Assessing determinants of exonic evolutionary rates in mammals

From studies investigating the differences in evolutionary rates between genes, gene compactness and gene expression level have been identified as important determinants of gene-level protein evolutionary rate, as represented by nonsynonymous to synonymous substitution rate (d(N)/d(S)) ratio. However, the causes of exon-level variances in d(N)/d(S) are less understood. Here, we use principal component regression to examine to what extent 13 exon features explain the variance in d(N), d(S), and the d(N)/d(S) ratio of human-rhesus macaque or human-mouse orthologous exons. The exon features were grouped into six functional categories: expression features, mRNA splicing features, structural-functional features, compactness features, exon duplicability, and other features, including G + C content and exon length. Although expression features are important for determining d(N) and d(N)/d(S) between exons of different genes, structural-functional features and splicing features explained more of the variance for exons of the same genes. Furthermore, we show that compactness features can explain only a relatively small percentage of variance in exon-level d(N) or d(N)/d(S) in either between-gene or within-gene comparison. By contrast, d(S) yielded inconsistent results in the human-mouse comparison and the human-rhesus macaque comparison. This inconsistency may suggest rapid evolutionary changes of the mutation landscape in mammals. Our results suggest that between-gene and within-gene variation in d(N)/d(S) (and d(N)) are driven by different evolutionary forces and that the role of mRNA splicing in causing the variation in evolutionary rates of coding sequences may be underappreciated.     

Gene expression induced by physical impedance in maize roots

Two cDNA clones, pIIG1 and pIIG2, corresponding to mRNAs that accumulate in maize root tips subjected to 10 min of physical impedance, were isolated by differential screening of a cDNA library. The deduced proteins, based on DNA sequence analysis, have molecular masses of 13 and 23 kDa for pIIG1 and pIIG2, respectively. pIIG1 showed 97% similarity at the nucleic acid level to a maize root cortical cell delineating protein (pZRP3) and was also similar to some bimodular proteins that are developmentally or stress regulated in other plant species. In situ localization of pIIG1 showed some expression in cortical cells of control maize roots; however, after a 10 min physical impedance treatment, pIIG1 accumulation increased greatly in cortical cells and extended to include the procambial region. pIIG2 did not show sequence similarity with any identified gene of known function, but a bipartite nuclear targeting sequence occurs in its deduced amino acid sequence which indicates it may function in the nucleus. Thus, rapid accumulation of specific mRNAs occurs in maize roots in response to impedance stress, and these mRNAs may be responsible for some responses of the roots to physical impedance.     

精氨酸甲基转移酶（PRMT）7通过IGF-1信号通路调控人骨髓间充质干细胞成脂分化的研究

目的 本研究旨在明确精氨酸甲基转移酶（PRMT）7在人骨髓间充质干细胞（hBMSCs）成脂分化过程中的变化以及是否调控hBMSCs成脂分化,进而探索相应的调控机制。方法 通过定量反转录PCR（qRT-PCR）和蛋白质印迹（Western blot）检测hBMSCs成脂分化过程中PRMT7的变化;通过qRT-PCR和Western blot实验证明PRMT7稳定敲低细胞系构建成功。进行油红O染色和定量分析,以及qRT-PCR和Western blot实验检测PRMT7稳定敲低细胞系成脂分化水平的变化;通过裸鼠体内异位成脂实验,油红O染色检测PRMT7稳定敲低细胞系体内异位成脂的效果;通过qRT-PCR和Western blot证明PRMT7稳定过表达细胞系构建成功。进行油红O染色和定量分析以及qRT-PCR和Western blot实验检测PRMT7稳定过表达细胞系成脂分化水平的变化;通过qRT-PCR和Western blot实验检测敲低PRMT7和过表达PRMT7的细胞中IGF-1表达水平的变化。在PRMT7稳定敲低细胞系中转染siIGF-1并通过qRT-PCR和Western blot检测IGF-1的表达水平验证敲低效率。通过油红O染色和定量分析,qRT-PCR实验检测转染siIGF-1的敲低组hBMSCs成脂分化水平的变化。结果 本文发现：在hBMSCs成脂过程中,PRMT7表达水平明显降低（P<0.01）;敲低PRMT7后hBMSCs的成脂分化能力增强（P<0.001）;敲低PRMT7后hBMSCs的体内异位成脂分化能力增强;过表达PRMT7后hBMSCs的成脂分化能力减弱（P<0.01）;PRMT7敲低后IGF-1表达水平增加（P<0.000 1）;PRMT7过表达后IGF-1表达水平降低（P<0.000 1）;转染siIGF-1后,各细胞系IGF-1表达水平明显降低（P<0.001）;敲低组转染siIGF-1后成脂分化能力明显降低（P<0.01）。结论 本研究通过细胞水平和裸鼠皮下移植实验发现PRMT7显著抑制hBMSCs成脂分化,机制研究发现PRMT7对hBMSCs成脂分化的调控作用依赖IGF-1信号通路。上述研究表明,PRMT7可能是治疗相关疾病的潜在分子靶点,为PRMT7和hBMSCs应用于相关疾病治疗提供了新思路。     

From pure C36 fullerene to cagelike nanocluster: a density functional study

The geometrical structures, energetics properties, and aromaticity of C_36-n Si _n (n?≤?18) fullerene-based clusters were studied using density functional theory calculations. The geometries of C_36-n Si _n clusters undergo strong structural deformation with the increase of Si substitution. For the most energy favorable structures of C_36-n Si _n , the silicon and carbon atoms form two distinct homogeneous segregations. Subsequently, the binding energy, HOMO–LUMO energy gap, vertical ionization potential, vertical electron affinity, and chemical hardness for the energetic favorable C_36-n Si _n geometries were computed and analyzed. In addition, the aromatic property of C_36-n Si _n cagelike clusters was investigated, and the result demonstrate that these C_36-n Si _n cagelike structures possess strong aromaticity.     

A novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with Comamonas sp. strain CNB-1

Comamonas sp. strain CNB-1 degrades nitrobenzene and chloronitrobenzene via the intermediates 2-aminomuconate and 2-amino-5-chloromuconate, respectively. Deamination of these two compounds results in the release of ammonia, which is used as a source of nitrogen for bacterial growth. In this study, a novel deaminase was purified from Comamonas strain CNB-1, and the gene (cnbZ) encoding this enzyme was cloned. The N-terminal sequence and peptide fingerprints of this deaminase were determined, and BLAST searches revealed no match with significant similarity to any functionally characterized proteins. The purified deaminase is a monomer (30 kDa), and its V(max) values for 2-aminomuconate and 2-amino-5-chloromuconate were 147 micromol x min(-1) x mg(-1) and 196 micromol x min(-1) x mg(-1), respectively. Its catalytic products from 2-aminomuconate and 2-amino-5-chloromuconate were 2-hydroxymuconate and 2-hydroxy-5-chloromuconate, respectively, which are different from those previously reported for the deaminases of Pseudomonas species. In the catalytic mechanism proposed, the alpha-carbon and nitrogen atoms (of both 2-aminomuconate and 2-amino-5-chloromuconate) were simultaneously attacked by a hydroxyl group and a proton, respectively. Homologs of cnbZ were identified in the genomes of Bradyrhizobium japonicum, Rhodopseudomonas palustris, and Roseiflexus sp. strain RS-1; these genes were previously annotated as encoding hypothetical proteins of unknown function. It is concluded that CnbZ represents a novel enzyme that deaminates xenobiotic compounds and/or alpha-amino acids.     

The Complete Genome of Comamonas testosteroni Reveals Its Genetic Adaptations to Changing Environments

Members of the gram-negative, strictly aerobic genus Comamonas occur in various environments. Here we report the complete genome of Comamonas testosteroni strain CNB-2. Strain CNB-2 has a circular chromosome that is 5,373,643 bp long and has a G+C content of 61.4%. A total of 4,803 open reading frames (ORFs) were identified; 3,514 of these ORFs are functionally assigned to energy production, cell growth, signal transduction, or transportation, while 866 ORFs encode hypothetical proteins and 423 ORFs encode purely hypothetical proteins. The CNB-2 genome has many genes for transportation (22%) and signal transduction (6%), which allows the cells to respond and adapt to changing environments. Strain CNB-2 does not assimilate carbohydrates due to the lack of genes encoding proteins involved in glycolysis and pentose phosphate pathways, and it contains many genes encoding proteins involved in degradation of aromatic compounds. We identified 66 Tct and nine TRAP-T systems and a complete tricarboxylic acid cycle, which may allow CNB-2 to take up and metabolize a range of carboxylic acids. This nutritional bias for carboxylic acids and aromatic compounds enables strain CNB-2 to occupy unique niches in environments. Four different sets of terminal oxidases for the respiratory system were identified, and they putatively functioned at different oxygen concentrations. This study conclusively revealed at the genomic level that the genetic versatility of C. testosteroni is vital for competition with other bacteria in its special niches.The members of the genus Comamonas are gram-negative, strict aerobes and frequently occur in diverse habitats, including activated sludge, marshes, marine habitats, and plant and animal tissues (4, 12, 13). They grow on organic acids, amino acids, and peptone, but they rarely attack carbohydrates. Some species, such as Comamonas testosteroni, can also mineralize complex and xenobiotic compounds, such as testosterone (17) and 4-chloronitrobenzene (CNB) (54). Their diversified niches make Comamonas species environmentally important and also suggest that the genus Comamonas represents a group of bacteria that can adapt very well, both ecologically and physiologically, to environments.To understand better how environmental microbes adapt to their environments, many well-known environmental microbes, such as Pseudomonas putida (53) and Rhodococcus sp. strain RAH1 (31), have been sequenced. The genome data for these organisms, as well as other environmental microbes, provide not only an understanding of physiological and environmental functions at the genetic level but also a starting point for systems biology analyses of these microbes. Until now, none of the Comamonas species has been sequenced, although these organisms represent an important group of environmental microbes.C. testosteroni strain CNB-1 was isolated from CNB-contaminated activated sludge and grows with CNB as a sole source of carbon and nitrogen, and it has been used successfully for rhizoremediation of CNB-polluted soil (25). Strain CNB-1 has a circular chromosome and a large plasmid, and the genes involved in the degradation of CNB on plasmid pCNB1 were identified previously (28). In the present study, the genome of strain CNB-2, which was derived from strain CNB-1, was sequenced, and a genome analysis was performed parallel to physiological experiments. The aim of this work was to obtain genetic insight into how C. testosteroni adapts to changing and diverse environments.