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1.
The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H+-dependent F0F1 type, one Na+-dependent V type).  相似文献   

2.
Mycobacterium vaccae is a rapidly growing, nontuberculous Mycobacterium species that is generally not considered a human pathogen and is of major pharmaceutical interest as an immunotherapeutic agent. We report here the annotated genome sequence of the M. vaccae type strain, ATCC 25954.  相似文献   

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4.
Erwinia amylovora causes the economically important disease fire blight that affects rosaceous plants, especially pear and apple. Here we report the complete genome sequence and annotation of strain ATCC 49946. The analysis of the sequence and its comparison with sequenced genomes of closely related enterobacteria revealed signs of pathoadaptation to rosaceous hosts.Erwinia amylovora, a plant-associated member of the Enterobacteriaceae, causes fire blight, a devastating disease of rosaceous plants, especially pear and apple (6). The complete genome of Ea273 (ATCC 49946), a virulent strain isolated from an infected apple tree in New York State, was sequenced. Total DNA was extracted and prepared in pMAQ1 shotgun libraries. The complete shotgun sequence was obtained by using dye terminator chemistry in ABI 3730 automated sequencers and contains 88,457 reads (11.12-fold coverage), yielding a theoretical coverage of the genome of 99.99%. The sequence was assembled, finished, and annotated as described previously (1, 5), using Artemis (4) to collate data and facilitate annotation.The genome of E. amylovora consists of a circular chromosome of 3,805,874 bp and two plasmids, AMYP1 (28,243 bp) and AMYP2 (71,487 bp). Coding regions in the chromosome account for 85.1% of the total sequence, with 3,483 identified coding sequences (CDS). Two hundred fifty-four (7%) of the CDSs do not have any matches in current NCBI databases; 114 (3.3%) correspond to conserved hypothetical proteins. Forty-nine CDSs (1.4%) are similar to genes from mobile elements such as integrases, transposases, and bacteriophages, and 110 CDSs (3.2%) were classified as pseudogenes due to interruptions or truncations of the CDSs. The remaining 2,956 annotated CDSs include among other categories genes involved in biosynthesis of the cellular envelope and modifications of surface proteins (299 CDSs [11%]) and genes involved in signal transduction and regulation (228 CDSs [8%]). Seven rRNA operons and 78 tRNA sequences were identified in the chromosome; two new clusters were identified (AMY1550-1575 and AMY2648-2676) that resemble the T3SS-encoding SSR-1 island of Sodalis glossinidius (2), and four clusters that contain genes for biosynthesis of flagella, which based on their location might be regulated independently.The smaller plasmid, AMYP1, had been reported as pEA29 (3); its sequence is nearly identical to the one reported here. The larger plasmid, AMYP2, renamed pEA72 for consistency in nomenclature, contains 87 predicted CDSs, with two predicted mobile-element-related CDSs and one pseudogene. Among the CDSs with annotated functions are a cluster of genes (AMYP2_49 to AMYP2_62) that encode a putative type IV fimbrial system (pil genes).The genome of E. amylovora is only 3.8 Mb long, whereas most free-living enterobacteria, including plant pathogens, have genomes of 4.5 Mb to 5.5 Mb. Comparison of the genome of Ea273 with the sequenced genomes of 15 closely related enterobacteria identified 21 lineage-specific regions, which might be considered genomic islands. E. amylovora has many more predicted pseudogenes, relative to other enterobacteria with similar lifestyles. Given its size and the preponderance of pseudogenes, genome reduction may have occurred via mutational inactivation and subsequent deletion with the following consequences: E. amylovora has fewer genes involved in anaerobic respiration and fermentation than are found in typical related enterobacteria; this likely result in a reduced capacity to live in anaerobic environments.The genome sequence of E. amylovora has revealed clear signs of pathoadaptation to the rosaceous plant environment. For example, T3SS-related proteins are present that are more similar to proteins of other plant pathogens than to proteins of closely related enterobacteria. These include type III effectors, homologous to those of plant-pathogenic pseudomonads, which confer virulence to E. amylovora in plants, and a sorbitol-metabolizing cluster that may confer a competitive advantage for survival in rosaceous plants. The reduced genome size and erosion or loss of genes involved in anaerobic respiration and nitrate assimilation are remarkable, relative to other plant- and animal-pathogenic members of the Enterobacteriaceae.  相似文献   

5.
Here we report the completely annotated genome sequence of the Helicobacter cinaedi type strain (ATCC BAA-847), which is an emerging pathogen that causes cellulitis and bacteremia. The genome sequence will provide new insights into the diagnosis, pathogenic mechanisms, and drug resistance of H. cinaedi.  相似文献   

6.
DS Yu  H Jeong  DH Lee  SK Kwon  JY Song  BK Kim  MS Park  GE Ji  TK Oh  JF Kim 《Journal of bacteriology》2012,194(17):4757-4758
Bifidobacterium bifidum, a common endosymbiotic inhabitant of the human gut, is considered a prominent probiotic microorganism that may promote health. We completely decrypted the 2.2-Mb genome sequence of B. bifidum BGN4, a strain that had been isolated from the fecal sample of a healthy breast-fed infant, and annotated 1,835 coding sequences.  相似文献   

7.
Endophytes live inside plant tissues without causing any harm and may even benefit plants. Here, we provide the high-quality genome sequence of Burkholderia sp. strain KJ006, an endophytic bacterium of rice with antifungal activity. The 6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains genes related to plant growth promotion or degradation of aromatic compounds.  相似文献   

8.
Cycloclasticus sp. strain P1 was isolated from deep-sea sediments of the Pacific Ocean and characterized as a unique bacterium in the degradation of pyrene, a four-ring polycyclic aromatic hydrocarbon (PAH). Here we report the complete genome of P1 and genes associated with PAH degradation.  相似文献   

9.
Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.  相似文献   

10.
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Clostridium carboxidivorans strain P7T is a strictly anaerobic acetogenic bacterium that produces acetate, ethanol, butanol, and butyrate. The C. carboxidivorans genome contains all the genes for the carbonyl branch of the Wood-Ljungdahl pathway for CO2 fixation, and it encodes enzymes for conversion of acetyl coenzyme A into butanol and butyrate.Clostridium carboxidivorans strain P7T (equivalent to ATCC BAA-624T and DSM 15243T) is an obligate anaerobe that can grow autotrophically with H2 and CO2 or CO (fixing carbon via the Wood-Ljungdahl pathway), or it can grow chemoorganotrophically with simple sugars (1). Acetate, ethanol, butanol, and butyrate are end products of metabolism.For slow-growing strict anaerobes such as Clostridium carboxidivorans, genome sequencing provides a rapid theoretical characterization of its metabolism compared to traditional methods. We isolated and amplified genomic C. carboxidivorans DNA using the Wizard genomic DNA purification kit (Promega, Madison, WI) and the REPLI-g kit (Qiagen). A single shotgun pyrosequencing run using a Genome Sequencer FLX system (454 Life Sciences, Branford, CT) resulted in 429,680 high-quality reads (mean read length, 231.6 bp) that were assembled using Newbler software (454 Life Sciences) into 225 contigs >500 bp long. Paired-end sequencing produced 111,154 reads (mean read length, 256.3 bp). Assembly of the paired-end and shotgun reads produced 73 scaffolds containing 216 large contigs with a mean sequence depth of 16.33 reads. PCR amplification and Sanger sequencing were conducted, followed by scaffold assembly using Sequencher (Gene Codes, Ann Arbor, MI). The 4.4-Mb final assembly has 33 scaffolds containing 69 contigs with a Phred-equivalent quality score of 40 or above (accuracy, >99.99%) (GenBank accession no. ADEK00000000).The sequence was annotated using Annotation Engine (J. Craig Venter Institute) and manually curated using Manatee (http://manatee.sourceforge.net/). The genome has 29.7% G+C content and contains 4,174 protein-coding sequences, 3 rRNA operons, 1 tmRNA (dual tRNA-like and mRNA-like nature), 6 noncoding RNAs (ncRNAs), and 48 tRNA genes. (6). Comparison of 16S rRNA genes showed that C. carboxidivorans is closely related to Clostridium scatologenes ATCC 25775T (97% sequence identity) and Clostridium drakei type strain SL1T (99% sequence identity). C. carboxidivorans shares 94% 16S rRNA sequence identity with Clostridium ljungdahlii (4.6 Mb), another solventogenic species.Pathway analyses indicated that C. carboxidivorans is similar to other anaerobic acetogens, such as Moorella thermoacetica (8), in having an incomplete reductive tricarboxylic acid (TCA) cycle where fumarate reductase is absent. Like other acetogenic clostridia, C. carboxidivorans uses the Wood-Ljungdahl pathway for fixing carbon dioxide to organic carbon via acetyl coenzyme A (acetyl-CoA) (5). Two of these genes encode carbon monoxide dehydrogenase (CODH) and acetyl-CoA synthase (ACS), which form a complex to catalyze the carbonyl branch of the pathway for carbon fixation and acetyl-CoA production. C. carboxidivorans has genes that encode phosphotransacetylase and acetate kinase for converting acetyl-CoA into acetate, yielding ATP (2).C. carboxidivorans is unique among other known acetogenic clostridia because it can fix carbon via the Wood-Ljungdahl pathway and convert acetyl-CoA into butanol, which is more energy dense than ethanol. Both C. carboxidivorans and Clostridium acetobutylicum encode NADPH-dependent butanol dehydrogenase (74% identity) to convert acetyl-CoA into butanol (3, 4), but C. acetobutylicum cannot fix CO2 or CO into acetyl-CoA. Conversely, C. ljungdahlii can fix CO and CO2, but it lacks butanol dehydrogenase and cannot convert acetyl-CoA into butanol. Therefore, P7 includes beneficial properties of both these industrially important strains. The genome sequence of C. carboxidivorans P7 could potentially accelerate research allowing its industrial application for biofuel production or to enable some of its pathways to be used directly in synthetic biology for biofuel production.  相似文献   

12.
The gene (aprI) encoding alkaline serine protease (AprI; subtilase) from Alteromonas sp. strain O-7 was cloned and sequenced. The nucleotide sequence of aprI has been identified. The deduced amino acid sequence indicated that aprI codes for a precursor of 715 amino acids and the precursor is composed of four regions including a signal peptide, an N-terminal pro-region, a mature protease region and a C-terminal extension region of 215 amino acids as previously described for aprII [H. Tsujibo et al., Gene, 136, 247–251 (1993)]. The amino acid sequence of the mature AprI (AprI-M) showed high sequence homology with those of other class I subtilases. The C-terminal region was characterized by a repeat of 94 amino acids residues, which showed about 50% similarity with those of the C-terminal pro-region of several known proteases from Gram-negative bacteria.  相似文献   

13.
14.
The Gram-negative bacterium Gluconacetobacter hansenii is considered a model organism for studying cellulose synthesis. We have determined the genome sequence of strain ATCC 23769.Plants produce cellulose, an unbranched chain of β-1,4-linked glucose units, as a structural polysaccharide. It is the most abundant polymer on earth, recently receiving much interest due to its potential use as a feedstock for bioethanol. Bacteria also produce cellulose. Among these, Gluconacetobacter hansenii (previously named Acetobacter xylinus) (4) has been extensively characterized and is a model system for cellulose biosynthesis (1, 2, 7). G. hansenii produces extracellular cellulose that is devoid of lignin or hemicellulose, making it an excellent source for pure cellulose. A lack of a completely sequenced genome for this organism has been a limiting factor in identifying other key proteins involved in cellulose synthesis.The whole-genome sequencing of G. hansenii ATCC 23769 was performed using the 454 FLX-Titanium pyrosequencing technology (5). A combinatorial sequencing approach using 489,201 reads obtained from the shotgun library and 195,088 reads from an 8-kb pair end library (3) produced a total of 221,294,116 bp. These reads were assembled using the Newbler assembler, producing 88 large contigs (>500 bp) and a chromosome-sized scaffold of 3,646,142 bp with an average coverage of ×50.5. This scaffold contained exclusively chromosomal DNA and no plasmid sequences. The gaps in the large scaffold were filled by primer walking and subsequent sequencing of the PCR products. The resulting high-quality draft assembly, consisting of a large scaffold with 71 contigs, was annotated using the Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) service of the National Institute of Biotechnology Information (NCBI).The chromosomal sequence of G. hansenii 23769 contains 3,547,122 bp, with a G+C content of 59%. The genome contains 3,351 genes, of which 3,308 are protein-encoding genes, accounting for 84% of the genome. There are 43 genes for tRNAs and 2 rRNA loci. The genes encoding proteins involved in cellulose synthesis are in an operon consisting of acsAB (GXY_04277), acsC (GXY_04282), and acsD (GXY_04292), as previously shown by Saxena et al. (7). Interestingly, there are two additional copies of acsAB, GXY_08864 and GXY_14452, which share 69% and 72% sequence identity, respectively, with the acsAB genes in the operon; the deduced amino acid sequences are 40% and 46% identical, respectively, with that deduced from acsAB in the operon. There are also two additional copies of acsC, GXY_08869 and GXY_014472, which share 72% and 65% DNA sequence identity, respectively, with the acsC gene in the operon; the deduced amino acid sequences share 28% and 30% amino acid identity, respectively, with that deduced from acsC. acsAB (GXY_08864) and acsC (GXY_08869) are only 17 bp apart, less than the distance (66 bp) between the acsAB and acsC genes in the operon. acsAB (GXY_14452) and acsC (GXY_14472) are separated by 3,299 bp, with three genes in between. However, acsD is present only in the operon, not duplicated elsewhere in the genome. The genome also contains three genes encoding diguanylate cyclase, as previously reported by Tal et al. (8). Diguanylate cyclase catalyzes the formation of cyclic di-GMP, a second messenger in bacteria that functions as an allosteric activator of cellulase synthase AcsAB (6).  相似文献   

15.
Mycoplasma wenyonii is a hemotrophic mycoplasma that causes acute and chronic infections in cattle. Here, we announce the first complete genome sequence of this organism. The genome is a single circular chromosome with 650,228 bp and G+C% of 33.9. Analyses of M. wenyonii genome will provide insights into its biology.  相似文献   

16.
Hydrocarboniphaga effusa strain AP103(T) (ATCC BAA-332(T)) is a member of the Gammaproteobacteria utilizing n-alkanes as the sole source of carbon and energy. Here we report the draft genome sequence of AP103(T), which consists of 5,193,926 bp with a G + C content of 65.18%.  相似文献   

17.
Mycoplasma hyorhinis is generally considered a swine pathogen yet is most commonly found infecting laboratory cell lines. An increasing body of evidence suggests that chronic infections with M. hyorhinis may cause oncogenic transformation. Here, we announce the complete genome sequence of M. hyorhinis strain HUB-1.Mycoplasma hyorhinis is generally considered to be a swine pathogen causing lung lesions, inflammation in the chest and abdominal lining, and arthritis (8). This agent also frequently contaminates laboratory cell cultures, impinging on many aspects of biological research (3). Recent studies have demonstrated that M. hyorhinis infections induce a malignant phenotype in human prostate (7) and gastric (4) cells, suggesting that M. hyorhinis infections are associated with oncogenic transformation. These properties of M. hyorhinis have increased its profile to researchers. The complete genome sequence of this microbe has yet to be determined.We sequenced the genome of M. hyorhinis strain HUB-1, a pathogenic strain isolated from the respiratory tract of swine. Whole-genome sequencing was performed by combining GS FLX (6) and Solexa paired-end sequencing technologies (1). Genomic libraries containing 3-kb inserts were constructed, and 308,604 reads (79.7% paired end) were produced using the GS FLX system, giving 65.9-fold coverage of the genome. About 93.4% of reads were assembled into one large scaffold using Newbler software (454 Life Sciences, Branford, CT). A total of 822,579 reads were generated using an Illumina Solexa Genome Analyzer IIx and were mapped to the scaffold using the Burrows-Wheeler alignment (BWA) tool (5). Gaps were filled by local assembly of the Solexa/Roche 454 reads or by sequencing PCR products by using an ABI 3730 capillary sequencer. Open reading frames containing more than 30 amino acid residues were predicted using Glimmer 3.0 (2) and verified by comparison with six other closely related genome sequences.The complete genome of M. hyorhinis HUB-1 consists of an 839,615-bp single circular chromosome with an average G+C content of 25.88%. A total of 654 protein-encoding genes are predicted. The average protein size is 364 amino acids, and the mean coding percentage is 85.2%. The genome includes 30 tRNA genes, and only a single copy of the 16S-23S rRNA operon can be found. The 5S rRNA operon is separate from the 16S-23S rRNA operon. Protein secretion occurs through a truncated membrane protein secretion system, consisting of SecA, SecD, SecY, PrsA, DnaK, Tig, and LepA. Additionally, 20 pseudogenes, which become truncated or inactivated, are identified in the genome.M. hyorhinis contains a special variable lipoprotein (Vlp) system that constitutes its major coat protein (9) and provides a mutational strategy for evasion of the host immune system. Different M. hyorhinis strains carry a variable number of vlp genes (9). M. hyorhinis HUB-1 is characterized to contain seven vlp genes displayed in the order 5′-vlpD-vlpE-vlpF-insertion sequence (IS)-vlpG-vlpA-IS-vlpB-vlpC-3′.This is the first complete genome sequence of M. hyorhinis, and its availability will provide a better-defined genetic background for future studies of gene expression and regulation.  相似文献   

18.
Enterococcus faecalis ATCC 29212, a vancomycin-sensitive strain, has been extensively used as a representative control strain for clinical and laboratory experiments. Here we report the draft genome and annotation of this strain, containing 3,027,060 bp, with a G+C content of 37.2% in 126 contigs (≥500 bp).  相似文献   

19.
Kadnikov  V. V.  Mardanov  A. V.  Beletsky  A. V.  Frank  Y. A.  Karnachuk  O. V.  Ravin  N. V. 《Microbiology》2019,88(4):461-468
Microbiology - Bacteria of the candidate phylum Bipolaricaulota, previously known as OP1 and Acetothermia, have been identified in various terrestrial and marine ecosystems as a result of molecular...  相似文献   

20.
Sphingomonas sp. strain ATCC 31555 can produce an anionic heteropolysaccharide, welan gum, which shows excellent stability and viscosity retention even at high temperatures. Here we present a 4.0-Mb assembly of its genome sequence. We have annotated 10 coding sequences (CDSs) responsible for the welan gum biosynthesis and 55 CDSs related to monosaccharide metabolism.  相似文献   

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