scholarly journals Metabolic potentials of Liquorilactobacillus nagelii AGA58 isolated from Shalgam based on genomic and functional analysis

2021 ◽  
Author(s):  
Ahmet Yetiman ◽  
Fatih ORTAKCI
Keyword(s):  
Gc Content ◽  
Pentose Phosphate ◽  
Trna Genes ◽  
Probiotic Potential ◽  
Hexose Sugars ◽  
Gastrointestinal Conditions ◽  
Flagellar Biosynthesis ◽  
Key Enzyme ◽  
Carbohydrate Fermentation ◽  
Genomic Characterization

The aim of present study was to perform functional and genomic characterization of a novel Liquorilactobacillus nagelii AGA58 isolated from Shalgam to understand its metabolic potentials. AGA58 is gram-positive,catalase-negative and appears as short-rods under light-microscope. The AGA58 chromosome composed of a single linear chromosome of 2,294,535 bp that is predicted to carry 2151 coding sequences, including 45 tRNA genes, 4 rRNA operons. Genome has a GC content of 36.9% includes 45 pseudogenes, 32 transposases and one intact-prophage. AGA58 is micro-anaerobic owing to shorter doubling time and faster growth rate achieved compared microaerofilic condition. It carries flagellar biosynthesis protein-encoding genes predicting motile behavior. AGA58 is an obligatory homofermentative where hexose sugars such as galactose, glucose, fructose, sucrose, mannose, N-acetyl glucosamine, maltose, trehalose are fermented to lactate thru glycolysis and no acid production from pentose sugars achieved due to lack of key enzyme namely phosphoketolase in pentose phosphate pathway. Carbohydrate fermentation tests showed AGA58 cannot ferment pentoses which was also confirmed in silico. Putative pyruvate metabolism revealed formate, malate, oxaloacetate, acetate, acetaldehyde, acetoin and lactate forms from pyruvate. AGA58 predicted to carry bacteriocin genes for type A2 lantipeptide, Blp family class II bacteriocins showing antimicrobial potential of this bacterium which can be linked to antagonism tests that AGA58 can inhibit E. coli O157:H7, S. Typhimurium ATCC14028, and K. pneumonia ATCC13883. Moreoever, AGA58 is tolerant to acid and bile concentrations simulating the human gastrointestinal conditions. L. nagelii AGA58 depicting the probiotic potential of AGA58 as a first report in literature within same species.

Isolation and characterization of Hena1 – a novel Erwinia amylovora bacteriophage

2020 ◽  
Vol 367 (9) ◽  
Author(s):  
Natalya V Besarab ◽  
Artur E Akhremchuk ◽  
Maryna A Zlatohurska ◽  
Liudmyla V Romaniuk ◽  
Leonid N Valentovich ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Fire Blight ◽  
Antimicrobial Agents ◽  
Erwinia Amylovora ◽  
Gc Content ◽  
Control Measures ◽  
Effective Control ◽  
Lytic Phage ◽  
Trna Genes ◽  
Isolation And Characterization

ABSTRACT Fire blight, caused by plant pathogenic bacterium Erwinia amylovora, is one of the most important diseases of Rosaceae plants. Due to the lack of effective control measures, fire blight infections pose a recurrent threat on agricultural production worldwide. Recently, bacterial viruses, or bacteriophages, have been proposed as environmentally friendly natural antimicrobial agents for fire blight control. Here, we isolated a novel bacteriophage Hena1 with activity against E. amylovora. Further analysis revealed that Hena1 is a narrow-host-range lytic phage belonging to Myoviridae family. Its genome consists of a linear 148,842 bp dsDNA (48.42% GC content) encoding 240 ORFs and 23 tRNA genes. Based on virion structure and genomic composition, Hena1 was classified as a new species of bacteriophage subfamily Vequintavirinae. The comprehensive analysis of Hena1 genome may provide further insights into evolution of bacteriophages infecting plant pathogenic bacteria.

scholarly journals Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection

Biomedicines ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 342
Author(s):  
Ahmed R. Sofy ◽  
Noha K. El-Dougdoug ◽  
Ehab E. Refaey ◽  
Rehab A. Dawoud ◽  
Ahmed A. Hmed
Keyword(s):  
Klebsiella Pneumoniae ◽  
Burst Size ◽  
Phylogenetic Analyses ◽  
Foodborne Pathogen ◽  
Gc Content ◽  
Full Genome Sequence ◽  
Multiple Drug ◽  
Lytic Phage ◽  
Trna Genes ◽  
Bacteriophage Therapy

Klebsiella pneumoniae is a hazardous opportunistic pathogen that is involved in many serious human diseases and is considered to be an important foodborne pathogen found in many food types. Multidrug resistance (MDR) K. pneumoniae strains have recently spread and increased, making bacteriophage therapy an effective alternative to multiple drug-resistant pathogens. As a consequence, this research was conducted to describe the genome and basic biological characteristics of a novel phage capable of lysing MDR K. pneumoniae isolated from food samples in Egypt. The host range revealed that KPP-5 phage had potent lytic activity and was able to infect all selected MDR K. pneumoniae strains from different sources. Electron microscopy images showed that KPP-5 lytic phage was a podovirus morphology. The one-step growth curve exhibited that KPP-5 phage had a relatively short latent period of 25 min, and the burst size was about 236 PFU/infected cells. In addition, KPP-5 phage showed high stability at different temperatures and pH levels. KPP-5 phage has a linear dsDNA genome with a length of 38,245 bp with a GC content of 50.8% and 40 predicted open reading frames (ORFs). Comparative genomics and phylogenetic analyses showed that KPP-5 is most closely associated with the Teetrevirus genus in the Autographviridae family. No tRNA genes have been identified in the KPP-5 phage genome. In addition, phage-borne virulence genes or drug resistance genes were not present, suggesting that KPP-5 could be used safely as a phage biocontrol agent.

scholarly journals A bacteriophage infecting Mesorhizobium species has a prolate capsid and shows similarities to a family of Caulobacter crescentus phages

2020 ◽  
pp. 1-14
Author(s):  
K.M. Damitha Gunathilake ◽  
Anupama P. Halmillawewa ◽  
Keith D. MacKenzie ◽  
Benjamin J. Perry ◽  
Christopher K. Yost ◽  
...  
Keyword(s):  
Caulobacter Crescentus ◽  
Gc Content ◽  
Nucleotide Metabolism ◽  
Gene Arrangement ◽  
Modular Organization ◽  
Trna Genes ◽  
Direct Repeats ◽  
Structural Genes ◽  
Replication Mechanism ◽  
Replication Module

Mesorhizobium phage vB_MloS_Cp1R7A-A1 was isolated from soil planted with chickpea in Saskatchewan. It is dissimilar in sequence and morphology to previously described rhizobiophages. It is a B3 morphotype virus with a distinct prolate capsid and belongs to the tailed phage family Siphoviridae. Its genome has a GC content of 60.3% and 238 predicted genes. Putative functions were predicted for 57 genes, which include 27 tRNA genes with anticodons corresponding to 18 amino acids. This represents the highest number of tRNA genes reported yet in a rhizobiophage. The gene arrangement shows a partially modular organization. Most of the structural genes are found in one module, whereas tRNA genes are in another. Genes for replication, recombination, and nucleotide metabolism form the third module. The arrangement of the replication module resembles the replication module of Enterobacteria phage T5, raising the possibility that it uses a recombination-based replication mechanism, but there is also a suggestion that a T7-like replication mechanism could be used. Phage termini appear to be long direct repeats of just over 12 kb in length. Phylogenetic analysis revealed that Cp1R7A-A1 is more closely related to PhiCbK-like Caulobacter phages and other B3 morphotype phages than to other rhizobiophages sequenced thus far.

scholarly journals The Bacillus subtilis yqjI Gene Encodes the NADP+-Dependent 6-P-Gluconate Dehydrogenase in the Pentose Phosphate Pathway

2004 ◽  
Vol 186 (14) ◽  
pp. 4528-4534 ◽  
Author(s):  
Nicola Zamboni ◽  
Eliane Fischer ◽  
Dietmar Laudert ◽  
Stéphane Aymerich ◽  
Hans-Peter Hohmann ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Glucose Dehydrogenase ◽  
Reducing Power ◽  
Pentose Phosphate ◽  
Gene Encoding ◽  
Metabolic Intermediates ◽  
The Third ◽  
Key Enzyme ◽  
Sequence Similarities

ABSTRACT Despite the importance of the oxidative pentose phosphate (PP) pathway as a major source of reducing power and metabolic intermediates for biosynthetic processes, almost no direct genetic or biochemical evidence is available for Bacillus subtilis. Using a combination of knockout mutations in known and putative genes of the oxidative PP pathway and 13C-labeling experiments, we demonstrated that yqjI encodes the NADP+-dependent 6-P-gluconate dehydrogenase, as was hypothesized previously from sequence similarities. Moreover, YqjI was the predominant isoenzyme during glucose and gluconate catabolism, and its role in the oxidative PP pathway could not be played by either of two homologues, GntZ and YqeC. This conclusion is in contrast to the generally held view that GntZ is the relevant isoform; hence, we propose a new designation for yqjI, gndA, the monocistronic gene encoding the principal 6-P-gluconate dehydrogenase. Although we demonstrated the NAD+-dependent 6-P-gluconate dehydrogenase activity of GntZ, gntZ mutants exhibited no detectable phenotype on glucose, and GntZ did not contribute to PP pathway fluxes during growth on glucose. Since gntZ mutants grew normally on gluconate, the functional role of GntZ remains obscure, as does the role of the third homologue, YqeC. Knockout of the glucose-6-P dehydrogenase-encoding zwf gene was primarily compensated for by increased glycolytic fluxes, but about 5% of the catabolic flux was rerouted through the gluconate bypass with glucose dehydrogenase as the key enzyme.

scholarly journals Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2137 ◽  
Author(s):  
Xiang-Xiao Meng ◽  
Yan-Fang Xian ◽  
Li Xiang ◽  
Dong Zhang ◽  
Yu-Hua Shi ◽  
...  
Keyword(s):  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Future Studies ◽  
Chloroplast Genomes ◽  
Close Relationship ◽  
Cp Genome ◽  
Sanguisorba Officinalis

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

scholarly journals Investigation of Heterologously Expressed Glucose-6-Phosphate Dehydrogenase Genes in a Yeast zwf1 Deletion

2020 ◽  
Vol 8 (4) ◽  
pp. 546 ◽  
Author(s):  
Jürgen J. Heinisch ◽  
Johannes Knuesting ◽  
Renate Scheibe
Keyword(s):  
Kluyveromyces Lactis ◽  
Expression System ◽  
Disulfide Bridge ◽  
Pentose Phosphate ◽  
Yeast Saccharomyces Cerevisiae ◽  
Physiological Properties ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Synthetic Media ◽  
Glucose 6 Phosphate Dehydrogenase

Glucose-6-phosphate dehydrogenase (G6PD) is a key enzyme of the oxidative part of the pentose phosphate pathway and serves as the major source of NADPH for metabolic reactions and oxidative stress response in pro- and eukaryotic cells. We here report on a strain of the model yeast Saccharomyces cerevisiae which lacks the G6PD-encoding ZWF1 gene and displays distinct growth retardation on rich and synthetic media, as well as a strongly reduced chronological lifespan. This strain was used as a recipient to introduce plasmid-encoded heterologous G6PD genes, synthesized in the yeast codon usage and expressed under the control of the native PFK2 promotor. Complementation of the hypersensitivity of the zwf1 mutant towards hydrogen peroxide to different degrees was observed for the genes from humans (HsG6PD1), the milk yeast Kluyveromyces lactis (KlZWF1), the bacteria Escherichia coli (EcZWF1) and Leuconostoc mesenteroides (LmZWF1), as well as the genes encoding three different plant G6PD isoforms from Arabidopsis thaliana (AtG6PD1, AtG6PD5, AtG6PD6). The plastidic AtG6PD1 isoform retained its redox-sensitive activity when produced in the yeast as a cytosolic enzyme, demonstrating the suitability of this host for determination of its physiological properties. Mutations precluding the formation of a disulfide bridge in AtG6PD1 abolished its redox-sensitivity but improved its capacity to complement the yeast zwf1 deletion. Given the importance of G6PD in human diseases and plant growth, this heterologous expression system offers a broad range of applications.

scholarly journals Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 61 ◽  
Author(s):  
Huyen-Trang Vu ◽  
Ngan Tran ◽  
Thanh-Diem Nguyen ◽  
Quoc-Luan Vu ◽  
My-Huyen Bui ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Complete Chloroplast Genome ◽  
Critically Endangered Species ◽  
Plastid Genomes ◽  
Chloroplast Genomes

Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.

scholarly journals  Bacteriocin-producing lactic acid bacteria as a probiotic potential from Thai indigenous chickens

2012 ◽  
Vol 57 (No. 3) ◽  
pp. 137-149 ◽  
Author(s):  
H. Musikasang ◽  
N. Sohsomboon ◽  
A. Tani ◽  
S. Maneerat
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Inhibitory Activity ◽  
Proteolytic Enzymes ◽  
Penicillin G ◽  
Probiotic Properties ◽  
Indigenous Chickens ◽  
Probiotic Potential ◽  
Gastrointestinal Conditions ◽  
Acti Vity

Bacteriocin-producing lactic acid bacteria (LAB) were isolated and screened from the gastrointestinal tract (GIT) of Thai indigenous chickens. The bacteriocinogenic activities and the primary probiotic properties were determined. The bacteriocins produced by 14 strains of selected LAB displayed inhibitory activity against indicator strains after the supernatants were neutralized with NaOH in the following species: Lactobacillus sakei subsp. sakei JCM1157, Enterococcus faecalis VanB, Bacillus sp., and Listeria monocytogenes. The antagonistic acti-vity of selected LAB was inactivated or decreased after being treated with proteolytic enzymes (α-chymotrypsin and trypsin). CR5-1 strain exhibited the highest level of activity (5120 AU/ml) in the stationary phase against L. sakei subsp. sakei JCM1157 in MRS broth at 37°C. The nine isolates of selected LAB were investigated for primary probiotic properties. The survival of the nine isolates was found to decrease approximately by 3 log CFU/ml after passing through the gastrointestinal conditions. All isolates exhibited protein digestion on agar plates but no isolates showed the ability to digest starch and lipid. Most of them showed high susceptibilities to some antibiotics (penicillin G, tetracycline and erythromycin). Thirteen LAB strains producing bacteriocin with strongly inhibitory activity were identified as Lactobacillus salivarius and only one strain was identified by 16S rDNA sequence analysis as Lactobacillus agilis.    

Identification and Characterization of Novel Human Glucose-6-Phosphate Dehydrogenase Inhibitors

2012 ◽  
Vol 18 (3) ◽  
pp. 286-297 ◽  
Author(s):  
Janina Preuss ◽  
Adam D. Richardson ◽  
Anthony Pinkerton ◽  
Michael Hedrick ◽  
Eduard Sergienko ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Basic Research ◽  
Pentose Phosphate ◽  
Screening Assay ◽  
High Throughput Screening Assay ◽  
Key Enzyme ◽  
Small Molecule Compound ◽  
Glucose 6 Phosphate Dehydrogenase ◽  
Identification And Characterization

Glucose-6-phosphate dehydrogenase (G6PD) is the key enzyme of the pentose phosphate pathway, converting glucose-6-phosphate to 6-phosphoglucono-δ-lactone with parallel reduction of NADP+. Several human diseases, including cancer, are associated with increased G6PD activity. To date, only a few G6PD inhibitors have been available. However, adverse side effects and high IC50 values hamper their use as therapeutics and basic research probes. In this study, we developed a high-throughput screening assay to identify novel human G6PD (hG6PD) inhibitors. Screening the LOPAC (Sigma-Aldrich; 1280 compounds), Spectrum (Microsource Discovery System; 1969 compounds), and DIVERSet (ChemBridge; 49 971 compounds) small-molecule compound collections revealed 139 compounds that presented ≥50% hG6PD inhibition. Hit compounds were further included in a secondary and orthogonal assay in order to identify false-positives and to determine IC50 values. The most potent hG6PD inhibitors presented IC50 values of <4 µM. Compared with the known hG6PD inhibitors dehydroepiandrosterone and 6-aminonicotinamide, the inhibitors identified in this study were 100- to 1000-fold more potent and showed different mechanisms of enzyme inhibition. One of the newly identified hG6PD inhibitors reduced viability of the mammary carcinoma cell line MCF10-AT1 (IC50 ~25 µM) more strongly than that of normal MCF10-A cells (IC50 >50 µM).

scholarly journals Complete genome sequence of Chryseobacterium sp. ZHDP1 with protease activity

2021 ◽  
Author(s):  
Huanshuai Zhao ◽  
Jianxin Wang ◽  
Jiamao Huang ◽  
Yuncheng Ma ◽  
Yunfei Chen ◽  
...  
Keyword(s):  
Complete Genome ◽  
Protease Activity ◽  
Fermentation Broth ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Rrna Gene ◽  
The Novel ◽  
Maximum Similarity ◽  
Insight Into

Abstract This study reported a complete genome of Chryseobacterium sp. ZHDP1 isolated from the soils of a seafood market. The ZHDP1 genome with a size of 4,917,748 bp and a GC content of 35.95% possessed 4,478 coding genes, 5 rRNA genes, 26 sRNA genes, and 89 tRNA genes. The 16S rRNA gene sequence of ZHDP1 had a maximum similarity of 99.07% with that of C. gambrini 5-1St1a. The maximum values of average nucleotide identity and DNA-DNA hybridization of ZHDP1 genome were 91.39 and 47.8, respectively, which were lower than the thresholds for a new genome. Different protease genes were annotated in the genome of ZHDP1, and the protease activity was also detected in the fermentation broth of ZHDP1. Furthermore, the activity of protease in the fermentation broth was optimized through temperature, pH, and metal irons, and the results showed that 60°C and pH 7.0 were the optimum conditions and Fe3+ could positively increase the protease activity of ZHDP1. This study provides the first insight into the novel genomic information of Chryseobacterium sp. ZHDP1 and its protein-degrading ability, thereby broadening our knowledge of the industrial potentials in genus Chryseobacterium strains.

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