大规模基因组重复序列识别与分类研究进展

重复序列在基因组中普遍存在,大量实验证实其在生物进化过程中起着重要作用.目前,重复序列的发现与识别技术已经成为基因组学的研究热点,文章分类总结了有关这方面的研究进展,并对相关工具的功能特点进行了简要分析,同时对重复序列发展趋势进行了总结和展望.     

Treat Me Well or Will Resist: Uptake of Mobile Genetic Elements Determine the Resistome of Corynebacterium striatum

Corynebacterium striatum, a bacterium that is part of the normal skin microbiota, is also an opportunistic pathogen. In recent years, reports of infections and in-hospital and nosocomial outbreaks caused by antimicrobial multidrug-resistant C. striatum strains have been increasing worldwide. However, there are no studies about the genomic determinants related to antimicrobial resistance in C. striatum. This review updates global information related to antimicrobial resistance found in C. striatum and highlights the essential genomic aspects in its persistence and dissemination. The resistome of C. striatum comprises chromosomal and acquired elements. Resistance to fluoroquinolones and daptomycin are due to mutations in chromosomal genes. Conversely, resistance to macrolides, tetracyclines, phenicols, beta-lactams, and aminoglycosides are associated with mobile genomic elements such as plasmids and transposons. The presence and diversity of insertion sequences suggest an essential role in the expression of antimicrobial resistance genes (ARGs) in genomic rearrangements and their potential to transfer these elements to other pathogens. The present study underlines that the resistome of C. striatum is dynamic; it is in evident expansion and could be acting as a reservoir for ARGs.     

Kinetic Analysis of the Interaction of Mos1 Transposase with its Inverted Terminal Repeats Reveals New Insight into the Protein–DNA Complex Assembly

Transposases are specific DNA‐binding proteins that promote the mobility of discrete DNA segments. We used a combination of physicochemical approaches to describe the association of MOS1 (an eukaryotic transposase) with its specific target DNA, an event corresponding to the first steps of the transposition cycle. Because the kinetic constants of the reaction are still unknown, we aimed to determine them by using quartz crystal microbalance on two sources of recombinant MOS1: one produced in insect cells and the other produced in bacteria. The prokaryotic‐expressed MOS1 showed no cooperativity and displayed a K_d of about 300 nM . In contrast, the eukaryotic‐expressed MOS1 generated a cooperative system, with a lower K_d (～2 nm) . The origins of these differences were investigated by IR spectroscopy and AFM imaging. Both support the conclusion that prokaryotic‐ and eukaryotic‐expressed MOS1 are not similarly folded, thereby resulting in differences in the early steps of transposition.     

High level arsenic resistance in bacteria present in biooxidation tanks used to treat gold-bearing arsenopyrite concentrates:A review

The microbial consortium used in continuous-flow, stirred tank processes to treat gold-bearing arsenopyrite concentrates became adapted to high concentrations of arsenic over a number of years. The dominant microorganisms, Acidithiobacillus caldus and Leptospirillum ferriphilum, were found to contain two sets of arsenic resistance genes. One set of ars genes was present in all isolates of a species irrespective of whether they were highly arsenic resistant or not. A second set of ars genes was present on Tn21-like transposons and was found in all strains tested that had been adapted to high concentrations of arsenic. The arsenic resistance transposons present in At. caldus and L. ferriphilum were closely related, but sufficiently different for them to have been acquired independently rather than having been passed from one bacterium to the other. The transposons were transpositionally active in Escherchia coli and were shown to confer higher levels of arsenic resistance than the chromosomally-located ars genes where it was possible to test this. Transposons containing arsenic resistance genes that were identical or closely related to the transposon from L. ferriphilum, originally found in South Africa, were also found in both L. ferrooxidans and L. ferriphilum isolates from South America and Europe. An arsB gene knockout of At. caldus was produced by homologous recombination that demonstrated both the ability of the chromosomal ars genes to confer low levels of arsenic resistance in At. caldus and the development of a genetic system for the creation of knock-out mutants.     

A family of vectors that facilitate transposon and insertional mutagenesis of cloned genes in yeast

This report describes two sets of plasmid vectors that facilitate the identification of regions of complementation in cloned genomic inserts via transposon or insertional mutagenesis. The first set contains ARS-H4 CEN6, a yeast selectable nutritional marker (HIS3, TRP1 or URA3), and neo for selection in Escherichia coli. These plasmids lack the Tn3 transposition immunity region present in pBR322 derived vectors, and are permissive recipients for Tn3 transposon mutagenesis. The second family of plasmids described facilitate gene disruption procedures performed in vitro. These vectors carry disruption cassettes that contain different yeast selectable markers (HIS3, LEU2, TRP1 or URA3) adjacent to the Tn5 neo gene. These genes can be excised as a cassette on a common restriction fragment and introduced into any desired restriction site with selection for kanamycin resistance.     

Unsupervised statistical identification of genomic islands using oligonucleotide distributions with application toVibrio genomes

Vibrio cholerae, Vibrio vulnificus, Vibrio parahaemolyticus and several other relatedVibrio species show distinctly similar two-chromosomal genome organization. However, the modes of pathogenicity are very different among these species, and this is largely attributed to externally acquired genetic elements. We develop some statistical methods to determine these external genetic elements or genomic islands in genomes based on their differential oligonucleotide usage patterns compared to the rest of the genome. Genomic islands identified by these unsupervised statistical methods include integron and pathogenicity islands. After statistical determination of the genomic islands, we investigate their gene contents and their possible association with the pathogenic behaviour of the correspondingVibrio species. These investigations lead to observations that are of evolutionary and biological significance.