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.     

The essential fatty acid status in phenylketonuria patients under treatment

Phenylketonuric patients are on a special diet that lacks certain essential fatty acids. This study evaluates the essential fatty acid status of a group of phenylketonuric patients in the Netherlands undergoing dietary treatment. To this end, the essential fatty acid status of nine phenylketonuria patients was studied. On the basis of age and gender, two control subjects were selected for each patient. The essential fatty acid composition of duplicate food portions and the essential fatty acid status of plasma and erythrocytes were analyzed. Phenylketonuria subjects had a different essential fatty acid profile from their peers, especially concerning the n-3 fatty acids. N-6 and n-3 fatty long-chain polyenes were hardly consumed by phenylketonuria subjects, in contrast to the control subjects. Linoleic acid, on the other hand, was consumed in significantly higher amounts by phenylketonuria subjects and made up about 40% of their daily fat consumption. The essential fatty acid consumption pattern of the phenylketonuria subjects is mirrored by the essential fatty acid concentrations in blood. The essential fatty acid status of the phenylketonuric diet should be improved in order to prevent deficiency in n-3 fatty acids.     

Essential gene acquisition destabilizes plasmid inheritance

Extra-chromosomal genetic elements are important drivers of evolutionary transformations and ecological adaptations in prokaryotes with their evolutionary success often depending on their ‘utility’ to the host. Examples are plasmids encoding antibiotic resistance genes, which are known to proliferate in the presence of antibiotics. Plasmids carrying an essential host function are recognized as permanent residents in their host. Essential plasmids have been reported in several taxa where they often encode essential metabolic functions; nonetheless, their evolution remains poorly understood. Here we show that essential genes are rarely encoded on plasmids; evolving essential plasmids in Escherichia coli we further find that acquisition of an essential chromosomal gene by a plasmid can lead to plasmid extinction. A comparative genomics analysis of Escherichia isolates reveals few plasmid-encoded essential genes, yet these are often integrated into plasmid-related functions; an example is the GroEL/GroES chaperonin. Experimental evolution of a chaperonin-encoding plasmid shows that the acquisition of an essential gene reduces plasmid fitness regardless of the stability of plasmid inheritance. Our results suggest that essential plasmid emergence leads to a dose effect caused by gene redundancy. The detrimental effect of essential gene acquisition on plasmid inheritance constitutes a barrier for plasmid-mediated lateral gene transfer and supplies a mechanistic understanding for the rarity of essential genes in extra-chromosomal genetic elements.     

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.     

微生物必需基因的理论研究现状

必需基因是生物体在优化条件下生长不可缺少的基因。近年来,对必需基因的研究已逐渐成为微生物学、基因组学和生物信息学研究领域的热点。文章首先描述了已经实验确定必需基因的微生物物种。然后,对必需基因的理论研究现状进行了综述。从进化保守性和序列组成两方面比较必需基因和非必需基因的差异,到必需基因的理论预测及必需基因在染色体上的分布等。最后,对这一重要研究领域的进展进行了总结和展望。     

Two- and Higher Point Correlation Functions in Proteins

Abstract

A method is presented for a more efficient sampling of the configurational space of proteins as compared to conventional sampling techniques such as molecular dynamics. The method is based on the large conformational changes in proteins revealed by the “essential dynamics” analysis. A form of constrained dynamics is performed, forcing the system to move along some of the essential coordinates. This results in a broader sampling of the essential subspace than in a comparable conventional molecular dynamics simulation without constraints. The new sampling method (essential dynamics sampling) was applied to the histidine-containing phosphocarrier protein HPr. The results indicate that the essential dynamics sampling method produces physically allowed structures, as estimated by the evaluation of many geometrical properties. In addition, a study of the motions in the essential subspace reveals a diffusion-like behavior.     

Bioactivity of selected plant essential oils against listeria monocytogenes

Ninety-three different commercial essential oils were screened for activity against 20 Listeria monocytogenes strains in vitro and the results correlated against the actual chemical composition of each oil. There was a substantial difference in the activity between different essential oils as expected, but there was also a difference in activity between different samples of the same essential oil. Strong anti- Listeria activity was often correlated with essential oils containing a high percentage of monoterpenes, eugenol, cinnamaldehyde, thymol, and sometimes with citronellol, limonene and geraniol. However, as there was often no correlation between the anti- Listeria activity and the main chemical components, it is possible that either there is a more complex relationship with the chemical composition (which includes the minor components) or that substantial adulteration had occurred in some essential oil samples. The possible use of a number of essential oils in a dual role as flavours and antimicrobials is discussed.     

Patterns of evolutionary conservation of essential genes correlate with their compensability

Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability—that is, by how easily they can be functionally replaced, for example through increased expression of other genes.     

Thematic Review Series: Living History of Lipids: Discovery of essential fatty acids

Dietary fat was recognized as a good source of energy and fat-soluble vitamins by the first part of the 20th century, but fatty acids were not considered to be essential nutrients because they could be synthesized from dietary carbohydrate. This well-established view was challenged in 1929 by George and Mildred Burr who reported that dietary fatty acid was required to prevent a deficiency disease that occurred in rats fed a fat-free diet. They concluded that fatty acids were essential nutrients and showed that linoleic acid prevented the disease and is an essential fatty acid. The Burrs surmised that other unsaturated fatty acids were essential and subsequently demonstrated that linolenic acid, the omega-3 fatty acid analog of linoleic acid, is also an essential fatty acid. The discovery of essential fatty acids was a paradigm-changing finding, and it is now considered to be one of the landmark discoveries in lipid research.     

两种精油熏蒸处理对金针菇贮藏品质的影响

为了开发高效的食用菌绿色保鲜剂,以新鲜的白色金针菇为供试材料,以花椒精油和丁香精油为供试熏蒸剂,分别在常温（25±1）℃和低温（4±1）℃条件下开展了适用于金针菇保鲜的精油种类和浓度的筛选试验,并对金针菇贮藏期内的感官评价、失重率、呼吸强度、褐变度、多酚氧化酶（PPO）活性、苯丙氨酸解氨酶（PAL）活性、丙二醛（MDA）以及总酚含量进行了测定。结果显示,常温（25±1）℃条件下用0.1 mL·kg-1花椒精油和0.5 mL·kg-1丁香精油保鲜效果优于其他处理,且有统计学意义（P<0.05）,0.1 mL·kg-1花椒精油和0.5 mL·kg-1丁香精油处理组感官评分分别高于对照组23.4%和27.8%,二者均能够抑制金针菇褐变、减轻腐败变质,且有统计学意义（P<0.05）;在低温（4±1）℃贮藏试验中发现,0.1 mL·kg-1花椒精油和0.5 mL·kg-1丁香精油均能有效抑制呼吸强度和PPO活性的升高（P<0.05）,其呼吸高峰较对照组分别降低了28.3%和39.6%;贮藏15 d后,精油处理组PPO活性较对照组分别降低了8.2%和16.6%;精油处理有效降低了MDA含量的产生,保持着较高的总酚含量、减轻腐烂褐变的程度。第15天时,对照组MDA含量为1.75 μmol·g-1,而花椒精油和丁香精油处理组MDA含量分别比对照组低0.15、0.40 μmol·g-1,丁香精油处理组显著低于花椒精油处理组和对照组（P<0.05）。研究结果表明,0.1 mL·kg-1花椒精油和0.5 mL·kg-1丁香精油均对金针菇采后贮藏保鲜效果显著,其中,0.5 mL·kg-1丁香精油的保鲜效果最明显,在15d的贮藏期内,金针菇依然保持着良好的品质,而对照组已经轻微褐变,部分开始腐烂。研究结果为花椒精油和丁香精油应用于金针菇采后贮藏保鲜提供了理论依据。     

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.     

Ancestry analysis indicates two different sets of essential genes in eukaryotic model species

Essential genes are so-called because they are crucial for organism perpetuation. Those genes are usually related to essential functions to cellular metabolism or multicellular homeostasis. Deleterious alterations on essential genes produce a spectrum of phenotypes in multicellular organisms. The effects range from the impairment of the fertilization process, disruption of fetal development, to loss of reproductive capacity. Essential genes are described as more evolutionarily conserved than non-essential genes. However, there is no consensus about the relationship between gene essentiality and gene age. Here, we identified essential genes in five model eukaryotic species (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, Caenorhabditis elegans, and Mus musculus) and estimate their evolutionary ancestry and their network properties. We observed that essential genes, on average, are older than other genes in all species investigated. The relationship of network properties and gene essentiality convey with previous findings, showing essential genes as important nodes in biological networks. As expected, we also observed that essential orthologs shared by the five species evaluated here are old. However, all the species evaluated here have a specific set of young essential genes not shared among them. Additionally, these two groups of essential genes are involved with distinct biological functions, suggesting two sets of essential genes: (i) a set of old essential genes common to all the evaluated species, regulating basic cellular functions, and (ii) a set of young essential genes exclusive to each species, which perform specific essential functions in each species.

     

Bactericidal activities of essential oils of basil and sage against a range of bacteria and the effect of these essential oils on Vibrio parahaemolyticus

Basil and sage essential oils were examined for bactericidal activity against a range of Gram-positive and Gram-negative bacteria by viable count determinations. Generally, Gram-positive bacteria showed higher resistance to basil and sage essential oils than Gram-negative bacteria. Vibrio species showed a high sensitivity to both essential oils. Stationary growth phase cells of selected bacteria showed higher resistance to these essential oils than exponential growth phase cells. Basil-resistant (b21) and sage-resistant (s20) strains of Vibrio parahaemolyticus were isolated. Both strains showed higher resistance to heat and H2O2 than parent strain. Conversely, heat-adapted V. parahaemolyticus also showed a higher resistance to these essential oils than nonadapted cells.     

The Role of Protein Interactions in Mediating Essentiality and Synthetic Lethality

Genes are characterized as essential if their knockout is associated with a lethal phenotype, and these “essential genes” play a central role in biological function. In addition, some genes are only essential when deleted in pairs, a phenomenon known as synthetic lethality. Here we consider genes displaying synthetic lethality as “essential pairs” of genes, and analyze the properties of yeast essential genes and synthetic lethal pairs together. As gene duplication initially produces an identical pair or sets of genes, it is often invoked as an explanation for synthetic lethality. However, we find that duplication explains only a minority of cases of synthetic lethality. Similarly, disruption of metabolic pathways leads to relatively few examples of synthetic lethality. By contrast, the vast majority of synthetic lethal gene pairs code for proteins with related functions that share interaction partners. We also find that essential genes and synthetic lethal pairs cluster in the protein-protein interaction network. These results suggest that synthetic lethality is strongly dependent on the formation of protein-protein interactions. Compensation by duplicates does not usually occur mainly because the genes involved are recent duplicates, but is more commonly due to functional similarity that permits preservation of essential protein complexes. This unified view, combining genes that are individually essential with those that form essential pairs, suggests that essentiality is a feature of physical interactions between proteins protein-protein interactions, rather than being inherent in gene and protein products themselves.     

Effect of some essential amino acid deficiency in the medium on the action of insulin on primary cultured hepatocytes of rats. Hepatocytes do not respond to insulin in some essential amino acid-deficient medium

1. The effects of insulin, glucagon and dexamethasone on the amino acid consumption by primary cultures of rat hepatocytes were studied in a medium containing all essential amino acids or in those deficient in some essential or nonessential amino acids. 2. The cells which were cultured in a medium containing all the essential amino acids responded to insulin by enhancing the consumption of amino acids and augmenting protein synthesis. 3. However, the cells did not respond to insulin significantly when they were cultured in a medium deficient in lysine or some other essential amino acids. 4. The results suggest that some essential amino acid deficiency impairs the transmission of the signal of insulin to the site of the metabolic changes induced by the hormone.     

Regional variation in the density of essential genes in mice

In most species, and particularly in vertebrates, the percentage of genes absolutely required for survival, the essential genes, has not been estimated. To obtain this estimation, we used the mouse as an experimental model to carry out high-efficiency N-ethyl-N-nitrosourea (ENU) mutagenesis screens in two balancer chromosome regions, and compared our results to a third previously published screen. The number of essential genes in each region was predicted based on allele frequencies. We determined that the density of essential genes differs by up to an order of magnitude among genomic regions. This indicates that extrapolating from regional estimates to genome-wide estimates of essential genes has a huge variance. A particularly high density of essential genes on mouse Chromosome 11 coincides with a high degree of regional linkage conservation, providing a possible causal explanation for the density variation. This is the first demonstration of regional variation in essential gene density in the mouse genome.     

The inhibitory effect of essential oils on herpes simplex virus type-1 replication in vitro

The antiviral effect of 12 essential oils on herpes simplex virus type-1 (HSV-1) replication was examined in vitro. The replication ability of HSV-1 was suppressed by incubation of HSV-1 with 1% essential oils at 4 C for 24 hr. Especially, lemongrass completely inhibited the viral replication even at a concentration of 0.1%, and its antiviral activity was dependent on the concentrations of the essential oil. When Vero cells were treated with the essential oil before or after viral adsorption, no antiviral activity was found, which suggests that the antiviral activity of essential oils including lemongrass may be due to the direct interaction with virions.     

Effect of oregano essential oil on the engraftment and development of Lewis carcinoma in F1 DBA C57 black hybrid mice

The effect of a low uptake dose of oregano essential oil with drinking water for three months (Origanum vulgare L.) on the degree of Lewis carcinoma engraftment and some parameters of oxidative stress has been studied in vivo using F1 DBA C57 Black hybrid mice. Oregano essential oil has been established to possess an anticancer activity. The degree of tumor engraftment decreased by 1.8 times, its size decreased by 1.5 times, and the development of tumor was significantly suppressed in sick mice under the effect of oregano essential oil. It was found that the uptake of essential oil did not affect the intensity of lipid peroxidation in the brain of mice and resulted in a significantly (by 36%) decreased content of secondary lipid oxidation products in the liver as shown in a reaction with thiobarbituric acid as compared to control subjects. The activity of antioxidant enzymes was found to increase after three months of essential oil uptake (by 1.5–3 times) as compared to the control group. This effect of essential oil supports the presence of bioantioxidant properties in this essential oil.     

马缨丹叶片精油化学成分及其对三种害虫的生物活性

【目的】为探讨马缨丹Lantana camara L.叶片精油化学成分以及其对3种害虫的生物活性,以应用于生物防治。【方法】马缨丹叶片经水蒸气蒸馏法提取精油,产率为0.21%。经过气-质联用仪(GCMS)分析,从马缨丹叶片精油中检测出主要的26种化合物,其中α-姜黄烯(α-curcumene,32.76%),β-石竹烯(β-caryophyllene,16.36%),石竹烯氧化物(Caryophyllene oxide,12.22%),桉油烯醇(Spathulenol,10.48%)含量较高,并对3种不同害虫进行生物活性测定。【结果】生物测定结果表明,马缨丹精油对米象Sitophilus oryzae成虫和Ⅳ龄埃及伊蚊Aedes aegypti幼虫的触杀效果显著,LC50分别为0.92 mg/cm2和32.33μg/m L。随着浓度的升高,对白蚁驱避作用增强,白蚁死亡率增加;高浓度精油对白蚁有触杀作用,但较低浓度对白蚁无显著影响。【结论】本研究证明马缨丹叶片精油对3种害虫有良好防治的效果。     

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.