Publications by authors named "Sagar M Utturkar"

28 Publications

  • Page 1 of 1

BRD9 Is a Critical Regulator of Androgen Receptor Signaling and Prostate Cancer Progression.

Cancer Res 2021 Feb 21;81(4):820-833. Epub 2020 Dec 21.

Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana.

Switch/sucrose-nonfermentable (SWI/SNF) chromatin-remodeling complexes are critical regulators of chromatin dynamics during transcription, DNA replication, and DNA repair. A recently identified SWI/SNF subcomplex termed GLTSCR1/1L-BAF (GBAF; or "noncanonical BAF", ncBAF) uniquely contains bromodomain-containing protein BRD9 and glioma tumor suppressor candidate region 1 (GLTSCR1) or its paralog GLTSCR1-like (GLTSCR1L). Recent studies have identified a unique dependency on GBAF (ncBAF) complexes in synovial sarcoma and malignant rhabdoid tumors, both of which possess aberrations in canonical BAF (cBAF) and Polybromo-BAF (PBAF) complexes. Dependencies on GBAF in malignancies without SWI/SNF aberrations, however, are less defined. Here, we show that GBAF, particularly its BRD9 subunit, is required for the viability of prostate cancer cell lines and for optimal xenograft tumor growth . BRD9 interacts with androgen receptor (AR) and CCCTC-binding factor (CTCF), and modulates AR-dependent gene expression. The GBAF complex exhibits overlapping genome localization and transcriptional targets as bromodomain and extraterminal domain-containing (BET) proteins, which are established AR coregulators. Our results demonstrate that GBAF is critical for coordinating SWI/SNF-BET cooperation and uncover a new druggable target for AR-positive prostate cancers, including those resistant to androgen deprivation or antiandrogen therapies. SIGNIFICANCE: Advanced prostate cancers resistant to androgen receptor antagonists are still susceptible to nontoxic BRD9 inhibitors, making them a promising alternative for halting AR signaling in progressed disease.
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http://dx.doi.org/10.1158/0008-5472.CAN-20-1417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8026650PMC
February 2021

The RNA helicase DDX5 supports mitochondrial function in small cell lung cancer.

J Biol Chem 2020 07 6;295(27):8988-8998. Epub 2020 May 6.

Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA. Electronic address:

DEAD-box helicase 5 (DDX5) is a founding member of the DEAD-box RNA helicase family, a group of enzymes that regulate ribonucleoprotein formation and function in every aspect of RNA metabolism, ranging from synthesis to decay. Our laboratory previously found that DDX5 is involved in energy homeostasis, a process that is altered in many cancers. Small cell lung cancer (SCLC) is an understudied cancer type for which effective treatments are currently unavailable. Using an array of methods, including short hairpin RNA-mediated gene silencing, RNA and ChIP sequencing analyses, and metabolite profiling, we show here that is overexpressed in SCLC cell lines and that its down-regulation results in various metabolic and cellular alterations. Depletion of resulted in reduced growth and mitochondrial dysfunction in the chemoresistant SCLC cell line H69AR. The latter was evidenced by down-regulation of genes involved in oxidative phosphorylation and by impaired oxygen consumption. Interestingly, depletion specifically reduced intracellular succinate, a TCA cycle intermediate that serves as a direct electron donor to mitochondrial complex II. We propose that the oncogenic role of DDX5, at least in part, manifests as up-regulation of respiration supporting the energy demands of cancer cells.
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http://dx.doi.org/10.1074/jbc.RA120.012600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7335798PMC
July 2020

Oct4-Mediated Inhibition of Lsd1 Activity Promotes the Active and Primed State of Pluripotency Enhancers.

Cell Rep 2020 02;30(5):1478-1490.e6

Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA. Electronic address:

An aberrant increase in pluripotency gene (PpG) expression due to enhancer reactivation could induce stemness and enhance the tumorigenicity of cancer stem cells. Silencing of PpG enhancers (PpGe) during embryonic stem cell differentiation involves Lsd1-mediated H3K4me1 demethylation and DNA methylation. Here, we observed retention of H3K4me1 and DNA hypomethylation at PpGe associated with a partial repression of PpGs in F9 embryonal carcinoma cells (ECCs) post-differentiation. H3K4me1 demethylation in F9 ECCs could not be rescued by Lsd1 overexpression. Given our observation that H3K4me1 demethylation is accompanied by strong Oct4 repression in P19 ECCs, we tested if Oct4 interaction with Lsd1 affects its catalytic activity. Our data show a dose-dependent inhibition of Lsd1 activity by Oct4 and retention of H3K4me1 at PpGe in Oct4-overexpressing P19 ECCs. These data suggest that Lsd1-Oct4 interaction in cancer stem cells could establish a "primed" enhancer state that is susceptible to reactivation, leading to aberrant PpG expression.
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http://dx.doi.org/10.1016/j.celrep.2019.11.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7316367PMC
February 2020

The origin and biosynthesis of the naphthalenoid moiety of juglone in black walnut.

Hortic Res 2018 1;5:67. Epub 2018 Nov 1.

1Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907 USA.

Several members of the family produce juglone, a specialized 1,4-naphthoquinone (1,4-NQ) natural product that is responsible for the notorious allelopathic effects of black walnut (). Despite its documented ecological roles and potential for being developed as a novel natural product-based herbicide, none of the genes involved in synthesizing juglone have been identified. Based on classical labeling studies, we hypothesized that biosynthesis of juglone's naphthalenoid moiety is shared with biochemical steps of the phylloquinone pathway. Here, using comparative transcriptomics in combination with targeted metabolic profiling of 1,4-NQs in various black walnut organs, we provide evidence that phylloquinone pathway genes involved in 1,4-dihydroxynaphthoic acid (DHNA) formation are expressed in roots for synthesis of a compound other than phylloquinone. Feeding experiments using axenic black walnut root cultures revealed that stable isotopically labeled l-glutamate incorporates into juglone resulting in the same mass shift as that expected for labeling of the quinone ring in phylloquinone. Taken together, these results indicate that , an intermediate from the phylloquinone pathway provides the naphthalenoid moiety of juglone. Moreover, this work shows that juglone can be synthesized in roots without the contribution of immediate precursors translocated from aerial tissues. The present study illuminates all genes involved in synthesizing the juglone naphthoquinone ring and provides RNA-sequencing datasets that can be used with functional screening studies to elucidate the remaining juglone pathway genes. Translation of the generated knowledge is expected to inform future metabolic engineering strategies for harnessing juglone as a novel natural product-based herbicide.
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http://dx.doi.org/10.1038/s41438-018-0067-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6210188PMC
November 2018

Unique organization and unprecedented diversity of the cellulosome system.

Biotechnol Biofuels 2017 7;10:211. Epub 2017 Sep 7.

Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.

Background: is an anaerobic, mesophilic, cellulolytic, cellulosome-producing clostridial bacterium capable of utilizing cellulose and cellobiose as carbon sources. Recently, we sequenced the genome, and subsequent comprehensive bioinformatic analysis, herein reported, revealed an unprecedented number of cellulosome-related components, including 78 cohesin modules scattered among 31 scaffoldins and more than 200 dockerin-bearing ORFs. In terms of numbers, the cellulosome system represents the most intricate, compositionally diverse cellulosome system yet known in nature.

Results: The organization of the cellulosome is unique compared to previously described cellulosome systems. In contrast to all other known cellulosomes, the cohesin types are reversed for all scaffoldins i.e., the type II cohesins are located on the enzyme-integrating primary scaffoldin, whereas the type I cohesins are located on the anchoring scaffoldins. Many of the type II dockerin-bearing ORFs include X60 modules, which are known to stabilize type II cohesin-dockerin interactions. In the present work, we focused on revealing the architectural arrangement of cellulosome structure in this bacterium by examining numerous interactions between the various cohesin and dockerin modules. In total, we cloned and expressed 43 representative cohesins and 27 dockerins. The results revealed various possible architectures of cell-anchored and cell-free cellulosomes, which serve to assemble distinctive cellulosome types via three distinct cohesin-dockerin specificities: type I, type II, and a novel-type designated R (distinct from type III interactions, predominant in ruminococcal cellulosomes).

Conclusions: The results of this study provide novel insight into the architecture and function of the most intricate and extensive cellulosomal system known today, thereby extending significantly our overall knowledge base of cellulosome systems and their components. The robust cellulosome system of with its unique binding specificities and reversal of cohesin-dockerin types, has served to amend our view of the cellulosome paradigm. Revealing new cellulosomal interactions and arrangements is critical for designing high-efficiency artificial cellulosomes for conversion of plant-derived cellulosic biomass towards improved production of biofuels.
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http://dx.doi.org/10.1186/s13068-017-0898-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590126PMC
September 2017

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.

Front Microbiol 2017 18;8:1272. Epub 2017 Jul 18.

Graduate School of Genome Science and Technology, University of TennesseeKnoxville, TN, United States.

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.
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http://dx.doi.org/10.3389/fmicb.2017.01272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5513972PMC
July 2017

Zymomonas mobilis as a model system for production of biofuels and biochemicals.

Microb Biotechnol 2016 11 15;9(6):699-717. Epub 2016 Sep 15.

National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.

Zymomonas mobilis is a natural ethanologen with many desirable industrial biocatalyst characteristics. In this review, we will discuss work to develop Z. mobilis as a model system for biofuel production from the perspectives of substrate utilization, development for industrial robustness, potential product spectrum, strain evaluation and fermentation strategies. This review also encompasses perspectives related to classical genetic tools and emerging technologies in this context.
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http://dx.doi.org/10.1111/1751-7915.12408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5072187PMC
November 2016

Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

Genome Announc 2016 Sep 29;4(5). Epub 2016 Sep 29.

Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA BioEnergy Science Center, Oak Ridge, Tennessee, USA

We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5043559PMC
http://dx.doi.org/10.1128/genomeA.01043-16DOI Listing
September 2016

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis.

Appl Environ Microbiol 2016 09 30;82(18):5698-708. Epub 2016 Aug 30.

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

Unlabelled: Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. Here, we describe a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots. This protocol achieved substantial reduction in contaminating plant DNA, allowed enrichment of endophytic bacteria away from the plant material, and enabled single-cell genomics analysis. Four single-cell genomes were selected for whole-genome amplification based on their rarity in the microbiome (potentially uncultured taxa) as well as their inferred abilities to form associations with plants. Bioinformatics analyses, including assembly, contamination removal, and completeness estimation, were performed to obtain single-amplified genomes (SAGs) of organisms from the phyla Armatimonadetes, Verrucomicrobia, and Planctomycetes, which were unrepresented in our previous cultivation efforts. Comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria.

Importance: Plant roots harbor a diverse collection of microbes that live within host tissues. To gain a comprehensive understanding of microbial adaptations to this endophytic lifestyle from strains that cannot be cultivated, it is necessary to separate bacterial cells from the predominance of plant tissue. This study provides a valuable approach for the separation and isolation of endophytic bacteria from plant root tissue. Isolated live bacteria provide material for microbiome sequencing, single-cell genomics, and analyses of genomes of uncultured bacteria to provide genomics information that will facilitate future cultivation attempts.
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http://dx.doi.org/10.1128/AEM.01285-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007785PMC
September 2016

Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7.

Genome Announc 2016 May 5;4(3). Epub 2016 May 5.

Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

Clostridium paradoxum strain JW-YL-7 is a moderately thermophilic anaerobic alkaliphile isolated from the municipal sewage treatment plant in Athens, GA. We report the near-complete genome sequence of C. paradoxum strain JW-YL-7 obtained by using PacBio DNA sequencing and Pilon for sequence assembly refinement with Illumina data.
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http://dx.doi.org/10.1128/genomeA.00229-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859166PMC
May 2016

Draft Genome Sequence of Pyrodictium occultum PL19T, a Marine Hyperthermophilic Species of Archaea That Grows Optimally at 105°C.

Genome Announc 2016 Feb 25;4(1). Epub 2016 Feb 25.

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

We report here the draft genome sequence of Pyrodictium occultum PL19(T), a marine hyperthermophilic archaeon. The genome provides insights into molecular and cellular adaptation mechanisms to life in extreme environments and the evolution of early organisms on Earth.
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http://dx.doi.org/10.1128/genomeA.00016-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767911PMC
February 2016

Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment.

Front Microbiol 2015 14;6:1118. Epub 2015 Oct 14.

Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA.

The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.
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http://dx.doi.org/10.3389/fmicb.2015.01118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604316PMC
November 2015

Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum.

Genome Announc 2015 Sep 24;3(5). Epub 2015 Sep 24.

Division of Biochemistry, University of Missouri, Columbia, Missouri, USA

The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45.
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http://dx.doi.org/10.1128/genomeA.01090-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582584PMC
September 2015

Draft Genome Sequence of Burkholderia sp. MR1, a Methylarsenate-Reducing Bacterial Isolate from Florida Golf Course Soil.

Genome Announc 2015 Jun 4;3(3). Epub 2015 Jun 4.

Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA

To elucidate the environmental organoarsenical biocycle, we isolated a soil organism, Burkholderia sp. MR1, which reduces relatively nontoxic pentavalent methylarsenate to the more toxic trivalent methylarsenite, with the goal of identifying the gene for the reductase. Here, we report the draft genome sequence of Burkholderia sp. MR1.
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http://dx.doi.org/10.1128/genomeA.00608-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457076PMC
June 2015

Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies.

Sci Data 2015 14;2:150014. Epub 2015 Apr 14.

Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37919, USA ; Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, USA.

During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequence datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.
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http://dx.doi.org/10.1038/sdata.2015.14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409012PMC
December 2015

Draft Genome Sequence of Brevibacterium linens AE038-8, an Extremely Arsenic-Resistant Bacterium.

Genome Announc 2015 Apr 16;3(2). Epub 2015 Apr 16.

Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA

To understand the arsenic biogeocycles in the groundwaters at Tucumán, Argentina, we isolated Brevibacterium linens sp. strain AE38-8, obtained from arsenic-contaminated well water. This strain is extremely resistant to arsenicals and has arsenic resistance (ars) genes in its genome. Here, we report the draft genome sequence of B. linens AE38-8.
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http://dx.doi.org/10.1128/genomeA.00316-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4400441PMC
April 2015

Draft Genome Sequence of Thalassotalea sp. Strain ND16A Isolated from Eastern Mediterranean Sea Water Collected from a Depth of 1,055 Meters.

Genome Announc 2014 Nov 26;2(6). Epub 2014 Nov 26.

Thalassotalea sp. strain ND16A belongs to the family Colwelliaceae and was isolated from eastern Mediterranean Sea water at a depth of 1,055 m. Members of Colwelliaceae are ubiquitous marine heterotrophs. Here, we report the draft genome sequence of Thalassotalea sp. strain ND16A, a member of the newly described genus Thalassotalea.
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http://dx.doi.org/10.1128/genomeA.01231-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246168PMC
November 2014

Draft Genome Sequence of Pseudoalteromonas sp. Strain ND6B, an Oil-Degrading Isolate from Eastern Mediterranean Sea Water Collected at a Depth of 1,210 Meters.

Genome Announc 2014 Nov 26;2(6). Epub 2014 Nov 26.

Here, we report the draft genome of Pseudoalteromonas sp. strain ND6B, which is able to grow with crude oil as a carbon source. Strain ND6B was isolated from eastern Mediterranean Sea deep water at a depth of 1,210 m. The genome of strain ND6B provides insight into the oil-degrading ability of the Pseudoalteromonas species.
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http://dx.doi.org/10.1128/genomeA.01212-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246160PMC
November 2014

Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology.

Genome Announc 2014 Sep 4;2(5). Epub 2014 Sep 4.

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

Pelosinus species can reduce metals such as Fe(III), U(VI), and Cr(VI) and have been isolated from diverse geographical regions. Five draft genome sequences have been published. We report the complete genome sequence for Pelosinus sp. strain UFO1 using only PacBio DNA sequence data and without manual finishing.
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http://dx.doi.org/10.1128/genomeA.00881-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155594PMC
September 2014

Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.

Bioinformatics 2014 Oct 14;30(19):2709-16. Epub 2014 Jun 14.

Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

Motivation: To assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences.

Results: Illumina, 454 and PacBio sequencing technologies were used to generate de novo and hybrid genome assemblies for four different bacteria, which were assessed for quality using summary statistics (e.g. number of contigs, N50) and in silico evaluation tools. Differences in predictions of multiple copies of rDNA operons for each respective bacterium were evaluated by PCR and Sanger sequencing, and then the validated results were applied as an additional criterion to rank assemblies. In general, assemblies using longer PacBio reads were better able to resolve repetitive regions. In this study, the combination of Illumina and PacBio sequence data assembled through the ALLPATHS-LG algorithm gave the best summary statistics and most accurate rDNA operon number predictions. This study will aid others looking to improve existing draft genome assemblies.

Availability And Implementation: All assembly tools except CLC Genomics Workbench are freely available under GNU General Public License.

Contact: brownsd@ornl.gov

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btu391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173024PMC
October 2014

Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals.

Genome Announc 2013 Jun 27;1(3). Epub 2013 Jun 27.

Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA.

Caulobacter sp. strain OR37 belongs to the class Alphaproteobacteria and was isolated from subsurface sediments in Oak Ridge, TN. Strain OR37 is noteworthy due to its tolerance to high concentrations of heavy metals, such as uranium, nickel, cobalt, and cadmium, and we present its draft genome sequence here.
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http://dx.doi.org/10.1128/genomeA.00322-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675514PMC
June 2013

Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential for Bioremediation.

Genome Announc 2013 Jun 27;1(3). Epub 2013 Jun 27.

Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA.

Ralstonia sp. strain OR214 belongs to the class Betaproteobacteria and was isolated from subsurface sediments in Oak Ridge, TN. A member of this genus has been described as a potential bioremediation agent. Strain OR214 is tolerant to various heavy metals, such as uranium, nickel, cobalt, and cadmium. We present its draft genome sequence here.
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http://dx.doi.org/10.1128/genomeA.00321-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675513PMC
June 2013

Draft Genome Sequence for Desulfovibrio africanus Strain PCS.

Genome Announc 2013 Apr 11;1(2):e0014413. Epub 2013 Apr 11.

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA;

Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated from sediment from Paleta Creek, San Diego, CA. Strain PCS is capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is predicted to produce methylmercury. We present the D. africanus PCS genome sequence.
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http://dx.doi.org/10.1128/genomeA.00144-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624683PMC
April 2013

Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides.

J Bacteriol 2012 Nov;194(21):5991-3

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.

To aid in the investigation of the Populus deltoides microbiome, we generated draft genome sequences for 21 Pseudomonas strains and 19 other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.
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http://dx.doi.org/10.1128/JB.01243-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3486089PMC
November 2012

Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7.

J Bacteriol 2012 Sep;194(18):5147-8

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.

Pelosinus fermentans 16S rRNA gene sequences have been reported from diverse geographical sites since the recent isolation of the type strain. We present the genome sequence of the P. fermentans type strain R7 (DSM 17108) and genome sequences for two new strains with different abilities to reduce iron, chromate, and uranium.
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http://dx.doi.org/10.1128/JB.01174-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430306PMC
September 2012

Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2.

J Bacteriol 2012 Jun;194(12):3290-1

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.

Clostridium thermocellum wild-type strain YS is an anaerobic, thermophilic, cellulolytic bacterium capable of directly converting cellulosic substrates into ethanol. Strain YS and a derived cellulose adhesion-defective mutant strain, AD2, played pivotal roles in describing the original cellulosome concept. We present their draft genome sequences.
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http://dx.doi.org/10.1128/JB.00473-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370843PMC
June 2012

Draft genome sequence for Microbacterium laevaniformans strain OR221, a bacterium tolerant to metals, nitrate, and low pH.

J Bacteriol 2012 Jun;194(12):3279-80

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.

Microbacterium laevaniformans strain OR221 was isolated from subsurface sediments obtained from the Field Research Center (FRC) in Oak Ridge, TN. It was characterized as a bacterium tolerant to heavy metals, such as uranium, nickel, cobalt, and cadmium, as well as nitrate and low pH. We present its draft genome sequence.
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http://dx.doi.org/10.1128/JB.00474-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370866PMC
June 2012

Draft genome sequence of Rhizobium sp. strain PDO1-076, a bacterium isolated from Populus deltoides.

J Bacteriol 2012 May;194(9):2383-4

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.

Rhizobium sp. strain PDO1-076 is a plant-associated bacterium isolated from Populus deltoides, and its draft genome sequence is reported.
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http://dx.doi.org/10.1128/JB.00198-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3347069PMC
May 2012