scholarly journals The serC-aro A operon of Escherichia coli. A mixed function operon encoding enzymes from two different amino acid biosynthetic pathways

1986 ◽  
Vol 234 (1) ◽  
pp. 49-57 ◽  
Author(s):  
K Duncan ◽  
J R Coggins
Keyword(s):  
Amino Acid ◽  
Biosynthetic Pathway ◽  
Shikimate Pathway ◽  
Biosynthetic Pathways ◽  
The Novel ◽  
Base Pairs ◽  
Reading Frame ◽  
E Coli ◽  
Phosphoserine Aminotransferase ◽  
Aroa Gene

Sub-cloning experiments aimed at precisely locating the E. coli aroA gene, which encodes the shikimate pathway enzyme 5-enolpyruvylshikimate 3-phosphate synthase, showed that in certain constructions, which remain capable of complementing an auxotrophic aroA mutation, expression of aroA is reduced. DNA sequence analysis revealed that a sequence approx. 1200 base pairs (bp) upstream of aroA is necessary for its expression. An open reading frame was identified in this region which encodes a protein of 362 amino acids with a calculated Mr of 39,834 and which ends 70 bp before the start of the aroA coding sequence. This gene has been identified as serC, the structural gene for 3-phosphoserine aminotransferase, an enzyme of the serine biosynthetic pathway. Both genes are expressed as a polycistronic message which is transcribed from a promotor located 58 bp upstream of serC. Evidence is presented which confirms that the aroA and serC genes constitute an operon which has the novel feature of encoding enzymes from two different amino acid biosynthetic pathways.

scholarly journals Mutations in Bartonella bacilliformis gyrB Confer Resistance to Coumermycin A1

1998 ◽  
Vol 42 (11) ◽  
pp. 2906-2913 ◽  
Author(s):  
James M. Battisti ◽  
Laura S. Smitherman ◽  
D. Scott Samuels ◽  
Michael F. Minnick
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Cell Extract ◽  
Natural Resistance ◽  
Temperature Sensitive ◽  
Bartonella Bacilliformis ◽  
Reading Frame ◽  
E Coli ◽  
Isolation And Characterization ◽  
Spontaneous Mutants

ABSTRACT This study describes the first isolation and characterization of spontaneous mutants conferring natural resistance to an antibiotic for any Bartonella species. The Bartonella bacilliformis gyrB gene, which encodes the B subunit of DNA gyrase, was cloned and sequenced. The gyrB open reading frame (ORF) is 2,079 bp and encodes a deduced amino acid sequence of 692 residues, corresponding to a predicted protein of ∼77.5 kDa. Sequence alignment indicates that B. bacilliformis GyrB is most similar to the GyrB protein from Bacillus subtilis (40.1% amino acid sequence identity) and that it contains the longest N-terminal tail (52 residues) of any GyrB characterized to date. The cloned B. bacilliformis gyrB was expressed in an Escherichia coli S30 cell extract and was able to functionally complement a temperature-sensitive E. coli Cour gyrB mutant (strain N4177). We isolated and characterized spontaneous mutants of B. bacilliformis resistant to coumermycin A1, an antibiotic that targets GyrB. Sequence analysis of gyrB from 12 Cour mutants ofB. bacilliformis identified single nucleotide transitions at three separate loci in the ORF. The predicted amino acid substitutions resulting from these transitions are Gly to Ser at position 124 (Gly124→Ser), Arg184→Gln, and Thr214→Ala or Thr214→Ile, which are analogous to mutated residues found in previously characterized resistant gyrB genes fromBorrelia burgdorferi, E. coli,Staphylococcus aureus, and Haloferax sp. The Cour mutants are three to five times more resistant to coumermycin A1 than the wild-type parental strain.

scholarly journals Conserved Pyridoxal 5'-Phosphate-Binding Protein YggS Impacts Amino Acid Metabolism through Pyridoxine 5'-Phosphate inEscherichia coli

2019 ◽  
Vol 85 (11) ◽  
Author(s):  
Tomokazu Ito ◽  
Kana Yamamoto ◽  
Ran Hori ◽  
Ayako Yamauchi ◽  
Diana M. Downs ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Metabolism ◽  
Biosynthetic Pathway ◽  
Acid Metabolism ◽  
Binding Protein ◽  
Protein Family ◽  
Pleiotropic Effects ◽  
Vitamin B ◽  
Content Type ◽  
E Coli

ABSTRACTEscherichia coliYggS (COG0325) is a member of the highly conserved pyridoxal 5′-phosphate (PLP)-binding protein (PLPBP) family. Recent studies suggested a role for this protein family in the homeostasis of vitamin B6and amino acids. The deletion or mutation of a member of this protein family causes pleiotropic effects in many organisms and is causative of vitamin B6-dependent epilepsy in humans. To date, little has been known about the mechanism by which lack of YggS results in these diverse phenotypes. In this study, we determined that the pyridoxine (PN) sensitivity observed inyggS-deficientE. coliwas caused by the pyridoxine 5′-phosphate (PNP)-dependent overproduction of Val, which is toxic toE. coli. The data suggest that theyggSmutation impacts Val accumulation by perturbing the biosynthetic of Thr from homoserine (Hse). Exogenous Hse inhibited the growth of theyggSmutant, caused further accumulation of PNP, and increased the levels of some intermediates in the Thr-Ile-Val metabolic pathways. Blocking the Thr biosynthetic pathway or decreasing the intracellular PNP levels abolished the perturbations of amino acid metabolism caused by the exogenous PN and Hse. Our data showed that a high concentration of intracellular PNP is the root cause of at least some of the pleiotropic phenotypes described for ayggSmutant ofE. coli.IMPORTANCERecent studies showed that deletion or mutation of members of the YggS protein family causes pleiotropic effects in many organisms. Little is known about the causes, mechanisms, and consequences of these diverse phenotypes. It was previously shown thatyggSmutations inE. coliresult in the accumulation of PNP and some metabolites in the Ile/Val biosynthetic pathway. This work revealed that some exogenous stresses increase the aberrant accumulation of PNP in theyggSmutant. In addition, the current report provides evidence indicating that some, but not all, of the phenotypes of theyggSmutant inE. coliare due to the elevated PNP level. These results will contribute to continuing efforts to determine the molecular functions of the members of the YggS protein family.

scholarly journals Characteristics of a New Enantioselective Thermostable Dipeptidase from Brevibacillus borstelensis BCS-1 and Its Application to Synthesis of a d-Amino-Acid-Containing Dipeptide

2004 ◽  
Vol 70 (3) ◽  
pp. 1570-1575 ◽  
Author(s):  
Dae Heoun Baek ◽  
Jae Jun Song ◽  
Seok-Joon Kwon ◽  
Chung Park ◽  
Chang-Min Jung ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Open Reading Frame ◽  
Nucleotide Sequence Analysis ◽  
Reading Frame ◽  
E Coli ◽  
Specificity Constant ◽  
Optimal Ph

ABSTRACT A new thermostable dipeptidase gene was cloned from the thermophile Brevibacillus borstelensis BCS-1 by genetic complementation of the d-Glu auxotroph Escherichia coli WM335 on a plate containing d-Ala-d-Glu. Nucleotide sequence analysis revealed that the gene included an open reading frame coding for a 307-amino-acid sequence with an M r of 35,000. The deduced amino acid sequence of the dipeptidase exhibited 52% similarity with the dipeptidase from Listeria monocytogenes. The enzyme was purified to homogeneity from recombinant E. coli WM335 harboring the dipeptidase gene from B. borstelensis BCS-1. Investigation of the enantioselectivity (E) to the P1 and P1′ site of Ala-Ala revealed that the ratio of the specificity constant (k cat /Km ) for l-enantioselectivity to the P1 site of Ala-Ala was 23.4 � 2.2 [E = (k cat /Km ) l,d /(k cat /Km ) d,d ], while the d-enantioselectivity to the P1′ site of Ala-Ala was 16.4 � 0.5 [E = (k cat /Km ) l,d /(k cat /Km ) l,l ] at 55�C. The enzyme was stable up to 55�C, and the optimal pH and temperature were 8.5 and 65�C, respectively. The enzyme was able to hydrolyze l-Asp-d-Ala, l-Asp-d-AlaOMe, Z-d-Ala-d-AlaOBzl, and Z-l-Asp-d-AlaOBzl, yet it could not hydrolyze d-Ala-l-Asp, d-Ala-l-Ala, d-AlaNH2, and l-AlaNH2. The enzyme also exhibited β-lactamase activity similar to that of a human renal dipeptidase. The dipeptidase successfully synthesized the precursor of the dipeptide sweetener Z-l-Asp-d-AlaOBzl.

scholarly journals Characterization and Complete Genome Analysis of a Novel Escherichia Phage, vB_EcoM-RPN242

2022 ◽  
Author(s):  
Napakhwan Imklin ◽  
Pattaraporn Sripras ◽  
Narut Thanantong ◽  
Porntippa Lekcharoensuk ◽  
Rujikan Nasanit
Keyword(s):  
Escherichia Coli ◽  
Nucleotide Sequence ◽  
Sequence Comparison ◽  
The Novel ◽  
Base Pairs ◽  
E Coli ◽  
Double Stranded Dna ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Complete Genome Analysis

Abstract The novel Escherichia phage vB_EcoM-RPN242 was isolated using a strain of Escherichia coli host originated from a diarrheal piglet. The phage was able to form plaques on the E. coli lawn at 15−45ºC. Moreover, it was stable over a wide pH (4−10) and temperature (4−70ºC) range. The vB_EcoM-RPN242 genome was found to be a linear, double-stranded DNA consisting of 154,840 base pairs. There were 195 protein-encoding genes and 2 tRNAs detected in the genome, however no unfavorable gene was found. According to the overall nucleotide sequence comparison, the vB_EcoM-RPN242 possibly represents a new phage species in the genus Agtrevirus.

Molecular and functional analysis of the novel cfr(D) linezolid resistance gene identified in Enterococcus faecium

2020 ◽  
Vol 75 (7) ◽  
pp. 1699-1703 ◽  
Author(s):  
François Guerin ◽  
Mohamed Sassi ◽  
Loren Dejoies ◽  
Asma Zouari ◽  
Sacha Schutz ◽  
...  
Keyword(s):  
Amino Acid ◽  
Enterococcus Faecium ◽  
Hybrid Approach ◽  
Amino Acid Identity ◽  
23S Rrna ◽  
The Novel ◽  
Resistance Phenotype ◽  
E Coli ◽  
Linezolid Resistance ◽  
Long Read

Abstract Objectives To characterize the novel cfr(D) gene identified in an Enterococcus faecium clinical isolate (15-307.1) collected from France. Methods The genome of 15-307.1 was entirely sequenced using a hybrid approach combining short-read (MiSeq, Illumina) and long-read (GridION, Oxford Nanopore Technologies) technologies in order to analyse in detail the genetic support and environment of cfr(D). Transfer of linezolid resistance from 15-307.1 to E. faecium BM4107 was attempted by filter-mating experiments. The recombinant plasmid pAT29Ωcfr(D), containing cfr(D) and its own promoter, was transferred to E. faecium HM1070, Enterococcus faecalis JH2-2 and Escherichia coli AG100A. Results As previously reported, 15-307.1 belonged to ST17 and was phenotypically resistant to linezolid (MIC, 16 mg/L), vancomycin and teicoplanin. A hybrid sequencing approach confirmed the presence of several resistance genes including vanA, optrA and cfr(D). Located on a 103 kb plasmid, cfr(D) encoded a 357 amino acid protein, which shared 64%, 64%, 48% and 51% amino acid identity with Cfr, Cfr(B), Cfr(C) and Cfr(E), respectively. Both optrA and cfr(D) were successfully co-transferred to E. faecium BM4107. When expressed in E. faecium HM1070 and E. faecalis JH2-2, pAT29Ωcfr(D) did not confer any resistance, whereas it was responsible for an expected PhLOPSA resistance phenotype in E. coli AG100A. Analysis of the genetic environment of cfr(D) showed multiple IS1216 elements, putatively involved in its mobilization. Conclusions Cfr(D) is a novel member of the family of 23S rRNA methyltransferases. While only conferring a PhLOPSA resistance phenotype when expressed in E. coli, enterococci could constitute an unknown reservoir of cfr(D).

Rapid Gene Cloning, Overexpression and Characterization of a Thermophilic Catalase in E. coli

2011 ◽  
Vol 365 ◽  
pp. 367-374 ◽  
Author(s):  
Hui Luo ◽  
Yao Zhou ◽  
Yan Hong Chang ◽  
Lian Xiong ◽  
Lin Zhi Liu
Keyword(s):  
Prokaryotic Expression ◽  
Bacillus Stearothermophilus ◽  
Base Pairs ◽  
Reading Frame ◽  
E Coli ◽  
Metal Affinity ◽  
Culture Optimization ◽  
Dna Mixture ◽  
Encoding Gene

A thermophilic catalase-encoding gene was rapidly obtained by means a PCR-based protocol with the genomic DNA mixture from compost culture as the template. The open reading frame of this gene is composed of 2208 base pairs, sharing 92.5% homology with the reported Bacillus stearothermophilus gene (NCBI genbank accession No. AB020234. 1). A prokaryotic expression plasmid pET-CATHis was constructed for the gene expression, and two recombinant E. coli, BL21(DE3)/pET-CATHis and BL21(DE3)pLysS/pET-CATHis were finally obtained. After culture optimization, the highest activities for these two strains in shaking flask culture were 74.3 U/ml and 1055.3 U/ml, respectively. The 6 His-tagged recombinant catalase was then purified by using immobilized metal affinity chromatography, and the properties of the purified protein were finally characterized.

Cystathionine β-lyase is involved in d-amino acid metabolism

2018 ◽  
Vol 475 (8) ◽  
pp. 1397-1410 ◽  
Author(s):  
Tetsuya Miyamoto ◽  
Masumi Katane ◽  
Yasuaki Saitoh ◽  
Masae Sekine ◽  
Hiroshi Homma
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Acid Metabolism ◽  
Environmental Changes ◽  
Biosynthetic Pathways ◽  
E Coli ◽  
Comparable Level ◽  
Multifunctional Enzymes ◽  
Dehydratase Activity ◽  
Amino Acid Racemase

Non-canonical d-amino acids play important roles in bacteria including control of peptidoglycan metabolism and biofilm disassembly. Bacteria appear to produce non-canonical d-amino acids to adapt to various environmental changes, and understanding the biosynthetic pathways is important. We identified novel amino acid racemases possessing the ability to produce non-canonical d-amino acids in Escherichia coli and Bacillus subtilis in our previous study, whereas the biosynthetic pathways of these d-amino acids still remain unclear. In the present study, we demonstrated that two cystathionine β-lyases (MetC and MalY) from E. coli produce non-canonical d-amino acids including non-proteinogenic amino acids. Furthermore, MetC displayed d- and l-serine (Ser) dehydratase activity. We characterised amino acid racemase, Ser dehydratase and cysteine lyase activities, and all were higher for MetC. Interestingly, all three activities were at a comparable level for MetC, although optimal conditions for each reaction were distinct. These results indicate that MetC and MalY are multifunctional enzymes involved in l-methionine metabolism and the production of d-amino acids, as well as d- and l-Ser metabolism. To our knowledge, this is the first evidence that cystathionine β-lyase is a multifunctional enzyme with three different activities.

scholarly journals A Tetrahydrofolate-Dependent O-Demethylase, LigM, Is Crucial for Catabolism of Vanillate and Syringate in Sphingomonas paucimobilis SYK-6

2005 ◽  
Vol 187 (6) ◽  
pp. 2030-2037 ◽  
Author(s):  
Tomokuni Abe ◽  
Eiji Masai ◽  
Keisuke Miyauchi ◽  
Yoshihiro Katayama ◽  
Masao Fukuda
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Double Mutant ◽  
Open Reading Frame ◽  
Sphingomonas Paucimobilis ◽  
Reading Frame ◽  
E Coli ◽  
Demethylase Activity ◽  
Specific Activities

ABSTRACT Vanillate and syringate are converted into protocatechuate (PCA) and 3-O-methylgallate (3MGA), respectively, by O-demethylases in Sphingomonas paucimobilis SYK-6. PCA is further degraded via the PCA 4,5-cleavage pathway, while 3MGA is degraded through multiple pathways in which PCA 4,5-dioxygenase (LigAB), 3MGA 3,4-dioxygenase (DesZ), and an unidentified 3MGA O-demethylase and gallate dioxygenase are participants. For this study, we isolated a 4.7-kb SmaI fragment that conferred on Escherichia coli the activity required for the conversion of vanillate to PCA. The nucleotide sequence of this fragment revealed an open reading frame of 1,413 bp (ligM), the deduced amino acid sequence of which showed 49% identity with that of the tetrahydrofolate (H4folate)-dependent syringate O-demethylase gene (desA). The metF and ligH genes, which are thought to be involved in H4folate-mediated C1 metabolism, were located just downstream of ligM. The crude LigM enzyme expressed in E. coli converted vanillate and 3MGA to PCA and gallate, respectively, with similar specific activities, and only in the presence of H4folate; however, syringate was not a substrate for LigM. The disruption of ligM led to significant growth retardation on both vanillate and syringate, indicating that ligM is involved in the catabolism of these substrates. The ability of the ligM mutant to transform vanillate was markedly decreased, and this mutant completely lost the 3MGA O-demethylase activity. A ligM desA double mutant completely lost the ability to transform vanillate, thus indicating that desA also contributes to vanillate degradation. All of these results indicate that ligM encodes vanillate/3MGA O-demethylase and plays an important role in the O demethylation of vanillate and 3MGA, respectively.

scholarly journals Improved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joanne M. L. Ho ◽  
Corwin A. Miller ◽  
Kathryn A. Smith ◽  
Jacob R. Mattia ◽  
Matthew R. Bennett
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Side Effects ◽  
Directed Evolution ◽  
Biosynthetic Pathway ◽  
Reporter Protein ◽  
Proteinogenic Amino Acid ◽  
E Coli ◽  
Rational Engineering ◽  
Fundamental Building Block

AbstractPyrrolysine (Pyl, O) exists in nature as the 22nd proteinogenic amino acid. Despite being a fundamental building block of proteins, studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, we improve Pyl biosynthesis via rational engineering and directed evolution of the entire biosynthetic pathway. To accommodate toxicity of Pyl biosynthetic genes in Escherichia coli, we also develop Alternating Phage Assisted Non-Continuous Evolution (Alt-PANCE) that alternates mutagenic and selective phage growths. The evolved pathway provides 32-fold improved yield of Pyl-containing reporter protein compared to the rationally engineered ancestor. Evolved PylB mutants are present at up to 4.5-fold elevated levels inside cells, and show up to 2.2-fold increased protease resistance. This study demonstrates that Alt-PANCE provides a general approach for evolving proteins exhibiting toxic side effects, and further provides an improved pathway capable of producing substantially greater quantities of Pyl-proteins in E. coli.

scholarly journals The biosynthetic pathway of ubiquinone contributes to pathogenicity of Francisella

2021 ◽  
Author(s):  
Katayoun Kazemzadeh ◽  
Mahmoud Hajj Chehade ◽  
Gautier Hourdoir ◽  
Camille Dorothée Brunet ◽  
Yvan Caspar ◽  
...  
Keyword(s):  
Francisella Tularensis ◽  
Biosynthetic Pathway ◽  
Galleria Mellonella ◽  
Competitive Inhibitor ◽  
Strictly Aerobic ◽  
Biosynthetic Pathways ◽  
Francisella Novicida ◽  
E Coli ◽  
Causative Bacterium

Francisella tularensis is the causative agent of tularemia. Because of its extreme infectivity and high mortality rate, this pathogen was classified as a biothreat agent. Francisella spp are strict aerobe and ubiquinone (UQ) has been previously identified in these bacteria. While the UQ biosynthetic pathways were extensively studied in Escherichia coli allowing the identification of fifteen Ubi-proteins to date, little is known about Francisella spp. In this study, and using Francisella novicida as a surrogate organism, we first identified UQ 8 as the major quinone found in the membranes of this bacterium. Then, we characterized the UQ biosynthetic pathway in F. novicida using a combination of bioinformatics, genetics and biochemical approaches. Our analysis disclosed the presence in Francisella of ten putative Ubi-proteins and we confirmed eight of them by heterologous complementation in E. coli . The UQ biosynthetic pathways from F. novicida and E. coli share a similar pattern. However, differences were highlighted: the decarboxylase remains unidentified in Francisella spp and homologs of the Ubi-proteins involved in the O 2 -independent UQ pathway are not present. This is in agreement with the strictly aerobic niche of this bacterium. Then, via two approaches, i.e. the use of an inhibitor (3-amino-4-hydroxybenzoic acid) and a transposon mutant, which both strongly impair the synthesis of UQ, we demonstrated that UQ is essential for the growth of F. novicida in a respiratory medium and contributes to its pathogenicity in Galleria mellonella used as an alternative animal model. Importance Francisella tularensis is the causative bacterium of tularemia and is classified as a biothreat agent. Using multidisciplinary approaches, we investigated the ubiquinone (UQ) biosynthetic pathway that operates in F. novicida used as a surrogate. We showed that UQ 8 is the major quinone identified in the membranes of Francisella novicida . We identified a new competitive inhibitor, which strongly decreased the biosynthesis of UQ. Our demonstration of the crucial role of UQ for the respiratory metabolism of F. novicida and for the involving in its pathogenicity in the Galleria mellonella model should stimulate the search for selective inhibitors of bacterial UQ biosynthesis.

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