Construction and expression of hybrid plasmids containing the structural gene of the Escherichia coli K-12 3-deoxy-2-oxo-D-gluconate transport system

Mandrand‐Berthelot, Marie‐Andrée; Ritzenthaler, Paul; Mata-Gilsinger, Mireille

doi:10.1128/jb.160.2.600-606.1984

Cited by 10 publications

(3 citation statements)

References 38 publications

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“…This gene encodes the permease for 3-deoxy-2-oxo-Dgluconate. It was located by genetic data, protein size, and comparison with the restriction map for the E. coli gene (31). The predicted gene product also showed similarity to the amino acid sequence of the analogous gene in Erwinia chrysanthemi (32) ( Table 2).…”

Section: I~~~~~~~~ĩ-mentioning

confidence: 94%

Analysis of theEscherichia coligenome. III. DNA sequence of the region from 87.2 to 89.2 minutes

et al. 1993

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The DNA sequence of 96.5 kilobases of the Escherichia coli K-12 genome has been determined, spanning the region between rrnA at 87.2 minutes and katG at 89.2 minutes on the genetic map. The sequence includes 84 open reading frames, of which 46 code for unidentified proteins. Six previously mapped but unsequenced genes have been identified in this span: mob, fdhD, rhaD, rhaA, rhaB, and kdgT. In addition, five new genes have been assigned: the heat shock genes hsIU and hsIV, and the genes fdoG, fdoH, and fdoI, which encode the three subunits of formate dehydrogenase-O. The arrangement of the genes relative to possible promoters and terminators suggests 57 potential transcription units. Other features include the precise location of the bacteriophage P2 attachment site attP2II, and eleven REP elements, including one containing 9 REP sequences--one of the largest such elements known. This segment brings the total length of contiguous finished sequence to 325 kilobases.

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Section: I~~~~~~~~ĩ-mentioning

confidence: 94%

Analysis of theEscherichia coligenome. III. DNA sequence of the region from 87.2 to 89.2 minutes

et al. 1993

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“…Pectin is degraded by a battery of pectinases for utilization as carbon source nutrients 33 . Resulting oligogalacturonide chains are transported into the periplasm space through anion-specific oligosaccharide KdgT porins 34 . The oligogalacturonides were further degraded into oligogalacturonides by the downstream pectinases, transported into the cytoplasm and ultimately degraded into pyruvate and 3-phosphoglyceraldehyde by the enzyme encoded by the eda gene (Fig.…”

Section: Utilization Of Plant-derived Nutrients E Coli Is Able To Cmentioning

confidence: 99%

Regulatory Role of PlaR (YiaJ) for Plant Utilization in Escherichia coli K-12

Shimada

Yokoyama

Anzai

et al. 2019

Sci Rep

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Outside a warm-blooded animal host, the enterobacterium Escherichia coli K-12 is also able to grow and survive in stressful nature. The major organic substance in nature is plant, but the genetic system of E. coli how to utilize plant-derived materials as nutrients is poorly understood. Here we describe the set of regulatory targets for uncharacterized IclR-family transcription factor YiaJ on the E. coli genome, using gSELEX screening system. Among a total of 18 high-affinity binding targets of YiaJ, the major regulatory target was identified to be the yiaLMNOPQRS operon for utilization of ascorbate from fruits and galacturonate from plant pectin. The targets of YiaJ also include the genes involved in the utilization for other plant-derived materials as nutrients such as fructose, sorbitol, glycerol and fructoselysine. Detailed in vitro and in vivo analyses suggest that L-ascorbate and α-D-galacturonate are the effector ligands for regulation of YiaJ function. These findings altogether indicate that YiaJ plays a major regulatory role in expression of a set of the genes for the utilization of plant-derived materials as nutrients for survival. PlaR was also suggested to play protecting roles of E. coli under stressful environments in nature, including the formation of biofilm. We then propose renaming YiaJ to PlaR (regulator of plant utilization). Bacteria constantly monitor environmental conditions, and respond for adaptation and survival by modulating the expression pattern of their genomes. Transcription, the major regulation step in gene expression, is carried out by a single species of RNA polymerase (RNAP). The intracellular concentration of RNAP core enzyme in growing Escherichia coli K-12 W3110 strain is about 2,000 molecules per genome, which is less than the total of about 4,500 genes on its genome 1,2. The expression pattern of a total of about 4,500 genes in its genome, however, can be modulated through alteration of the promoter selectivity of RNAP after interaction with two groups of the regulatory proteins, i.e., seven species of the promoter recognition subunit sigma 1,3,4 and about 300 species of the DNA-binding transcription factors (TFs) 5,6. Based on the protein structure of DNA-binding motifs, these TFs were classified into 54 families (5; TEC database [www.shigen.nig.ac.jp/ecoli/tec/]). Up to the present time, more than 80% of the estimated 300 TFs in E. coli K-12 have been linked to at least one regulatory target gene or operon in its genome. The search for regulatory targets of these TFs has been carried out in vivo using both the ordinary molecular genetic approaches and the modern methodologies such as transcriptome using DNA microarrays and chromatin immunoprecipitation (ChIP) approaches. Using only in vivo analyses, however, it is difficult to get the complete set of regulatory targets because the binding in vivo of test TFs to their DNA targets is interfered with by both approximately 300 species of co-existing TFs and a number of nucleoid-associated DNA-binding proteins 5. The regulato...

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“…KDG is also an important intermediate for the degradation of extracellular pectin, which is processed and incorporated into cells and then converted to KDG intracellularly in Erwinia chrysanthemi (Hugouvieux-Cotte-Pattat et al, 1996). Extracellular KDG is also utilized by incorporation via the KDG transporter in Escherichia coli (Mandrand-Berthelot et al, 1984) and Er. chrysanthemi (Hugouvieux-Cotte-Pattat et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

Crystallization and preliminary crystallographic analysis of 2-keto-3-deoxygluconate kinase fromThermus thermophilus

Inagaki¹,

Ukita

Kumei

et al. 2004

Acta Crystallogr D Biol Cryst

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2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate. Two crystal forms of KDGK from Thermus thermophilus were obtained by vapour-diffusion and microbatch methods. Crystals in the form of triangular plates (TtKDGK-1) were obtained that belong to space group P3, with unit-cell parameters a = b = 145.83, c = 74.63 A, and diffract to 3.2 A. These crystals exhibited nearly perfect hemihedral twinning. Assigning six subunits of TtKDGK to the asymmetric unit of the crystal corresponds to a 46.2% solvent content. A single plate-like crystal (TtKDGK-2) belonged to space group P6(3), with unit-cell parameters a = b = 84.83, c = 168.49 A, and diffracts to 2.25 A. This crystal exhibits only partial hemihedral twinning, with a twin fraction of 24.4%. Diffraction-quality crystals of TtKDGK with bound ATP (TtKDGK-ATP), a = b = 84.72, c = 321.61 A and with bound KDG plus the ATP analogue AMP-PNP (TtKDGK-ATP-KDG), with unit-cell parameters a = b = 84.32, c = 168.7 A, were also prepared and characterized.

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Construction and expression of hybrid plasmids containing the structural gene of the Escherichia coli K-12 3-deoxy-2-oxo-D-gluconate transport system

Cited by 10 publications

References 38 publications

Analysis of theEscherichia coligenome. III. DNA sequence of the region from 87.2 to 89.2 minutes

Analysis of theEscherichia coligenome. III. DNA sequence of the region from 87.2 to 89.2 minutes

Regulatory Role of PlaR (YiaJ) for Plant Utilization in Escherichia coli K-12

Crystallization and preliminary crystallographic analysis of 2-keto-3-deoxygluconate kinase fromThermus thermophilus

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