Exploring the relationship between fractal features and bacterial essential genes

Essential genes are indispensable for the survival of an organism in optimal conditions.Rapid and accurate identifications of new essential genes are of great theoretical and practical significance.Exploring features with predictive power is fundamental for this.Here,we calculate six fractal features from primary gene and protein sequences and then explore their relationship with gene essentiality by statistical analysis and machine learning-based methods.The models are applied to all the currently available identified genes in 27 bacteria from the database of essential genes（DEG）.It is found that the fractal features of essential genes generally differ from those of non-essential genes.The fractal features are used to ascertain the parameters of two machine learning classifiers：Na¨？ve Bayes and Random Forest.The area under the curve（AUC） of both classifiers show that each fractal feature is satisfactorily discriminative between essential genes and non-essential genes individually.And,although significant correlations exist among fractal features,gene essentiality can also be reliably predicted by various combinations of them.Thus,the fractal features analyzed in our study can be used not only to construct a good essentiality classifier alone,but also to be significant contributors for computational tools identifying essential genes.

Establishment of a system for screening and identification of novel bactericide targets in the plant pathogenic bacterium Xanthomonas oryzae pv. oryzae using Tn-seq and SPR

Xanthomonas spp. cause severe bacterial diseases. However, effective strategies for prevention and management of these diseases are scarce. Thus, it is necessary to improve the efficiency of control of diseases caused by Xanthomonas. In this study, Xanthomonas oryzae pv. oryzae(Xoo), which causes rice bacterial leaf blight, has been studied as a representative. A transposon insertion library of Xoo, comprising approximately 200,000 individual insertion mutants, was generated. Transposon sequencing data indicated that the mariner C9 transposase mapped at 35.7–36.4% of all potential insertion sites, revealing 491 essential genes required for the growth of Xoo in rich media. The results show that, compared to the functions of essential genes of other bacteria, the functions of some essential genes of Xoo are unknown, 25 genes might be dangerous for the Xanthomonas group, and 3 are specific to Xanthomonas. High-priority candidates for developing broad-spectrum, Xanthomonas-specific, and environment-friendly bactericides were identified in this study. In addition, this study revealed the possible targets of dioctyldiethylenetriamine using surface plasmon resonance(SPR) in combination with high performance liquid chromatography–mass spectrometry(HPLC–MS). The study also provided references for the research of some certain bactericides with unknown anti-bacterial mode of action. In conclusion, this study urged a better understanding of Xanthomonas,provided meaningful data for the management of bacterial leaf blight, and disclosed selected targets of a novel bactericide.

Essential cellular modules for the proliferation of the primitive cell

Bacteria appeared early in the evolution of cellular life on planet Earth, and therefore the universally essential genes or biological pathways found across bacterial domains may represent fundamental genetic or cellular systems used in early life. The essential genes and the minimal gene set required to support bacterial life have recently been experimentally and computationally identified. It is, however,still hard to estimate the ancient genes present in primitive cells compared to the essential genes in contemporary bacteria, because we do not know how ancestral primitive cells lived and proliferated, and therefore cannot directly evaluate the essentiality of the genes in ancestral primitive cells. The cell wall is normally essential for bacterial proliferation and cellular division of walled bacterial cells is normally highly controlled by the essential FtsZ cell division machinery. But, bacteria are capable of reverting to their cell wall deficient ancestral form, called the ＂L-form＂. Unlike ＂normal＂ cells, L-forms divide by a simple physical mechanism based on the effects of membrane dynamics, suggesting a mode of primitive proliferation before the appearance of the cell wall. In this review, we summarize the experimental and computational investigations of minimal gene sets and discuss the minimal cellular modules required to support the proliferation of primitive cells, based on L-form proliferation.

Association between essential hypertension and polymorphisms of beta 1 adrenergic receptor gene G1165C (Gly389Arg) in Chinese Mongolian population

BACKGROUND： The prevalences of hypertension, cerebrovascular diseases, etc. are higher in Mongolian population because of the influence of various factors including genetics, geography, diet, etc. Therefore, it is helpful to develop researches on the genetics of various diseases including hypertension in Mongolian population. OBJECTIVE： To analyze the association between the polymorphism of beta1 adrenergic receptor （β1-AR） gene G1165C （Arg389Gly）, an important candidate gene for various diseases of cardiovascular system, and essential hypertension in Mongolian population. DESIGN ： A cross-sectional study SETTINGS： Department of Neurology, the First Affiliated Hospital of Inner Mongolia Medical College; Wulate Houqi Red Cross Society. PARTICIPANTS： The survey was carried out from February 2003 to March 2005. Totally 239 Mongolian residents, whose blood relations of 3 generations were all Mongolians, were selected from Wulate Houqi, Inner Mongolia, and they were all informed with the survey and detected items. Based on the diagnostic standard of hypertension set by WHO in 1999, the subjects were divided into two groups according to the level blood pressure： ① Normal blood pressure group （n=117）： systolic blood pressure （SBP） 〈 140 mm Hg （1 mm Hg =0.133 kPa）, diastolic blood pressure （DBP） 〈 90 mm Hg, and those having histories of cerebrovascular disease, heart disease, diseases of liver, kidney and tiroides, and diabetes mellitus were excluded. ② Essential hypertension group （n=122）： including 51 patients with simple high SBP. All the enrolled subjects had no blood relationship with each other, and had no history of miscegenation. METHODS ： The body height, body mass, waist circumference and blood lipids were measured routinely, and their habits of smoking and drinking were also investigated. Penpheral venous blood （5 mL） was drawn, the genome DNA was extracted, and the polymorphisms of the β1-AR Gl165C （Gly389Arg） genotype were detected with the Sequenom system. Polymerase chain reaction （PCR） experiment and SNP detection were performed in Huada Gene Laboratory of Bejing, then the univariate analysis of variance was applied in the sample comparison among groups, and the chi-square test was used to compare the genotypes and allele frequencies. The odd ratio （OR） and 95% confidence interval （CO were calculated. MAIN OUTCOME MEASURES： The distributions of β1-AR Gl165C （Gly389Arg） genotypes and alleles were observed. RESULTS： A11 the 239 subjects were involved in the analysis of results, and no one missed, ①Comparison of β1-AR G1165C （Gly389Arg） genotypes and allele distnbutions： In Mongolian population, the frequencies of CC and GG＋GC genotypes at β1-AR G1165C （Gly389Arg） site in the essential hypertension group （72%, 28%） were not significantly different from those in the normal blood pressure group （67%, 33%） （xz=0.841, P=-0.359; OR 0.773, 95%Cl： 0.445-1.342）; The frequencies of C and G alleles also had no significant differences between the essential hypertension group （85%, 15%） and the normal blood pressure group （82%, 18%） （x^2=1.136, P=-0.287; OR： 0.769, 95%Cl： 0.747-1.248）. ②The frequencies of CC and GG＋GC genotypes at β1-AR G1165C （Gly389Arg） site had no significant differences between the patients with simple high SBP （71%, 29%） and the normal blood pressure group （x^2=0.250, P=-0.617; OR： 0.833, 95%C/： 0.408-1.703）; The frequencies of C and G alleles were not significantly different between the patients with simple high SBP （86%, 14%） and the normal blood pressure group （x^2=0.670, P=-0.413; OR 0.766, 95%Cl： 0.404-1.453）. CONCLUSION： In Mongolian population, the distributions of the genotypes and alleles of β1-AR Gl165C （Gly389Arg） have no obvious differences between the subjects with normal blood pressure and the patients with essential hypertension （including simple SBP increase）, which suggests that G1165C （Glu389Asp） site of β1-AR gene may be not a genetic mark of essential hypertension and simple high SBP in Mongolian population.

Association of Connexin Gene Polymorphism with Essential Hypertension in Kazak and Han Chinese in Xinjiang,China

Essential hypertension（EH） is affected by both genetic and environmental factors.The polymorphism of connexin（Cx） genes is found associated with the development of hypertension.However,the association of the polymorphism of Cxs with EH has not been investigated.This study aimed to investigate the association of the polymorphism of connexin（Cx） genes Cx37,Cx40,and Cx43 with EH in Kazak and Han Chinese in Xinjiang,China.Polymerase chain reaction-restriction fragment length polymorphism（PCR-RFLP） method and matrix-assisted laser desorption ionization time-of-flight mass spectrometry（MALDI-TOF-MS） were used to analyze the polymorphism of Cx genes in Kazak and Han EH patients as well as their normotensive controls.The results showed that there were no significant differences in the frequencies of different three genotypes（A/A,A/G,and G/G） and A and G alleles of Cx40 rs35594137 and rs11552588 between EH patients and normotensive controls.However,in Kazak EH patients,the frequencies of three genotypes（A/A,A/G,and G/G） of Cx37 rs1630310 were 24.8%,47.2% and 28.0%,respectively,which were significantly different from those in Han EH patients.In Han EH patients,the frequencies of the three genotypes（C/C,C/G and G/G） of Cx43 rs1925223 were 6.4%,35.6% and 58.0%,respectively.Frequencies of the other four genotypes had no statistical differences among Kazak and Han EH patients and their normotensive controls.These results suggest polymorphisms of Cx37 rs1630310 and Cx43 rs1925223 genes may be associated with the pathogenesis of EH.Carrying Cx37 rs1630310-A or Cx43 rs1925223-G genotypes may protect against the development of EH.

POLYMORPHISM OF ANGIOTENSIN I TYPE 1 RECEPTOR GENE IN ELDERLY PATIENTS WITH ESSENTIAL HYPERTENSION

Objective To detect the A/C1165 polymorphism of angiotensin Ⅱ type Ⅰ receptor (AT1-R)gene in essential hypertensive elderly. Methods The A/C1166 polymorphism of AT1-R gene was assessed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in a case-control study of 87 essential hypertensive elders (EH) and 55 normolensive elders (NT). Results The genotype frequencies of AA, AC, CC were 0 .805 , 0.161, 0 .034 in EH group and 0 .927 ,0 .073 ,0 .000 in NT group respectively. The frequency of C61166 allele was higher in EH group (0.115) than in NT group (0 .036 )(P<0 .05 ). Conclusion The resultsindicate that A/C1166 polymorphism of AT1-R gene may be associated with essential hypertension in elderly.

Association of angiotensin Ⅱ type 1 receptor gene polymorphism with essential hypertension

Objective To determine whether the polymorphism A1166C in the angiotensin Ⅱ type 1 receptor (AT1R) gene is associated with essential hypertension Methods A casecontrol study was carried out using 125 hypertensive and 103 normotensive subjects The AC variant at position 1166 (A1166C) of the AT 1R gene was identified by polymerase chain reaction (PCR) and PCR/restriction fragment length polymorphism (PCR/RFLP) analysis The digestion products were separated on 2% agarose gels and visualized with ethidium bromide under ultraviolet ray Results The differences in C1166 allele frequency and in the AC genotype distribution of the AT 1R gene between the hypertensive and normotensive groups were statistically significant (C allele: 0.092 vs 0.034, χ2=6.1.86,P<0.05; AC genotype: 0.184 vs 0.068, χ2=6.654,P<0.05) Conclusion The AC genotype is associated with essential hypertension, and the C allele may be a marker for predisposition to hypertension in Chinese Han population

Systematic Analysis of 42 Autographa Californica Multiple Nucleopolyhedrovirus Genes Identifies An Additional Six Genes Involved in the Production of Infectious Budded Virus

Baculoviruses have been widely used as a vector for expressing foreign genes.Among numerous baculoviruses,Autographa californica multiple nucleopolyhedrovirus(AcMNPV)is the most frequently used and it encodes 155 open reading frames(ORFs).Here,we systematically investigated the impact of 42 genes of AcMNPV on the production of infectious budded viruses(BVs)by constructing gene-knockout bacmids and subsequently conducting transfection and infection assays.The results showed that among the 39 functionally unverified genes and 3 recently reported genes,36 are dispensable for infectious BV production,as the one-step growth curves of the gene-knockout viruses were not significantly different from those of the parental virus.Three genes(ac62,ac82 and ac106/107)are essential for infectious BV production,as deletions thereof resulted in complete loss of infectivity while the repaired viruses showed no significant difference in comparison to the parental virus.In addition,three genes(ac13,ac51 and ac120)are important but not essential for infectious BV production,as gene-knockout viruses produced significantly lower BV levels than that of the parental virus or repaired viruses.We then grouped the 155 AcMNPV genes into three categories(Dispensable,Essential,or Important for infectious BV production).Based on our results and previous publications,we constructed a schematic diagram of a potential mini-genome of AcMNPV,which contains only essential and important genes.The results shed light on our understanding of functional genomics of baculoviruses and provide fundamental information for future engineering of baculovirus expression system.

Association of Renin Binding Protein(RnBP) Gene Polymorphisms with Essential Hypertension in the Hani Minority of Southwestern China

Essential hypertension is one of the most common multi- factorial diseases, affecting 20%--30% of the human popula- tion （Ibrahim and Damasceno, 2012）. Based on the results of twin studies, adoption studies and statistical analyses of blood pressure （BP） across various pedigrees, it has been estimated that 30%--50% of the variability in blood pressure among the general population is genetically determined （Garcia et al., 2003）. Although the genetic mechanisms of essential hyper- tension have not been studied well, investigations for the genes that constitute the renin-angiotensin system （RAS） appear to be particularly promising, since this system plays a central role in the regulation of blood pressure （Ferrario, 2010）.

Less Is More, Natural Loss-of-Function Mutation Is a Strategy for Adaptation

Gene gain and loss are crucial factors that shape the evolutionary success of diverse organisms.In the past two decades,more attention has been paid to the significance of gene gain through gene duplication or de novo genes.However,gene loss through natural loss-of-function(LoF)mutations,which isprevalent in the genomes of diverse organisms,has been largely ignored.With the development of sequencing techniques,many genomes have been sequenced across diverse species and can be used to study the evolutionary patterns of gene loss.In this review,we summarize recent advances in research on various aspects of LoF mutations,including their identification,evolutionary dynamics in natural populations,and functional effects.In particular,we discuss how LoF mutations can provide insights into the minimum gene set(or the essential gene set)of an organism.Furthermore,we emphasize their potential impact on adaptation.At the genome level,although most LoF mutations are neutral or deleterious,at least some of them are under positive selection and may contribute to biodiversity and adaptation.Overall,we highlight the importance of natural LoF mutations as a robust framework for understanding biological questions in general.

Comparative analysis of metabolic network of pathogens

BACKGROUND： Metabolic networks are complex and system of highly connected chemical reactions and hence it needs a system level computational approach to identify the genotype- phenotype relationship. The study of essential genes and reactions and synthetic lethality of genes and reactions plays a crucial role in explaining functional links between genes and gene function predictions. METHODS： Flux balance analysis （FBA） has been developed as a powerful method for the in silico analyses of metabolic networks. In this study, we present the comparative analysis of the genomic scale metabolic networks of the four microorganisms i.e. Salmonella typhimurium, Mycobacterium tuberculosis, Staphylococcus aureus, and Helicobacter pylori. The fluxes of all reaction were obtained and the growth rate of the organism was calculated by setting the biomass reaction as the objective function. RESULTS ＆ CONCLUSIONS： The average lethality fraction of all the four organisms studied ranged from 0.2 to 0.6. It was also observed that there are very few metabolites which are highly connected. Those metabolites that are highly connected are supposed to be the ‘global players＇ similar to the hub protein in the protein - protein interaction network.

How to make a minimal genome for synthetic minimal cell

As a key focus of synthetic biology,building a minimal artificial cell has given rise to many discussions.A synthetic minimal cell will provide an appropriate chassis to integrate functional synthetic parts,devices and systems with functions that cannot generally be found in nature.The design and construction of a functional minimal genome is a key step while building such a cell/chassis since all the cell functions can be traced back to the genome.Kinds of approaches,based on bioinformatics and molecular biology,have been developed and proceeded to derive essential genes and minimal gene sets for the synthetic minimal genome.Experiments about streamlining genomes of model bacteria revealed genome reduction led to unanticipated beneficial properties,such as high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains.Recent achievements in chemical synthesis technology for large DNA segments together with the rapid development of the wholegenome sequencing,have transferred synthesis of genes to assembly of the whole genomes based on oligonucleotides,and thus created strong preconditions for synthesis of artificial minimal genome.Here in this article,we review briefly the history and current state of research in this field and summarize the main methods for making a minimal genome.We also discuss the impacts of minimized genome on metabolism and regulation of artificial cell.