scholarly journals Vibrio natriegens, a new genomic powerhouse

2016 ◽  
Author(s):  
Henry H. Lee ◽  
Nili Ostrov ◽  
Brandon G. Wong ◽  
Michaela A. Gold ◽  
Ahmad S. Khalil ◽  
...  
Keyword(s):  
Recombinant Dna ◽  
Open Reading Frames ◽  
Host Organism ◽  
Recombinant Dna Technology ◽  
Free Living ◽  
Growth Properties ◽  
Culturing Conditions ◽  
Laboratory Culturing ◽  
Tools And Techniques ◽  
Reading Frames

Recombinant DNA technology has revolutionized biomedical research with continual innovations advancing the speed and throughput of molecular biology. Nearly all these tools, however, are reliant onEscherichia colias a host organism, and its lengthy growth rate increasingly dominates experimental time. Here we report the development ofVibrio natriegens, a free-living bacteria with the fastest generation time known, into a genetically tractable host organism. We systematically characterize its growth properties to establish basic laboratory culturing conditions. We provide the first completeVibrio natriegensgenome, consisting of two chromosomes of 3,248,023 bp and 1,927,310 bp that together encode 4,578 open reading frames. We reveal genetic tools and techniques for working withVibrio natriegens. These foundational resources will usher in an era of advanced genomics to accelerate biological, biotechnological, and medical discoveries.

scholarly journals DNA Engineering and Hepatitis B Virus Replication

2021 ◽  
Vol 12 ◽  
Author(s):  
Chun-yang Gan ◽  
Jing Cui ◽  
Wen-lu Zhang ◽  
Yu-wei Wang ◽  
Ai-long Huang ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Recombinant Dna ◽  
Core Protein ◽  
Surface Protein ◽  
Open Reading Frames ◽  
Recombinant Dna Technology ◽  
Systematic Analysis ◽  
B Virus ◽  
Exogenous Genes

Recombinant DNA technology is a vital method in human hepatitis B virus (HBV), producing reporter viruses or vectors for gene transferring. Researchers have engineered several genes into the HBV genome for different purposes; however, a systematic analysis of recombinant strategy is lacking. Here, using a 500-bp deletion strategy, we scanned the HBV genome and identified two regions, region I (from nt 2,118 to 2,814) and region II (from nt 99 to 1,198), suitable for engineering. Ten exogenous genes, including puromycin N-acetyl transferase gene (Pac), blasticidin S deaminase gene (BSD), Neomycin-resistance gene (Neo), Gaussia luciferase (Gluc), NanoLuc (Nluc), copGFP, mCherry, UnaG, eGFP, and tTA1, were inserted into these two regions and fused into the open reading frames of hepatitis B core protein (HBC) and hepatitis B surface protein (HBS) via T2A peptide. Recombination of 9 of the 10 genes at region 99–1198 and 5 of the 10 genes at region 2118–2814 supported the formation of relaxed circular (RC) DNA. HBV DNA and HBV RNA assays implied that exogenous genes potentially abrogate RC DNA by inducing the formation of adverse secondary structures. This hypothesis was supported because sequence optimization of the UnaG gene based on HBC sequence rescued RC DNA formation. Findings from this study provide an informative basis and a valuable method for further constructing and optimizing recombinant HBV and imply that DNA sequence might be intrinsically a potential source of selective pressure in the evolution of HBV.

scholarly journals Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea

Open Biology ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 200302
Author(s):  
Maura Rojas-Pirela ◽  
Diego Andrade-Alviárez ◽  
Verónica Rojas ◽  
Ulrike Kemmerling ◽  
Ana J. Cáceres ◽  
...  
Keyword(s):  
Phosphoglycerate Kinase ◽  
Glycolytic Enzyme ◽  
Open Reading Frames ◽  
Activity Regulation ◽  
Free Living ◽  
Structural Domains ◽  
Domains Of Life ◽  
Moonlighting Functions ◽  
Reading Frames ◽  
Structural Aspects

Phosphoglycerate kinase (PGK) is a glycolytic enzyme that is well conserved among the three domains of life. PGK is usually a monomeric enzyme of about 45 kDa that catalyses one of the two ATP-producing reactions in the glycolytic pathway, through the conversion of 1,3-bisphosphoglycerate (1,3BPGA) to 3-phosphoglycerate (3PGA). It also participates in gluconeogenesis, catalysing the opposite reaction to produce 1,3BPGA and ADP. Like most other glycolytic enzymes, PGK has also been catalogued as a moonlighting protein, due to its involvement in different functions not associated with energy metabolism, which include pathogenesis, interaction with nucleic acids, tumorigenesis progression, cell death and viral replication. In this review, we have highlighted the overall aspects of this enzyme, such as its structure, reaction kinetics, activity regulation and possible moonlighting functions in different protistan organisms, especially both free-living and parasitic Kinetoplastea. Our analysis of the genomes of different kinetoplastids revealed the presence of open-reading frames (ORFs) for multiple PGK isoforms in several species. Some of these ORFs code for unusually large PGKs. The products appear to contain additional structural domains fused to the PGK domain. A striking aspect is that some of these PGK isoforms are predicted to be catalytically inactive enzymes or ‘dead’ enzymes. The roles of PGKs in kinetoplastid parasites are analysed, and the apparent significance of the PGK gene duplication that gave rise to the different isoforms and their expression in Trypanosoma cruzi is discussed.

scholarly journals Prediction of cellulolytic and hemicellulolytic bacterial diversity in the gut of Coptotermes gestroi in the Southern Vietnam

2020 ◽  
Vol 17 (3) ◽  
pp. 537-544
Author(s):  
Nguyen Thi Thao ◽  
Do Thi Huyen ◽  
Truong Nam Hai
Keyword(s):  
Bacterial Species ◽  
Abundant Species ◽  
Open Reading Frames ◽  
Metagenomic Dna ◽  
Free Living ◽  
Southern Vietnam ◽  
Degrading Bacteria ◽  
Coptotermes Gestroi ◽  
Reading Frames ◽  
Living Bacteria

In lower termite such as Coptotermes gestroi, cellulose and hemicellulose are hydrolysed by cellulases and hemicellulases secreted from bacteria, archaea, protozoa and fungy in the hindgut. In which, majority of the enzymes are contributed by protozoa. From the metagenomic DNA data (125,423 open reading frames -ORFs) of free-living bacteria in the gut of C. gestroi harvested in Southern Vietnam and by MEGA 4.0 software, 100.340 ORFs were classified into 1,368 species, 628 genera, 217 families, 97 orders, 41 classes and 22 phyla (Do et al., 2014). Among these, 2,131 ORFs (2,12%) belong to 24 bacterial species (account 1,75% bacterial species), 11 families, 9 orders, 8 classes and 5 phyla were predicted have ability to produce cellulases; 679 ORFs belong to 18 bacterial species 8 families, 6 orders, 5 classes, 4 phyla were predicted have ability to produce hemicellulase. Majority of cellulase producers were species which of Firmicutes (15/24 species), accumulated in class Clostridia, order Clostridiales. The most abundant cellulase producer was Pseudomonas fluorescens (1,258 ORFs) of order Pseudomonadaceae. Out of the 18 hemicellulase producers, the most abundant species was Clostridium thermocellum (113 ORFs) in the phylum Firmicutes, followed by 3 species belonging to the phylum Bacteroidetes. The species predicted to produce both cellulase, hemicellulase were C. thermocellum, Ruminococcusns flavefaciens and Bacillus subtilis. Our study provides  a data of gut cellulose and hemicellulose - degrading bacteria composition of C. gestroi

Enzymatic Synthesis of 15N-L-aspartic Acid Using Recombinant Aspartase from Escherichia Coli K12

2008 ◽  
Vol 59 (11) ◽  
Author(s):  
Iulia Lupan ◽  
Sergiu Chira ◽  
Maria Chiriac ◽  
Nicolae Palibroda ◽  
Octavian Popescu
Keyword(s):  
Amino Acids ◽  
Aspartic Acid ◽  
Enzymatic Synthesis ◽  
Large Scale ◽  
Recombinant Dna ◽  
Industrial Enzymes ◽  
Recombinant Dna Technology ◽  
Bacterial Fermentation ◽  
Natural Protein ◽  
Novel Method

Amino acids are obtained by bacterial fermentation, extraction from natural protein or enzymatic synthesis from specific substrates. With the introduction of recombinant DNA technology, it has become possible to apply more rational approaches to enzymatic synthesis of amino acids. Aspartase (L-aspartate ammonia-lyase) catalyzes the reversible deamination of L-aspartic acid to yield fumaric acid and ammonia. It is one of the most important industrial enzymes used to produce L-aspartic acid on a large scale. Here we described a novel method for [15N] L-aspartic synthesis from fumarate and ammonia (15NH4Cl) using a recombinant aspartase.

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