A. Holtel - Academia.edu (original) (raw)
Papers by A. Holtel
metabolism of aromatics. plasmid pWW0 of Pseudomonas putida for promoters of the catabolic pathwa... more metabolism of aromatics. plasmid pWW0 of Pseudomonas putida for promoters of the catabolic pathways of TOL Transcriptional induction kinetics from the
The Lancet Infectious Diseases, 2009
FEMS Microbiology Letters, 1998
Pseudomonas putida grows on benzylamine as a sole source of carbon/energy and nitrogen. Synthesis... more Pseudomonas putida grows on benzylamine as a sole source of carbon/energy and nitrogen. Synthesis of an inducible benzylamine dehydrogenase (BMDH) depends on the specific RNA polymerase sigma factor c SR and is subject to carbon source-dependent inhibition. The presence of TOL plasmid pWW0 harboring the genetic information for the catabolism of toluene exerts strong inhibition of induction of BMDH activity.
Molecular & general genetics : MGG, 1989
The role of the Klebsiella pneumoniae PII protein (encoded by glnB) in nitrogen regulation has be... more The role of the Klebsiella pneumoniae PII protein (encoded by glnB) in nitrogen regulation has been studied using two classes of glnB mutants. In Class I mutants PII appears not to be uridylylated in nitrogen-limiting conditions and in Class II mutants PII is not synthesised. The effects of these mutations on expression from nitrogen-regulated promoters indicate that PII is not absolutely required for nitrogen control. Furthermore the uridylylated form of PII (PII-UMP) plays a significant role in the response to changes in nitrogen status by counteracting the effect of PII on NtrB-mediated dephosphorylation of NtrC. PII is not involved in the nif-specific response to changes in nitrogen status mediated by NifL.
Research in microbiology
IIANtr, encoded within the rpoN operons of many Gram-negative bacteria, is a homologue of a class... more IIANtr, encoded within the rpoN operons of many Gram-negative bacteria, is a homologue of a class of phosphoryl transfer proteins of the phosphoenolpyruvate: sugar phosphotransferase system. We have used a xylS operon-lacZ fusion from the TOL plasmid of Pseudomonas putida to show that IIANtr influences sigma 54-dependent transcription when the xylS operon is expressed in Escherichia coli. Loss of IIANtr influences, but does not abolish cyclic AMP-independent carbon catabolite repression.
Research in Microbiology, 1996
IIANtr, encoded within the rpoN operons of many Gram-negative bacteria, is a homologue of a class... more IIANtr, encoded within the rpoN operons of many Gram-negative bacteria, is a homologue of a class of phosphoryl transfer proteins of the phosphoenolpyruvate: sugar phosphotransferase system. We have used a xylS operon-lacZ fusion from the TOL plasmid of Pseudomonas putida to show that IIANtr influences σ54-dependent transcription when the xylS operon is expressed in Escherichia coli. Loss of IIANtr influences,
Journal of …, 1995
Regulation of the xyl gene operons of the Pseudomonas putida TOL plasmid is mediated by the produ... more Regulation of the xyl gene operons of the Pseudomonas putida TOL plasmid is mediated by the products of the downstream clustered and divergently oriented xylR and xylS regulatory genes. The xylR-xylS intergenic region contains the xylR and xylS promoters Pr and Ps, respectively. A binding site for the XylR activator protein is located upstream of Ps and overlapping Pr. DNase I footprint experiments showed that one of these sites, which overlaps the recognition site for XylR activator, as well as an AT-rich region comprising the Ps promoter consensus were protected by integration host factor (IHF). IHF was found to act negatively in the in vivo activation of the Ps promoter, since the activity of a Ps promoter::lacZ fusion was elevated in an Escherichia coli mutant lacking IHF. In contrast, no alteration in the synthesis of XylR protein in the E. coli IHF-deficient mutant was detected.
Nucleic acids research, 1992
The xyIR and xylS genes, which encode the positive regulators of the TOL plasmid catabolic pathwa... more The xyIR and xylS genes, which encode the positive regulators of the TOL plasmid catabolic pathways, are adjacent genes on the TOL plasmid and are transcribed from divergent promoters. Transcription from the xylS gene promoter, Ps, is positively regulated by effectoractivated XyIR protein and requires the specific RNA polymerase sigma54 subunit (RpoN). Deletions and point mutations in the Ps upstream region localized the site of XyIR interaction to the region between-133 bp and-207 bp (with respect to the transcriptional start of the xylS messenger), which contains an inverted sequence repeat largely homologous to the motif recognised by XyIR in the XyIR-regulated 'upper' catabolic pathway promoter, Pu. Gel retardation experiments showed binding of IHF to the Ps promoter region. Corresponding sequences showing good homology to the IHF-binding consensus were identified close to the Ps Promoter (between-35 bp and-47 bp, Ps proximal site) and further upstream overlapping the XyIR recognition sequence (Ps distal site). In the latter case IHF recognition motifs were found well conserved on both strands at nearly the same position (between-140 bp and-152 bp on the upper and between-141 bp and-153 bp on the lower strand). Expression from Ps, either under inducing or noninducing conditions, was, however, only slightly influenced by the absence of IHF in an IHF-deficient mutant and thus activation of Ps, like that of other sigma54-dependent promoters which are rich in Ts, does not absolutely require IHF protein.
Journal of …, 1994
JOURNAL OF BACrERIOLOGY, May 1994, p. 2517-2524 0021-9193/94/$04.00+0 Copyright © 1994, American ... more JOURNAL OF BACrERIOLOGY, May 1994, p. 2517-2524 0021-9193/94/$04.00+0 Copyright © 1994, American Society for Microbiology ... Transcriptional Induction Kinetics from the Promoters of the ... Catabolic Pathways of TOL Plasmid pWWO of Pseudomonas
Journal of …, 1994
TOL plasmid-encoded degradation of benzyl alcohol by Pseudomonas putida is inhibited by glucose a... more TOL plasmid-encoded degradation of benzyl alcohol by Pseudomonas putida is inhibited by glucose and other compounds relatedto the main carbohydrate metabolismin Pseudomonas species. We report here that this effect is exerted at the level of expression of the xyl ...
Molecular …, 1990
Stimulation of transcription from the Pseudomonas TOL plasmid xylS gene promoter (Ps) and the upp... more Stimulation of transcription from the Pseudomonas TOL plasmid xylS gene promoter (Ps) and the upperpathway operon promoter (Pu) is dependent on the positive regulator protein XylR activated by an effector molecule such as 3-cholorotoluene, and on RpoN, an RNA polymerase sigma factor. Mutational analysis of the Ps and Pu promoters showed that upstream activator sequences located between-110 and-218bp upstream of the main transcription initiation point are required for regulated expression from these promoters. A search for homologous nucleotide sequences in the-110to-218bp region in Pu and Ps revealed conserved sequences that may act as putative recognition sequences for the XylR protein. Ps and Pu exhibit another well-conserved region at around 50 bp, which is homologous to corresponding sites in other RpoN-dependent promoters and may constitute a binding site for integration host factor (IHF)
Archives of Microbiology, 1985
Depending on the growth conditions Paracoccus denitrificans synthesizes two different carriers me... more Depending on the growth conditions Paracoccus denitrificans synthesizes two different carriers mediating uptake of methylamine. When used as a nitrogen source, methylamine is transported via a NH2 carrier, and its transport is inhibited by NH + but not by ethylamine. When used as a carbon source, methylamine is transported by a specific alkylamine carrier, and its transport is inhibited by ethylamine but not by NH~. The NH~-carrier is under nitrogen control, the alkylamine carrier under carbon control.
Integration host factor (IHF) is a DNA-binding and-bending protein that has been found in a numbe... more Integration host factor (IHF) is a DNA-binding and-bending protein that has been found in a number of gram-negative bacteria. Here we describe the cloning, sequencing, and functional analysis of the genes coding for the two subunits of IHF from Pseudomonas putida. Both the ihfA and ihfB genes of P. putida code for 100-amino-acid-residue polypeptides that are 1 and 6 residues longer than the Escherichia coli IHF subunits, respectively. The P. putida ihfA and ihfB genes can effectively complement E. coli ihf mutants, suggesting that the P. putida IHF subunits can form functional heterodimers with the IHF subunits of E. coli. Analysis of the amino acid differences between the E. coli and P. putida protein sequences suggests that in the evolution of IHF, amino acid changes were mainly restricted to the N-terminal domains and to the extreme C termini. These changes do not interfere with dimer formation or with DNA recognition. We constructed a P. putida mutant strain carrying an ihfA gene knockout and demonstrated that IHF is essential for the expression of the P U promoter of the xyl operon of the upper pathway of toluene degradation. It was further shown that the ihfA P. putida mutant strain carrying the TOL plasmid was defective in the degradation of the aromatic model compound benzyl alcohol, proving the unique role of IHF in xyl operon promoter regulation.
Seventeen genes specifically required for nitrogen fixation are clustered on the chromosome of Kl... more Seventeen genes specifically required for nitrogen fixation are clustered on the chromosome of Klebsiella pneumoniae and form a complex regulon that is organized into eight transcriptional units. The nif promoters are representative of a new class of promoter, the members of which lack the consensus sequences normally found in prokaryotic promoters, nif gene transcription is positively controlled and requires: (1) the ntrA gene product, which replaces the rpoD -encoded sigma subunit of RNA polymerase to allow recognition of nif promoter sequences; and (2) the product of either the nitrogen regulation gene ntrC or the specific nif regulatory gene, nifA , which are both transcriptional activators. Most nif promoters require an upstream activator sequence (UAS) for nifA -mediated activation. The UAS acts independently of orientation and can function when placed 2 kilobases upstream from the transcription start site. Current evidence suggests that activation requires an interaction between proteins bound at the UAS and at the downstream nif promoter consensus, possibly via a loop in the DNA structure. Transcription of nif is modulated by the ntrB and nifL gene products. Both proteins can ‘sense’ environmental changes: ntrB prevents activation by ntrC in response to excess nitrogen whereas nifL prevents activation by nifA in response to fixed nitrogen and oxygen. The C-terminal end of ntrB shows clear homology at the amino acid level with a number of diverse control proteins involved in regulation or sensory transduction. Each member of this family interacts with another protein component showing homology to the N-terminal sequence of ntrC , but not to nifA . The significance of these protein homologies is discussed.
An open-reading frame (ORF111) upstream of the glutamine synthetase I structural gene (glnA) in R... more An open-reading frame (ORF111) upstream of the glutamine synthetase I structural gene (glnA) in Rhizobium leguminosarum biovar viceae encodes a protein which is highly homologous to the Ptt protein (encoded by glnB) of enteric bacteria. ORFlll was cloned in a number of different plasmid vectors and shown to complement a K. pneumoniae glnB mutant. We propose that ORFlll encodes the PIt protein of R. leguminosarum and that it should be designated glnB. 2. INTRODUCTION The main pathway for nitrogen assimilation in the Rhizobiaceae is that provided by the coordinated activities of glutamine synthetase (GS) and glutamate synthase [1]. The Rhizobiaceae, which include the genera Rhizobium, Bradyrhizobium and Agrobacterium are distinct from other bacteria in that they have two isoforms of GS [2]. The form termed GSI is structurally and enzymatically typi
SummaryThe role of theKlebsiella pneumoniae PII protein (encoded byglnB) in nitrogen regulation h... more SummaryThe role of theKlebsiella pneumoniae PII protein (encoded byglnB) in nitrogen regulation has been studied using two classes ofglnB mutants. In Class I mutants PII appears not to be uridylylated in nitrogen-limiting conditions and in Class II mutants PII is not synthesised. The effects of these mutations on expression from nitrogen-regulated promoters indicate that PII is not absolutely required for nitrogen control. Furthermore the uridylylated form of PII(PII-UMP) plays a significant role in the response to changes in nitrogen status by counteracting the effect of PII on NtrB-mediated dephosphorylation of NtrC. PII is not involved in thenif-specific response to changes in nitrogen status mediated by NifL.
Journal of …, 1998
The xylR and xylS genes are divergent and control transcription of the TOL plasmid catabolic path... more The xylR and xylS genes are divergent and control transcription of the TOL plasmid catabolic pathways for toluene metabolism. Four promoters are found in the 300-bp intergenic region: Pr1 and Pr2 are constitutive 70 -dependent tandem promoters that drive expression of ...
metabolism of aromatics. plasmid pWW0 of Pseudomonas putida for promoters of the catabolic pathwa... more metabolism of aromatics. plasmid pWW0 of Pseudomonas putida for promoters of the catabolic pathways of TOL Transcriptional induction kinetics from the
The Lancet Infectious Diseases, 2009
FEMS Microbiology Letters, 1998
Pseudomonas putida grows on benzylamine as a sole source of carbon/energy and nitrogen. Synthesis... more Pseudomonas putida grows on benzylamine as a sole source of carbon/energy and nitrogen. Synthesis of an inducible benzylamine dehydrogenase (BMDH) depends on the specific RNA polymerase sigma factor c SR and is subject to carbon source-dependent inhibition. The presence of TOL plasmid pWW0 harboring the genetic information for the catabolism of toluene exerts strong inhibition of induction of BMDH activity.
Molecular & general genetics : MGG, 1989
The role of the Klebsiella pneumoniae PII protein (encoded by glnB) in nitrogen regulation has be... more The role of the Klebsiella pneumoniae PII protein (encoded by glnB) in nitrogen regulation has been studied using two classes of glnB mutants. In Class I mutants PII appears not to be uridylylated in nitrogen-limiting conditions and in Class II mutants PII is not synthesised. The effects of these mutations on expression from nitrogen-regulated promoters indicate that PII is not absolutely required for nitrogen control. Furthermore the uridylylated form of PII (PII-UMP) plays a significant role in the response to changes in nitrogen status by counteracting the effect of PII on NtrB-mediated dephosphorylation of NtrC. PII is not involved in the nif-specific response to changes in nitrogen status mediated by NifL.
Research in microbiology
IIANtr, encoded within the rpoN operons of many Gram-negative bacteria, is a homologue of a class... more IIANtr, encoded within the rpoN operons of many Gram-negative bacteria, is a homologue of a class of phosphoryl transfer proteins of the phosphoenolpyruvate: sugar phosphotransferase system. We have used a xylS operon-lacZ fusion from the TOL plasmid of Pseudomonas putida to show that IIANtr influences sigma 54-dependent transcription when the xylS operon is expressed in Escherichia coli. Loss of IIANtr influences, but does not abolish cyclic AMP-independent carbon catabolite repression.
Research in Microbiology, 1996
IIANtr, encoded within the rpoN operons of many Gram-negative bacteria, is a homologue of a class... more IIANtr, encoded within the rpoN operons of many Gram-negative bacteria, is a homologue of a class of phosphoryl transfer proteins of the phosphoenolpyruvate: sugar phosphotransferase system. We have used a xylS operon-lacZ fusion from the TOL plasmid of Pseudomonas putida to show that IIANtr influences σ54-dependent transcription when the xylS operon is expressed in Escherichia coli. Loss of IIANtr influences,
Journal of …, 1995
Regulation of the xyl gene operons of the Pseudomonas putida TOL plasmid is mediated by the produ... more Regulation of the xyl gene operons of the Pseudomonas putida TOL plasmid is mediated by the products of the downstream clustered and divergently oriented xylR and xylS regulatory genes. The xylR-xylS intergenic region contains the xylR and xylS promoters Pr and Ps, respectively. A binding site for the XylR activator protein is located upstream of Ps and overlapping Pr. DNase I footprint experiments showed that one of these sites, which overlaps the recognition site for XylR activator, as well as an AT-rich region comprising the Ps promoter consensus were protected by integration host factor (IHF). IHF was found to act negatively in the in vivo activation of the Ps promoter, since the activity of a Ps promoter::lacZ fusion was elevated in an Escherichia coli mutant lacking IHF. In contrast, no alteration in the synthesis of XylR protein in the E. coli IHF-deficient mutant was detected.
Nucleic acids research, 1992
The xyIR and xylS genes, which encode the positive regulators of the TOL plasmid catabolic pathwa... more The xyIR and xylS genes, which encode the positive regulators of the TOL plasmid catabolic pathways, are adjacent genes on the TOL plasmid and are transcribed from divergent promoters. Transcription from the xylS gene promoter, Ps, is positively regulated by effectoractivated XyIR protein and requires the specific RNA polymerase sigma54 subunit (RpoN). Deletions and point mutations in the Ps upstream region localized the site of XyIR interaction to the region between-133 bp and-207 bp (with respect to the transcriptional start of the xylS messenger), which contains an inverted sequence repeat largely homologous to the motif recognised by XyIR in the XyIR-regulated 'upper' catabolic pathway promoter, Pu. Gel retardation experiments showed binding of IHF to the Ps promoter region. Corresponding sequences showing good homology to the IHF-binding consensus were identified close to the Ps Promoter (between-35 bp and-47 bp, Ps proximal site) and further upstream overlapping the XyIR recognition sequence (Ps distal site). In the latter case IHF recognition motifs were found well conserved on both strands at nearly the same position (between-140 bp and-152 bp on the upper and between-141 bp and-153 bp on the lower strand). Expression from Ps, either under inducing or noninducing conditions, was, however, only slightly influenced by the absence of IHF in an IHF-deficient mutant and thus activation of Ps, like that of other sigma54-dependent promoters which are rich in Ts, does not absolutely require IHF protein.
Journal of …, 1994
JOURNAL OF BACrERIOLOGY, May 1994, p. 2517-2524 0021-9193/94/$04.00+0 Copyright © 1994, American ... more JOURNAL OF BACrERIOLOGY, May 1994, p. 2517-2524 0021-9193/94/$04.00+0 Copyright © 1994, American Society for Microbiology ... Transcriptional Induction Kinetics from the Promoters of the ... Catabolic Pathways of TOL Plasmid pWWO of Pseudomonas
Journal of …, 1994
TOL plasmid-encoded degradation of benzyl alcohol by Pseudomonas putida is inhibited by glucose a... more TOL plasmid-encoded degradation of benzyl alcohol by Pseudomonas putida is inhibited by glucose and other compounds relatedto the main carbohydrate metabolismin Pseudomonas species. We report here that this effect is exerted at the level of expression of the xyl ...
Molecular …, 1990
Stimulation of transcription from the Pseudomonas TOL plasmid xylS gene promoter (Ps) and the upp... more Stimulation of transcription from the Pseudomonas TOL plasmid xylS gene promoter (Ps) and the upperpathway operon promoter (Pu) is dependent on the positive regulator protein XylR activated by an effector molecule such as 3-cholorotoluene, and on RpoN, an RNA polymerase sigma factor. Mutational analysis of the Ps and Pu promoters showed that upstream activator sequences located between-110 and-218bp upstream of the main transcription initiation point are required for regulated expression from these promoters. A search for homologous nucleotide sequences in the-110to-218bp region in Pu and Ps revealed conserved sequences that may act as putative recognition sequences for the XylR protein. Ps and Pu exhibit another well-conserved region at around 50 bp, which is homologous to corresponding sites in other RpoN-dependent promoters and may constitute a binding site for integration host factor (IHF)
Archives of Microbiology, 1985
Depending on the growth conditions Paracoccus denitrificans synthesizes two different carriers me... more Depending on the growth conditions Paracoccus denitrificans synthesizes two different carriers mediating uptake of methylamine. When used as a nitrogen source, methylamine is transported via a NH2 carrier, and its transport is inhibited by NH + but not by ethylamine. When used as a carbon source, methylamine is transported by a specific alkylamine carrier, and its transport is inhibited by ethylamine but not by NH~. The NH~-carrier is under nitrogen control, the alkylamine carrier under carbon control.
Integration host factor (IHF) is a DNA-binding and-bending protein that has been found in a numbe... more Integration host factor (IHF) is a DNA-binding and-bending protein that has been found in a number of gram-negative bacteria. Here we describe the cloning, sequencing, and functional analysis of the genes coding for the two subunits of IHF from Pseudomonas putida. Both the ihfA and ihfB genes of P. putida code for 100-amino-acid-residue polypeptides that are 1 and 6 residues longer than the Escherichia coli IHF subunits, respectively. The P. putida ihfA and ihfB genes can effectively complement E. coli ihf mutants, suggesting that the P. putida IHF subunits can form functional heterodimers with the IHF subunits of E. coli. Analysis of the amino acid differences between the E. coli and P. putida protein sequences suggests that in the evolution of IHF, amino acid changes were mainly restricted to the N-terminal domains and to the extreme C termini. These changes do not interfere with dimer formation or with DNA recognition. We constructed a P. putida mutant strain carrying an ihfA gene knockout and demonstrated that IHF is essential for the expression of the P U promoter of the xyl operon of the upper pathway of toluene degradation. It was further shown that the ihfA P. putida mutant strain carrying the TOL plasmid was defective in the degradation of the aromatic model compound benzyl alcohol, proving the unique role of IHF in xyl operon promoter regulation.
Seventeen genes specifically required for nitrogen fixation are clustered on the chromosome of Kl... more Seventeen genes specifically required for nitrogen fixation are clustered on the chromosome of Klebsiella pneumoniae and form a complex regulon that is organized into eight transcriptional units. The nif promoters are representative of a new class of promoter, the members of which lack the consensus sequences normally found in prokaryotic promoters, nif gene transcription is positively controlled and requires: (1) the ntrA gene product, which replaces the rpoD -encoded sigma subunit of RNA polymerase to allow recognition of nif promoter sequences; and (2) the product of either the nitrogen regulation gene ntrC or the specific nif regulatory gene, nifA , which are both transcriptional activators. Most nif promoters require an upstream activator sequence (UAS) for nifA -mediated activation. The UAS acts independently of orientation and can function when placed 2 kilobases upstream from the transcription start site. Current evidence suggests that activation requires an interaction between proteins bound at the UAS and at the downstream nif promoter consensus, possibly via a loop in the DNA structure. Transcription of nif is modulated by the ntrB and nifL gene products. Both proteins can ‘sense’ environmental changes: ntrB prevents activation by ntrC in response to excess nitrogen whereas nifL prevents activation by nifA in response to fixed nitrogen and oxygen. The C-terminal end of ntrB shows clear homology at the amino acid level with a number of diverse control proteins involved in regulation or sensory transduction. Each member of this family interacts with another protein component showing homology to the N-terminal sequence of ntrC , but not to nifA . The significance of these protein homologies is discussed.
An open-reading frame (ORF111) upstream of the glutamine synthetase I structural gene (glnA) in R... more An open-reading frame (ORF111) upstream of the glutamine synthetase I structural gene (glnA) in Rhizobium leguminosarum biovar viceae encodes a protein which is highly homologous to the Ptt protein (encoded by glnB) of enteric bacteria. ORFlll was cloned in a number of different plasmid vectors and shown to complement a K. pneumoniae glnB mutant. We propose that ORFlll encodes the PIt protein of R. leguminosarum and that it should be designated glnB. 2. INTRODUCTION The main pathway for nitrogen assimilation in the Rhizobiaceae is that provided by the coordinated activities of glutamine synthetase (GS) and glutamate synthase [1]. The Rhizobiaceae, which include the genera Rhizobium, Bradyrhizobium and Agrobacterium are distinct from other bacteria in that they have two isoforms of GS [2]. The form termed GSI is structurally and enzymatically typi
SummaryThe role of theKlebsiella pneumoniae PII protein (encoded byglnB) in nitrogen regulation h... more SummaryThe role of theKlebsiella pneumoniae PII protein (encoded byglnB) in nitrogen regulation has been studied using two classes ofglnB mutants. In Class I mutants PII appears not to be uridylylated in nitrogen-limiting conditions and in Class II mutants PII is not synthesised. The effects of these mutations on expression from nitrogen-regulated promoters indicate that PII is not absolutely required for nitrogen control. Furthermore the uridylylated form of PII(PII-UMP) plays a significant role in the response to changes in nitrogen status by counteracting the effect of PII on NtrB-mediated dephosphorylation of NtrC. PII is not involved in thenif-specific response to changes in nitrogen status mediated by NifL.
Journal of …, 1998
The xylR and xylS genes are divergent and control transcription of the TOL plasmid catabolic path... more The xylR and xylS genes are divergent and control transcription of the TOL plasmid catabolic pathways for toluene metabolism. Four promoters are found in the 300-bp intergenic region: Pr1 and Pr2 are constitutive 70 -dependent tandem promoters that drive expression of ...