Activity, stability, and structure of metagenome-derived LC11-RNase H1, a homolog of Sulfolobus tokodaii RNase H1

Metagenome‐derived LC11‐RNase H1 is a homolog of Sulfolobus tokodaii RNase H1 (Sto‐RNase H1). It lacks a C‐terminal tail, which is responsible for hyperstabilization of Sto‐RNase H1. Sto‐RNase H1 is characterized by its ability to cleave not only an RNA/DNA hybrid but also a double‐stranded RNA (dsRNA). To examine whether LC11‐RNase H1 also exhibits both RNase H and dsRNase activities, LC11‐RNase H1 was overproduced in Escherichia coli, purified, and characterized. LC11‐RNase H1 exhibited RNase H activity with similar metal ion preference, optimum pH, and cleavage mode of substrate with those of Sto‐RNase H1. However, LC11‐RNase H1 did not exhibit dsRNase activity at any condition examined. LC11‐RNase H1 was less stable than Sto‐RNases H1 and its derivative lacking the C‐terminal tail (Sto‐RNase H1ΔC6) by 37 and 13°C in T_m, respectively. To understand the structural bases for these differences, the crystal structure of LC11‐RNase H1 was determined at 1.4 Å resolution. The LC11‐RNase H1 structure is highly similar to the Sto‐RNase H1 structure. However, LC11‐RNase H1 has two grooves on protein surface, one containing the active site and the other containing DNA‐phosphate binding pocket, while Sto‐RNase H1 has one groove containing the active site. In addition, LC11‐RNase H1 contains more cavities and buried charged residues than Sto‐RNase H1. We propose that LC11‐RNase H1 does not exhibit dsRNase activity because dsRNA cannot fit to the two grooves on protein surface and that LC11‐RNase H1 is less stable than Sto‐RNase H1ΔC6 because of the increase in cavity volume and number of buried charged residues.     

A Novel Bioinformatics Strategy for Function Prediction of Poorly-Characterized Protein Genes Obtained from Metagenome Analyses

As a result of remarkable progresses of DNA sequencing technology, vast quantities of genomic sequences have been decoded. Homology search for amino acid sequences, such as BLAST, has become a basic tool for assigning functions of genes/proteins when genomic sequences are decoded. Although the homology search has clearly been a powerful and irreplaceable method, the functions of only 50% or fewer of genes can be predicted when a novel genome is decoded. A prediction method independent of the homology search is urgently needed. By analyzing oligonucleotide compositions in genomic sequences, we previously developed a modified Self-Organizing Map ‘BLSOM’ that clustered genomic fragments according to phylotype with no advance knowledge of phylotype. Using BLSOM for di-, tri- and tetrapeptide compositions, we developed a system to enable separation (self-organization) of proteins by function. Analyzing oligopeptide frequencies in proteins previously classified into COGs (clusters of orthologous groups of proteins), BLSOMs could faithfully reproduce the COG classifications. This indicated that proteins, whose functions are unknown because of lack of significant sequence similarity with function-known proteins, can be related to function-known proteins based on similarity in oligopeptide composition. BLSOM was applied to predict functions of vast quantities of proteins derived from mixed genomes in environmental samples.     

不同风化时间碳酸岩表面古菌群落结构与功能特征

【背景】古菌群落是碳酸岩表面微生物群落的重要成员,也是碳酸岩表面生物演替的先锋生物,能够促进碳酸岩风化和加快土壤形成,在生物地球化学循环中起重要作用。【目的】揭示在不同风化时间碳酸岩表面风化残积物中的古菌群落结构及生态功能。方法】采集19-213年风化时间段废弃碳酸岩墓碑表面风化残积物样品(n=18),基于宏基因组测序技术分析其古菌群落结构与功能特征。【结果】门水平上,优势门有广古菌门(Euryarchaeota),随后为奇古菌门(Thaumarchaeota)、未鉴定古菌门(unclassified Archaea)、深古菌门(Bathyarchaeota)和泉古菌门(Crenarchaeota);属水平上,优势属主要由甲烷八叠球菌属(Methanosarcina)、甲烷丝状菌属(Methanothrix)、Methanoperedens、氨氧化古菌属(Nitrosocosmicus)、亚硝化球菌属(Nitrososphaera)及其他未鉴定属组成;C/N、C/P、N/P是显著影响碳酸岩表面古菌群落的主要环境因子。进一步分析发现,碳酸岩表面古菌群落功能丰富,其中新陈代谢(metabo...     

嗜热菌群降解偶氮染料的特性及机制

【背景】印染废水的出水温度高,抑制了微生物对偶氮染料的降解,而关于嗜热菌在高温下降解偶氮染料的报道较少。【目的】富集能在高温下降解偶氮染料的嗜热微生物菌群,并研究其降解潜力和基因组特征。【方法】通过富集的方法获得嗜热微生物菌群,利用分光光度法测定其降解特性;采用全波长扫描、傅里叶变换红外吸收光谱(Fourier transform infrared spectroscopy,FTIR)和气相质谱(gas chromatography-mass spectrometer,GC-MS)分析其降解机理;采用植物毒性的方法比较偶氮染料降解前后的毒性;采用高通量测序技术分析其功能基因和群落结构。【结果】该菌群(SD1)可以在65℃降解偶氮染料,Caldibacillus、unclassified＿f＿＿Bacillaceae、Geobacillus等为优势属,在降解过程中起关键作用;菌群SD1能在较宽泛的p H (5.0-9.0)、温度(50-75℃)、染料浓度(100-500 mg/L)和盐度(1%-5%)降解酸性大红GR;偶氮还原酶和NADH-DCIP是主要的降解酶,GC-MS和FTIR结果...     

Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting

The functional basis for species sorting theory remains elusive, especially for microbial community assembly in deep‐sea environments. Using artificial surface‐based biofilm models, our recent work revealed taxonomic succession during biofilm development in a newly defined cold seep system, the Thuwal cold seeps II, which comprises a brine pool and the adjacent normal bottom water (NBW) to form a metacommunity via the potential immigration of organisms from one patch to another. Here, we designed an experiment to investigate the effects of environmental switching between the brine pool and the NBW on biofilm assembly, which could reflect environmental filtering effects during bacterial immigration to new environments. Analyses of 16S rRNA genes of 71 biofilm samples suggested that the microbial composition of biofilms established in new environments was determined by both the source community and the incubation conditions. Moreover, a comparison of 18 metagenomes provided evidence for biofilm community assembly that was based primarily on functional features rather than taxonomic identities; metal ion resistance and amino acid metabolism were the major species sorting determinants for the succession of biofilm communities. Genome binning and pathway reconstruction of two bacterial species (Marinobacter sp. and Oleispira sp.) further demonstrated metal ion resistance and amino acid metabolism as functional traits conferring the survival of habitat generalists in both the brine pool and NBW. The results of this study shed new light on microbial community assembly in special habitats and bridge a gap in species sorting theory.     

瘤胃微生物元基因组来源的新的组成型启动子获取

【目的】自极端环境来源的微生物的基因组中筛选新型的可用于合成生物学底盘细胞设计的启动子元件。【方法】本研究以含有绿色荧光蛋白结构基因和核糖体结合位点的探针型质粒pUC18-GFP为载体,通过构建瘤胃微生物元基因组质粒文库,从文库中快速高效筛选具有启动子功能的DNA片段。并且通过基于神经网络的启动子预测分析,获得可能的启动子区域。以绿色荧光蛋白和施氏假单胞菌Pseudomonas stutzeri来源的麦芽四糖淀粉酶作为报告基因验证所获得的新启动子片段的功能。【结果】我们从约3750个转化子中筛选到22条具有组成型启动子功能的DNA片段。这些片段与NCBI数据库中已报道的基因序列同源性较低,启动效率高低不等。我们通过启动子预测和亚克隆的方法获得两条全新的启动子片段RFa1p2 (76 bp)和RFb4p (547 bp)。此新的组成型启动子可以在不添加任何诱导剂的情况下启动异源蛋白在大肠杆菌基因工程菌中高效表达。     

Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families

Functional classification of proteins from sequences alone has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of the evolution of living organisms and for biotechnological applications. ProfileView is a sequence-based computational method, designed to functionally classify sets of homologous sequences. It relies on two main ideas: the use of multiple profile models whose construction explores evolutionary information in available databases, and a novel definition of a representation space in which to analyze sequences with multiple profile models combined together. ProfileView classifies protein families by enriching known functional groups with new sequences and discovering new groups and subgroups. We validate ProfileView on seven classes of widespread proteins involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions. ProfileView agrees with the large set of functional data collected for these proteins from the literature regarding the organization into functional subgroups and residues that characterize the functions. In addition, ProfileView resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of novel biological functions. On protein families with complex domain architecture, ProfileView functional classification reconciles domain combinations, unlike phylogenetic reconstruction. ProfileView proves to outperform the functional classification approach PANTHER, the two k-mer-based methods CUPP and eCAMI and a neural network approach based on Restricted Boltzmann Machines. It overcomes time complexity limitations of the latter.     

新型海洋微生物β-葡萄糖苷酶基因的克隆、表达及重组酶性质

通过功能筛选方法,从中国南海海洋表层海水微生物元基因组文库筛选得到了6个β-葡萄糖苷酶阳性克隆。对其中的一个阳性克隆pSB47B2进一步亚克隆和序列分析,获得一新型β-葡萄糖苷酶基因(命名为bgl1B)开放阅读框。以pET22b(+)为载体、Escherichia coli BL21(DE3)为宿主菌,bgl1B被高效活性重组表达。通过Ni-NTA亲和层析柱纯化了重组Bgl1B(rBgl1B)。纯化的rBgl1B催化pNPG水解反应的最适pH为6.5,最适温度为40oC。在最适反应条件下,rBgl1B水解pNPG的活性达到39.7U/mg,Km和Vmax分别为0.288mmol/L、36.9μmol/min。纤维二糖是rBgl1B的有效作用底物,其Km和Vmax分别为0.173mmol/L、35μmol/min。但rBgl1B不能催化转化蔗糖、乳糖、麦芽糖以及CMC。rBgl1B催化pNPG的水解反应对高浓度的Na+有较好的耐受性,而低浓度的Ca2+、Mn2+对该酶活有一定促进作用。不同于许多来源于真菌的酸性β-葡萄糖苷酶,rBgl1B在pH7.0～9.0范围内具有比较高的酶活力并具有较好的稳定性。