Low Divergence of Clonorchis sinensis in China Based on Multilocus Analysis

Clonorchis sinensis, an ancient parasite that infects a number of piscivorous mammals, attracts significant public health interest due to zoonotic exposure risks in Asia. The available studies are insufficient to reflect the prevalence, geographic distribution, and intraspecific genetic diversity of C. sinensis in endemic areas. Here, a multilocus analysis based on eight genes (ITS1, act, tub, ef-1a, cox1, cox3, nad4 and nad5 [4.986 kb]) was employed to explore the intra-species genetic construction of C. sinensis in China. Two hundred and fifty-six C. sinensis isolates were obtained from environmental reservoirs from 17 provinces of China. A total of 254 recognized Multilocus Types (MSTs) showed high diversity among these isolates using multilocus analysis. The comparison analysis of nuclear and mitochondrial phylogeny supports separate clusters in a nuclear dendrogram. Genetic differentiation analysis of three clusters (A, B, and C) showed low divergence within populations. Most isolates from clusters B and C are geographically limited to central China, while cluster A is extraordinarily genetically diverse. Further genetic analyses between different geographic distributions, water bodies and hosts support the low population divergence. The latter haplotype analyses were consistent with the phylogenetic and genetic differentiation results. A recombination network based on concatenated sequences showed a concentrated linkage recombination population in cox1, cox3, nad4 and nad5, with spatial structuring in ITS1. Coupled with the history record and archaeological evidence of C. sinensis infection in mummified desiccated feces, these data point to an ancient origin of C. sinensis in China. In conclusion, we present a likely phylogenetic structure of the C. sinensis population in mainland China, highlighting its possible tendency for biogeographic expansion. Meanwhile, ITS1 was found to be an effective marker for tracking C. sinensis infection worldwide. Thus, the present study improves our understanding of the global epidemiology and evolution of C. sinensis.     

Horizontal gene transfer in an acid mine drainage microbial community

Background

Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance.

Results

Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT.

Conclusions

Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1720-0) contains supplementary material, which is available to authorized users.     

Water-protein interplay reveals the specificity of α-lytic protease

Wild type and mutant α-lytic protease, differing by only one amino acid, have distinct specificities. Previous studies have shown that motion patterns of the binding pocket play an important role. However, it is still unclear how these differences are generated from a single amino acid mutation. Based on comparative molecular dynamics simulations using explicit and implicit solvent models, we studied the dynamic properties of both protein and water. The explicit solvent simulations showed specificity related differences in the energy landscapes and the power spectra between the two enzymes, whereas implicit solvent simulations did not. Moreover, the explicit solvent simulations demonstrated obvious distinctions in dynamic behaviors of water, such as their residence behaviors and hydrogen bonding. These results suggest that the interplay between water and enzyme is essential in determining the substrate specificity, and the detail knowledge of such interplay can greatly improve our understanding of bio-molecules.     

Melanin in a Meristematic Mutant of Fonsecaea monophora Inhibits the Production of Nitric Oxide and Th1 Cytokines of Murine Macrophages

Melanin is a complex polymer which is secreted outside or constitutes the structure of fungal cell wall. It is considered as an important virulence factor in opportunistic pathogenic fungi. In this study, one albino mutant (CBS 125149) was generated from a parent meristematic mutant (CBS 122845) of Fonsecaea monophora. Transmission electron microscopy profiles showed that melanin in the parent strains appeared as electron-dense granules which located on the cell wall surface. We extracted the cell wall fractions from the two different strains by an alkali–acid method. The different strains or its cell wall fractions were interacted with the activated RAW264.7. The pigmented strain and its cell wall fraction could reduce the expression of inducible nitric oxide synthase gene and inhibit the synthesis of nitric oxide in vitro (P < 0.05). Exacerbated Th2 and inhibited Th1 response occurred in the interaction between activated RAW264.7 and the pigmented strain or its cell wall fraction. Collectively, our results suggest that melanin plays an important role in escaping the killing of oxidative burst in vitro. The exacerbated Th2 response probably accelerates the persistence of the fungus.     

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes

Background

Shine-Dalgarno (SD) signal has long been viewed as the dominant translation initiation signal in prokaryotes. Recently, leaderless genes, which lack 5'-untranslated regions (5'-UTR) on their mRNAs, have been shown abundant in archaea. However, current large-scale in silico analyses on initiation mechanisms in bacteria are mainly based on the SD-led initiation way, other than the leaderless one. The study of leaderless genes in bacteria remains open, which causes uncertain understanding of translation initiation mechanisms for prokaryotes.

Results

Here, we study signals in translation initiation regions of all genes over 953 bacterial and 72 archaeal genomes, then make an effort to construct an evolutionary scenario in view of leaderless genes in bacteria. With an algorithm designed to identify multi-signal in upstream regions of genes for a genome, we classify all genes into SD-led, TA-led and atypical genes according to the category of the most probable signal in their upstream sequences. Particularly, occurrence of TA-like signals about 10 bp upstream to translation initiation site (TIS) in bacteria most probably means leaderless genes.

Conclusions

Our analysis reveals that leaderless genes are totally widespread, although not dominant, in a variety of bacteria. Especially for Actinobacteria and Deinococcus-Thermus, more than twenty percent of genes are leaderless. Analyzed in closely related bacterial genomes, our results imply that the change of translation initiation mechanisms, which happens between the genes deriving from a common ancestor, is linearly dependent on the phylogenetic relationship. Analysis on the macroevolution of leaderless genes further shows that the proportion of leaderless genes in bacteria has a decreasing trend in evolution.

     

Molecular cloning, characterization and differential expression of Cdc42 in Fonsecaea monophora

The cell divisions cycle 42 (Cdc42) gene has been characterized in the fungi, such as Candida albicans, Penicillium marneffei, and Wangiella (Exophiala) dermatitidis, which plays important roles during growth and development. The partial cDNA sequence of Cdc42 of Fonsecaea monophora (F. monophora), designated FmCdc42, was obtained using degenerate primers based on the conserved domain of the other fungi Cdc42. Then the complete cDNA sequence of FmCdc42 was obtained by 5′ and 3′ RACE. The full-length cDNA is 1,510 bp in size which had an open reading frame (ORF) of 582 bp, encoding 193 amino acid residues. The predicted molecular mass of FmCdc42 is 21.5 kDa with an estimated theoretical isoelectric point of 5.67. The deduced amino acid sequence of FmCdc42 shows 99% identity to that of Wangiella (Exophiala) dermatitidis. 5 exons and 4 introns are identified within the 1,617 bp FmCdc42 genomic DNA sequence of F. monophora. The ORF could be subcloned into the pCDNA6/myc-His B expression vector. The recombinant protein about 27.5 kD infusion protein had high expression level in Vero cells with SDS-PAGE and Western blot analysis. Quantitative real time RT-PCR revealed that FmCdc42 was the highest expression in the sclerotic bodies’ stage compared with that in the mycelia and conidia stages, which indicated that the FmCdc42 may be involved in formation of F. monophora sclerotic bodies.     

冷榨花生粕蛋白胨质量分析及其在枯草芽胞杆菌增殖中的应用

为降低微生物培养基制备成本和实现冷榨花生粕蛋白质的深加工,本试验以双酶协同酶解（胃蛋白酶+碱性蛋白酶）冷榨花生粕蛋白质制备植物蛋白胨,从一般性状检查和化学指标两个方面对冷榨花生粕蛋白胨进行了质量分析。参考《微生物培养基的制造与应用》和《中国生物制品主要原辅材料质控标准》对蛋白胨进行了质量评价,并以枯草芽胞杆菌为试验菌进行了冷榨花生粕蛋白胨对细菌的增殖培养试验以评价其质量优劣。结果表明,双酶协同酶解制备得到的冷榨花生粕蛋白胨各项指标均满足生化蛋白胨的质量标准,与标准蛋白胨（胰蛋白胨）的对照试验发现两者差异不显著（p>0.05）,冷榨花生粕蛋白胨可完全替代胰蛋白胨用于枯草芽胞杆菌的增殖培养。