. Understanding how different classes of genes evolve is essential for a full understanding of evolutionary biology, and may have medical relevance in the design of new antibacterial agents. We therefore performed an investigation into the properties of essential and nonessential genes. Analysis of evolutionary conservation, protein length distribution and amino acid usage between essential and nonessential genes in Escherichia coli K12 demonstrated that essential genes are relatively preserved throughout the bacterial kingdom when compared to nonessential genes. Furthermore, results show that essential genes, compared to nonessential genes, have a significantly higher proportion of large (>534 amino acids) and small proteins (<139 amino acids) relative to medium-sized proteins. The pattern of amino acids usage shows a similar trend for essential and nonessential genes, although some notable exceptions are observed. These findings help to clarify our understanding of the evolutionary mechanisms of essential and nonessential genes, relevant to the study of mutagenesis and possibly allowing prediction of gene properties in other poorly understood organisms.