拟南芥中一个新的snoRNA基因簇的鉴定及结构分析

在拟南芥中发现和鉴定了Z2 snoRNA基因簇, 该基因簇由4个相同的 Z2 snoRNA 基因组成,分别命名为Z2a, Z2b, Z2c和Z2d. 在Z2 snoRNA基因簇的基因间隔区中没有发现已知的植物snoRNA基因保守的启动元件,因此,Z2 snoRNA基因簇是由一个上游启动子控制转录的. 对Z2 snoRNA基因间隔区序列的二级结构分析也表明,在3个基因间隔区中都编码一种与酿酒酵母snoRNA前体切割加工的识别信号类似的发夹结构. Z2 snoRNA基因簇的发现,揭示出植物snoRNA基因具有多拷贝的特点,并为进一步研究植物snoRNA基因簇的转录和转录后的加工机制提供了一个良好的研究体系.     

深圳市新甲型H1N1流感病毒感染病例的血清学及分子特点分析

本研究通过对深圳市4名甲流重症患者的血清抗体及其所感染的新甲型H1N1流感病毒的抗原性和分子特点的分析,发现这些患者在感染后短期内产生的血清中和抗体滴度均不超过1:20,不能起到有效的保护作用;交叉血凝抑制实验的结果显示新H1N1病毒与季节性H1N1和H3N2流感病毒无任何交叉反应,抗原性差异很大,而患者所感染的病毒与标准株的抗原性则没有太大差异;分子特点的分析表明新H1N1病毒进入人群后依然属于经典的猪流感亚系,4名重症患者感染的病毒不具备高致病性流感病毒的遗传特点,几个氨基酸位点的变异没有影响病毒的毒力和致病性,只有一株毒株的NA蛋白发生了His275Tyr的突变,产生了对达菲等神经氨酸酶抑制剂的耐药性。     

变孢毛霉的一个新变种及对Mucor luteus Linnemann和M.variosporus Schipper的合格化

根据国际植物命名法规,对两个不合格发表的毛霉种名：Ｍｕｃｏｒ　ｌｕｔｅｕｓ　Ｌｉｎｎｅｍａｎｎ和ＭｕｃｏｒｖａｒｉｏｓｐｏｒｕｓＳｃｈｉｐｐｅｒ进行了合格化。对变孢毛霉（Ｍｉｃｏｒｖａｒｉｏｓｐｏｒｕｓ）的一个新变种进行了描述。     

Different expression strategy: multiple intronic gene clusters of box H/ACA snoRNA in Drosophila melanogaster

The high degree of rRNA pseudouridylation in Drosophila melanogaster provides a good model for studying the genomic organization, structural and functional diversity of box H/ACA small nucleolar RNAs (snoRNAs). Accounting for both conserved sequence motifs and secondary structures, we have developed a computer-assisted method for box H/ACA snoRNA searching. Ten snoRNA clusters containing 42 box H/ACA snoRNAs were identified from D.melanogaster. Strikingly, they are located in the introns of eight protein-coding genes. In contrast to the mode of one snoRNA per intron so far observed in all animals, our results demonstrate for the first time a novel polycistronic organization that implies a different expression strategy for a box H/ACA snoRNA gene when compared to box C/D snoRNAs in D.melanogaster. Mutiple isoforms of the box H/ACA snoRNAs, from which most clusters are made up, were observed in D.melanogaster. The degree of sequence similarity between the isoforms varies from 99% to 70%, implying duplication events in different periods and a trend of enlarging the intronic snoRNA clusters. The variation in the functional elements of the isoforms could lead to partial alternation of snoRNA's function in loss or gain of rRNA complementary sequences and probably contributes to the great diversity of rRNA pseudouridylation in D.melanogaster.     

Functionality and substrate specificity of human box H/ACA guide RNAs

A large number of box H/ACA RNAs have been identified in human cells, and have been predicted to account for nearly all pseudouridylation sites in human rRNAs. However, the function of these mammalian H/ACA RNAs in directing pseudouridylation has been verified experimentally in only two cases. In this study, we used three in vitro reconstitution systems, including yeast and mammalian systems, to test the function of seven H/ACA RNAs guiding16 pseudouridylation sites. Our results verified 12 of these sites; four predictions were incorrect. Further analyses indicated that three components, including the stability of the hairpin structure harboring the pseudouridylation pocket, the stability of guide sequence–target RNA base-pairing interaction, and the distance between the target uridine and the box H or ACA, were critical for the guide function, as changes in these components were sufficient to alter the functionality and specificity of the pseudouridylation pocket. The dynamic functional changes in response to changes in these three important components were further tested in vivo, and the results were completely consistent with the in vitro results. Finally, we compared our results with predictions made by two computer programs, as well as predictions made by human experts using visual inspection. We found that the predictions of one program (snoGPS) agreed with our experimental results with 100% sensitivity (12/12) and 75% specificity (3/4).     

Long-distance placement of substrate RNA by H/ACA proteins

The structural basis for accurate placement of substrate RNA by H/ACA proteins is studied using a nonintrusive fluorescence assay. A model substrate RNA containing 2-aminopurine immediately 3′ of the uridine targeted for modification produces distinct fluorescence signals that report the substrate's docking status within the enzyme active site. We combined substrate RNA with complete and subcomplexes of H/ACA ribonucleoprotein particles and monitored changes in the substrate conformation. Our results show that each of the three accessory proteins, as well as an active site residue, have distinct effects on substrate conformations, presumably as docking occurs. Interestingly, in some cases these effects are exerted far from the active site. Application of our data to an available structural model of the holoenzyme, enables the functional role of each accessory protein in substrate placement to come into view.     

18S rRNA processing requires base pairings of snR30 H/ACA snoRNA to eukaryote‐specific 18S sequences

The H/ACA RNAs represent an abundant, evolutionarily conserved and functionally diverse class of non‐coding RNAs. Many H/ACA RNAs direct pseudouridylation of rRNAs and snRNAs, while members of the rapidly growing group of ‘orphan’ H/ACA RNAs participate in pre‐rRNA processing, telomere synthesis and probably, in other nuclear processes. The yeast snR30 ‘orphan’ H/ACA snoRNA has long been known to function in the nucleolytic processing of 18S rRNA, but its molecular role remained unknown. Here, we provide biochemical and genetic evidence demonstrating that during pre‐rRNA processing, two evolutionarily conserved sequence elements in the 3′‐hairpin of snR30 base‐pair with short pre‐rRNA sequences located in the eukaryote‐specific internal region of 18S rRNA. The newly discovered snR30‐18S base‐pairing interactions are essential for 18S rRNA production and they constitute a complex snoRNA target RNA transient structure that is novel to H/ACA RNAs. We also demonstrate that besides the 18S recognition motifs, the distal part of the 3′‐hairpin of snR30 contains an additional snoRNA element that is essential for 18S rRNA processing and that functions most likely as a snoRNP protein‐binding site.     

Computational prediction of Caenorhabditis box H/ACA snoRNAs using genomic properties of their host genes

Identification of small nucleolar RNAs (snoRNAs) in genomic sequences has been challenging due to the relative paucity of sequence features. Many current prediction algorithms rely on detection of snoRNA motifs complementary to target sites in snRNAs and rRNAs. However, recent discovery of snoRNAs without apparent targets requires development of alternative prediction methods. We present an approach that combines rule-based filters and a Bayesian Classifier to identify a class of snoRNAs (H/ACA) without requiring target sequence information. It takes advantage of unique attributes of their genomic organization and improved species-specific motif characterization to predict snoRNAs that may otherwise be difficult to discover. Searches in the genomes of Caenorhabditis elegans and the closely related Caenorhabditis briggsae suggest that our method performs well compared to recent benchmark algorithms. Our results illustrate the benefits of training gene discovery engines on features restricted to particular phylogenetic groups and the utility of incorporating diverse data types in gene prediction.     

Structural and Sequence Evolution of U17 Small Nucleolar RNA (snoRNA) and Its Phylogenetic Congruence in Chelonians

Vertebrate U17 RNA is an intron-encoded H/CA box containing snoRNA, which has been intensively studied in the last decade, though its precise role in ribosome biogenesis is not yet clear. A consensus secondary structure for the U17 RNA molecule has been derived from the comparative sequence and structural evolution analysis of U17 snoRNA among vertebrates. Its phylogenetic congruence above class level has been tested and preliminary data on chelonians suggest that also in this order, U17 snoRNA evolved congruently with phylogeny. We herein extend our analysis to other components of this reptile group. According to the sequence data that have also emerged from chelonians, the U17 RNA molecule can be divided into two main domains: the 5-variable domain, which presents the sequence motifs capable of base-pairing with the 18S rRNA target and spanning STEM1, -2, and -3, and the 3-conserved domain, consisting of STEM4. In vertebrates, the latter RNA region shows a high conservation both in secondary structure and in the presence of the three sequence motifs 5-AUUCCUA-3, 5-U(G/U)ACU-3, and 5-AACCC-3. We tested the phylogenetic congruence of U17 evolution with chelonian relationships: Our results are significantly similar to those emerging from mtDNA and morphological systematics. Some discrepancies (e.g., the position of Platysternon) need to be addressed in greater depth.