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1.  Genome Sequence of Pseudomonas putida Strain SJTE-1, a Bacterium Capable of Degrading Estrogens and Persistent Organic Pollutants 
Journal of Bacteriology  2012;194(17):4781-4782.
Pseudomonas putida strain SJTE-1 can utilize 17β-estradiol and other environmental estrogens/toxicants, such as estrone, and naphthalene as sole carbon sources. We report the draft genome sequence of strain SJTE-1 (5,551,505 bp, with a GC content of 62.25%) and major findings from its annotation, which could provide insights into its biodegradation mechanisms.
doi:10.1128/JB.01060-12
PMCID: PMC3415482  PMID: 22887678
2.  Genome Sequence of Pseudomonas aeruginosa Strain SJTD-1, a Bacterium Capable of Degrading Long-Chain Alkanes and Crude Oil 
Journal of Bacteriology  2012;194(17):4783-4784.
Pseudomonas aeruginosa strain SJTD-1 can utilize long-chain alkanes, diesel oil, and crude oil as sole carbon sources. We report the draft genome sequence of strain SJTD-1 (6,074,058 bp, with a GC content of 66.83%) and major findings from its annotation, which could provide insights into its petroleum biodegradation mechanism.
doi:10.1128/JB.01061-12
PMCID: PMC3415508  PMID: 22887679
3.  Revised Genome Sequence of Burkholderia thailandensis MSMB43 with Improved Annotation 
Journal of Bacteriology  2012;194(17):4749-4750.
There is growing interest in discovery of novel bioactive natural products from Burkholderia thailandensis. Here we report a significantly improved genome sequence and reannotation of Burkholderia thailandensis MSMB43, which will facilitate the discovery of new natural products through genome mining and studies of the metabolic versatility of this bacterium.
doi:10.1128/JB.00931-12
PMCID: PMC3415525  PMID: 22887659
4.  The Genome of Salmonella enterica Serovar Gallinarum: Distinct Insertions/Deletions and Rare Rearrangements 
Journal of Bacteriology  2005;187(14):4720-4727.
Salmonella enterica serovar Gallinarum is a fowl-adapted pathogen, causing typhoid fever in chickens. It has the same antigenic formula (1,9,12:—:—) as S. enterica serovar Pullorum, which is also adapted to fowl but causes pullorum disease (diarrhea). The close relatedness but distinct pathogeneses make this pair of fowl pathogens good models for studies of bacterial genomic evolution and the way these organisms acquired pathogenicity. To locate and characterize the genomic differences between serovar Gallinarum and other salmonellae, we constructed a physical map of serovar Gallinarum strain SARB21 by using I-CeuI, XbaI, and AvrII with pulsed-field gel electrophoresis techniques. In the 4,740-kb genome, we located two insertions and six deletions relative to the genome of S. enterica serovar Typhimurium LT2, which we used as a reference Salmonella genome. Four of the genomic regions with reduced lengths corresponded to the four prophages in the genome of serovar Typhimurium LT2, and the others contained several smaller deletions relative to serovar Typhimurium LT2, including regions containing srfJ, std, and stj and gene clusters encoding a type I restriction system in serovar Typhimurium LT2. The map also revealed some rare rearrangements, including two inversions and several translocations. Further characterization of these insertions, deletions, and rearrangements will provide new insights into the molecular basis for the specific host-pathogen interactions and mechanisms of genomic evolution to create a new pathogen.
doi:10.1128/JB.187.14.4720-4727.2005
PMCID: PMC1169526  PMID: 15995186
5.  Genomic Diversification among Archival Strains of Salmonella enterica Serovar Typhimurium LT7 
Journal of Bacteriology  2003;185(7):2131-2142.
To document genomic changes during long periods of storage, we analyzed Salmonella enterica serovar Typhimurium LT7, a mutator strain that was previously reported to have higher rates of mutations compared to other serovar Typhimurium strains such as LT2. Upon plating directly from sealed agar stabs that had been stocked at room temperature for up to four decades, many auxotrophic mutants derived from LT7 gave rise to colonies of different sizes. Restreaking from single colonies consistently yielded colonies of diverse sizes even when we repeated single-colony isolation nine times. Colonies from the first plating had diverse genomic changes among and even within individual vials, including translocations, inversions, duplications, and point mutations, which were detected by rare-cutting endonuclease analysis with pulsed-field gel electrophoresis. Interestingly, even though the colony size kept diversifying, all descendents of the same single colonies from the first plating had the same sets of detected genomic changes. We did not detect any colony size or genome structure diversification in serovar Typhimurium LT7 stocked at −70°C or in serovar Typhimurium LT2 stocked either at −70°C or at room temperature. These results suggest that, although colony size diversification occurred during rapid growth, all detected genomic changes took place during the storage at room temperature and were carried over to their descendents without further changes during rapid growth in rich medium. We constructed a genomic cleavage map on the LT7 strain that had been stocked at −70°C and located all of the detected genomic changes on the map. We speculated on the significance of mutators for survival and evolution under environmentally stressed conditions.
doi:10.1128/JB.185.7.2131-2142.2003
PMCID: PMC151480  PMID: 12644482
6.  The Evolving Genome of Salmonella enterica Serovar Pullorum 
Journal of Bacteriology  2002;184(10):2626-2633.
Salmonella enterica serovar Pullorum is a fowl-adapted bacterial pathogen that causes dysentery (pullorum disease). Host adaptation and special pathogenesis make S. enterica serovar Pullorum an exceptionally good system for studies of bacterial evolution and speciation, especially regarding pathogen-host interactions and the acquisition of pathogenicity. We constructed a genome map of S. enterica serovar Pullorum RKS5078, using I-CeuI, XbaI, AvrII, and SpeI and Tn10 insertions. Pulsed-field gel electrophoresis was employed to separate the large DNA fragments generated by the endonucleases. The genome is 4,930 kb, which is similar to most salmonellas . However, the genome of S. enterica serovar Pullorum RKS5078 is organized very differently from the majority of salmonellas, with three major inversions and one translocation. This extraordinary genome structure was seen in most S. enterica serovar Pullorum strains examined, with different structures in a minority of S. enterica serovar Pullorum strains. We describe the coexistence of different genome structures among the same bacteria as genomic plasticity. Through comparisons with S. enterica serovar Typhimurium, we resolved seven putative insertions and eight deletions ranging in size from 12 to 157 kb. The genomic plasticity seen among S. enterica serovar Pullorum strains supported our hypothesis about its association with bacterial evolution: a large genomic insertion (157 kb in this case) disrupted the genomic balance, and rebalancing by independent recombination events in individual lineages resulted in diverse genome structures. As far as the structural plasticity exists, the S. enterica serovar Pullorum genome will continue evolving to reach a further streamlined and balanced structure.
doi:10.1128/JB.184.10.2626-2633.2002
PMCID: PMC135040  PMID: 11976291
7.  Characterization of CRISPR RNA Biogenesis and Cas6 Cleavage-Mediated Inhibition of a Provirus in the Haloarchaeon Haloferax mediterranei 
Journal of Bacteriology  2013;195(4):867-875.
The adaptive immune system comprising CRISPR (clustered regularly interspaced short palindromic repeats) arrays and cas (CRISPR-associated) genes has been discovered in a wide range of bacteria and archaea and has recently attracted comprehensive investigations. However, the subtype I-B CRISPR-Cas system in haloarchaea has been less characterized. Here, we investigated Cas6-mediated RNA processing in Haloferax mediterranei. The Cas6 cleavage site, as well as the CRISPR transcription start site, was experimentally determined, and processing of CRISPR transcripts was detected with a progressively increasing pattern from early log to stationary phase. With genetic approaches, we discovered that the lack of Cas1, Cas3, or Cas4 unexpectedly resulted in a decrease of CRISPR transcripts, while Cas5, Cas6, and Cas7 were found to be essential in stabilizing mature CRISPR RNA (crRNA). Intriguingly, we observed a CRISPR- and Cas3-independent inhibition of a defective provirus, in which the putative Cascade (CRISPR-associated complex for antiviral defense) proteins (Cas5, Cas6, Cas7, and Cas8b) were indispensably required. A sequence carried by a proviral transcript was found to be homologous to the CRISPR repeat RNA and vulnerable to Cas6-mediated cleavage, implying a distinct interference mechanism that may account for this unusual inhibition. These results provide fundamental information for the subtype I-B CRISPR-Cas system in halophilic archaea and suggest diversified mechanisms and multiple physiological functions for the CRISPR-Cas system.
doi:10.1128/JB.01688-12
PMCID: PMC3562093  PMID: 23243301
8.  Genome Sequence of the Aerobic Bacterium Bacillus sp. Strain FJAT-13831 
Journal of Bacteriology  2012;194(23):6633.
Bacillus sp. strain FJAT-13831 was isolated from the no. 1 pit soil of Emperor Qin's Terracotta Warriors in Xi'an City, People's Republic of China. The isolate showed a close relationship to the Bacillus cereus group. The draft genome sequence of Bacillus sp. FJAT-13831 was 4,425,198 bp in size and consisted of 5,567 genes (protein-coding sequences [CDS]) with an average length of 782 bp and a G+C value of 36.36%.
doi:10.1128/JB.01072-12
PMCID: PMC3497504  PMID: 23144388
9.  Genome Sequence of the Biocontrol Agent Microbacterium barkeri Strain 2011-R4 
Journal of Bacteriology  2012;194(23):6666-6667.
Microbacterium barkeri strain 2011-R4 is a Gram-positive epiphyte which has been confirmed as a biocontrol agent against several plant pathogens in our previous studies. Here, we present the draft genome sequence of this strain, which was isolated from the rice rhizosphere in Tonglu city, Zhejiang province, China.
doi:10.1128/JB.01468-12
PMCID: PMC3497549  PMID: 23144410
10.  Complete Genome Sequence of the Metabolically Versatile Halophilic Archaeon Haloferax mediterranei, a Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Producer 
Journal of Bacteriology  2012;194(16):4463-4464.
Haloferax mediterranei, an extremely halophilic archaeon, has shown promise for production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) from unrelated cheap carbon sources. Here we report the complete genome (3,904,707 bp) of H. mediterranei CGMCC 1.2087, consisting of one chromosome and three megaplasmids.
doi:10.1128/JB.00880-12
PMCID: PMC3416209  PMID: 22843593
11.  Whole-Genome Sequence of Staphylococcus aureus Strain LCT-SA112 
Journal of Bacteriology  2012;194(15):4124.
Staphylococcus aureus is a facultative anaerobic Gram-positive coccal bacterium. S. aureus is the most common species of Staphylococcus to cause staphylococcal infections, which are very common in clinical medicine. Here we report the genome sequence of S. aureus strain LCT-SA112, which was isolated from S. aureus subsp. aureus CGMCC 1.230.
doi:10.1128/JB.00710-12
PMCID: PMC3416511  PMID: 22815443
12.  Whole-Genome Sequence of Klebsiella pneumonia Strain LCT-KP214 
Journal of Bacteriology  2012;194(12):3281.
Klebsiella pneumoniae is a Gram-negative, nonmotile, encapsulated, lactose-fermenting, facultative anaerobic, rod-shaped bacterium found in the normal flora of the mouth, skin, and intestines. Here we present the fine-draft genome sequence of K. pneumoniae strain LCT-KP214, which originated from K. pneumoniae strain CGMCC 1.1736.
doi:10.1128/JB.00531-12
PMCID: PMC3370881  PMID: 22628509
13.  OnpA, an Unusual Flavin-Dependent Monooxygenase Containing a Cytochrome b5 Domain 
Journal of Bacteriology  2012;194(6):1342-1349.
ortho-Nitrophenol 2-monooxygenase (EC 1.14.13.31) from Alcaligenes sp. strain NyZ215 catalyzes monooxygenation of ortho-nitrophenol to form catechol via ortho-benzoquinone. Sequence analysis of this onpA-encoded enzyme revealed that it contained a flavin-binding monooxygenase domain and a heme-binding cytochrome b5 domain. OnpA was purified to homogeneity as a His-tagged protein and was considered a monomer, as determined by gel filtration. FAD and heme were identified by high-performance liquid chromatography (HPLC) and HPLC-mass spectrometry (HPLC-MS) as cofactors in this enzyme, and quantitative analysis indicated that 1 mol of the purified recombinant OnpA contained 0.66 mol of FAD and 0.20 mol of heme. However, the enzyme activity of OnpA was increased by 60% and 450% after addition of FAD and hemin, respectively, suggesting that the optimal stoichiometry was 1:1:1. In addition, site-directed mutagenesis experiments confirmed that two highly conserved histidines located in the cytochrome b5 domain were associated with binding of the heme, and the cytochrome b5 domain was involved in the OnpA activity. These results indicate that OnpA is an unusual FAD-dependent monooxygenase containing a fused cytochrome b5 domain that is essential for its activity. Therefore, we here demonstrate a link between cytochrome b5 and flavin-dependent monooxygenases.
doi:10.1128/JB.06411-11
PMCID: PMC3294848  PMID: 22267507
14.  Complete Genome Sequence of Salmonella enterica Serovar Pullorum RKS5078 
Journal of Bacteriology  2012;194(3):744.
Salmonella enterica serovar Pullorum is a chicken-adapted pathogen, causing pullorum disease. Its strict host adaptation has been suspected to result in gene decay. To validate this hypothesis and identify the decayed genes, we sequenced the complete genome of S. Pullorum RKS5078. We found 263 pseudogenes in this strain and conducted functional analyses of the decayed genes.
doi:10.1128/JB.06507-11
PMCID: PMC3264078  PMID: 22247537
15.  Complete Genome Sequence of Haloarcula hispanica, a Model Haloarchaeon for Studying Genetics, Metabolism, and Virus-Host Interaction 
Journal of Bacteriology  2011;193(21):6086-6087.
Haloarcula hispanica is an extremely halophilic archaeon that has an unusually low restriction barrier and is therefore significant for studying archaeal genetics, metabolism, and virus-host interactions. Here we report the complete genome sequence (3,890,005 bp) of H. hispanica strain CGMCC 1.2049, consisting of two chromosomes and one megaplasmid.
doi:10.1128/JB.05953-11
PMCID: PMC3194904  PMID: 21994921
16.  Genome Sequence of the Tobacco Bacterial Wilt Pathogen Ralstonia solanacearum 
Journal of Bacteriology  2011;193(21):6088-6089.
Ralstonia solanacearum is a causal agent of plant bacterial wilt with thousands of distinct strains in a heterogeneous species complex. Here we report the genome sequence of a phylotype IB strain, Y45, isolated from tobacco (Nicotiana tabacum) in China. Compared with the published genomes of eight strains which were isolated from other hosts and habitats, 794 specific genes and many rearrangements/inversion events were identified in the tobacco strain, demonstrating that this strain represents an important node within the R. solanacearum complex.
doi:10.1128/JB.06009-11
PMCID: PMC3194909  PMID: 21994922
17.  Complete Genome Sequence of the Industrial Strain Ketogulonicigenium vulgare WSH-001 
Journal of Bacteriology  2011;193(21):6108-6109.
Ketogulonicigenium vulgare is an industrial organism commonly used in the vitamin C industry. Here, we report the finished, annotated, and compared 3.28-Mbp high-quality genome sequence of Ketogulonicigenium vulgare WSH-001, a 2-keto-l-gulonic acid-producing industrial strain stocked in our laboratory.
doi:10.1128/JB.06007-11
PMCID: PMC3194925  PMID: 21994934
18.  Complete Genome Sequence of the Industrial Strain Bacillus megaterium WSH-002 
Journal of Bacteriology  2011;193(22):6389-6390.
Bacillus megaterium, an industrial strain, has been widely used in protein production and the vitamin C industry. Here we reported a finished, annotated, and compared 4.14-Mbp high-quality genome sequence of B. megaterium WSH-002, which is the companion strain for Ketogulonicigenium vulgare in the vitamin C industry and is stocked in our laboratory.
doi:10.1128/JB.06066-11
PMCID: PMC3209192  PMID: 22038958
19.  Genome Sequence of the Halotolerant Marine Bacterium Myxococcus fulvus HW-1 
Journal of Bacteriology  2011;193(18):5015-5016.
Myxococcus fulvus HW-1 (ATCC BAA-855) is a halotolerant marine myxobacterium. This strain exhibits complex social behaviors in the presence of low concentrations of seawater but adopts an asocial living pattern under oceanic conditions. The whole genome of M. fulvus HW-1 will enable us to further investigate the details of its evolution.
doi:10.1128/JB.05516-11
PMCID: PMC3165639  PMID: 21868801
20.  Draft Genome Sequence of Gordonia neofelifaecis NRRL B-59395, a Cholesterol-Degrading Actinomycete▿ 
Journal of Bacteriology  2011;193(18):5045-5046.
We report a draft sequence of the genome of Gordonia neofelifaecis NRRL B-59395, a cholesterol-degrading actinomycete isolated from fresh feces of a clouded leopard (Neofelis nebulosa). As predicted, the reported genome contains several gene clusters for cholesterol degradation. This is the second available genome sequence of the family Gordoniaceae.
doi:10.1128/JB.05531-11
PMCID: PMC3165644  PMID: 21742880
21.  Genome Sequence of the Repetitive-Sequence-Rich Mycoplasma fermentans Strain M64▿ 
Journal of Bacteriology  2011;193(16):4302-4303.
Mycoplasma fermentans is a microorganism commonly found in the genitourinary and respiratory tracts of healthy individuals and AIDS patients. The complete genome of the repetitive-sequence-rich M. fermentans strain M64 is reported here. Comparative genomics analysis revealed dramatic differences in genome size between this strain and the recently completely sequenced JER strain.
doi:10.1128/JB.05228-11
PMCID: PMC3147699  PMID: 21642450
22.  Whole Genome Sequences of Four Brucella Strains ▿ 
Journal of Bacteriology  2011;193(14):3674-3675.
Brucella melitensis and Brucella suis are intracellular pathogens of livestock and humans. Here we report four genome sequences, those of the virulent strain B. melitensis M28-12 and vaccine strains B. melitensis M5 and M111 and B. suis S2, which show different virulences and pathogenicities, which will help to design a more effective brucellosis vaccine.
doi:10.1128/JB.05155-11
PMCID: PMC3133323  PMID: 21602346
23.  Whole-Genome Sequences of Four Mycobacterium bovis BCG Vaccine Strains ▿ 
Journal of Bacteriology  2011;193(12):3152-3153.
Mycobacterium bovis Bacille Calmette-Guérin (BCG) is the only vaccine available against tuberculosis (TB). A number of BCG strains are in use, and they exhibit biochemical and genetic differences. We report the genome sequences of four BCG strains representing different lineages, which will help to design more effective TB vaccines.
doi:10.1128/JB.00405-11
PMCID: PMC3133212  PMID: 21478353
24.  Structural and Mechanical Properties of Klebsiella pneumoniae Type 3 Fimbriae▿ §  
Journal of Bacteriology  2011;193(7):1718-1725.
This study investigated the structural and mechanical properties of Klebsiella pneumoniae type 3 fimbriae, which constitute a known virulence factor for the bacterium. Transmission electron microscopy and optical tweezers were used to understand the ability of the bacterium to survive flushes. An individual K. pneumoniae type 3 fimbria exhibited a helix-like structure with a pitch of 4.1 nm and a three-phase force-extension curve. The fimbria was first nonlinearly stretched with increasing force. Then, it started to uncoil and extended several micrometers at a fixed force of 66 ± 4 pN (n = 22). Finally, the extension of the fimbria shifted to the third phase, with a characteristic force of 102 ± 9 pN (n = 14) at the inflection point. Compared with the P fimbriae and type 1 fimbriae of uropathogenic Escherichia coli, K. pneumoniae type 3 fimbriae have a larger pitch in the helix-like structure and stronger uncoiling and characteristic forces.
doi:10.1128/JB.01395-10
PMCID: PMC3067671  PMID: 21239584
25.  Complete Genome Sequence of Metallosphaera cuprina, a Metal Sulfide-Oxidizing Archaeon from a Hot Spring▿ 
Journal of Bacteriology  2011;193(13):3387-3388.
The genome of the metal sulfide-oxidizing, thermoacidophilic strain Metallosphaera cuprina Ar-4 has been completely sequenced and annotated. Originally isolated from a sulfuric hot spring, strain Ar-4 grows optimally at 65°C and a pH of 3.5. The M. cuprina genome has a 1,840,348-bp circular chromosome (2,029 open reading frames [ORFs]) and is 16% smaller than the previously sequenced Metallosphaera sedula genome. Compared to the M. sedula genome, there are no counterpart genes in the M. cuprina genome for about 480 ORFs in the M. sedula genome, of which 243 ORFs are annotated as hypothetical protein genes. Still, there are 233 ORFs uniquely occurring in M. cuprina. Genome annotation supports that M. cuprina lives a facultative life on CO2 and organics and obtains energy from oxidation of sulfidic ores and reduced inorganic sulfuric compounds.
doi:10.1128/JB.05038-11
PMCID: PMC3133273  PMID: 21551305

Results 1-25 (408)