病原微生物致病岛的研究

致病岛是病原微生物通过基因水平转移获得的外源DNA,它是在研究致病性肠道菌的基因组结构和致病性的基础上发展起来的,并在其他革兰氏阴性和阳性致病菌中得到证实。本就各类病原菌致病岛的研究近况作一综述,同时介绍了致病岛的特征,讨论了致病岛在微生物进化中的意义及与tRNA基因的关系。     

病原菌毒力岛研究进展

毒力岛作为基因组岛的一种亚类,是细菌染色体上具有特定结构和功能特征的可移动基因大片段,经基因水平转移（转导、接合或转化）获得,可使细菌基因组进化在短期内发生“量的飞跃”,直接或间接增强细菌的生态适应性,与病原菌的致病性密切相关。毒力岛存在于多种动植物病原细菌中,对于细菌的毒力变异、遗传进化甚至新病原亚种形成有重要意义。简要综述了病原菌毒力岛的研究进展,介绍了毒力岛的结构、功能特征及其在病原菌进化中作用。     

Bacterial Genomic Islands: Organization,Function, and Evolutionary Role

Data on the structural organization and evolutionary role of specific bacterial DNA regions known as genomic islands are reviewed. Emphasis is placed on the most extensively studied genomic islands, pathogenicity islands (PAIs), which are present in the chromosome of Gram-negative and Gram-positive pathogenic bacteria and absent from related nonpathogenic strains. PAIs are long DNA regions that harbor virulence genes and often differ in GC content from the remainder of the bacterial genome. Many PAI occur in the tRNA gene loci, which provide a convenient target for foreign gene insertion. Some PAI are highly homologous to each other and contain sequences similar to ISs, phage att sites, and plasmid ori sites, along with functional or defective integrase and transposase genes, suggesting horizontal transfer of PAI among bacteria.     

致病岛及其分泌系统

致病岛是指细菌染色体上一段具有典型结构特征的基因簇,主要编码与细菌的毒力及代谢等功能相关的产物。病原菌必须要有一套高效的分泌系统才能将致病因子分泌到细菌表面或转运出细胞,并尽可能进入宿主细胞。现在已经发现了至少5套不同的蛋白分泌系统。本文就致病岛及其分泌系统的相关研究进展作一综述。     

Bacteriophage Transcription Factor Cro Regulates Virulence Gene Expression in Enterohemorrhagic Escherichia coli

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MS2噬菌体衣壳蛋白与包装位点结合特异性及其生物学应用进展

MS2噬菌体为正义单链RNA噬菌体,基因组含有3569个核苷酸,编码成熟酶蛋白、衣壳蛋白、复制酶蛋白和裂解蛋白。MS2噬菌体复制酶编码基因5'端一个由19个碱基组成的茎环结构(又称包装位点)是衣壳蛋白二聚体与RNA相互作用的部位,二者相互作用形成的复合物是启动噬菌体自我包装的信号。MS2噬菌体衣壳蛋白与包装位点结合的特异性已被应用于RNA病毒核酸检测的标准物质、校准品和质控品的研究,实时动态监测活细胞内RNA的运动,以及RNA体内递送载体的研究等领域。     

Structure of the Marine Siphovirus TW1: Evolution of Capsid-Stabilizing Proteins and Tail Spikes

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Pisodonophis boro (ophichthidae: anguilliformes): Specialization for head‐first and tail‐first burrowing?

The rice paddy eel, Pisodonophis boro (P. boro), is of special interest because of its peculiar burrowing habits. P. boro penetrates the substrate tail-first, a technique common for ophichthids, but it is able to burrow head-first as well. P. boro exhibits three feeding modes: inertial feeding, grasping, and spinning. Rotational feeding is a highly specialized feeding mode, adopted by several elongate, aquatic vertebrates and it is likely that some morphological modifications are related to this feeding mode. The detailed morphology of the head and tail of P. boro is examined with the goal to apportion the anatomical specializations among head-first burrowing, tail-first burrowing, and rotational feeding. The reduced eyes, covered with thick corneas may be beneficial for protection during head-first burrowing, but at the same time decreased visual acuity may have an impact on other sensory systems (e.g. cephalic lateral line system). The elongated and pointed shape of the skull is beneficial for substrate penetration. The cranial bones and their joints, which are fortified, are advantageous for resisting high mechanical loads during head-first burrowing. The aponeurotic connection between epaxial and jaw muscles is considered beneficial for transferring these forces from the body to the head during rotational feeding. Hypertrophied jaw muscles facilitate a powerful bite, which is required to hold prey during spinning movements and variability in the fiber angles of subdivisions of jaw muscles may be beneficial for preventing the lower jaw from being dislodged or opened. Furthermore, firm upper (premaxillo-ethmovomerine complex) and lower jaws (with robust coronoid processes) and high neurocranial rigidity are advantageous for a solid grip to hold prey during rotational feeding. The pointed shape of the tail and the consolidated caudal skeleton are beneficial for their tail-first burrowing habits. It is quite likely that the reduction of the caudal musculature is related to the tail-first burrowing behavior because the subtle movements of the caudal fin rays are no longer required.     

Genomic islands: tools of bacterial horizontal gene transfer and evolution

Bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. Besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. The horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. A significant part of the horizontal gene transfer is or has been facilitated by genomic islands (GEIs). GEIs are discrete DNA segments, some of which are mobile and others which are not, or are no longer mobile, which differ among closely related strains. A number of GEIs are capable of integration into the chromosome of the host, excision, and transfer to a new host by transformation, conjugation or transduction. GEIs play a crucial role in the evolution of a broad spectrum of bacteria as they are involved in the dissemination of variable genes, including antibiotic resistance and virulence genes leading to generation of hospital 'superbugs', as well as catabolic genes leading to formation of new metabolic pathways. Depending on the composition of gene modules, the same type of GEIs can promote survival of pathogenic as well as environmental bacteria.     

IGIPT - Integrated genomic island prediction tool

IGIPT is a web-based integrated platform for the identification of genomic islands (GIs). It incorporates thirteen parametric measures based on anomalous nucleotide composition on a single platform, thus improving the predictive power of a horizontally acquired region, since it is known that no single measure can absolutely predict a horizontally transferred region. The tool filters putative GIs based on standard deviation from genomic average and also provides raw output in MS excel format for further analysis. To facilitate the identification of various structural features, viz., tRNA integration sites, repeats, etc. in the vicinity of GIs, the tool provides option to extract the predicted regions and its flanking regions. AVAILABILITY: The database is available for free at http://bioinf.iiit.ac.in/IGIPT/     

Prediction of pathogenicity islands in Enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes

The genome of lethal animal pathogenic bacterium Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is characterized by the presence of multiple pathogenicity islands (PAIs). Computational methods have been developed to identify PAIs based on the distinguishing G + C levels in some PAI versus non-PAI regions. We observed that PAIs can have a very similar G + C level to that of the host chromosome, which may have led to false negative predictions using these methods. We have applied a novel method of genomic barcodes to identify PAIs. Using this technique, we have successfully identified both known and novel PAIs in the genomes of three strains of EHEC O157:H7.     

Isolation and genetic characterization of a novel filamentous bacteriophage,a deleted form of phage f237, from a pandemic Vibrio parahaemolyticus O4:K68 strain

We isolated a filamentous bacteriophage, VfO4K68, from the pandemic Vibrio parahaemolyticus strain belonging to 04:K68 serovar. The VfO4K68 DNA lacked a 1,893-bp fragment present in that of the distinctive region of f237, a filamentous phage isolated from a pandemic 03:K6 strain (Nasu, H. et al., J. Clin. Microbiol., 38, 2156-2161, 2000). The deletion resulted in the formation of a novel open reading frame (ORF) that possesses homology to the ORF 27 of ETA phage and staphylococcal enterotoxin E (SEE) of Staphylococcus aureus. VfO4K68 was able to infect the recipient 03:K6 serovar strains. These results suggest that VfO4K68 might act as a genetic transmitter and play some roles in the pandemic V. parahaemolyticus infection.     

Chaperonin-mediated folding of bacteriophage T4 major capsid protein. II. Production of gene product 23 deletion mutants

Folding of bacteriophage T4 major capsid protein, gene product 23 (534 a.a.), is aided by two proteins: E. coli GroEL chaperonin and viral gp31 co-chaperonin. In the present work a set of mutants with extensive deletions inside gene 23 using controlled digestion with Bal31 nuclease has been constructed. Proteins with deletions were co-expressed from plasmid vectors with phage gp31 co-chaperonin. Deletions from 8 to 33 a.a. in the N-terminal region of the gp23 molecule covering the protein proteolytic cleavage site during capsid maturation have no influence on the mutants' ability to produce in E. coli cells proteins which form regular structures—polyheads. Deletions in other regions of the polypeptide chain (187-203 and 367-476 a.a.) disturb the correct folding and subsequent assembly of gp23 into polyheads.     

Laterally transferred genomic islands in Xanthomonadales related to pathogenicity and primary metabolism.

Lateral gene transfer (LGT) is considered as one of the drivers in bacterial genome evolution, usually associated with increased fitness and/or changes in behavior, especially if one considers pathogenic vs. non-pathogenic bacterial groups. The genomes of two phytopathogens, Xanthomonas campestris pv. campestris and Xanthomonas axonopodis pv. citri, were previously inspected for genome islands originating from LGT events, and, in this work, potentially early and late LGT events were identified according to their altered nucleotide composition. The biological role of the islands was also assessed, and pathogenicity, virulence and secondary metabolism pathways were functions highly represented, especially in islands that were found to be recently transferred. However, old islands are composed of a high proportion of genes related to cell primary metabolic functions. These old islands, normally undetected by traditional atypical composition analysis, but confirmed as product of LGT by atypical phylogenetic reconstruction, reveal the role of LGT events by replacing core metabolic genes normally inherited by vertical processes.