Enzymatic characterization of Catalase from Bacillus anthracis and prediction of critical residues using information theoretic measure of Relative Entropy

In order to cope up with the reactive oxygen species (ROS) generated by host innate immune response, most of the intracellular organisms express Catalase for the enzymatic destruction/detoxification of hydrogen peroxide, to combat its deleterious effects. Catalase thus, scavenges ROS thereby playing a pivotal role in facilitating the survival of the pathogen within the host, and thus contributes to its pathogenesis. Bacillus anthracis harbors five isoforms of Catalase, but none of them has been studied so far. Thus, this study is the first attempt to delineate the biochemical and functional characteristics of one of the isoforms of Catalase (Cat1.4) of B. anthracis, followed by identification of residues critical for catalysis. The general strategy used, so far for mutational analysis in Catalases is structure based, i.e. the residues in the vicinity of heme were mutated to decipher the enzymatic mechanism. However, in the present study, protein sequence analysis was used for the prediction of catalytically important residues of Catalase. Essential measures were adopted to ensure the accuracy of predictions like after retrieval of well-annotated sequences from the database with EC 1.11.1.6, preprocessing was done to remove irrelevant sequences. The method used for multiple alignment of sequences, was guided by structural alignment and thereafter, an information theoretic measure, Relative Entropy was used for the critical residue prediction. By exploiting this strategy, we identified two previously known essential residues, H55 and Y338 in the active site which were demonstrated to be crucial for the activity. We also identified six novel crucial residues (Q332, Y117, H215, W257, N376 and H146) located distantly from the active site. Thus, the present study highlights the significance of this methodology to identify not only those crucial residues which lie in the active site of Catalase, but also the residues located distantly.     

Manganese and Arsenic Oxidation Performance of Bacterium-Yunotaki 86 (BY86) from Hokkaido,Japan, and the Bacterium's Phylogeny

We examined the Mn(II) oxidation performance of a bacterium, BY86, collected at Yunotaki Falls Hokkaido, Japan. The bacterium showed rapid oxidation of Mn(II), and brown precipitates containing Mn formed within a few days of incubation. The presence of higher oxidation states of Mn than Mn(II) was ascertained by the UV-vis and XANES sutdy. This bacterium did not oxidize As(III) to As(V) in the absence of Mn. In the presence of Mn, however, As(III) was rapidly oxidized to As(V) on the cell surfaces. These findings indicate that BY86 does not have the ability to directly oxidize As(III) to As(V) within a short period of contact, but indirectly oxidizes it by the Mn oxides generated on the cell surfaces. A phylogenetical study disclosed that BY86 was most closely related to Bacillus cereus with an identity of 99.90%. It is expected that our findings in this study will contribute to the study of Mn(II)-oxidizing bacteria, which play an important role in the biogeochemical cycling of Mn as well as other trace elements including As.     

天名精倍半萜内酯化合物

从菊科天名精全草中分得天名精内酯酮,特勒内酯,11（13）－二氢特勒内酯和异埃瓦内酯。其中11（13）－二氢特勒内酯和异埃瓦内酯为新的天然产物。     

生物素对地衣芽孢杆菌生长和乳酸形成的影响

生物素对地衣芽孢杆菌生长和乳酸形成的影响胡尚勤（重庆师范学院生物系重庆６３００４７）地衣芽孢杆菌（Ｂａｃｉｌｕｓｌｉｃｇｅｎｉｆｏｒｍｉｓ）是我国９０年代首次从正常待产妇阴道拭子分离出来的一个无毒新菌株。现在国内已经用它来生产“整肠生”活菌剂。它是一...     

Role of lipopeptides produced by Bacillus subtilis GA1 in the reduction of grey mould disease caused by Botrytis cinerea on apple

AIM: Test of Bacillus subtilis strain GA1 for its potential to control grey mould disease of apple caused by Botrytis cinerea. METHODS AND RESULTS: GA1 was first tested for its ability to antagonize in vitro the growth of a wide variety of plant pathogenic fungi responsible for diseases of economical importance. The potential of strain GA1 to reduce post-harvest infection caused by B. cinerea was tested on apples by treating artificially wounded fruits with endospore suspensions. Strain GA1 was very effective at reducing disease incidence during the first 5 days following pathogen inoculation and a 80% protection level was maintained over the next 10 days. Treatment of fruits with an extract of GA1 culture supernatant also exerted a strong preventive effect on the development of grey mould. Further analysis of this extract revealed that strain GA1 produces a wide variety of antifungal lipopeptide isomers from the iturin, fengycin and surfactin families. A strong evidence for the involvement of such compounds in disease reduction arose from the recovery of fengycins from protected fruit sites colonized by bacterial cells. CONCLUSIONS: The results presented here demonstrate that, despite unfavourable pH, B. subtilis endospores inoculated on apple pulp can readily germinate allowing significant cell populations to establish and efficient in vivo synthesis of lipopeptides which could be related to grey mould reduction. SIGNIFICANCE AND IMPACT OF THE STUDY: This work enables for the first time to correlate the strong protective effect of a particular B. subtilis strain against grey mould with in situ production of fengycins in infected sites of apple fruits.     

Diversity of commensal Bacillus cereus sensu lato isolated from the common sow bug (Porcellio scaber, Isopoda)

Although Bacillus cereus sensu lato are important both from an ecological and an economical point of view, little is known about their population structure, ecology, and relationships with other organisms. In the present work, the genotypic similarity of arthropod-borne B. cereus s.l. isolates, and their symbiotic relationship with the host are assessed. Bacilli of this group were recovered from the digestive tracts of sow bugs (Porcellio scaber) collected in three closely located sites. Their genotypic diversity was investigated using pulse-field gel electrophoresis (PFGE) following the whole-genome DNA digestions with NotI and AscI, and PCR amplification of virulence genes. The majority of the sow-bug Bacillus cereus sensu stricto isolates originating from the same but also from different sites displayed identical PFGE patterns, virulence gene content and enterotoxicity, indicating strong genetic and genomic relationships. The sow-bug Bacillus mycoides/Bacillus pseudomycoides strains displayed a higher diversity. The isopod-B. cereus s.l. relationship was also evaluated using antibiotic-resistant derivatives of B. cereus s.s., B. mycoides/B. pseudomycoides and Bacillus thuringiensis reintroduced into sow bugs. Both spores and vegetative cells of B. cereus s.l. were recovered from sow bugs over a 30-day period, strongly suggesting that these bacteria are natural residents of terrestrial isopods.     

黑水虻肠道细菌抗菌筛选及其活性物质分子鉴定

【目的】从昆虫黑水虻分离的肠道细菌进行抗植物病原菌的拮抗菌筛选,对获得有拮抗活性的肠道细菌进行活性物质的分子鉴定。【方法】用稀释涂布法从水虻肠道中分离菌株,采用平板对峙法进行抗菌筛选,对有抗菌活性的菌株通过生理生化实验、16S rRNA鉴定和进化树分析确定其种属。参考已知脂肽合成关键基因设计引物,以拮抗菌总DNA为模板进行PCR扩增,对目的片段进行测序。【结果】通过抗菌筛选获得一株对水稻黄单胞菌以及小麦纹枯病病原菌等有很强抑制效果的水虻肠道细菌BSF-CL,经鉴定为枯草芽胞杆菌。脂肽合成关键基因PCR结果显示BSF-CL菌株具有脂肽Iturin和Surfactin合成的关键基因。推测BSF-CL很可能合成脂肽Iturin和Surfactin。【结论】从水虻肠道中分离出对水稻黄单胞菌有很强抑菌活性的菌株,分离菌被鉴定为一种枯草芽胞杆菌,通过活性物质的分子克隆鉴定初步推测其活性物质可能为脂肽Iturin和Surfactin。     

yhcZ基因在苏云金芽胞杆菌生长中的功能研究

在枯草芽胞杆菌和蜡样芽胞杆菌中,yhcZ基因和yhcY基因组成双组分系统调控细菌生长,但yhcZ基因在苏云金芽胞杆菌中发挥的生物学功能尚未明确。本研究通过基因功能注释、上下游基因排列分析和氨基酸序列比对,证实苏云金芽胞杆菌库斯塔克亚种HD73中HD73_5824基因为yhcZ基因,推测其与HD73_5825基因(yhcY基因)共同组成双组份系统调控细菌生长。利用同源重组技术敲除HD73菌株中的yhcZ基因获得缺失突变体HD (ΔyhcZ),其在LB和SSM培养基中生长均慢于野生型HD73,而互补菌株HD(ΔyhcZ::yhcZ)菌株则能够部分恢复生长,表明yhcZ基因的缺失影响了该菌株细胞的生长。在以0.4%葡萄糖为唯一碳源的M9培养基中,HD (ΔyhcZ)生长速度快于HD73,表明yhcZ基因在该菌株吸收利用葡萄糖的过程中发挥重要作用。Biolog实验显示HD (ΔyhcZ)的单孔颜色变化率低于HD73,且对D/L-丝氨酸、甲酸、D-葡糖酸、L-组胺,D-乳酸甲酯以及柠檬酸等的吸收利用能力低于HD73,表明yhcZ基因能显著影响HD73菌株对碳源的利用。同时,HD(ΔyhcZ)对8% NaCl的耐受能力弱于HD73,表明该基因可能参与细菌细胞应力响应相关基因的表达与调控。以上结果表明yhcZ基因在HD73菌株生长过程中对葡萄糖及其他碳源的利用具有重要的促进作用。本研究结果为解析yhcZ基因调控葡萄糖及碳源利用的分子机制奠定基础,且为进一步研究细菌生长及发酵提供参考。     

Biocatalytic asymmetric hydroxylation of hydrocarbons by free and immobilized Bacillus megaterium cells

Screening of soil bacteria with allylbenzene resulted in a Bacillus megaterium strain, which hydroxylates simple hydrocarbons in high enantiomeric excess (ee up to 99%). Benzylic and nonbenzylic hydroxylation products were obtained, without the usually observed high preference for the benzylic position. The immobilization of the B. megaterium cells in alginate gel effectively improved the stability of the cells and increased the amounts of products formed, without loss of enantioselectivity. The product ratio ( vs. β hydroxylation) was shifted towards benzylic hydroxylation, which suggests that at least two hydroxylating enzymes with distinct regioselectivity are involved. Comparison to free-cell fermentations in small- and large-scale bioreactors (up to 2000 ml) showed that the use of immobilized cells is advantageous, as they are easier to handle and yield higher amounts of oxidation products.     

Structure and function of psychrophilic alanine racemase

We describe the structure and function of psychrophilic alanine racemases from Bacillus psychrosaccharolyticus and Pseudomonas fluorescens. These enzymes showed high catalytic activities even at 0°C and were extremely labile at temperatures over 35°C. The enzymes were also found to be less resistant to organic solvents than alanine racemases from thermophilic and mesophilic bacteria, both in vivo and in vitro. Both enzymes have a dimeric structure and contain 2 mol of pyridoxal 5′-phosphate (PLP) per mol as a coenzyme. The enzyme from B. psychrosaccharolyticus was found to have a markedly large K_m value (5.0 μM) for PLP in comparison with other reported alanine racemases, and was stable at temperatures up to 50°C in the presence of excess amounts of PLP. The dissociation of PLP from the P. fluorescens enzyme may trigger the unfolding of the secondary structure. The enzyme from B. psychrosaccharolyticus has a distinguishing hydrophilic region around residue no. 150 in its deduced amino acid sequence, whereas the corresponding regions of other Bacillus alanine racemases are hydrophobic. The position of this region in the three dimensional structure of this enzyme was predicted to be in a surface loop surrounding the active site. This hydrophilic region may interact with solvent, reduce the compactness of the active site, and destabilize the enzyme.