A5071426268- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Enzyme Structure and Function
- Protist diversity and phylogeny
- Microbial Fuel Cells and Bioremediation
- Radioactive element chemistry and processing
- Connexins and lens biology
- RNA and protein synthesis mechanisms
- Insect symbiosis and bacterial influences
- Microbial Metabolic Engineering and Bioproduction
- Bacteriophages and microbial interactions
- DNA Repair Mechanisms
- Microbial bioremediation and biosurfactants
- Microbial metabolism and enzyme function
- Bacterial Genetics and Biotechnology
- Polyamine Metabolism and Applications
- Metal-Catalyzed Oxygenation Mechanisms
- Biochemical Acid Research Studies
- Research in Cotton Cultivation
- Plant and Fungal Interactions Research
- Methane Hydrates and Related Phenomena
- Metabolism and Genetic Disorders
- Parasitic Diseases Research and Treatment
- Microbial Natural Products and Biosynthesis
- Radioactive contamination and transfer
National Center for Biotechnology Information
2004-2024
National Institutes of Health
2003-2024
Sumy State University
2020
United States National Library of Medicine
2006-2007
Russian Academy of Sciences
2006
Uniformed Services University of the Health Sciences
2001-2005
University of Hawaiʻi at Mānoa
2004
University of Hawaii System
2004
Pacific Northwest National Laboratory
2004
University of Minnesota
2004
NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with location conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated models that make use 3D structure to refine provide insights into sequence/structure/function relationships. Manually are organized hierarchically if they describe families clearly related by common descent. As also imports family variety external sources, it partially...
ABSTRACT The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has been determined by shotgun approach. consists a 3.94-Mb chromosome and 192-kb megaplasmid that contains majority genes responsible for solvent production. Comparison C. to Bacillus subtilis reveals significant local conservation gene order, which not seen in comparisons other genomes with similar, or, some cases closer, phylogenetic proximity. This allows prediction many previously...
Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required fertility survival of human filarial parasitic nematode Brugia malayi. Although, quantitatively, even more degraded than those closely related Rickettsia species, Wolbachia has retained intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, nucleotides likely be Wolbachia's principal contribution mutualistic relationship,...
Deinococcus radiodurans is extremely resistant to ionizing radiation. How this bacterium can grow under chronic γ radiation [50 grays (Gy) per hour] or recover from acute doses greater than 10 kGy unknown. We show that D. accumulates very high intracellular manganese and low iron levels compared with radiation-sensitive bacteria resistance exhibits a concentration-dependent response manganous chloride [Mn(II)]. Among the most radiation-resistant bacterial groups reported, Deinococcus,...
Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but molecular mechanisms underlying this phenotype remain poorly understood. To define repertoire DEIRA genes responding acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases recovery by using DNA microarrays covering ≈94% predicted genes. At least at one time point during recovery, 832 (28%...
Abstract Background The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this in wide range environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated pure culture. We recently reported cultivation initial characterization an extremely acidophilic methanotrophic member the , strain V4, from Hell's Gate geothermal area New Zealand....
Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile radiodurans was first member this group whose genome completely sequenced. Analysis sequence D. radiodurans, however, failed identify unique DNA repair systems. To further delineate genes underlying resistance phenotypes, we report whole-genome a second species, thermophile geothermalis, which at its optimal growth temperature is as IR, UV desiccation...
Abstract Background Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. is thermophile, which relatively sensitive ionizing radiation desiccation, whereas D. mesophile, highly radiation- desiccation-resistant. Here we present an in-depth comparison of the genomes these two related differently adapted bacteria. Results By reconstructing evolution after divergence from their common ancestor, demonstrate high level...
Abstract Background Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - opposed homologous enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction metabolic pathways in a variety organisms. In 1998, systematic search for enzymes resulted identification 105 Enzyme Commission (EC) numbers included two or more...
We report the complete genome sequence of deep-sea γ-proteobacterium, Idiomarina loihiensis , isolated recently from a hydrothermal vent at 1,300-m depth on Lōihi submarine volcano, Hawaii. The I. comprises single chromosome 2,839,318 base pairs, encoding 2,640 proteins, four rRNA operons, and 56 tRNA genes. A comparison to genomes other γ-proteobacteria reveals abundance amino acid transport degradation enzymes, but loss sugar systems certain enzymes metabolism. This finding suggests that...
Bacterial and mammalian AlkB proteins are iron(II)- 2-oxoglutarate-dependent dioxygenases that reverse methylation damage, such as 1-methyladenine 3-methylcytosine, in RNA DNA. An AlkB-domain is encoded by the genome of numerous single-stranded, plant-infecting viruses, majority which belong to Flexiviridae family. Our phylogenetic analysis sequences suggests a single plant virus might have acquired relatively recently, followed horizontal dissemination among other viruses via recombination....
We describe a simple theoretical framework for identifying orthologous sets of genes that deviate from clock-like model evolution. The approach used is based on comparing the evolutionary distances within set orthologs to standard intergenomic distance, which was defined as median distribution between all one-to-one orthologs. Under model, points plot intergenic versus are expected fit straight line. A statistical technique identify significant deviations behavior described. For several...
Abstract Background Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, processed foods gelatin milk powder. flavithermus is a facultatively anaerobic bacterium super-saturated silica solutions opaline sinter. The ability A. to grow makes it an ideal subject study processes sinter formation, which might be similar biomineralization that occurred at dawn life. Results We report here complete genome...
We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) ( https://ncbi.nlm.nih.gov/genome/cgv/ ). CGV visualizes pairwise same-species and cross-species alignments provided by National Center Biotechnology Information (NCBI) using assembly alignment algorithms developed us others. Researchers can examine large structural differences spanning chromosomes, such as inversions or translocations. Users also navigate to...
ABSTRACT The ionizing radiation (IR) dose that yields 20% survival (D 20 ) of Shewanella oneidensis MR-1 is lower by factors and 200 than those for Escherichia coli Deinococcus radiodurans , respectively. Transcriptome analysis was used to identify the genes responding 40 Gy ). We observed induction 170 repression 87 in during a 1-h recovery period after irradiation. genomic response IR very similar its UV (254 nm), which included systems involved DNA repair prophage synthesis absence...
A Gram-negative, aerobic, heterotrophic, non-pigmented, dimorphic prosthecate bacterium was isolated from tundra wetland soil and designated strain Z-0023 T . Cells of this had a life cycle developed non-adhesive stalk at site not coincident with the centre cell pole, characteristic typical representatives genus Asticcacaulis highly distinctive feature cells presence conical, bell-shaped sheath when grown low temperature. This psychrotolerant, moderately acidophilic organism capable growth...
The iron(II)- and 2-oxoglutarate (2OG)-dependent dioxygenase AlkB from Escherichia coli (EcAlkB) repairs alkylation damage in DNA by direct reversal. EcAlkB substrates include methylated bases, such as 1-methyladenine (m1A) 3-methylcytosine (m3C), well certain bulkier lesions, for example the exocyclic adduct 1,N6-ethenoadenine (εA). is only bacterial protein characterized to date, we here present an extensive bioinformatics functional analysis of proteins. Based on sequence phylogeny, show...
We have recently shown that Deinococcus radiodurans and other radiation resistant bacteria accumulate exceptionally high intracellular manganese low iron levels. In comparison, the dissimilatory metal-reducing bacterium Shewanella oneidensis accumulates Fe but not Mn is extremely sensitive to radiation. proposed for Fe-rich, Mn-poor cells killed at doses which cause very little DNA damage, cell death might be induced by release of Fe(II) from proteins during irradiation, leading additional...
Abstract Background The arylalkylamine N -acetyltransferase (AANAT) family is divided into structurally distinct vertebrate and non-vertebrate groups. Expression of AANATs limited primarily to the pineal gland retina, where it plays a role in controlling circadian rhythm melatonin synthesis. Based on biological timing, AANAT has been given moniker "the Timezyme". Non-vertebrate AANATs, which occur fungi protists, are thought play detoxification not known be associated with specific tissue....
We have previously identified a gelsolin-like protein (C/L-gelsolin) as corneal crystallin in zebrafish. Here we show by phylogenetic analysis that there are at least six genes encoding proteins based on their gelsolin domains zebrafish: gsna and gsnb group with the vertebrate gene, scina scinb scinderin (adseverin) scinla scinlb novel scinderin-like genes. RT-PCR showed scinla, scinlb, preferentially expressed adult cornea whereas is to similar extent cornea, lens, brain, heart; expression...
Abstract We report a new visualization tool for analysis of whole genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) ( https://ncbi.nlm.nih.gov/genome/cgv/ ). CGV visualizes pairwise same-species and cross-species alignments provided by NCBI using assembly alignment algorithms developed us others. Researchers can examine between two assemblies alternate views: chromosome ideogram- based view or 2D dotplot. Whole views expose large structural differences spanning...