Genome Sequence of Luminous Piezophile Photobacterium phosphoreum ANT-2200

Zhang, Sheng-Da; Barbe, Valérie; Garel, Marc; Zhang, Weijia; Chen, Haitao; Santini, Claire‐Lise; Murat, Dorothée; Jing, Hongmei; Zhao, Yuan; Lajus, Aurélie; Martini, Séverine; Pradel, Nathalie; Tamburini, Christian; Wu, Long‐Fei

doi:10.1128/genomea.00096-14

Cited by 7 publications

(5 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The efficiency of RecET direct cloning is limited by the need for the linear vector and the target genomic segment to simultaneously enter one E. coli cell before productive HR can take place. To associate the two DNA molecules in vitro before electroporation into E. coli , we evaluated a variety of exonucleases and annealing protocols using a model experiment based on direct cloning of a 14kb fragment encoding the lux gene cluster from the Gram-negative luminous piezophile marine bacterium P. phosphoreum ANT-2200 ( 14 ) (Figure 1A ). The basic protocol involved mixing restriction digested genomic DNA (10 μg) with a linear direct cloning vector (2.2 kb p15A-cm; 200 ng) that was flanked by short sequence regions (homology arms) identical to the ends of the 14 kb lux restriction fragment.…”

Section: Resultsmentioning

confidence: 99%

ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes

Wang

Jia

et al. 2017

Nucleic Acids Research

102

View full text Add to dashboard Cite

The exponentially increasing volumes of DNA sequence data highlight the need for new DNA cloning methods to explore the new information. Here, we describe ‘ExoCET’ (Exonuclease Combined with RecET recombination) to directly clone any chosen region from bacterial and mammalian genomes with nucleotide precision into operational plasmids. ExoCET combines in vitro exonuclease and annealing with the remarkable capacity of full length RecET homologous recombination (HR) to retrieve specified regions from genomic DNA preparations. Using T4 polymerase (T4pol) as the in vitro exonuclease for ExoCET, we directly cloned large regions (>50 kb) from bacterial and mammalian genomes, including DNA isolated from blood. Employing RecET HR or Cas9 cleavage in vitro, the directly cloned region can be chosen with nucleotide precision to position, for example, a gene into an expression vector without the need for further subcloning. In addition to its utility for bioprospecting in bacterial genomes, ExoCET presents straightforward access to mammalian genomes for various applications such as region-specific DNA sequencing that retains haplotype phasing, the rapid construction of optimal, haplotypic, isogenic targeting constructs or a new way to genotype that presents advantages over Southern blotting or polymerase chain reaction. The direct cloning capacities of ExoCET present new freedoms in recombinant DNA technology.

show abstract

Section: Resultsmentioning

confidence: 99%

ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes

Wang

Jia

et al. 2017

Nucleic Acids Research

102

View full text Add to dashboard Cite

show abstract

“…The classic rib -gene organization in Photobacterium is rib E-B-H-A. However, it is worth noting that the absence of rib E is described for some P. phosphoreum strains (Urbanczyk et al, 2011; Dunlap, 2014) and not in some others (Lee et al, 1994; Sung and Lee, 2004; Zhang et al, 2014). Interestingly, in V. campbellii , only one gene, rib B, coding for a key step of the riboflavin-complex synthetase, can be found (Swartzman, 1990; Dunlap, 2014).…”

Section: Resultsmentioning

confidence: 99%

“…In this study, we have chosen to use Photobacterium phosphoreum ANT-2200, a luminous piezomesophilic bacterium (Martini et al, 2013), which entire genome has been sequenced (Zhang et al, 2014). We focused on the relationship between growth and light emission through physiological, genomic and, transcriptomic approaches at atmospheric pressure.…”

Section: Introductionmentioning

confidence: 99%

Bacterial Bioluminescence: Light Emission in Photobacterium phosphoreum Is Not Under Quorum-Sensing Control

et al. 2019

Self Cite

View full text Add to dashboard Cite

Bacterial-bioluminescence regulation is often associated with quorum sensing. Indeed, many studies have been made on this subject and indicate that the expression of the light-emission-involved genes is density dependent. However, most of these studies have concerned two model species, Aliivibrio fischeri and Vibrio campbellii . Very few works have been done on bioluminescence regulation for the other bacterial genera. Yet, according to the large variety of habitats of luminous marine bacteria, it would not be surprising to find different light-regulation systems. In this study, we used Photobacterium phosphoreum ANT-2200, a piezophilic bioluminescent strain isolated from Mediterranean deep-sea waters (2200-m depth). To answer the question of whether or not the bioluminescence of P. phosphoreum ANT-2200 is under quorum-sensing control, we focused on the correlation between growth and light emission through physiological, genomic and, transcriptomic approaches. Unlike A. fischeri and V. campbellii , the light of P. phosphoreum ANT-2200 immediately increases from its initial level. Interestingly, the emitted light increases at much higher rate at the low cell density than it does for higher cell-density values. The expression level of the light-emission-involved genes stays constant all along the exponential growth phase. We also showed that, even when more light is produced, when the strain is cultivated at high hydrostatic pressure, no change in the transcription level of these genes can be detected. Through different experiments and approaches, our results clearly indicate that, under the tested conditions, the genes, directly involved in the bioluminescence in P. phosphoreum ANT-2200, are not controlled at a transcriptomic level. Quite obviously, these results demonstrate that the light emission of the strain is not density dependent, which means not under quorum-sensing control. Through this study, we point out that bacterial-bioluminescence regulation should not, from now on, be always linked with the quorum-sensing control.

show abstract

“…Both expression of TMAO reductase and kinetics of TMAO reduction are increased under HHP condition, which eventually result in improved pressure tolerance in deep-sea bacteria V. fluvialis QY27 when TMAO is presented (Yin et al, 2018). Pressure inducible TMAO reductase has been reported in several deepsea bacteria (Vezzi et al, 2005;Le Bihan et al, 2013;Zhang et al, 2014Zhang et al, , 2016, it is plausible to deduce that TMAO improved pressure tolerance may be present in other strains as well. However, none of the 32 strains analyzed in this study exhibited improved pressure tolerance at 30 MPa when supplemented with TMAO, indicating the remarkable phenomenon might be a species-specific feature of Vibrio fluvialis.…”

Section: Discussionmentioning

confidence: 95%

Contribution of trimethylamine N-oxide on the growth and pressure tolerance of deep-sea bacteria

Yin

Zhang

et al. 2018

J. Ocean. Limnol.

Self Cite

View full text Add to dashboard Cite

Trimethylamine N-oxide (TMAO) is widely dispersed in marine environments and plays an important role in the biogeochemical cycle of nitrogen. Diverse marine bacteria utilize TMAO as carbon and nitrogen sources or as electron acceptor in anaerobic respiration. Alteration of respiratory component according to the pressure is a common trait of deep-sea bacteria. Deep-sea bacteria from different genera harbor high hydrostatic pressure (HHP) inducible TMAO reductases that are assumed to be constitutively expressed in the deep-sea piezosphere and facilitating quick reaction to TMAO released from fish which is a potential nutrient for bacterial growth. However, whether deep-sea bacteria universally employ this strategy remains unknown. In this study, 237 bacterial strains affiliated to 23 genera of Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria were isolated from seawater, sediment or amphipods collected at different depths. The pressure tolerance and the utilization of TMAO were examined in 74 strains. The results demonstrated no apparent correlation between the depth where the bacteria inhabit and their pressure tolerance, regarding to our samples. Several deep-sea strains from the genera of Alteromonas,

show abstract

Genome Sequence of Luminous Piezophile Photobacterium phosphoreum ANT-2200

Cited by 7 publications

References 6 publications

ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes

ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes

Bacterial Bioluminescence: Light Emission in Photobacterium phosphoreum Is Not Under Quorum-Sensing Control

Contribution of trimethylamine N-oxide on the growth and pressure tolerance of deep-sea bacteria

Contact Info

Product

Resources

About