Bacterial Lifestyle in a Deep-sea Hydrothermal Vent Chimney Revealed by the Genome Sequence of the Thermophilic Bacterium Deferribacter desulfuricans SSM1

The complete genome sequence of the thermophilic sulphur-reducing bacterium, Deferribacter desulfuricans SMM1, isolated from a hydrothermal vent chimney has been determined. The genome comprises a single circular chromosome of 2 234 389 bp and a megaplasmid of 308 544 bp. Many genes encoded in the genome are most similar to the genes of sulphur- or sulphate-reducing bacterial species within Deltaproteobacteria. The reconstructed central metabolisms showed a heterotrophic lifestyle primarily driven by C1 to C3 organics, e.g. formate, acetate, and pyruvate, and also suggested that the inability of autotrophy via a reductive tricarboxylic acid cycle may be due to the lack of ATP-dependent citrate lyase. In addition, the genome encodes numerous genes for chemoreceptors, chemotaxis-like systems, and signal transduction machineries. These signalling networks may be linked to this bacterium''s versatile energy metabolisms and may provide ecophysiological advantages for D. desulfuricans SSM1 thriving in the physically and chemically fluctuating environments near hydrothermal vents. This is the first genome sequence from the phylum Deferribacteres.     

Genome sequence of benzo(a)pyrene-degrading bacterium Novosphingobium pentaromativorans US6-1

Novosphingobium pentaromativorans US6-1 showed a good ability to degrade high-molecular-weight polycyclic aromatic hydrocarbons. We report the draft genome sequence of strain US6-1, which contains a main chromosome (5,096,413 bp, G+C content of 63.1%) and two plasmids (188,476 and 60,085 bp). The majority of the aromatic-hydrocarbon-degrading genes are encoded in the larger plasmid.     

Complete Genomic Structure of the Bloom-forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843

The nucleotide sequence of the complete genome of a cyanobacterium,Microcystis aeruginosa NIES-843, was determined. The genomeof M. aeruginosa is a single, circular chromosome of 5 842 795base pairs (bp) in length, with an average GC content of 42.3%.The chromosome comprises 6312 putative protein-encoding genes,two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species,and genes for tmRNA, the B subunit of RNase P, SRP RNA, and6Sa RNA. Forty-five percent of the putative protein-encodingsequences showed sequence similarity to genes of known function,32% were similar to hypothetical genes, and the remaining 23%had no apparent similarity to reported genes. A total of 688kb of the genome, equivalent to 11.8% of the entire genome,were composed of both insertion sequences and miniature inverted-repeattransposable elements. This is indicative of a plasticity ofthe M. aeruginosa genome, through a mechanism that involveshomologous recombination mediated by repetitive DNA elements.In addition to known gene clusters related to the synthesisof microcystin and cyanopeptolin, novel gene clusters that maybe involved in the synthesis and modification of toxic smallpolypeptides were identified. Compared with other cyanobacteria,a relatively small number of genes for two component systemsand a large number of genes for restriction-modification systemswere notable characteristics of the M. aeruginosa genome.     

Multicopy plasmid stability in Escherichia coli requires host-encoded functions that lead to plasmid site-specific recombination

Summary The heritable stability of the multicopy plasmid ColE1 and its natural relatives, requires the presence in the plasmid of a site (cer in ColE1) that acts as a substrate for site-specific recombination, thereby maintaining plasmids in the monomeric state. Multimerization, promoted by homologous recombination, leads to plasmid loss. Here we show that the Escherichia coli chromosome encodes at least two unlinked functions that act on cer and its analogous sites, to promote stabilizing site-specific recombination. One of these functions is encoded by a gene residing on a cosmid that also contains the argI and pyrB genes, mapping it to the 96–97 min region of the E. coli map.     

Comparative mapping of HKT genes in wheat, barley, and rice, key determinants of Na+ transport, and salt tolerance

Salt tolerance of plants depends on HKT transporters (High-affinityK⁺ Transporter), which mediate Na⁺-specific transport or Na⁺-K⁺co-transport. Gene sequences closely related to rice HKT geneswere isolated from hexaploid bread wheat (Triticum aestivum)or barley (Hordeum vulgare) for genomic DNA southern hybridizationanalysis. HKT gene sequences were mapped on chromosomal armsof wheat and barley using wheat chromosome substitution linesand barley–wheat chromosome addition lines. In addition,HKT gene members in the wild diploid wheat ancestors, T. monococcum(A^m genome), T. urartu (A^u genome), and Ae. tauschii (D^t genome)were investigated. Variation in copy number for individual HKTgene members was observed between the barley, wheat, and ricegenomes, and between the different wheat genomes. HKT2;1/2-like,HKT2;3/4-like, HKT1;1/2-like, HKT1;3-like, HKT1;4-like, andHKT1;5-like genes were mapped to the wheat–barley chromosomegroups 7, 7, 2, 6, 2, and 4, respectively. Chromosomal regionscontaining HKT genes were syntenic between wheat and rice exceptfor the chromosome regions containing the HKT1;5-like gene.Potential roles of HKT genes in Na⁺ transport in rice, wheat,and barley are discussed. Determination of the chromosome locationsof HKT genes provides a framework for future physiological andgenetic studies investigating the relationships between HKTgenes and salt tolerance in wheat and barley. Key words: Barley, comparative mapping, HKT, rice, salt tolerance, sodium transport, wheat     

Complete Nucleotide Sequences of 93-kb and 3.3-kb Plasmids of an Enterohemorrhagic Escherichia coli O157:H7 Derived from Sakai Outbreak

Enterohemorrhagic Escherichia coli (EHEC) O157:H7, derived froman outbreak in Sakai city, Japan in 1996, possesses two kindsof plasmids: a 93-kb plasmid termed pO157, found in clinicalEHEC isolates world-wide and a 3.3-kb plasmid termed pOSAK1,prevalent in EHEC strains isolated in Japan. Complete nucleotidesequences of both plasmids have been determined, and the putativefunctions of the encoded proteins and the cis-acting DNA sequenceshave been analyzed. pO157 shares strikingly similar genes andDNA sequences with F-factor and the transmissible drug-resistantplasmid R100 for DNA replication, copy number control, plasmidsegregation, conjugative functions and stable maintenance inthe host, although it is defective in DNA transfer by conjugationdue to the truncation and deletion of the required genes andDNA sequences. In addition, it encodes several proteins implicatedin EHEC pathogenicity such as an EHEC hemolysin (HlyA), a catalase-peroxidase(KatP), a serine protease (EspP) and type II secretion system.pOSAK1 possesses a ColE1-like replication system, and the DNAsequence is extremely similar to that of a drug-resistant plasmid,NTP16, derived from Salmonella typhimurium except that it lacksdrug resistance transposons.     

Complete Nucleotide Sequence of the Chloroplast Genome from the Tasmanian Blue Gum, Eucalyptus globulus (Myrtaceae)

The complete nucleotide sequence of the chloroplast genome ofthe hardwood species Eucalyptus globulus is presented and comparedwith chloroplast genomes of tree and non-tree angiosperms andtwo softwood tree species. The 160 286 bp genome is similarin gene order to that of Nicotiana, with an inverted repeat(IR) (26 393 bp) separated by a large single copy (LSC) regionof 89 012 bp and a small single copy region of 18 488 bp. Thereare 128 genes (112 individual gene species and 16 genes duplicatedin the inverted repeat) coding for 30 transfer RNAs, 4 ribosomalRNAs and 78 proteins. One pseudogene (-infA) and one pseudo-ycf(-ycf15) were identified. The chloroplast genome of E. globulusis essentially co-linear with that of another hardwood treespecies, Populus trichocarpa, except that the latter lacks rps16and rpl32, and the IR has expanded in Populus to include rps19(part of the LSC in E. globulus). Since the chloroplast genomeof E. globulus is not significantly different from other treeand non-tree angiosperm taxa, a comparison of hardwood and softwoodchloroplasts becomes, in essence, a comparison of angiospermand gymnosperm chloroplasts. When compared with E. globulus,Pinus chloroplasts have a very small IR, two extra tRNAs andfour additional photosynthetic genes, lack any functional ndhgenes and have a significantly different genome arrangement.There does not appear to be any correlation between plant habitand chloroplast genome composition and arrangement.     

Complete Mitochondrial Genome of Anoplocephala magna Solidifying the Species

The 2 species of the genus Anoplocephala (Anoplocephalidae), A. perfoliata and A. magna, are among the most important equine cestode parasites. However, there is little information about their differences at the molecular level. The present study revealed that the mitochondrial (mt) genome of A. magna was 13,759 bp in size and 700 bp shorter than that of A. perfoliata. The 2 species includes 2 rRNA, 22 tRNA, and 12 protein-coding genes each. The size of each of the 36 genes was the same as that of A. perfoliata, except for cox1, rrnL, trnC, trnS2(UCN), trnG, trnH, trnQ, and trnP. In the full mitochondrial genome, the sequence similarity was 87.1%. The divergence in the nucleotide and amino acid sequences of individual protein-coding genes ranged from 11.1% to 16% and 6.8% to 16.4%, respectively. The 2 noncoding regions of the mt genome of A. magna were 199 bp and 271 bp in length, while the equivalent regions in A. perfoliata were 875 bp and 276 bp, respectively. The results of this study support the proposal that A. magna and A. perfoliata are separate species, consistent with previous morphological analyses.     

The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite

We sequenced the genome of Rickettsia felis, a flea-associated obligate intracellular α-proteobacterium causing spotted fever in humans. Besides a circular chromosome of 1,485,148 bp, R. felis exhibits the first putative conjugative plasmid identified among obligate intracellular bacteria. This plasmid is found in a short (39,263 bp) and a long (62,829 bp) form. R. felis contrasts with previously sequenced Rickettsia in terms of many other features, including a number of transposases, several chromosomal toxin–antitoxin genes, many more spoT genes, and a very large number of ankyrin- and tetratricopeptide-motif-containing genes. Host-invasion-related genes for patatin and RickA were found. Several phenotypes predicted from genome analysis were experimentally tested: conjugative pili and mating were observed, as well as β-lactamase activity, actin-polymerization-driven mobility, and hemolytic properties. Our study demonstrates that complete genome sequencing is the fastest approach to reveal phenotypic characters of recently cultured obligate intracellular bacteria.     

Fine mapping of the human pentraxin gene region on chromosome 1q23

 The 1q21 to 25 region of human chromosome 1 contains genes which encode proteins with immune- and inflammation-associated functions. These include the pentraxin genes, for C-reactive protein (CRP), serum amyloid P (SAP) protein (APCS), and a CRP pseudogene (CRPP1). The region of chromosome 1 containing this cluster is syntenic with distal mouse chromosome 1. We constructed an approximately 1.4 megabase yeast artificial chromosome (YAC) contig with the pentraxin genes at its core. This four-YAC contig includes other genes with immune functions including the FCER1A gene, which encodes the α-subunit of the IgE high-affinity Fc receptor and the IFI-16 gene, an interferon-γ-induced gene. In addition, it contains the histone H3F2 and H4F2 genes and the gene for erythroid α-spectrin (SPTA1). The gene order is cen.-SPTA1-H4F2-H3F2-IFI-16-CRP-CRPP1-APCS-FCER1A- tel. The contig thus consists of a cluster of genes whose products either have immunological importance, bind DNA, or both. Received: 13 December 1995 / 6 February 1996     

李氏大足蝗线粒体全基因组序列分析

采用长距PCR 扩增及保守引物步移法测定并注释了李氏大足蝗( Aeropus licenti Chang)的线粒体基因组全序列。结果表明,李氏大足蝗的线粒体基因组全长15 597 bp,A+T 含量为74.8%,37个基因位置与飞蝗的一致,基因间隔序列共计17处105 bp,间隔长度从1～21 bp不等;有10对基因间存在58 bp重叠,重叠碱基数在1～17 bp之间。13个蛋白质编码基因中找到4种可能的起始密码子;有12个基因在基因3'端找到完全的TAA或TAG 终止密码子,只有ND5基因终止密码子为不完整的T。除tRNA^Ser（AGN）外,其余21个tRNA基因的二级结构均属典型的三叶草结构。tRNA^Ser（AGN）的DHU臂缺失,在相应的位置上只形成一个环。预测的lrRNA二级结构总共有6个结构域（结构域Ⅲ缺失）,47个茎环结构;预测的srRNA的二级结构包含3个结构域,31个茎环结构。A+T 丰富区长度为712 bp。     

Complete genome sequence of the hydrogenotrophic Archaeon Methanobacterium sp. Mb1 isolated from a production-scale biogas plant

Methanobacterium sp. Mb1, a hydrogenotrophic methanogenic Archaeon, was isolated from a rural biogas plant producing methane-rich biogas from maize silage and cattle manure in Germany. Here we report the complete genome sequence of the novel methanogenic isolate Methanobacterium sp. Mb1 harboring a 2,029,766 bp circular chromosome featuring a GC content of 39.74%. The genome encodes two rRNA operons, 41 tRNA genes and 2021 coding sequences and represents the smallest genome currently known within the genus Methanobacterium.     

Cloning and Sequencing of a 36-kb Region of the Bacillus subtilis Genome between the gnt and iol Operons

Within the framework of an international project for the sequencingof the entire Bacillus subtilis genome, a 36-kb chromosome segment,which covers the region between the gnt and iol operons, hasbeen cloned and sequenced. This region (36447 bp) contains 33complete open reading frames (ORFs; genes) including the fourgnt genes and one partial gene. A homology search for the productsof the 33 complete ORFs revealed significant homology to knownproteins in 16 of them such as tetracycline resistance protein(Clostridium perfringens), asparagine synthetase (Arabidopsisthaliana), aldehyde dehydrogenase (Pseudomonas oleovorans),2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (P. paucimobilis),heat shock protein HtpG (Escherichia coli), galactose-protonsymporter (E. coli), auxin-induced protein (common tobacco),glucitol operon repressor (E. coli) and methylmalonate-semialdehydedehydrogenase (P. aeruginosa). Unlike the regions we sequencedso far, this region contained two short sequence multiplications:one was a tandem sequence duplication (409 and 410 bp), andthe other a triplication consisting of two highly conserved118-bp tandem sequences preceded by a less conserved similarsequence (129 bp). The reasons for the presence of these sequencemultiplications in the gnt to iol region were deduced.     

一株污水源多重耐药大肠杆菌的耐药性检测及全基因组测序分析

【背景】水体环境分布广、流动性强,是耐药菌和耐药基因传播的主要媒介。【目的】了解北方污水厂大肠杆菌携带的耐药基因及可移动遗传元件情况。【方法】从北方污水厂筛选出一株多重耐药大肠杆菌,通过药敏试验进行耐药性检验,采用96孔板法测定菌株的最小抑菌浓度,利用酶标仪探究亚抑菌浓度抗生素对菌株生长的影响,并对菌株进行全基因组测序,对其携带的耐药基因及可移动遗传元件进行预测。【结果】大肠杆菌WEC对四环素、环丙沙星、诺氟沙星和红霉素具有耐药性,亚抑菌浓度的四环素、环丙沙星和诺氟沙星能够延缓或抑制菌株的生长。WEC菌株的基因组中包含一条大小为4 782 114 bp的环状染色体和2个大小分别为60 306 bp (pWEC-1)和92 065 bp (pWEC-2)的环状质粒。菌株共携带129个耐药基因,其中128个位于染色体上,在染色体上预测到原噬菌体、基因岛及插入序列的存在,部分可移动遗传元件携带有耐药基因。质粒pWEC-1中无耐药基因,pWEC-2含有1个耐药基因,在质粒基因组中预测到原噬菌体和插入序列。【结论】污水源大肠杆菌WEC是一株多重耐药菌株,其基因组中携带耐药基因和多种可移动遗传元件...     

Structure of the Mutant Fibrillin-1 Gene in the Tight Skin (TSK) Mouse

Mice carrying the tight skin (TSK) mutation harbors a 3.0-kbgenomic duplication (exons 17–40) of the fibrillin-1 gene(Fbn-1) locatedon band F of chromosome 2 as TSK mutation. Wecloned and sequenced the mutated Fbn-1 gene, since it is believedto be responsible for TSK syndrome. Sequence analysis showednumerous amino aciddifferences in the 5' and 3' segments betweenthe TSK mutation and wild-type fbn-1 gene, but any amino aciddifference between the TSK mutation and C57BL/6 mice. (TSK andC57Bl/6 mice are genetically similar, differing only by TSKmutation.) Four amino acid differences were observed betweentwo copies of TSK's fbn-1 gene encoded by exons 17–40.Our results suggest that the majority of structural differencesoccurred in the N and C termini segments during strain divergenceand only a few after the duplication event.     

The Genome Sequence of Rickettsia felis Identifies the First Putative Conjugative Plasmid in an Obligate Intracellular Parasite

We sequenced the genome of Rickettsia felis, a flea-associated obligate intracellular α-proteobacterium causing spotted fever in humans. Besides a circular chromosome of 1,485,148 bp, R. felis exhibits the first putative conjugative plasmid identified among obligate intracellular bacteria. This plasmid is found in a short (39,263 bp) and a long (62,829 bp) form. R. felis contrasts with previously sequenced Rickettsia in terms of many other features, including a number of transposases, several chromosomal toxin–antitoxin genes, many more spoT genes, and a very large number of ankyrin- and tetratricopeptide-motif-containing genes. Host-invasion-related genes for patatin and RickA were found. Several phenotypes predicted from genome analysis were experimentally tested: conjugative pili and mating were observed, as well as β-lactamase activity, actin-polymerization-driven mobility, and hemolytic properties. Our study demonstrates that complete genome sequencing is the fastest approach to reveal phenotypic characters of recently cultured obligate intracellular bacteria.