Complete Genome Sequence of Acidovorax sp. Strain KKS102, a Polychlorinated-Biphenyl Degrader

Ohtsubo, Yoshiyuki; Maruyama, Fumito; Mitsui, Hisayuki; Nagata, Yasunobu; Tsuda, Masashi

doi:10.1128/jb.01848-12

Cited by 121 publications

(109 citation statements)

References 15 publications

(1 reference statement)

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“…Draft genome sequencing was carried out using the HiSeq 1000 sequencing system (Illumina, San Diego, CA) and the 454 GS FLX titanium system (Roche, Mannheim, Germany), and mutation sites were identified by using ShortReadManager software (34). An RNeasy minikit (Qiagen, Hilden, Germany) was used to prepare total cellular RNA from B. multivorans cells cultivated in liquid medium.…”

Section: Methodsmentioning

confidence: 99%

The Small Protein HemP Is a Transcriptional Activator for the Hemin Uptake Operon in Burkholderia multivorans ATCC 17616

Sato

Nonoyama

Kimura

et al. 2017

Appl Environ Microbiol

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Iron and heme play very important roles in various metabolic functions in bacteria, and their intracellular homeostasis is maintained because high concentrations of free forms of these molecules greatly facilitate the Fenton reaction-mediated production of large amounts of reactive oxygen species that severely damage various biomolecules. The ferric uptake regulator (Fur) from Burkholderia multivorans ATCC 17616 is an iron-responsive global transcriptional regulator, and its fur deletant exhibits pleiotropic phenotypes. In this study, we found that the phenotypes of the fur deletant were suppressed by an additional mutation in hemP. The transcription of hemP was negatively regulated by Fur under iron-replete conditions and was constitutive in the fur deletant. Growth of a hemP deletant was severely impaired in a medium containing hemin as the sole iron source, demonstrating the important role of HemP in hemin utilization. HemP was required as a transcriptional activator that specifically binds the promoter-containing region upstream of a Fur-repressive hmuRSTUV operon, which encodes the proteins for hemin uptake. A hmuR deletant was still able to grow using hemin as the sole iron source, albeit at a rate clearly lower than that of the wild-type strain. These results strongly suggested (i) the involvement of HmuR in hemin uptake and (ii) the presence in ATCC 17616 of at least part of other unknown hemin uptake systems whose expression depends on the HemP function. Our in vitro analysis also indicated high-affinity binding of HemP to hemin, and such a property might modulate transcriptional activation of the hmu operon.IMPORTANCE Although the hmuRSTUV genes for the utilization of hemin as a sole iron source have been identified in a few Burkholderia strains, the regulatory expression of these genes has remained unknown. Our analysis in this study using B. multivorans ATCC 17616 showed that its HemP protein is required for expression of the hmuRSTUV operon, and the role of HemP in betaproteobacterial species was elucidated for the first time, to our knowledge, in this study. The HemP protein was also found to have two additional properties that have not been reported for functional homologues in other species; one is that HemP is able to bind to the promotercontaining region of the hmu operon to directly activate its transcription, and the other is that HemP is also required for the expression of an unknown hemin uptake system.

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Section: Methodsmentioning

confidence: 99%

The Small Protein HemP Is a Transcriptional Activator for the Hemin Uptake Operon in Burkholderia multivorans ATCC 17616

Sato

Nonoyama

Kimura

et al. 2017

Appl Environ Microbiol

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“…Acidovorax is a common environmental isolate, with some species known to cause plant disease (Acidovorax citrulii) (Burdman and Walcott 2012), and others known to reduce nitrogen (Ohtsubo et al 2012;Chakraborty and Picardal 2013). The Acidovorax OTU which accounts for almost all of the sequences in the genera was BLAST-matched to A. valerianellae, which has been implicated in disease in the edible plant species Valerianellae locusta (commonly called Corn Salad) (Gardan et al 2003;Thiele et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Characterizing bacterial assemblages in sediments and aerosols at a dry lake bed in Australia using high-throughput sequencing

et al. 2015

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Dust storms are responsible for the transport of a large quantity of bacteria from arid regions. A severe drought in the first decade of the new millennium in Australia increased the incidence of dust transport further. The major aims of this study were to characterize the bacterial communities in aerosols and their associated source sediments using high-throughput sequencing (HTS) and to investigate the possibility of using HTS to link dust to its source, which has not been previously performed in this way. Four field campaigns were conducted at the recently evaporated saline playa Lake Gnarpurt in the Australian state of Victoria between 2008 and 2010 (3 in the austral summer, 1 in winter) to collect aerosol and sediment samples. Aerosol samples were collected on filters up to 150 m above the lake bed using a tethered heliumfilled balloon. DNA was extracted from all samples using commercial kits, and the bacterial communities were examined using 454 HTS on the 16S rRNA gene. Over 200,000 sequences from 29 samples were analysed. In both sediment and aerosol samples, Salinimicrobium was the most abundant taxon; however, there was great variation and diversity across all samples. Analysis of similarities of the bacterial communities indicated that there was a significant overlap between the sediment samples and the aerosols collected above that location, showing that the bacteria in the air was derived from a subset of dust from a nearby source. The challenge remains to use bacterial profiling to link an aerosol sample to a distant source.

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“…The 799 Mb paired-end sequences were assembled into 259 scaffolds larger than 500 bp using Newbler v2.6 (Roche Applied Science, Branford, CT, USA) with the default parameters. Subsequently, each sequence gap in scaffolds was checked and re-assembled using sequence reads belonging to gap extremes by GenoFinisher [13]. Branching contigs, one connected to multiple other contigs, were also examined and misassembled linkages were corrected.…”

Section: Genome Sequencing Informationmentioning

confidence: 99%

Draft genome sequence of Streptomyces sp. TP-A0867, an alchivemycin producer

Komaki

Ichikawa²,

Oguchi³

et al. 2016

Stand in Genomic Sci

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Streptomyces sp. TP-A0867 (=NBRC 109436) produces structurally complex polyketides designated alchivemycins A and B. Here, we report the draft genome sequence of this strain together with features of the organism and assembly, annotation, and analysis of the genome sequence. The 9.9 Mb genome of Streptomyces sp. TP-A0867 encodes 8,385 putative ORFs, of which 7,232 were assigned with COG categories. We successfully identified a hybrid polyketide synthase (PKS)/ nonribosomal peptide synthetase (NRPS) gene cluster that could be responsible for alchivemycin biosynthesis, and propose the biosynthetic pathway. The alchivemycin biosynthetic gene cluster is also present in Streptomyces rapamycinicus NRRL 5491T, Streptomyces hygroscopicus subsp. hygroscopicus NBRC 16556, and Streptomyces ascomycinicus NBRC 13981T, which are taxonomically highly close to strain TP-A0867. This study shows a representative example that distribution of secondary metabolite genes is correlated with evolution within the genus Streptomyces.

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Complete Genome Sequence of Acidovorax sp. Strain KKS102, a Polychlorinated-Biphenyl Degrader

Abstract: bWe report the complete genome sequence of Acidovorax sp. strain KKS102, a polychlorinated-biphenyl-degrading strain isolated from a soil sample in Tokyo. The genome contains a single circular 5,196,935-bp chromosome and no plasmids.

Cited by 121 publications

References 15 publications

The Small Protein HemP Is a Transcriptional Activator for the Hemin Uptake Operon in Burkholderia multivorans ATCC 17616

The Small Protein HemP Is a Transcriptional Activator for the Hemin Uptake Operon in Burkholderia multivorans ATCC 17616

Characterizing bacterial assemblages in sediments and aerosols at a dry lake bed in Australia using high-throughput sequencing

Draft genome sequence of Streptomyces sp. TP-A0867, an alchivemycin producer

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