scholarly journals From Genome to Function: Systematic Analysis of the Soil BacteriumBacillus subtilis

2001 ◽  
Vol 2 (1) ◽  
pp. 22-24 ◽  
Author(s):  
Colin R. Harwood ◽  
Samuel G. Crawshaw ◽  
Anil Wipat
Keyword(s):  
Functional Analysis ◽  
Bacillus Subtilis ◽  
Genome Sequence ◽  
Water Sources ◽  
Natural Environments ◽  
Positive Bacterium ◽  
Systematic Analysis ◽  
Analysis Programme ◽  
Analytical Approaches

Bacillus subtilisis a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. Whilst this bacterium has been studied extensively in the laboratory, relatively few studies have been undertaken to study its activity in natural environments. The publication of theB. subtilisgenome sequence and subsequent systematic functional analysis programme have provided an opportunity to develop tools for analysing the role and expression ofBacillusgenesin situ. In this paper we discuss analytical approaches that are being developed to relate genes to function in environments such as the rhizosphere.

scholarly journals From Gene Regulation to Gene Function: Regulatory Networks inBacillus subtilis

2002 ◽  
Vol 3 (1) ◽  
pp. 37-41 ◽  
Author(s):  
Colin R. Harwood ◽  
Ivan Moszer
Keyword(s):  
Functional Analysis ◽  
Gene Regulation ◽  
Bacillus Subtilis ◽  
Genome Sequence ◽  
Gene Function ◽  
In Silico ◽  
Regulatory Networks ◽  
Water Sources ◽  
Positive Bacterium ◽  
Gram Positive

Bacillus subtilisis a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. The publication of theB. subtilisgenome sequence and subsequent systematic functional analysis and gene regulation programmes, together with an extensive understanding of its biochemistry and physiology, makes this micro-organism a prime candidate in which to model regulatory networksin silico.In this paper we discuss combined molecular biological and bioinformatical approaches that are being developed to model this organism's responses to changes in its environment.

scholarly journals Complete Genome Sequence of Undomesticated Bacillus subtilis Strain NCIB 3610

2017 ◽  
Vol 5 (20) ◽  
Author(s):  
Taylor M. Nye ◽  
Jeremy W. Schroeder ◽  
Daniel B. Kearns ◽  
Lyle A. Simmons
Keyword(s):  
Bacillus Subtilis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Experimental System ◽  
Subtilis Strain ◽  
Positive Bacterium ◽  
Gram Positive ◽  
Content Type

ABSTRACT Bacillus subtilis is a Gram-positive bacterium that serves as an important experimental system. B. subtilis NCIB 3610 is an undomesticated strain that exhibits phenotypes lost from the more common domesticated laboratory strains. Here, we announce the complete genome sequence of DK1042, a genetically competent derivative of NCIB 3610.

scholarly journals The complete genome sequence of the Gram-positive bacterium Bacillus subtilis

Nature ◽  
10.1038/36786 ◽  
1997 ◽  
Vol 390 (6657) ◽  
pp. 249-256 ◽  
Author(s):  
F. Kunst ◽  
N. Ogasawara ◽  
I. Moszer ◽  
A. M. Albertini ◽  
G. Alloni ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Positive Bacterium ◽  
Gram Positive ◽  
Bacterium Bacillus Subtilis ◽  
Bacterium Bacillus

scholarly journals Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Naomi Shimokawa-Chiba ◽  
Claudia Müller ◽  
Keigo Fujiwara ◽  
Bertrand Beckert ◽  
Koreaki Ito ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Stop Codon ◽  
Release Factor ◽  
Positive Bacterium ◽  
Gram Positive ◽  
E Coli ◽  
Cryo Electron Microscopy ◽  
Dead End ◽  
Bacterium Bacillus Subtilis ◽  
Bacterium Bacillus

AbstractRescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some Gram-negative species possess alternative and release factor (RF)-dependent rescue factors, which enable an RF to catalyze stop-codon-independent polypeptide release. We now discover that the Gram-positive Bacillus subtilis has an evolutionarily distinct ribosome rescue factor named BrfA. Genetic analysis shows that B. subtilis requires the function of either trans-translation or BrfA for growth, even in the absence of proteotoxic stresses. Biochemical and cryo-electron microscopy (cryo-EM) characterization demonstrates that BrfA binds to non-stop stalled ribosomes, recruits homologous RF2, but not RF1, and induces its transition into an open active conformation. Although BrfA is distinct from E. coli ArfA, they use convergent strategies in terms of mode of action and expression regulation, indicating that many bacteria may have evolved as yet unidentified ribosome rescue systems.

scholarly journals In-Situ Synthesis of TiO2@GO Nanosheets for Polymers Degradation in a Natural Environment

Polymers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 2158
Author(s):  
Yueqin Shi ◽  
Zhanyang Yu ◽  
Zhengjun Li ◽  
Xiaodong Zhao ◽  
Yongjun Yuan
Keyword(s):  
Natural Environment ◽  
New Technologies ◽  
Separation Efficiency ◽  
Basic Mechanism ◽  
Chemical Degradation ◽  
Natural Environments ◽  
Additional Energy ◽  
Photogenerated Electrons ◽  
Main Components

Plastic photodegradation naturally takes 300–500 years, and their chemical degradation typically needs additional energy or causes secondary pollution. The main components of global plastic are polymers. Hence, new technologies are urgently required for the effective decomposition of the polymers in natural environments, which lays the foundation for this study on future plastic degradation. This study synthesizes the in-situ growth of TiO2 at graphene oxide (GO) matrix to form the TiO2@GO photocatalyst, and studies its application in conjugated polymers’ photodegradation. The photodegradation process could be probed by UV-vis absorption originating from the conjugated backbone of polymers. We have found that the complete decomposition of various polymers in a natural environment by employing the photocatalyst TiO2@GO within 12 days. It is obvious that the TiO2@GO shows a higher photocatalyst activity than the TiO2, due to the higher crystallinity morphology and smaller size of TiO2, and the faster transmission of photogenerated electrons from TiO2 to GO. The stronger fluorescence (FL) intensity of TiO2@GO compared to TiO2 at the terephthalic acid aqueous solution indicates that more hydroxyl radicals (•OH) are produced for TiO2@GO. This further confirms that the GO could effectively decrease the generation of recombination centers, enhance the separation efficiency of photoinduced electrons and holes, and increase the photocatalytic activity of TiO2@GO. This work establishes the underlying basic mechanism of polymers photodegradation, which might open new avenues for simultaneously addressing the white pollution crisis in a natural environment.

scholarly journals Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Catarina Leal ◽  
Florence Fontaine ◽  
Aziz Aziz ◽  
Conceiçao Egas ◽  
Christophe Clément ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Vitis Vinifera ◽  
Genome Sequence ◽  
Draft Genome ◽  
Rhizospheric Soil ◽  
Bioactive Substances ◽  
Protein Coding ◽  
Genes Encoding ◽  
Stimulate Plant Growth ◽  
Biocontrol Potential

Abstract Background Bacillus subtilis strains have been widely studied for their numerous benefits in agriculture, including viticulture. Providing several assets, B. subtilis spp. are described as promising plant-protectors against many pathogens and as influencers to adaptations in a changing environment. This study reports the draft genome sequence of the beneficial Bacillus subtilis PTA-271, isolated from the rhizospheric soil of healthy Vitis vinifera cv. Chardonnay at Champagne Region in France, attempting to draw outlines of its full biocontrol capacity. Results The PTA-271 genome has a size of 4,001,755 bp, with 43.78% of G + C content and 3945 protein coding genes. The draft genome of PTA-271 putatively highlights a functional swarming motility system hypothesizing a colonizing capacity and a strong interacting capacity, strong survival capacities and a set of genes encoding for bioactive substances. Predicted bioactive compounds are known to: stimulate plant growth or defenses such as hormones and elicitors, influence beneficial microbiota, and counteract pathogen aggressiveness such as effectors and many kinds of detoxifying enzymes. Conclusions Plurality of the putatively encoded biomolecules by Bacillus subtilis PTA-271 genome suggests environmentally robust biocontrol potential of PTA-271, protecting plants against a broad spectrum of pathogens.

scholarly journals Riboflavin Production in Lactococcus lactis: Potential for In Situ Production of Vitamin-Enriched Foods

2004 ◽  
Vol 70 (10) ◽  
pp. 5769-5777 ◽  
Author(s):  
Catherine Burgess ◽  
Mary O'Connell-Motherway ◽  
Wilbert Sybesma ◽  
Jeroen Hugenholtz ◽  
Douwe van Sinderen
Keyword(s):  
Functional Analysis ◽  
Lactic Acid ◽  
Lactococcus Lactis ◽  
Regulatory Region ◽  
Northern Hybridization ◽  
Vitamin B ◽  
Fermented Foods ◽  
Riboflavin Production ◽  
In Situ Production

ABSTRACT This study describes the genetic analysis of the riboflavin (vitamin B2) biosynthetic (rib) operon in the lactic acid bacterium Lactococcus lactis subsp. cremoris strain NZ9000. Functional analysis of the genes of the L. lactis rib operon was performed by using complementation studies, as well as by deletion analysis. In addition, gene-specific genetic engineering was used to examine which genes of the rib operon need to be overexpressed in order to effect riboflavin overproduction. Transcriptional regulation of the L. lactis riboflavin biosynthetic process was investigated by using Northern hybridization and primer extension, as well as the analysis of roseoflavin-induced riboflavin-overproducing L. lactis isolates. The latter analysis revealed the presence of both nucleotide replacements and deletions in the regulatory region of the rib operon. The results presented here are an important step toward the development of fermented foods containing increased levels of riboflavin, produced in situ, thus negating the need for vitamin fortification.

Difficulty of in situ detection of HTLV-I proviral genome sequence

1992 ◽  
Vol 92 (2) ◽  
pp. 231-232 ◽  
Author(s):  
Mitsuo Narita ◽  
Mutsuo Shibata ◽  
Takehiro Togashi
Keyword(s):  
Genome Sequence ◽  
Proviral Genome ◽  
In Situ Detection
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