scholarly journals The Complete Genome of Comamonas testosteroni Reveals Its Genetic Adaptations to Changing Environments

2009 ◽  
Vol 75 (21) ◽  
pp. 6812-6819 ◽  
Author(s):  
Ying-Fei Ma ◽  
Yun Zhang ◽  
Jia-Yue Zhang ◽  
Dong-Wei Chen ◽  
Yongqian Zhu ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Carboxylic Acids ◽  
Aromatic Compounds ◽  
Complete Genome ◽  
Strictly Aerobic ◽  
Hypothetical Proteins ◽  
Comamonas Testosteroni ◽  
Circular Chromosome ◽  
Changing Environments ◽  
Genes Encoding

ABSTRACT Members of the gram-negative, strictly aerobic genus Comamonas occur in various environments. Here we report the complete genome of Comamonas testosteroni strain CNB-2. Strain CNB-2 has a circular chromosome that is 5,373,643 bp long and has a G+C content of 61.4%. A total of 4,803 open reading frames (ORFs) were identified; 3,514 of these ORFs are functionally assigned to energy production, cell growth, signal transduction, or transportation, while 866 ORFs encode hypothetical proteins and 423 ORFs encode purely hypothetical proteins. The CNB-2 genome has many genes for transportation (22%) and signal transduction (6%), which allows the cells to respond and adapt to changing environments. Strain CNB-2 does not assimilate carbohydrates due to the lack of genes encoding proteins involved in glycolysis and pentose phosphate pathways, and it contains many genes encoding proteins involved in degradation of aromatic compounds. We identified 66 Tct and nine TRAP-T systems and a complete tricarboxylic acid cycle, which may allow CNB-2 to take up and metabolize a range of carboxylic acids. This nutritional bias for carboxylic acids and aromatic compounds enables strain CNB-2 to occupy unique niches in environments. Four different sets of terminal oxidases for the respiratory system were identified, and they putatively functioned at different oxygen concentrations. This study conclusively revealed at the genomic level that the genetic versatility of C. testosteroni is vital for competition with other bacteria in its special niches.

scholarly journals Complete Genome Sequence of Actinomyces hongkongensis HKU8T Isolated from Human Blood

2017 ◽  
Vol 5 (14) ◽  
Author(s):  
Yan-xia Gao ◽  
Yu-yan Zhou ◽  
Ying Xie ◽  
Man Wang ◽  
Shu-juan Wang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Human Blood ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Human Diseases ◽  
Circular Chromosome ◽  
Content Type ◽  
Genes Encoding

ABSTRACT Members of the genus Actinomyces are strongly associated with human diseases. We present here the complete genome sequence of Actinomyces hongkongensis HKU8T, which consists of one circular chromosome. The strain characteristically contains various genes encoding for enzymes involved in arylamidase utilization.

scholarly journals Complete Genome Sequence ofCaulobacter crescentusSiphophage Seuss

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Jordan M. Sloan ◽  
Jennifer L. Keene ◽  
Jesse L. Cahill ◽  
Eric S. Rasche ◽  
Gabriel F. Kuty Everett
Keyword(s):  
Life Cycle ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Caulobacter Crescentus ◽  
Hypothetical Proteins ◽  
Genes Encoding ◽  
Key Features

Caulobacter crescentusis a water-dwelling bacterium known to have a dimorphic life cycle. Here, we announce the complete genome of Seuss, aC. crescentusicosahedral siphophage, and describe key features. Seuss is unique among phages deposited in GenBank, with genes encoding novel hypothetical proteins composing 45% of its genome.

scholarly journals Complete Genome Sequence of the Novel Psychrobacter sp. Strain AJ006, Which Has the Potential for Biomineralization

2020 ◽  
Vol 9 (41) ◽  
Author(s):  
Jun Ho Lee ◽  
Pyung Cheon Lee
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The Novel ◽  
Antarctic Soil ◽  
Circular Chromosome ◽  
Biomineralization Process ◽  
Chromosomal Genes ◽  
Genes Encoding ◽  
Single Circular Chromosome

ABSTRACT A novel Psychrobacter sp. strain, AJ006, was isolated from Antarctic soil. Its complete genome sequence consists of a single circular chromosome (3,032,533 bp; G+C content, 44.0%) and a single linear plasmid (49,070 bp; G+C content, 41.7%). Chromosomal genes encoding carbonic anhydrase and urease, key enzymes in a biomineralization process, were predicted.

scholarly journals Complete Genome Sequence of Yellow Pigment-Producing Sphingobium sp. Strain HAL-16

2020 ◽  
Vol 9 (41) ◽  
Author(s):  
Soon Jae Kwon ◽  
Pyung Cheon Lee
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Soil Samples ◽  
Yellow Pigment ◽  
Antarctic Soil ◽  
Circular Chromosome ◽  
Genes Encoding ◽  
Single Circular Chromosome ◽  
Β Carotene

ABSTRACT Sphingobium sp. strain HAL-16, which was isolated from Antarctic soil samples, synthesizes a yellow pigment. The complete genome consists of a single circular chromosome (4,372,398 bp, with a G+C content of 62.7%) and a single circular plasmid (57,025 bp, with a G+C content of 59.4%). Five genes encoding carotenogenic enzymes were identified, suggesting that the yellow pigment is a hydroxy/keto-β-carotene.

scholarly journals Analysis of the Complete Genome of the Alkaliphilic and Phototrophic Firmicute Heliorestis convoluta Strain HHT

2020 ◽  
Vol 8 (3) ◽  
pp. 313
Author(s):  
Emma D. Dewey ◽  
Lynn M. Stokes ◽  
Brad M. Burchell ◽  
Kathryn N. Shaffer ◽  
Austin M. Huntington ◽  
...  
Keyword(s):  
Complete Genome ◽  
Gc Content ◽  
Soda Lake ◽  
Amino Acid Residues ◽  
Gene Encoding ◽  
Circular Chromosome ◽  
Genes Encoding ◽  
Complete Set ◽  
Close Relatives ◽  
Encoding Genes

Despite significant interest and past work to elucidate the phylogeny and photochemistry of species of the Heliobacteriaceae, genomic analyses of heliobacteria to date have been limited to just one published genome, that of the thermophilic species Heliobacterium (Hbt.) modesticaldum str. Ice1T. Here we present an analysis of the complete genome of a second heliobacterium, Heliorestis (Hrs.) convoluta str. HHT, an alkaliphilic, mesophilic, and morphologically distinct heliobacterium isolated from an Egyptian soda lake. The genome of Hrs. convoluta is a single circular chromosome of 3.22 Mb with a GC content of 43.1% and 3263 protein-encoding genes. In addition to culture-based observations and insights gleaned from the Hbt. modesticaldum genome, an analysis of enzyme-encoding genes from key metabolic pathways supports an obligately photoheterotrophic lifestyle for Hrs. convoluta. A complete set of genes encoding enzymes for propionate and butyrate catabolism and the absence of a gene encoding lactate dehydrogenase distinguishes the carbon metabolism of Hrs. convoluta from its close relatives. Comparative analyses of key proteins in Hrs. convoluta, including cytochrome c553 and the Fo alpha subunit of ATP synthase, with those of related species reveal variations in specific amino acid residues that likely contribute to the success of Hrs. convoluta in its highly alkaline environment.

Use of a dynamic gassing-out method for activity and oxygen diffusion coefficient estimation in biofilms

1998 ◽  
Vol 37 (4-5) ◽  
pp. 171-175
Author(s):  
Artem Khlebnikov ◽  
Falilou Samb ◽  
Paul Péringer
Keyword(s):  
Diffusion Coefficient ◽  
Oxygen Uptake ◽  
Oxygen Diffusion ◽  
Fixed Bed ◽  
Biofilm Reactor ◽  
Strictly Aerobic ◽  
Comamonas Testosteroni ◽  
Respiration Activity ◽  
Oxygen Diffusion Coefficient ◽  
Biofilm Development

p-toluenesulphonic acid degradation by Comamonas testosteroni T-2 in multi-species biofilms was studied in a fixed bed biofilm reactor. The polypropylene static mixer elements (Sulzer Chemtech Ltd., Switzerland) were used as a support matrix for biofilm formation. Biofilm respiration was estimated using the dynamic gassing-out oxygen uptake method. A strong relation between oxygen uptake and reactor degradation efficiency was observed, because p-toluenesulphonate degradation is a strictly aerobic process. This technique also allowed us to estimate the thickness of the active layer in the studied system. The mean active thickness was in order of 200 μm, which is close to maximum oxygen penetration depth in biofilms. A transient mathematical model was established to evaluate oxygen diffusitivity in non-steady-state biofilms. Based on the DO concentration profiles, the oxygen diffusion coefficient and the maximum respiration activity were calculated. The oxygen diffusion coefficient obtained (2 10−10-1.2 10−9 m2 s−1) is in good agreement with published values. The DO diffusion coefficient varied with biofilm development. This may be, most likely, due to the biofilm density changes during the experiments. The knowledge of diffusivity changes in biofilms is particularly important for removal capacity estimation and appropriate reactor design.

scholarly journals Genes encoding components of the olfactory signal transduction cascade contain a DNA binding site that may direct neuronal expression.

1993 ◽  
Vol 13 (9) ◽  
pp. 5805-5813 ◽  
Author(s):  
M M Wang ◽  
R Y Tsai ◽  
K A Schrader ◽  
R R Reed
Keyword(s):  
Signal Transduction ◽  
Dna Binding ◽  
Binding Site ◽  
Binding Sites ◽  
Consensus Sequence ◽  
Initiation Site ◽  
Olfactory Neuron ◽  
Promoter Regions ◽  
Transcriptional Initiation ◽  
Genes Encoding

Genes which mediate odorant signal transduction are expressed at high levels in neurons of the olfactory epithelium. The molecular mechanism governing the restricted expression of these genes likely involves tissue-specific DNA binding proteins which coordinately activate transcription through sequence-specific interactions with olfactory promoter regions. We have identified binding sites for the olfactory neuron-specific transcription factor, Olf-1, in the sequences surrounding the transcriptional initiation site of five olfactory neuron-specific genes. The Olf-1 binding sites described define the consensus sequence YTCCCYRGGGAR. In addition, we have identified a second binding site, the U site, in the olfactory cyclic nucleotide gated channel and type III cyclase promoters, which binds factors present in all tissue examined. These experiments support a model in which expression of Olf-1 in the sensory neurons coordinately activates a set of olfactory neuron-specific genes. Furthermore, expression of a subset of these genes may be modulated by additional binding factors.

scholarly journals Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
So-Ra Han ◽  
Byeollee Kim ◽  
Jong Hwa Jang ◽  
Hyun Park ◽  
Tae-Jin Oh
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cold Adaptation ◽  
Gc Content ◽  
Glycogen Metabolism ◽  
Extreme Environment ◽  
Circular Chromosome ◽  
Cold Regions ◽  
Insight Into

Abstract Background The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. Results Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. Conclusions We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

scholarly journals Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species

2021 ◽  
Vol 13 (3) ◽  
Author(s):  
Xiuqin Zhong ◽  
Max Lundberg ◽  
Lars Råberg
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Immune Function ◽  
Sequence Divergence ◽  
Expression Divergence ◽  
Functional Categories ◽  
Coding Sequence ◽  
Immune Genes ◽  
Genes Encoding ◽  
Signal Transduction Proteins

Abstract Differences in immune function between species could be a result of interspecific divergence in coding sequence and/or expression of immune genes. Here, we investigate how the degree of divergence in coding sequence and expression differs between functional categories of immune genes, and if differences between categories occur independently of other factors (expression level, pleiotropy). To this end, we compared spleen transcriptomes of wild-caught yellow-necked mice and bank voles. Immune genes expressed in the spleen were divided into four categories depending on the function of the encoded protein: pattern recognition receptors (PRR); signal transduction proteins; transcription factors; and cyto- and chemokines and their receptors. Genes encoding PRR and cyto-/chemokines had higher sequence divergence than genes encoding signal transduction proteins and transcription factors, even when controlling for potentially confounding factors. Genes encoding PRR also had higher expression divergence than genes encoding signal transduction proteins and transcription factors. There was a positive correlation between expression divergence and coding sequence divergence, in particular for PRR genes. We propose that this is a result of that divergence in PRR coding sequence leads to divergence in PRR expression through positive feedback of PRR ligand binding on PRR expression. When controlling for sequence divergence, expression divergence of PRR genes did not differ from other categories. Taken together, the results indicate that coding sequence divergence of PRR genes is a major cause of differences in immune function between species.

scholarly journals Complete Genome Sequence of Lanthionine-Producing Lactobacillus brevis Strain 100D8, Generated by PacBio Sequencing

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Min-Jung Kim ◽  
Hye Sun Kim ◽  
Sam Churl Kim ◽  
Youn-Sig Kwak
Keyword(s):  
Antifungal Activity ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Lactobacillus Brevis ◽  
Pacbio Sequencing ◽  
Circular Chromosome ◽  
Coding Sequences ◽  
Content Type

Lactobacillus brevis strain 100D8 was isolated from rye silage and showed rapid acidification ability in vitro and antifungal activity against mycotoxin-producing fungi. We report here the complete genome sequence of L. brevis strain 100D8, which has a circular chromosome (2,351,988 bp, 2,304 coding sequences [CDSs]) and three plasmids (45,061 bp, 57 CDSs; 40,740 bp, 40 CDSs; and 39,943 bp, 57 CDSs).

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