Middleton, WI, United States
Middleton, WI, United States
SEARCH FILTERS
Time filter
Source Type

Schoenfeld T.W.,Lucigen Inc. | Murugapiran S.K.,University of Nevada, Las Vegas | Dodsworth J.A.,University of Nevada, Las Vegas | Floyd S.,Lucigen Inc. | And 3 more authors.
Molecular Biology and Evolution | Year: 2013

Bioinformatics and functional screens identified a group of Family A-type DNA Polymerase (polA) genes encoded by viruses inhabiting circumneutral and alkaline hot springs in Yellowstone National Park and the US Great Basin. The proteins encoded by these viral polA genes (PolAs) shared no significant sequence similarity with any known viral proteins but were remarkably similar to PolAs encoded by two of three families of the bacterial phylum Aquificae and by several apicoplast-targeted PolA-like proteins found in the eukaryotic phylum Apicomplexa, which includes the obligate parasites Plasmodium, Babesia, and Toxoplasma. The viral gene products share signature elements previously associated only with Aquificae and Apicomplexa PolA-like proteins and were similar to proteins encoded by prophage elements of a variety of otherwise unrelated Bacteria, each of which additionally encoded a prototypical bacterial PolA. Unique among known viral DNA polymerases, the viral PolA proteins of this study share with the Apicomplexa proteins large amino-terminal domains with putative helicase/primase elements but low primary sequence similarity. The genomic context and distribution, phylogeny, and biochemistry of these PolA proteins suggest that thermophilic viruses transferred polA genes to the Apicomplexa, likely through secondary endosymbiosis of a virus-infected proto-apicoplast, and to the common ancestor of two of three Aquificae families, where they displaced the orthologous cellular polA gene. On the basis of biochemical activity, gene structure, and sequence similarity, we speculate that the xenologous viral-type polA genes may have functions associated with diversity-generating recombination in both Bacteria and Apicomplexa. © 2013 The Author.


Christopherson M.R.,University of Wisconsin - Madison | Suen G.,University of Wisconsin - Madison | Bramhacharya S.,University of Wisconsin - Madison | Jewell K.A.,University of Wisconsin - Madison | And 4 more authors.
PLoS ONE | Year: 2013

Actinobacteria in the genus Cellulomonas are the only known and reported cellulolytic facultative anaerobes. To better understand the cellulolytic strategy employed by these bacteria, we sequenced the genome of the Cellulomonas fimi ATCC 484T. For comparative purposes, we also sequenced the genome of the aerobic cellulolytic "Cellvibrio gilvus" ATCC 13127T. An initial analysis of these genomes using phylogenetic and whole-genome comparison revealed that "Cellvibrio gilvus" belongs to the genus Cellulomonas. We thus propose to assign "Cellvibrio gilvus" to the genus Cellulomonas. A comparative genomics analysis between these two Cellulomonas genome sequences and the recently completed genome for Cellulomonas flavigena ATCC 482T showed that these cellulomonads do not encode cellulosomes but appear to degrade cellulose by secreting multi-domain glycoside hydrolases. Despite the minimal number of carbohydrate-active enzymes encoded by these genomes, as compared to other known cellulolytic organisms, these bacteria were found to be proficient at degrading and utilizing a diverse set of carbohydrates, including crystalline cellulose. Moreover, they also encode for proteins required for the fermentation of hexose and xylose sugars into products such as ethanol. Finally, we found relatively few significant differences between the predicted carbohydrate-active enzymes encoded by these Cellulomonas genomes, in contrast to previous studies reporting differences in physiological approaches for carbohydrate degradation. Our sequencing and analysis of these genomes sheds light onto the mechanism through which these facultative anaerobes degrade cellulose, suggesting that the sequenced cellulomonads use secreted, multidomain enzymes to degrade cellulose in a way that is distinct from known anaerobic cellulolytic strategies. © 2013 Christopherson et al.


PubMed | Lucigen Inc.
Type: Journal Article | Journal: Molecular biology and evolution | Year: 2013

Bioinformatics and functional screens identified a group of Family A-type DNA Polymerase (polA) genes encoded by viruses inhabiting circumneutral and alkaline hot springs in Yellowstone National Park and the US Great Basin. The proteins encoded by these viral polA genes (PolAs) shared no significant sequence similarity with any known viral proteins but were remarkably similar to PolAs encoded by two of three families of the bacterial phylum Aquificae and by several apicoplast-targeted PolA-like proteins found in the eukaryotic phylum Apicomplexa, which includes the obligate parasites Plasmodium, Babesia, and Toxoplasma. The viral gene products share signature elements previously associated only with Aquificae and Apicomplexa PolA-like proteins and were similar to proteins encoded by prophage elements of a variety of otherwise unrelated Bacteria, each of which additionally encoded a prototypical bacterial PolA. Unique among known viral DNA polymerases, the viral PolA proteins of this study share with the Apicomplexa proteins large amino-terminal domains with putative helicase/primase elements but low primary sequence similarity. The genomic context and distribution, phylogeny, and biochemistry of these PolA proteins suggest that thermophilic viruses transferred polA genes to the Apicomplexa, likely through secondary endosymbiosis of a virus-infected proto-apicoplast, and to the common ancestor of two of three Aquificae families, where they displaced the orthologous cellular polA gene. On the basis of biochemical activity, gene structure, and sequence similarity, we speculate that the xenologous viral-type polA genes may have functions associated with diversity-generating recombination in both Bacteria and Apicomplexa.


Lucigen Inc. | Entity website

RNAse Inhibitor is a potent inhibitor of ribonucleases such as RNase A, RNase B, and RNase C. The 52 kDa protein is a fusion of the porcine RNAse Inhibitor gene with a proprietary 22 ...


Highest quality deoxynucleotides, 2'-deoxynucleoside 5'-triphosphates, at a great value, formulated for your convenience. These nucleotides are also suitable for: sequencing nick translation cDNA synthesis TdT-tailing reactions fill-in reactions 2 ...


Lucigen Inc. | Entity website

Executive Management Ralph Kauten, M.B ...


Lucigen Inc. | Entity website

The services for ordering custom cells were very easy to use. I was also very pleased with the prompt delivery ...


Lucigen Inc. | Entity website

HomeCompetent CellsCRISPR, Large or Difficult Fragment CloningCJ236 Electrocompetent Cells < Back CJ236 Electrocompetent Cells High efficiency cells to create uracil-containing DNA for site-directed mutagenesis Sole source of highly efficient Electrocompetent cells (1 109 cfu/g) ung- and dut- mutations to generate DNA with some uracil residues Ideal genotype and efficiency for Kunkel directed mutagenesis method1. 1 Kunkel T ...


Originally aired 29 October 2015, GenomeWeb Presented by Mark Liles, Auburn University, Bob Klein, USDA, and David Smith, Mayo Clinic. This webinar will focus on a range of research and clinical applications enabled by improvements in mate pair technology for whole genome sequencing ...

Loading Lucigen Inc. collaborators
Loading Lucigen Inc. collaborators