Liu Rigo | Universidade Federal do Paraná (original) (raw)

Papers by Liu Rigo

Current Plant Science and Biotechnology in Agriculture

Research in Microbiology, 2004

The Azospirillum brasilense transcription regulator NifA and the nitrogen-status signaling protei... more The Azospirillum brasilense transcription regulator NifA and the nitrogen-status signaling proteins GlnB, GlnZ and GlnK were expressed in Escherichia coli and analyzed for their ability to activate nif gene expression. When expressed separately, none of the proteins were able to activate nifH promoter expression in any tested conditions; in contrast, nifH expression was observed in cells grown in the absence of ammonium and oxygen and when expressing simultaneously NifA and GlnB proteins, but not when expressing NifA and GlnZ or GlnK. Our results show that the GlnB protein is required for transcription activation by Azospirillum brasilense NifA and it cannot be replaced by GlnZ or GlnK.

Journal of Bacteriology, 2012

Herbaspirillum lusitanum strain P6-12 (DSM 17154) is, so far, the only species of Herbaspirillum ... more Herbaspirillum lusitanum strain P6-12 (DSM 17154) is, so far, the only species of Herbaspirillum isolated from plant root nodules. Here we report a draft genome sequence of this organism.

BMC Microbiology, 2011

Background The PII protein family comprises homotrimeric proteins which act as transducers of the... more Background The PII protein family comprises homotrimeric proteins which act as transducers of the cellular nitrogen and carbon status in prokaryotes and plants. In Herbaspirillum seropedicae, two PII-like proteins (GlnB and GlnK), encoded by the genes glnB and glnK, were identified. The glnB gene is monocistronic and its expression is constitutive, while glnK is located in the nlmAglnKamtB operon and is expressed under nitrogen-limiting conditions. Results In order to determine the involvement of the H. seropedicae glnB and glnK gene products in nitrogen fixation, a series of mutant strains were constructed and characterized. The glnK - mutants were deficient in nitrogen fixation and they were complemented by plasmids expressing the GlnK protein or an N-truncated form of NifA. The nitrogenase post-translational control by ammonium was studied and the results showed that the glnK mutant is partially defective in nitrogenase inactivation upon addition of ammonium while the glnB mutant...

Nitrogen Fixation with Non-Legumes, 1989

Several ethylenediamine (EDA)-resistant mutants of A. brasilense were isolated and found to depre... more Several ethylenediamine (EDA)-resistant mutants of A. brasilense were isolated and found to depress nitrogenase in the presence of high NH 4 + concentrations. These mutants were defective in NH 4 + uptake and capable of excreting NH4 + in N-free semi-solid medium. A gene library of H. seropedicae strain HZ78 was constructed in cosmid pVK102. A recombinant plasmid pEMS1, capable of complementing a nifA - mutant of A. brasilense, was isolated and is being characterized.

PLoS genetics, 2011

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazot... more The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme--GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected b...

The FEBS Journal, 2016

Herbaspirillum seropedicae is a diazotrophic β-Proteobacterium found endophytically associated wi... more Herbaspirillum seropedicae is a diazotrophic β-Proteobacterium found endophytically associated with gramineae (Poaceae or graminaceous plants) such as rice, sorghum and sugar cane. In this work we show that nitrate-dependent growth in this organism is regulated by the master nitrogen regulatory two-component system NtrB-NtrC, and by NtrY-NtrX, which functions to specifically regulate nitrate metabolism. NtrY is a histidine kinase sensor protein predicted to be associated with the membrane and NtrX is the response regulator partner. The ntrYntrX genes are widely distributed in Proteobacteria. In α-Proteobacteria they are frequently located downstream from ntrBC, whereas in β-Proteobacteria these genes are located downstream from genes encoding an RNA methyltransferase and a proline-rich protein with unknown function. The NtrX protein of α-Proteobacteria has an AAA+ domain, absent in those from β-Proteobacteria. An ntrY mutant of H. seropedicae showed the wild-type nitrogen fixation phenotype, but the nitrate-dependent growth was abolished. Gene fusion assays indicated that NtrY is involved in the expression of genes coding for the assimilatory nitrate reductase as well as the nitrate-responsive two-component system NarX-NarL (narK and narX promoters, respectively). The purified NtrX protein was capable of binding the narK and narX promoters, and the binding site at the narX promoter for the NtrX protein was determined by DNA footprinting. In silico analyses revealed similar sequences in other promoter regions of H. seropedicae that are related to nitrate assimilation, supporting the role of the NtrY-NtrX system in regulating nitrate metabolism in H. seropedicae.

Canadian Journal of Microbiology, 1991

Several spontaneous ethylenediamine-resistant mutants of Azospirillum brasilense strain FP2 (Sp7,... more Several spontaneous ethylenediamine-resistant mutants of Azospirillum brasilense strain FP2 (Sp7, NalR SmR) were isolated. Four mutants, HM053, HM14, HM26, and HM210, were found to fix nitrogen constitutively in the presence of high concentration of NH4+ and to excrete NH4+ derived from nitrogen fixation. They also showed lower rates of NH4+ uptake than the wild-type strain, FP2. All of the mutants were prototrophic for glutamine or glutamate. Their glutamate synthase and glutamate dehydrogenase activities were similar to those of the wild-type strain. However, they presented different patterns of glutamine synthetase activity. Mutant HM14 showed low levels of normally regulated glutamine synthetase activity, while the other mutants showed low levels (HM053) or wild-type levels (HM26 and HM210) of constitutively adenylylated glutamine synthetase activity. The mutants are probably defective in the adenylylation system. Key words: Azospirillum brasilense, ammonium excretion, ethylenediamine resistance, glutamine synthetase.

Can J Microbiol, 1994

The pathway for the breakdown of L-rhamnose by the yeast Piclzia stipitis NRC 5568 was shown to i... more The pathway for the breakdown of L-rhamnose by the yeast Piclzia stipitis NRC 5568 was shown to involve nonphosphorylated intermediates and to produce pyruvate and L-lactaldehyde. The activities of the enzymes and the nature of several intermediates were determined. The enzymes involved are L-rhamnose dehydrogenase, L-rhamnonate dehydratase, and 2-keto-3-deoxy-~-1.ha1nnonate aldolase. This pathway was found to be inducible by L-rhamnose and repressed by D-glucose. These enzymes were also present in a mutant of P. stipitis (PR I) resistant to catabolite repression and in Debar?lonlyces polymorph~ts 1747. Cell-free extracts of P. stipitis and D. ~~o l y r n o~h~~~ grown in L-rhamnose as sole carbon source were found to contain NADf-dependent aldehyde dehydrogenase activities.

Journal of Bacteriology

The activity of a truncated form of Herbaspirillum seropedicae NifA in different genetic backgrou... more The activity of a truncated form of Herbaspirillum seropedicae NifA in different genetic backgrounds showed that its regulatory domain is involved in nitrogen control but not in O 2 sensitivity or Fe dependence. The model for nitrogen control involving PII could thus apply to the proteobacteria at large. NifA may have a role in controlling ADP-ribosylation of nitrogenase in Azospirillum brasilense.

Journal of bacteriology, 1989

The pathway for L-arabinose metabolism in Herbaspirillum seropedicae was shown to involve nonphos... more The pathway for L-arabinose metabolism in Herbaspirillum seropedicae was shown to involve nonphosphorylated intermediates and to produce alpha-ketoglutarate. The activities of the enzymes and the natures of several intermediates were determined. The pathway was inducible by L-arabinose, and two key enzymes, L-arabinose dehydrogenase and 2-keto-glutarate semialdehyde dehydrogenase, were present in all strains of H. seropedicae tested.

Archives of …, 2007

Random mutagenesis using transposons with promoterless reporter genes has been widely used to exa... more Random mutagenesis using transposons with promoterless reporter genes has been widely used to examine differential gene expression patterns in bacteria. Using this approach, we have identified 26 genes of the endophytic nitrogen-fixing bacterium Herbaspirillum seropedicae regulated in response to ammonium content in the growth medium. These include nine genes involved in the transport of nitrogen compounds, such as the high-affinity ammonium transporter AmtB, and uptake systems for alternative nitrogen sources; nine genes coding for proteins responsible for restoring intracellular ammonium levels through enzymatic reactions, such as nitrogenase, amidase, and arginase; and a third group includes metabolic switch genes, coding for sensor kinases or transcription regulation factors, whose role in metabolism was previously unknown. Also, four genes identified were of unknown function. This paper describes their involvement in response to ammonium limitation. The results provide a preliminary profile of the metabolic response of Herbaspirillum seropedicae to ammonium stress.

PLoS genetics, 2011

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazot... more The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme--GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected b...

Environmental Microbiology, 2016

Herbaspirillum seropedicae is a nitrogen-fixing β-proteobacterium that associates with roots of g... more Herbaspirillum seropedicae is a nitrogen-fixing β-proteobacterium that associates with roots of gramineous plants. In silico analyses revealed that H. seropedicae genome has genes encoding a putative respiratory (NAR) and an assimilatory nitrate reductase (NAS). To date, little is known about nitrate metabolism in H. seropedicae, and, as this bacterium cannot respire nitrate, the function of NAR remains unknown. This study aimed to investigate the function of NAR in H. seropedicae and how it metabolizes nitrate in a low aerated-condition. RNA-seq transcriptional profiling in the presence of nitrate allowed us to pinpoint genes important for nitrate metabolism in H. seropedicae, including nitrate transporters and regulatory proteins. Additionally, both RNA-seq data and physiological characterization of a mutant in the catalytic subunit of NAR (narG mutant) showed that NAR is not required for nitrate assimilation but is required for: (i) production of high levels of nitrite, (ii) production of NO, and (iii) dissipation of redox power, which in turn lead to carbon consumption. In addition, wheat plants showed an increase in shoot dry weight only when inoculated with H. seropedicae wild type, but not with the narG mutant, suggesting that NAR is important to H. seropedicae-wheat interaction. This article is protected by copyright. All rights reserved.

FEMS Microbiology Ecology

AbstractA clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of t... more AbstractA clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of the Brazilian Atlantic Forest soil. The DNA insert of LP001 was fully sequenced, and 38 ORFs were identified. Comparison of ORFs, %G + C content and gene organization with sequenced bacterial genomes suggested that the fosmid DNA insert belongs to an organism of the Acidobacteria phylum. Protein domain analysis and inactivation by transposon insertion showed that the protein encoded by ORF29 was responsible for the lipase activity and was named LipAAc. The purified LipAAc lipase was capable of hydrolyzing a broad range of substrates, showing the highest activity against p‐nitrophenol (pNP) decanoate. The lipase was active over a pH range of 5.0–10.0 and was insensitive to divalent cations. LipAAc is moderately thermostable with optimum temperature between 50 and 60 °C and was thermally activated (80% activity increase) after 1 h incubation at 50 °C. Phylogenetic analysis suggested that th...

Biochimica et biophysica acta, Jan 14, 1976

Growth of Pullularia pullulans on L-rhamnose induces formation of L-rhamnofuranose dehydrogenase,... more Growth of Pullularia pullulans on L-rhamnose induces formation of L-rhamnofuranose dehydrogenase, whichreversibly converts L-rhamnofuranose to L-rhamnono-gamma-lactone with the concomitant reduction of NAD, but not of NADP. The dehydrogenase was purified 100-fold by MnCl(2) treatment...

Memórias do Instituto Oswaldo Cruz, 2010

Thirty-eight strains of Shiga toxin-producing Escherichia coli (STEC) were characterised in terms... more Thirty-eight strains of Shiga toxin-producing Escherichia coli (STEC) were characterised in terms of biochemical properties, enterohaemolysin production and plasmid carriage. A wide variation in the biochemical properties was observed among the STEC, with 14 distinct biotypes identified. Biotype 1 was the most common, found in 29% of the strains. Enterohaemolysin production was detected in 29% of the strains. Most of the bacterial strains (95%) carried one or more plasmids and considerable heterogeneity in size and combinations was observed. Seven distinct plasmid profiles were identified. The most common profile, characterised by the presence of a single plasmid of ~90 kb, was found in 50% of these strains. These data indicate extensive diversity among STEC strains. No correlation was found among biotype, serotype, enterohaemolysin production and plasmid profile.

FEMS Microbiology Ecology, 2012

A clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of the Brazi... more A clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of the Brazilian Atlantic Forest soil. The DNA insert of LP001 was fully sequenced, and 38 ORFs were identified. Comparison of ORFs, % G + C content and gene organization with sequenced bacterial genomes suggested that the fosmid DNA insert belongs to an organism of the Acidobacteria phylum. Protein domain analysis and inactivation by transposon insertion showed that the protein encoded by ORF29 was responsible for the lipase activity and was named LipAAc. The purified LipAAc lipase was capable of hydrolyzing a broad range of substrates, showing the highest activity against p-nitrophenol (pNP) decanoate. The lipase was active over a pH range of 5.0 -10.0 and was insensitive to divalent cations. LipAAc is moderately thermostable with optimum temperature between 50 and 60°C and was thermally activated (80% activity increase) after 1 h incubation at 50°C. Phylogenetic analysis suggested that the LipAAc is a member of family I of bacterial lipases and clusters with other moderately thermostable lipases of this group. Comparisons of the DNA insert of fosmid LP001 with other acidobacterial genomes and sequence database suggest that lipAAc gene has a fungal origin and was acquired by horizontal transfer.

Environmental Microbiology Reports, 2011

Lipases are the most investigated class of enzymes in metagenomics. Phylogenetic classification o... more Lipases are the most investigated class of enzymes in metagenomics. Phylogenetic classification of bacterial lipases comprises eight families. Here we describe the construction and screening of three metagenomic libraries from Brazilian Atlantic Forest soil and identification of a new lipase family. The metagenomic libraries, MAF1, MAF2 and MAF3, contained 34 560, 29 280 and 36 288 clones respectively.

Canadian Journal of Microbiology, 1991

A genomic library of Herbaspirillum seropedicae was constructed and screened for the nifA gene by... more A genomic library of Herbaspirillum seropedicae was constructed and screened for the nifA gene by complementation of a nifA mutant of Azospirillum brasilense (FP10). A recombinant plasmid, pEMS1, capable of restoring acetylene reduction activity in the mutant FP10, was isolated and found to hybridize to the nifA gene of Klebsiella pneumoniae. The results suggest that nifA is involved in the regulation of nif genes in H. seropedicae.

Current Plant Science and Biotechnology in Agriculture

Research in Microbiology, 2004

The Azospirillum brasilense transcription regulator NifA and the nitrogen-status signaling protei... more The Azospirillum brasilense transcription regulator NifA and the nitrogen-status signaling proteins GlnB, GlnZ and GlnK were expressed in Escherichia coli and analyzed for their ability to activate nif gene expression. When expressed separately, none of the proteins were able to activate nifH promoter expression in any tested conditions; in contrast, nifH expression was observed in cells grown in the absence of ammonium and oxygen and when expressing simultaneously NifA and GlnB proteins, but not when expressing NifA and GlnZ or GlnK. Our results show that the GlnB protein is required for transcription activation by Azospirillum brasilense NifA and it cannot be replaced by GlnZ or GlnK.

Journal of Bacteriology, 2012

Herbaspirillum lusitanum strain P6-12 (DSM 17154) is, so far, the only species of Herbaspirillum ... more Herbaspirillum lusitanum strain P6-12 (DSM 17154) is, so far, the only species of Herbaspirillum isolated from plant root nodules. Here we report a draft genome sequence of this organism.

BMC Microbiology, 2011

Background The PII protein family comprises homotrimeric proteins which act as transducers of the... more Background The PII protein family comprises homotrimeric proteins which act as transducers of the cellular nitrogen and carbon status in prokaryotes and plants. In Herbaspirillum seropedicae, two PII-like proteins (GlnB and GlnK), encoded by the genes glnB and glnK, were identified. The glnB gene is monocistronic and its expression is constitutive, while glnK is located in the nlmAglnKamtB operon and is expressed under nitrogen-limiting conditions. Results In order to determine the involvement of the H. seropedicae glnB and glnK gene products in nitrogen fixation, a series of mutant strains were constructed and characterized. The glnK - mutants were deficient in nitrogen fixation and they were complemented by plasmids expressing the GlnK protein or an N-truncated form of NifA. The nitrogenase post-translational control by ammonium was studied and the results showed that the glnK mutant is partially defective in nitrogenase inactivation upon addition of ammonium while the glnB mutant...

Nitrogen Fixation with Non-Legumes, 1989

Several ethylenediamine (EDA)-resistant mutants of A. brasilense were isolated and found to depre... more Several ethylenediamine (EDA)-resistant mutants of A. brasilense were isolated and found to depress nitrogenase in the presence of high NH 4 + concentrations. These mutants were defective in NH 4 + uptake and capable of excreting NH4 + in N-free semi-solid medium. A gene library of H. seropedicae strain HZ78 was constructed in cosmid pVK102. A recombinant plasmid pEMS1, capable of complementing a nifA - mutant of A. brasilense, was isolated and is being characterized.

PLoS genetics, 2011

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazot... more The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme--GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected b...

The FEBS Journal, 2016

Herbaspirillum seropedicae is a diazotrophic β-Proteobacterium found endophytically associated wi... more Herbaspirillum seropedicae is a diazotrophic β-Proteobacterium found endophytically associated with gramineae (Poaceae or graminaceous plants) such as rice, sorghum and sugar cane. In this work we show that nitrate-dependent growth in this organism is regulated by the master nitrogen regulatory two-component system NtrB-NtrC, and by NtrY-NtrX, which functions to specifically regulate nitrate metabolism. NtrY is a histidine kinase sensor protein predicted to be associated with the membrane and NtrX is the response regulator partner. The ntrYntrX genes are widely distributed in Proteobacteria. In α-Proteobacteria they are frequently located downstream from ntrBC, whereas in β-Proteobacteria these genes are located downstream from genes encoding an RNA methyltransferase and a proline-rich protein with unknown function. The NtrX protein of α-Proteobacteria has an AAA+ domain, absent in those from β-Proteobacteria. An ntrY mutant of H. seropedicae showed the wild-type nitrogen fixation phenotype, but the nitrate-dependent growth was abolished. Gene fusion assays indicated that NtrY is involved in the expression of genes coding for the assimilatory nitrate reductase as well as the nitrate-responsive two-component system NarX-NarL (narK and narX promoters, respectively). The purified NtrX protein was capable of binding the narK and narX promoters, and the binding site at the narX promoter for the NtrX protein was determined by DNA footprinting. In silico analyses revealed similar sequences in other promoter regions of H. seropedicae that are related to nitrate assimilation, supporting the role of the NtrY-NtrX system in regulating nitrate metabolism in H. seropedicae.

Canadian Journal of Microbiology, 1991

Several spontaneous ethylenediamine-resistant mutants of Azospirillum brasilense strain FP2 (Sp7,... more Several spontaneous ethylenediamine-resistant mutants of Azospirillum brasilense strain FP2 (Sp7, NalR SmR) were isolated. Four mutants, HM053, HM14, HM26, and HM210, were found to fix nitrogen constitutively in the presence of high concentration of NH4+ and to excrete NH4+ derived from nitrogen fixation. They also showed lower rates of NH4+ uptake than the wild-type strain, FP2. All of the mutants were prototrophic for glutamine or glutamate. Their glutamate synthase and glutamate dehydrogenase activities were similar to those of the wild-type strain. However, they presented different patterns of glutamine synthetase activity. Mutant HM14 showed low levels of normally regulated glutamine synthetase activity, while the other mutants showed low levels (HM053) or wild-type levels (HM26 and HM210) of constitutively adenylylated glutamine synthetase activity. The mutants are probably defective in the adenylylation system. Key words: Azospirillum brasilense, ammonium excretion, ethylenediamine resistance, glutamine synthetase.

Can J Microbiol, 1994

The pathway for the breakdown of L-rhamnose by the yeast Piclzia stipitis NRC 5568 was shown to i... more The pathway for the breakdown of L-rhamnose by the yeast Piclzia stipitis NRC 5568 was shown to involve nonphosphorylated intermediates and to produce pyruvate and L-lactaldehyde. The activities of the enzymes and the nature of several intermediates were determined. The enzymes involved are L-rhamnose dehydrogenase, L-rhamnonate dehydratase, and 2-keto-3-deoxy-~-1.ha1nnonate aldolase. This pathway was found to be inducible by L-rhamnose and repressed by D-glucose. These enzymes were also present in a mutant of P. stipitis (PR I) resistant to catabolite repression and in Debar?lonlyces polymorph~ts 1747. Cell-free extracts of P. stipitis and D. ~~o l y r n o~h~~~ grown in L-rhamnose as sole carbon source were found to contain NADf-dependent aldehyde dehydrogenase activities.

Journal of Bacteriology

The activity of a truncated form of Herbaspirillum seropedicae NifA in different genetic backgrou... more The activity of a truncated form of Herbaspirillum seropedicae NifA in different genetic backgrounds showed that its regulatory domain is involved in nitrogen control but not in O 2 sensitivity or Fe dependence. The model for nitrogen control involving PII could thus apply to the proteobacteria at large. NifA may have a role in controlling ADP-ribosylation of nitrogenase in Azospirillum brasilense.

Journal of bacteriology, 1989

The pathway for L-arabinose metabolism in Herbaspirillum seropedicae was shown to involve nonphos... more The pathway for L-arabinose metabolism in Herbaspirillum seropedicae was shown to involve nonphosphorylated intermediates and to produce alpha-ketoglutarate. The activities of the enzymes and the natures of several intermediates were determined. The pathway was inducible by L-arabinose, and two key enzymes, L-arabinose dehydrogenase and 2-keto-glutarate semialdehyde dehydrogenase, were present in all strains of H. seropedicae tested.

Archives of …, 2007

Random mutagenesis using transposons with promoterless reporter genes has been widely used to exa... more Random mutagenesis using transposons with promoterless reporter genes has been widely used to examine differential gene expression patterns in bacteria. Using this approach, we have identified 26 genes of the endophytic nitrogen-fixing bacterium Herbaspirillum seropedicae regulated in response to ammonium content in the growth medium. These include nine genes involved in the transport of nitrogen compounds, such as the high-affinity ammonium transporter AmtB, and uptake systems for alternative nitrogen sources; nine genes coding for proteins responsible for restoring intracellular ammonium levels through enzymatic reactions, such as nitrogenase, amidase, and arginase; and a third group includes metabolic switch genes, coding for sensor kinases or transcription regulation factors, whose role in metabolism was previously unknown. Also, four genes identified were of unknown function. This paper describes their involvement in response to ammonium limitation. The results provide a preliminary profile of the metabolic response of Herbaspirillum seropedicae to ammonium stress.

PLoS genetics, 2011

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazot... more The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme--GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected b...

Environmental Microbiology, 2016

Herbaspirillum seropedicae is a nitrogen-fixing β-proteobacterium that associates with roots of g... more Herbaspirillum seropedicae is a nitrogen-fixing β-proteobacterium that associates with roots of gramineous plants. In silico analyses revealed that H. seropedicae genome has genes encoding a putative respiratory (NAR) and an assimilatory nitrate reductase (NAS). To date, little is known about nitrate metabolism in H. seropedicae, and, as this bacterium cannot respire nitrate, the function of NAR remains unknown. This study aimed to investigate the function of NAR in H. seropedicae and how it metabolizes nitrate in a low aerated-condition. RNA-seq transcriptional profiling in the presence of nitrate allowed us to pinpoint genes important for nitrate metabolism in H. seropedicae, including nitrate transporters and regulatory proteins. Additionally, both RNA-seq data and physiological characterization of a mutant in the catalytic subunit of NAR (narG mutant) showed that NAR is not required for nitrate assimilation but is required for: (i) production of high levels of nitrite, (ii) production of NO, and (iii) dissipation of redox power, which in turn lead to carbon consumption. In addition, wheat plants showed an increase in shoot dry weight only when inoculated with H. seropedicae wild type, but not with the narG mutant, suggesting that NAR is important to H. seropedicae-wheat interaction. This article is protected by copyright. All rights reserved.

FEMS Microbiology Ecology

AbstractA clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of t... more AbstractA clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of the Brazilian Atlantic Forest soil. The DNA insert of LP001 was fully sequenced, and 38 ORFs were identified. Comparison of ORFs, %G + C content and gene organization with sequenced bacterial genomes suggested that the fosmid DNA insert belongs to an organism of the Acidobacteria phylum. Protein domain analysis and inactivation by transposon insertion showed that the protein encoded by ORF29 was responsible for the lipase activity and was named LipAAc. The purified LipAAc lipase was capable of hydrolyzing a broad range of substrates, showing the highest activity against p‐nitrophenol (pNP) decanoate. The lipase was active over a pH range of 5.0–10.0 and was insensitive to divalent cations. LipAAc is moderately thermostable with optimum temperature between 50 and 60 °C and was thermally activated (80% activity increase) after 1 h incubation at 50 °C. Phylogenetic analysis suggested that th...

Biochimica et biophysica acta, Jan 14, 1976

Growth of Pullularia pullulans on L-rhamnose induces formation of L-rhamnofuranose dehydrogenase,... more Growth of Pullularia pullulans on L-rhamnose induces formation of L-rhamnofuranose dehydrogenase, whichreversibly converts L-rhamnofuranose to L-rhamnono-gamma-lactone with the concomitant reduction of NAD, but not of NADP. The dehydrogenase was purified 100-fold by MnCl(2) treatment...

Memórias do Instituto Oswaldo Cruz, 2010

Thirty-eight strains of Shiga toxin-producing Escherichia coli (STEC) were characterised in terms... more Thirty-eight strains of Shiga toxin-producing Escherichia coli (STEC) were characterised in terms of biochemical properties, enterohaemolysin production and plasmid carriage. A wide variation in the biochemical properties was observed among the STEC, with 14 distinct biotypes identified. Biotype 1 was the most common, found in 29% of the strains. Enterohaemolysin production was detected in 29% of the strains. Most of the bacterial strains (95%) carried one or more plasmids and considerable heterogeneity in size and combinations was observed. Seven distinct plasmid profiles were identified. The most common profile, characterised by the presence of a single plasmid of ~90 kb, was found in 50% of these strains. These data indicate extensive diversity among STEC strains. No correlation was found among biotype, serotype, enterohaemolysin production and plasmid profile.

FEMS Microbiology Ecology, 2012

A clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of the Brazi... more A clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of the Brazilian Atlantic Forest soil. The DNA insert of LP001 was fully sequenced, and 38 ORFs were identified. Comparison of ORFs, % G + C content and gene organization with sequenced bacterial genomes suggested that the fosmid DNA insert belongs to an organism of the Acidobacteria phylum. Protein domain analysis and inactivation by transposon insertion showed that the protein encoded by ORF29 was responsible for the lipase activity and was named LipAAc. The purified LipAAc lipase was capable of hydrolyzing a broad range of substrates, showing the highest activity against p-nitrophenol (pNP) decanoate. The lipase was active over a pH range of 5.0 -10.0 and was insensitive to divalent cations. LipAAc is moderately thermostable with optimum temperature between 50 and 60°C and was thermally activated (80% activity increase) after 1 h incubation at 50°C. Phylogenetic analysis suggested that the LipAAc is a member of family I of bacterial lipases and clusters with other moderately thermostable lipases of this group. Comparisons of the DNA insert of fosmid LP001 with other acidobacterial genomes and sequence database suggest that lipAAc gene has a fungal origin and was acquired by horizontal transfer.

Environmental Microbiology Reports, 2011

Lipases are the most investigated class of enzymes in metagenomics. Phylogenetic classification o... more Lipases are the most investigated class of enzymes in metagenomics. Phylogenetic classification of bacterial lipases comprises eight families. Here we describe the construction and screening of three metagenomic libraries from Brazilian Atlantic Forest soil and identification of a new lipase family. The metagenomic libraries, MAF1, MAF2 and MAF3, contained 34 560, 29 280 and 36 288 clones respectively.

Canadian Journal of Microbiology, 1991

A genomic library of Herbaspirillum seropedicae was constructed and screened for the nifA gene by... more A genomic library of Herbaspirillum seropedicae was constructed and screened for the nifA gene by complementation of a nifA mutant of Azospirillum brasilense (FP10). A recombinant plasmid, pEMS1, capable of restoring acetylene reduction activity in the mutant FP10, was isolated and found to hybridize to the nifA gene of Klebsiella pneumoniae. The results suggest that nifA is involved in the regulation of nif genes in H. seropedicae.