16S rRNA二级结构的研究进展及其在系统分类中的应用

16S rRNA作为研究系统进化的生物大分子极受重视,是系统分类中必不可少的一个指标。然而,在进行系统发育分析时通常的序列联配方法有明显的局限性,即无法摆脱一级结构的束缚。20世纪80年代以来,一些研究者把目光投向了16S rRNA二级结构的分析研究,并且已经取得了相当不错的进展。研究表明,16S rRNA二级结构可能作为一个新的分类指标,成为系统分类的一个重要补充。     

鸡葡萄球菌的生物学特性及快速鉴定

目的探讨鸡葡萄球菌的生物学特性、可能存在的毒力因子及快速检测方法。方法首先观察鸡葡萄球菌的培养特性,镜下观察菌体结构。采用自动微生物分析仪（VITEK60、VITEK-Ⅱ）和分子生物学方法（细菌的通用引物16S rRNA进行PCR扩增）进行鉴定。以金黄色葡萄球菌的5种毒力因子基因序列设计引物,采用PCR方法扩增鸡葡萄球菌相应的毒力因子,同时采用悬浮芯片技术对该菌进行快速检测。结果鸡葡萄球菌的初始菌落形态与金黄色葡萄球菌类似,48h后菌落变粗糙,颜色加深;在VITEK60上细菌不能鉴定,在VITEK—Ⅱ上鉴定为鸡葡萄球菌并且该菌的16S rRNA的PCR产物序列与标准序列同源性达99％;鸡葡萄球菌的毒力因子均为阴性,悬浮芯片技术可以在4—6h内检测出鸡葡萄球菌。结论VITEK-Ⅱ可以鉴定鸡葡萄球菌等罕见细菌,分子生物学方法可以对该菌进行快速准确鉴定;鸡葡萄球菌的致病性和毒力有限;鸡葡萄球菌可能引起新的人畜共患病,应引起足够重视。     

油菜叶绿体16SrRNA基因的一级结构分析

本文报道了油菜叶绿体16S rRNA基因的全顺序及其5′端上游的156bp和3′端下游的101bp的核苷酸顺序。油菜叶绿体16s rRNA基因长为1491bp,和烟草、玉米相比,同源程度分别为98.5％、96.1％。油菜叶绿体16S rRNA基因5′端上游及3′端下游的顺序能互补而形成一个较大的茎环结构,但与烟草相比,由于3′端下游顺序有79bp的缺失,因此,该结构中的茎部分大小仅为烟草的二分之一。     

油菜叶绿体16S rRNA基因前导顺序的一级结构

质粒pBN119的3.2kb BamHI片段的PvuⅡ-BglⅡ片段全顺序长为840bp,其中含油菜叶绿体16S rRNA基因5′端的140bp。通过寻找GTTC顺序,发现在395至468位核苷酸之间是tRNA~(Val)基因;在73至118位核苷酸之间是一个蛋白阅读框。和已发表的玉米叶绿体16S rRNA前导顺序进行比较,同样存在三个相应的大肠杆菌RNA聚合酶的结合位点。和大肠杆菌的启动子及相应基因作比较,表明叶绿体基因组具有很明显的原核性,但其tRNA~(Val)基因没有CCA3′顺序。在16S rRNA基因、tRNA~(Val)基因及蛋白阅读框的5′端附近均能找到一个比较稳定的茎环结构。我们推测这些茎环结构可能和位于反问重复顺序上的某些基因的转录调节有关。     

红足壮异蝽Urochela quadrinotata Reuter线粒体基因组的测定与分析

研究测定并分析了红足壮异蝽Urochela quadrinotata Reuter的线粒体基因组全序列。该线粒体基因组全长16585bp(GenBank登录号为JQ743678),A+T含量为75.4%,共编码35个基因,包括13个蛋白质基因、20个tRNA基因(两个tRNA基因,即tRNAIle和tRNAGln未被检测到)、2个rRNA基因及一段较长的非编码区(控制区,亦称A+T富含区)。基因排序与大部分昆虫的线粒体基因排列方式相同,没有发生基因重排。除tRNASer(AGN)的DHU臂无法形成典型的茎环结构,其余tRNA基因均能稳定形成典型的三叶草二级结构。预测了红足壮异蝽16S和12S rRNA的二级结果,分别包括6个结构域43个茎环和3个结构域27茎环。控制区含一个长1652bp的串联重复区域,由16个串联重复单元组成。     

菌种1137116S rRNA序列分析及鉴定

通过PCR方法扩增菌种11371的16S rRNA基因并测序,将序列提交GenBank(登录号:DQ531606),并与其他链霉菌属种进行比较,通过DNAStar软件得到菌种16S rRNA基因序列进化树。同时采用插片法、显微镜观察等方法对株菌11371进行形态特征、培养特征、生理生化特征鉴定。结果表明,11371的16S rRNA序列与其他链霉菌具有一定的同源性,结合生理、生化指标鉴定结果,进一步确定菌种为不吸水链霉菌一株新亚种(Streptomyces ahygroscopicus subsp.wuzhouensis n.sub-sp.),菌株11371 16S rRNA序列为GenBank中首例Streptomyces ahygroscopicus的16S rRNA序列。     

乌鳢肝5S rRNA的核苷酸序列

应用Peattie,Maxum等化学裂解法,辅以酶解直读法等测定了乌醴(Ophiocephalus argus)肝5S rRNA的核苷酸序列;与已知的虹鳟鱼和纵带泥鳅5S rRNA序列比较,发现它们之间的核苷酸序列具有高度的保守性.利用其一级结构所给出的信息,初步提出二级结构模型.     

乌鳢肝5S rRNA的核苷酸序列

应用Peattie,Maxum等化学裂解法,辅以酶解直读法等测定了乌醴(Ophiocephalus argus)肝5S rRNA的核苷酸序列;与已知的虹鳟鱼和纵带泥鳅5S rRNA序列比较,发现它们之间的核苷酸序列具有高度的保守性.利用其一级结构所给出的信息,初步提出二级结构模型.     

脱氮除磷假单胞菌的筛选及定量检测

【目的】筛选具有较强脱氮除磷能力的细菌,建立结合S1酶保护分析的分子探针技术,以分析该菌在发酵过程中的数量变化情况。【方法】采用缺磷培养基厌氧培养、富磷培养基好氧培养和硝酸盐还原产气实验进行脱氮除磷菌筛选。通过16S rRNA基因序列分析及同源性比对,结合菌株的生理生化鉴定试验,鉴定筛选株。设计相应的16S rRNA探针组,建立结合S1酶保护分析的分子探针技术。【结果】筛选的菌株被鉴定为假单胞菌Pseudomonas sp.,命名为LY10。菌株LY10在富磷培养基中好氧培养24 h,总磷去除率达90.01%。在反硝化聚磷培养基中培养48 h,总氮和总磷去除率分别为84.71%和89.37%。针对假单胞菌16S rRNA基因序列设计了一组用于结合S1酶保护分析的分子探针Probe-P.sp,该探针具有很高的甄别灵敏度,能够将LY10与丛毛单胞属(Commonas)等5种细菌区分开;分子探针定量分析假单胞菌LY10,其细胞量与吸光值呈线性关系,检测的线性范围为103~106 cells/mL,线性方程为:y=-0.967 87+0.372 99x(R2=0.996 7,n=5)。【结论】新筛的假单胞菌LY10的脱氮除磷能力较强,具有生物脱氮除磷的工业化应用潜质。所建立的结合S1酶保护分析的分子探针技术的特异性和灵敏度良好,有望应用于混菌体系中的假单胞菌的定性定量分析。     

16S rRNA二级结构可变区图形分析在放线菌分类中的应用

采用16S rRNA可变区二级结构图形分析,比较了姜氏菌属及几个相关属种可变区二级结构的变化。结果表明,在9个可变区二级结构中茎的长度、环的数目和类型、茎的碱基对、以及环内部碱基均有不同。尤其在V5和V6两个区,这种差别尤为明显。这为姜氏菌属的建立提供了又一个证据,并认为16S rRNA可变区二级结构分析,可以应用于属以上原核生物的分类。     

Use of Subtractive Hybridization To Design Habitat-Based Oligonucleotide Probes for Investigation of Natural Bacterial Communities

We describe a rapid oligonucleotide probe design strategy based on subtractive hybridization which yields probes for 16S rRNA or rRNA genes of individual members of microbial communities that are specific within the context of those communities. This strategy circumvents the need to sequence many similar or identical clones of dominant members of a community. Radioactively labeled subfragments of a cloned 16S rRNA gene sequence for which a probe is required (target) were hybridized with biotinylated total 16S ribosomal DNA (rDNA) amplified from the microbial community, and the hybrids formed were subsequently discarded. The remaining enriched fragments were used to screen a library consisting of cloned subfragments of the target sequence by colony hybridization in order to identify the variable regions of the 16S rRNA gene with the required specificity. The sequencing of random clones in one 16S rDNA library demonstrated that only those clones with 100% sequence identity with the probe fragment were detected by it. Moreover, sequencing of other, randomly selected, probe-positive clones revealed 100% sequence identity with the probe. Probes developed in this way tended to correspond to more variable regions of the 16S rRNA if the target sequences were similar to the sequences of other clones in the library and to less variable regions if the target sequences were phylogenetically isolated within the clone library. Although the absolute specificity of the latter probes, as assessed by comparison with available database sequences, was lower than the absolute specificity of the probes from the more variable regions, they were specific within the context of the environmental samples from which they were derived.     

Proteins neighboring 18S rRNA conserved sequences 609-618 and 1047-1061 within the 40S human ribosomal subunit

The structure of human 40S ribosomal subunits has been probed by a cross-linking strategy based on the use of oligonucleotide derivatives that modify proteins in the vicinity of specific 18S rRNA sequences. The oligonucleotide derivatives carried a p-azidoperfluorobenzamide group at the 5' ends and were complementary to 18S rRNA sequences 609-618 and 1047-1061, homologous to the highly conserved regions designated as the "530 stem-loop" and "790 stem-loop", respectively, in Escherichia coli 16S rRNA. Ribosomal proteins surrounding these sequences were the main targets of the cross-linking. Proteins S3 and S5 were cross-linked to the derivative complementary to the sequence 609-618, and proteins S2 and S3 were modified by the derivative complementary to the sequence 1047-1061. Cross-linking was not affected by binding of 40S subunits to either poly(U) or poly(U) and Phe-tRNA(Phe).     

Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts

Cyanobacteria are common members of sponge-associated bacterial communities and are particularly abundant symbionts of coral reef sponges. The unicellular cyanobacterium Synechococcus spongiarum is the most prevalent photosynthetic symbiont in marine sponges and inhabits taxonomically diverse hosts from tropical and temperate reefs worldwide. Despite the global distribution of S. spongiarum , molecular analyses report low levels of genetic divergence among 16S ribosomal RNA (rRNA) gene sequences from diverse sponge hosts, resulting either from the widespread dispersal ability of these symbionts or the low phylogenetic resolution of a conserved molecular marker. Partial 16S rRNA and entire 16S–23S rRNA internal transcribed spacer (ITS) genes were sequenced from cyanobacteria inhabiting 32 sponges (representing 18 species, six families and four orders) from six geographical regions. ITS phylogenies revealed 12 distinct clades of S. spongiarum that displayed 9% mean sequence divergence among clades and less than 1% sequence divergence within clades. Symbiont clades ranged in specificity from generalists to specialists, with most (10 of 12) clades detected in one or several closely related hosts. Although multiple symbiont clades inhabited some host sponges, symbiont communities appear to be structured by both geography and host phylogeny. In contrast, 16S rRNA sequences were highly conserved, exhibiting less than 1% sequence divergence among symbiont clades. ITS gene sequences displayed much higher variability than 16S rRNA sequences, highlighting the utility of ITS sequences in determining the genetic diversity and host specificity of S. spongiarum populations among reef sponges. The genetic diversity of S. spongiarum revealed by ITS sequences may be correlated with different physiological capabilities and environmental preferences that may generate variable host–symbiont interactions.     

Phylogenetic diversity of bacterial symbionts of Solemya hosts based on comparative sequence analysis of 16S rRNA genes.

The bacterial endosymbionts of two species of the bivalve genus Solemya from the Pacific Ocean, Solemya terraeregina and Solemya pusilla, were characterized. Prokaryotic cells resembling gram-negative bacteria were observed in the gills of both host species by transmission electron microscopy. The ultrastructure of the symbiosis in both host species is remarkably similar to that of all previously described Solemya spp. By using sequence data from 16S rRNA, the identity and evolutionary origins of the S. terraeregina and S. pusilla symbionts were also determined. Direct sequencing of PCR-amplified products from host gill DNA with primers specific for Bacteria 16S rRNA genes gave a single, unambiguous sequence for each of the two symbiont species. In situ hybridization with symbiont-specific oligonucleotide probes confirmed that these gene sequences belong to the bacteria residing in the hosts gills. Phylogenetic analyses of the 16S rRNA gene sequences by both distance and parsimony methods identify the S. terraeregina and S. pusilla symbionts as members of the gamma subdivision of the Proteobacteria. In contrast to symbionts of other bivalve families, which appear to be monophyletic, the S. terraeregina and S. pusilla symbionts share a more recent common ancestry with bacteria associating endosymbiotically with bivalves of the superfamily Lucinacea than with other Solemya symbionts (host species S. velum, S. occidentalis, and S. reidi). Overall, the 16S rRNA gene sequence data suggest that the symbionts of Solemya hosts represent at least two distinct bacterial lineages within the gamma-Proteobacteria. While it is increasingly clear that all extant species of Solemya live in symbiosis with specific bacteria, the associations appear to have multiple evolutionary origins.     

Questionable 16S ribosomal RNA gene annotations are frequent in completed microbial genomes

According to recent reports, many ribosomal RNA gene annotations are still questionable, and the use of inappropriate tools for annotation has been blamed. However, we believe that the abundant 16S rRNA partial sequence in the databases, mainly created by culture-independent PCR methods, is another main cause of the ambiguous annotations of 16S rRNA. To examine the current status of 16S rRNA gene annotations in complete microbial genomes, we used as a criterion the conserved anti-SD sequence, located at the 3′ end of the 16S rRNA gene, which is commonly overlooked by culture-independent PCR methods. In our large survey, 859 16S rRNA gene sequences from 252 different species of the microbial complete genomes were inspected. 67 species (234 genes) were detected with ambiguous annotations. The common anti-SD sequence and other conserved 16S rRNA sequence features could be detected in the downstream-intergenic regions for almost every questionable sequence, indicating that many of the 16S rRNA genes were annotated incorrectly. Furthermore, we found that more than 91.5% of the 93,716 sequences of the available 16S rRNA in the main databases are partial sequences. We also performed BLAST analysis for every questionable rRNA sequence, and most of the best hits in the analysis were rRNA partial sequences. This result indicates that partial sequences are prevalent in the databases, and that these sequences have significantly affected the accuracy of microbial genomic annotation. We suggest that the annotation of 16S rRNA genes in newly complete microbial genomes must be done in more detail, and that revision of questionable rRNA annotations should commence as soon as possible.     

Polymorphisms in 16S rRNA genes of Flavobacterium psychrophilum correlate with elastin hydrolysis and tetracycline resistance

Flavobacterium psychrophilum is the etiological agent of bacterial coldwater disease, which causes significant problems to aquaculture worldwide. A recent study (Soule M, Cain K, LaFrentz S, Call DR [2005] Infect Immun 73:3799-3802) identified two 16S rRNA gene sequence variants (6 base differences) within the variable stem-loop region 3 for F. psychrophilum strains ATCC 49418 and CSF 259-93. That study also hypothesized that F. psychrophilum is composed of at least 2 distinct genetic lineages (I and II) described by a microarray-based comparative genomics study. In the present study, we augmented an existing 16S rDNA microarray to detect both 16S rRNA sequence variants from F. psychrophilum. Subsequent microarray experiments showed that CSF 259-93 hybridized as expected, but ATCC 49418 was positive for both sequence variants. We then developed a PCR-restriction fragment length polymorphism (RFLP) assay (MnlI and MaeIII) to distinguish between the 2 sequences. Gel isolation of PCR-RFLP products, cloning, and sequencing confirmed that ATCC 49418 harbors both 16S rRNA sequences. Microarray experiments showed that 11 of 14 strains from genetic Lineage I harbor both the CSF 259-93 and ATCC 49418 16S rRNA sequence variants, whereas all 15 Lineage II strains were only positive for the CSF 259-93 sequence (p < 0.0001). Elastin hydrolysis and tetracycline resistance were most closely associated with the latter strains (p < 0.0001 and p = 0.024, respectively). These data support the hypothesis that F. psychrophilum is composed of at least 2 distinct genetic lineages that are closely associated with host origin.     

Oligonucleotide probes complementary to variable regions of ribosomal RNA discriminate between Mycoplasma species

On the basis of information from computer-assisted sequence comparison of the Mycoplasma pneumoniae 16S ribosomal RNA (rRNA) sequences with sequences from various other mycoplasmal and bacterial species, we constructed M. pneumoniae-specific oligonucleotide probes complementary to variable regions in the 16S rRNA molecule. Using a DNA/RNA dot blot hybridization procedure, it was possible to detect less than 1 X 10(3) mycoplasmas. This test is a most sensitive assay for species-specific detection of bacteria. It can easily be adapted for detection and identification of other bacterial species and may have wide medical and industrial application.     

Cytidine deamination assay to differentiate Staphylococcus aureus from other staphylococci

AIMS: Adoption of the property of cytidine (cytosine-beta-d-riboside) deamination in staphylococci to distinguish Staphylococcus aureus from other staphylococci. METHODS AND RESULTS: A total of 560 staphylococcal strains were examined. The test demonstrated a sensitivity of 97.1% and a specificity of 98.8%. Of the 249 S. aureus strains (115 oxacillin-resistant) 58 strains were coagulase-negative S. aureus and another 16 strains were clumping factor-negative S. aureus. The 74 deficient S. aureus strains were identified by 16S rRNA gene sequencing and further investigated by spa typing and 13 spa types were found. CONCLUSIONS: The cytidine deaminase test (CDT) is useful especially for distinguishing coagulase- and clumping factor-negative S. aureus from other staphylococci and the results correlated well with 16S rRNA sequencing and the polymerase chain reaction (PCR) amplification of the nuc gene. SIGNIFICANCE AND IMPACT OF THE STUDY: Cytidine deamination assay differentiates S. aureus from other staphylococci. This method is fast (6 h) and reliable in distinguishing between non-S. aureus and the defective (coagulase-negative, clumping factor-negative) S. aureus isolates which could have major consequences for therapy.     

Analysis of 23S rRNA genes in metagenomes - a case study from the Global Ocean Sampling Expedition

As an evolutionary marker, 23S ribosomal RNA (rRNA) offers more diagnostic sequence stretches and greater sequence variation than 16S rRNA. However, 23S rRNA is still not as widely used. Based on 80 metagenome samples from the Global Ocean Sampling (GOS) Expedition, the usefulness and taxonomic resolution of 23S rRNA were compared to those of 16S rRNA. Since 23S rRNA is approximately twice as large as 16S rRNA, twice as many 23S rRNA gene fragments were retrieved from the GOS reads than 16S rRNA gene fragments, with 23S rRNA gene fragments being generally about 100 bp longer. Datasets for 16S and 23S rRNA sequences revealed similar relative abundances for major marine bacterial and archaeal taxa. However, 16S rRNA sequences had a better taxonomic resolution due to their significantly larger reference database.Reevaluation of the specificity of previously published PCR amplification primers and group specific fluorescence in situ hybridization probes on this metagenomic set of non-amplified 23S rRNA sequences revealed that out of 16 primers investigated, only two had more than 90% target group coverage. Evaluations of two probes, BET42a and GAM42a, were in accordance with previous evaluations, with a discrepancy in the target group coverage of the GAM42a probe when evaluated against the GOS metagenomic dataset.