scholarly journals Bacterial methionine biosynthesis

Microbiology ◽  
2014 ◽  
Vol 160 (8) ◽  
pp. 1571-1584 ◽  
Author(s):  
Matteo P. Ferla ◽  
Wayne M. Patrick
Keyword(s):  
Bacterial Species ◽  
Sequencing Data ◽  
Methionine Biosynthesis ◽  
Gene Encoding ◽  
Metabolic Intermediates ◽  
E Coli ◽  
True Diversity ◽  
Preceding Step ◽  
Adenosyl Methionine ◽  
Key Steps

Methionine is essential in all organisms, as it is both a proteinogenic amino acid and a component of the cofactor, S-adenosyl methionine. The metabolic pathway for its biosynthesis has been extensively characterized in Escherichia coli; however, it is becoming apparent that most bacterial species do not use the E. coli pathway. Instead, studies on other organisms and genome sequencing data are uncovering significant diversity in the enzymes and metabolic intermediates that are used for methionine biosynthesis. This review summarizes the different biochemical strategies that are employed in the three key steps for methionine biosynthesis from homoserine (i.e. acylation, sulfurylation and methylation). A survey is presented of the presence and absence of the various biosynthetic enzymes in 1593 representative bacterial species, shedding light on the non-canonical nature of the E. coli pathway. This review also highlights ways in which knowledge of methionine biosynthesis can be utilized for biotechnological applications. Finally, gaps in the current understanding of bacterial methionine biosynthesis are noted. For example, the paper discusses the presence of one gene (metC) in a large number of species that appear to lack the gene encoding the enzyme for the preceding step in the pathway (metB), as it is understood in E. coli. Therefore, this review aims to move the focus away from E. coli, to better reflect the true diversity of bacterial pathways for methionine biosynthesis.

scholarly journals The yhhP Gene Encoding a Small Ubiquitous Protein Is Fundamental for Normal Cell Growth ofEscherichia coli

1998 ◽  
Vol 180 (8) ◽  
pp. 2257-2261 ◽  
Author(s):  
Takafumi Yamashino ◽  
Mototoshi Isomura ◽  
Chiharu Ueguchi ◽  
Takeshi Mizuno
Keyword(s):  
Fusion Gene ◽  
Bacterial Species ◽  
Luria Broth ◽  
Major Constituent ◽  
Gene Encoding ◽  
Logarithmic Growth Phase ◽  
E Coli ◽  
Archaeal Species ◽  
Enhanced Expression ◽  
The Stability

ABSTRACT H-NS is a major constituent of the Escherichia colinucleoid, whereas ςS is a stress-induced sigma factor. Anhns null mutation affects the cellular content of ςS in such a way that a remarkable accumulation of ςS is observed in the logarithmic growth phase, which results in enhanced expression of a number of ςS-dependent genes, including the katE gene. We isolated an extragenic mutation that affects the expression of thekatE-lacZ fusion gene in the Δhns background. The relevant gene was identified as yhhP, which encodes a small polypeptide of 81 amino acids. Lesion of this gene seemed to affect the stability of ςS. A deletion analysis ofyhhP revealed that this small protein plays a fundamental role in the general physiology of E. coli. TheyhhP-deficient cell is not capable of growing in standard laboratory rich medium (i.e., Luria broth), resulting in the formation of filamentous cells. Homologs of this intriguing protein occur in a wide variety of bacterial species, including archaeal species.

scholarly journals Effects of Deregulation of Methionine Biosynthesis on Methionine Excretion in Escherichia coli

2005 ◽  
Vol 71 (6) ◽  
pp. 3228-3234 ◽  
Author(s):  
Yoshihiro Usuda ◽  
Osamu Kurahashi
Keyword(s):  
Escherichia Coli ◽  
Wild Type Strain ◽  
Methionine Biosynthesis ◽  
Gene Encoding ◽  
Deletion Mutations ◽  
E Coli ◽  
Mutant Strains ◽  
Resistant Mutants ◽  
Adenosylmethionine Synthetase ◽  
Expression Plasmids

ABSTRACT Several regulators of methionine biosynthesis have been reported in Escherichia coli, which might represent barriers to the production of excess l-methionine (Met). In order to examine the effects of these factors on Met biosynthesis and metabolism, deletion mutations of the methionine repressor (metJ) and threonine biosynthetic (thrBC) genes were introduced into the W3110 wild-type strain of E. coli. Mutations of the metK gene encoding S-adenosylmethionine synthetase, which is involved in Met metabolism, were detected in 12 norleucine-resistant mutants. Three of the mutations in the metK structural gene were then introduced into metJ and thrBC double-mutant strains; one of the resultant strains was found to accumulate 0.13 g/liter Met. Mutations of the metA gene encoding homoserine succinyltransferase were detected in α-methylmethionine-resistant mutants, and these mutations were found to encode feedback-resistant enzymes in a 14C-labeled homoserine assay. Three metA mutations were introduced, using expression plasmids, into an E. coli strain that was shown to accumulate 0.24 g/liter Met. Combining mutations that affect the deregulation of Met biosynthesis and metabolism is therefore an effective approach for the production of Met-excreting strains.

scholarly journals Replicon typing characterization of plasmids encoding resistance to gentamicin and apramycin inEscherichia coliandSalmonella typhimuriumisolated from human and animal sources in Belgium

1993 ◽  
Vol 111 (2) ◽  
pp. 229-238 ◽  
Author(s):  
P. Pohl ◽  
Y. Glupczynski ◽  
M. Marin ◽  
G. Van Robaeys ◽  
P. Lintermans ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Bacterial Species ◽  
Gene Encoding ◽  
E Coli ◽  
Molecular Weights ◽  
Electrophoretic Patterns ◽  
Rapid Spread ◽  
Hospital Patients ◽  
Resistance Patterns ◽  
Gentamicin Resistance

SummaryEscherichia coliand salmonella strains with plasmids conferring resistance to gentamicin and apramycin have been isolated with increasing frequency both from cattle and hospital patients in Belgium. The apramycin-gentamicin resistance plasmids were characterized in recipient strains by their profiles and molecular weights using agarose gel electrophoresis, by their antimicrobial resistance patterns and by replicon typing using a series of DNA probes specific for the genes controlling their systems of replication. Overall, most of the plasmids differed in their DNA electrophoretic patterns. Seventeen different antimicrobial resistance profiles were observed, and there were six different types of replicons. However, two replication genes predominated and had a preferential distribution in different bacterial species. The rep FIC.a plus rep Q multireplicon was found mainly in plasmids recovered from gentamicin- and apramycin-resistantE. coliwhile replicon of the type rep FIC.b largely prevailed inS. typhimurium. Identical replication genes were found in most animal and human strains, hence suggesting a high homology between apramycin- gentamicin plasmids in these communities. Finally, our results indicate that the rapid spread of apramycin-gentamicin-resistance in several species of Enterobacteriaceae isolated from animals and from humans in Belgium is not due to a single plasmid, but rather that the gene encoding AAC(3)-IV is carried by various replicons.

scholarly journals Probe design for exploiting gene encoding pectinesterase from dna metagenome data of bacteria in goat rumen and co-expression of gpecs1 gen with chaperone pg-kje8 in Escherichia coli

2018 ◽  
Vol 40 (1) ◽  
pp. 84-91
Author(s):  
Nguyen Khanh Hoang Viet ◽  
Do Thi Huyen ◽  
Le Tung Lam ◽  
Phung Thi Lan ◽  
Phung Thu Nguyet ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Dna Sequences ◽  
Soluble Form ◽  
Probe Design ◽  
Sequencing Data ◽  
Gene Encoding ◽  
E Coli ◽  
Environmental Treatment ◽  
Query Coverage ◽  
Goat Rumen

This article introduces the steps of constructing and using probe to exploit the gene encoding pectinesterase from metagenome DNA sequencing data by next generation gene sequencing tools. Probe was used to exploit and select the gene encoding for pectinesterase from the metagenome DNA sequences of bacteria in goat rumen and thereby select a sequence to express in E. coli. According to the CAZy classification system, pectinesterase belongs to the family of carbohydrates esterases CE8 is an enzyme that has many applications in the food processing industry, environmental treatment, animal feed processing and medicine. As the results, 3 sequences of CE8 was retrieved from CAZy database and one probe was designed, this probe length was 367 amino acids contained all the conserved amino acid residues: 200 conserved residues in all sequence, 72 residues similar in almost sequences and residues conserved in many sequences and homologus; choosed highest alkalinity index. Using the probe designed, we filtered four coding sequences for pectinesterase from metagenome DNA sequencing data of bacteria in goat rumen. Spatial structure estimation with Phyre2 has only one sequencing (code 46301) with 100% sequence identity and 90% query coverage with pectinesterase. A artificial gene were synthesized and inserted into the vector pET22b (+) at the NcoI, XhoI to co-express with chaperone pG-KJE8 in E. coli. The recombinant pectinesterase enzyme is expressed in soluble form and has a pectin substrate biodegradation activity. The results demonstrate that using probe for gene extraction is feasible.

Efficacy of Silver Nanoparticles Synthesized from Hymenocallis species (Spider Lilly) Leaf Extract as Antimicrobial Agents

2019 ◽  
Vol 12 (5) ◽  
pp. 4644-4647
Author(s):  
K.K. Gupta ◽  
Neha Kumari ◽  
Neha Sinha ◽  
Akruti Gupta
Keyword(s):  
Silver Nanoparticles ◽  
Leaf Extract ◽  
Antimicrobial Agents ◽  
Color Change ◽  
Bacterial Species ◽  
Antimicrobial Property ◽  
Biogenic Synthesis ◽  
E Coli ◽  
Light Yellow ◽  
Antibiotic Property

Biogenic synthesis of silver nanoparticles synthesized from Hymenocallis species (Spider Lilly) leaf extract was subjected for investigation of its antimicrobial property against four bacterial species (E. coli, Salmonella sp., Streptococcus sp. & Staphylococcus sp.). The results revealed that synthesized nanoparticles solution very much justify the color change property from initial light yellow to final reddish brown during the synthesis producing a characteristics absorption peak in the range of 434-466 nm. As antimicrobial agents, their efficacy was evaluated by analysis of variance in between the species and among the different concentration of AgNPs solution, which clearly showed that there was significant variation in the antibiotic property between the four different concentrations of AgNPs solution and also among four different species of bacteria taken under studies. However, silver nanoparticles solution of 1: 9 and 1:4 were proved comparatively more efficient as antimicrobial agents against four species of bacteria.

Substituted 6,7-dimethoxy-5-oxo-2,3,5,9b-tetrahydrothiazolo[2,3-a]isoindole- 3-1,1-dioxide Derivatives with Antimicrobial Activity and Docking Assisted Prediction of the Mechanism of their Antibacterial and Antifungal Properties

2020 ◽  
Vol 20 (29) ◽  
pp. 2681-2691
Author(s):  
Athina Geronikaki ◽  
Victor Kartsev ◽  
Phaedra Eleftheriou ◽  
Anthi Petrou ◽  
Jasmina Glamočlija ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Antifungal Activity ◽  
Drug Targets ◽  
Bacterial Species ◽  
Pharmaceutical Research ◽  
Docking Studies ◽  
Fungal Species ◽  
Docking Analysis ◽  
E Coli ◽  
Antibacterial And Antifungal

Background: Although a great number of the targets of antimicrobial therapy have been achieved, it remains among the first fields of pharmaceutical research, mainly because of the development of resistant strains. Docking analysis may be an important tool in the research for the development of more effective agents against specific drug targets or multi-target agents 1-3. Methods: In the present study, based on docking analysis, ten tetrahydrothiazolo[2,3-a]isoindole derivatives were chosen for the evaluation of the antimicrobial activity. Results: All compounds showed antibacterial activity against eight Gram-positive and Gram-negative bacterial species being, in some cases, more potent than ampicillin and streptomycin against all species. The most sensitive bacteria appeared to be S. aureus and En. Cloacae, while M. flavus, E. coli and P. aeruginosa were the most resistant ones. The compounds were also tested for their antifungal activity against eight fungal species. All compounds exhibited good antifungal activity better than reference drugs bifonazole (1.4 – 41 folds) and ketoconazole (1.1 – 406 folds) against all fungal species. In order to elucidate the mechanism of action, docking studies on different antimicrobial targets were performed. Conclusion: According to docking analysis, the antifungal activity can be explained by the inhibition of the CYP51 enzyme for most compounds with a better correlation of the results obtained for the P.v.c. strain (linear regression between estimated binding Energy and log(1/MIC) with R 2 =0.867 and p=0.000091 or R 2 = 0.924, p= 0.000036, when compound 3 is excluded.

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

scholarly journals Evolution of Chi motifs in Proteobacteria

2021 ◽  
Author(s):  
Angélique Buton ◽  
Louis-Marie Bobay
Keyword(s):  
Sequence Similarity ◽  
Bacterial Species ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Large Dataset ◽  
High Sequence Similarity ◽  
Strand Breaks ◽  
E Coli ◽  
Dna Motif ◽  
And Staphylococcus Aureus

Abstract Homologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex allows bacteria to repair DNA double strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized in Escherichia coli and analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species: E. coli, Haemophilus influenzae, Bacillus subtilis, Lactococcus lactis and Staphylococcus aureus. In this study we detected putative Chi motifs in a large dataset of Proteobacteria and we identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif of E. coli in 85 species of Proteobacteria. Most Chi motifs were detected in Enterobacteriaceae and this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.

scholarly journals SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

scholarly journals Characterization of Escherichia coli Strains Derived from Cow Milk of Subclinical and Clinical Cases of Mastitis

2021 ◽  
Vol 11 (2) ◽  
pp. 541
Author(s):  
Katarzyna Grudlewska-Buda ◽  
Krzysztof Skowron ◽  
Ewa Wałecka-Zacharska ◽  
Natalia Wiktorczyk-Kapischke ◽  
Jarosław Bystroń ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Subclinical Mastitis ◽  
Clinical Mastitis ◽  
Economic Problem ◽  
Cow Milk ◽  
P Value ◽  
Dairy Herds ◽  
E Coli ◽  
Bonferroni Test

Mastitis is a major economic problem in dairy herds, as it might decrease fertility, and negatively affect milk quality and milk yield. Out of over 150 bacterial species responsible for the udder inflammation, Escherichia coli is one of the most notable. This study aimed to assess antimicrobial susceptibility, resistance to dipping agents and biofilm formation of 150 E. coli strains isolated from milk of cows with subclinical and clinical mastitis. The strains came from three dairy herds located in Northern and Central Poland. The statistical analyses were performed with post-hoc Bonferroni test and chi-square test (including Yates correction). The data with a p value of <0.05 were considered significant. We found that the tested strains were mostly sensitive to antimicrobials and dipping agents. It was shown that 37.33% and 4.67% of strains were resistant and moderately resistant to at least one antimicrobial agent, respectively. No extended-spectrum beta-lactamases (ESBL)-producing E. coli were detected. The majority of strains did not possess the ability to form biofilm or formed a weak biofilm. The strong biofilm formers were found only among strains derived from cows with subclinical mastitis. The lowest bacteria number was noted for subclinical mastitis cows’ strains, after stabilization with iodine (3.77 log CFU × cm−2) and chlorhexidine (3.96 log CFU × cm−2) treatment. In the present study, no statistically significant differences in susceptibility to antibiotics and the ability to form biofilm were found among the strains isolated from cows with subclinical and clinical mastitis. Despite this, infections in dairy herds should be monitored. Limiting the spread of bacteria and characterizing the most common etiological factors would allow proper treatment.

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