Sequence and structural organization of a nifA-like gene and part of a nifB-like gene of Herbaspirillum seropedicae strain Z78

Souza, Emanuel Maltempi de; Funayama, S.; Rigo, L. U.; Yates, M. G.; Pedrosa, F. O.

doi:10.1099/00221287-137-7-1511

Cited by 45 publications

(40 citation statements)

References 42 publications

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“…It is possible that the sequences close to the 5h end of the NifA UAS play a regulatory role in NifA activation of the k24\k12 promoter. The sequence "50 bp upstream from the NifA UAS may constitute an IHF binding site (Souza et al, 1991a). Presumably the IHF could inhibit NifA binding and hence transcription in the absence of a NtrC UAS.…”

Section: Discussionmentioning

confidence: 99%

“…The PII protein probably participates in the regulation of NifA protein activity since a glnB null mutant of A. brasilense is Nif − even when the nifA gene is expressed constitutively (de Zamaroczy et al, 1993 ;Arsene et al, 1996). The promoter region of the nifA gene of H. seropedicae was found to contain sequences homologous to a k24\k12 type promoter, together with NifA and NtrC binding sites (Souza et al, 1991a), suggesting participation of these proteins in the expression of the nifA gene. The activity of the NifA protein from H. seropedicae is controlled by ammonium ions and oxygen (Souza et al, 1999).…”

Section: Introductionmentioning

confidence: 99%

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Expression of the nifA gene of Herbaspirillum seropedicae: role of the NtrC and NifA binding sites and of the −24/−12 promoter element

et al. 2000

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Expression of the nifA gene of Herbaspirillum seropedicae: role of the NtrC and NifA binding sites and of the −24/−12 promoter element

et al. 2000

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“…4), where the upstream regions are specially AϩT rich (Ϸ60%) with respect to coding regions (Ϸ47.5%). They also contain conserved Ϫ24͞Ϫ12 consensus sequences for 54 -dependent promoters (25) and two or three putative NifA-binding sites (26,27). Moreover, in the nifH upstream region, there are two more interesting features that stress the relevance of its regulatory function: an inverted repeat comprising the ATG translation start codon and a DNA region with high bending index between the two NifA-binding sites (data not shown).…”

Section: Ammonium Starvation-induced Nif Genes Under Aerobic Conditionsmentioning

confidence: 99%

Gene function analysis in environmental isolates: The nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans

Parro

Moreno‐Paz

2003

Proc. Natl. Acad. Sci. U.S.A.

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A random genomic library from an environmental isolate of the Gram-negative bacterium Leptospirillum ferrooxidans has been printed on a microarray. Gene expression analysis was carried out with total RNA extracted from L. ferrooxidans cultures in the presence or absence of ammonium as nitrogen source under aerobic conditions. Although practically nothing is known about the genome sequence of this bacterium, this approach allowed us the selection and sequencing of only those clones bearing genes that showed an altered expression pattern. By sequence comparison, we have identified most of the genes of nitrogen fixation regulon in L. ferrooxidans, like the nifHDKENX operon, encoding the structural components of Mo-Fe nitrogenase; nifSU-hesBhscBA-fdx operon, for Fe-S cluster assembly; the amtB gene (ammonium transporter); modA (molybdenum ABC type transporter); some regulatory genes like ntrC, nifA (the specific activator of nif genes); or two glnB-like genes (encoding the PII regulatory protein). Our results show that shotgun DNA microarrays are very powerful tools to accomplish gene expression studies with environmental bacteria whose genome sequence is still unknown, avoiding the time and effort necessary for whole genome sequencing projects.shotgun DNA microarrays ͉ gene expression ͉ nitrogen fixation ͉ iron oxidizer G ene expression analysis by DNA microarrays (biochips) has enjoyed a tremendous increase during the last few years (1). As whole genome sequences are available at increasing rates, DNA microarrays are used for the functional analysis of the newly and already characterized genes. A previous knowledge of DNA sequence usually is a prerequisite for biochip construction from already known genes. It is possible to spot all ORFs of complete genomes from bacteria to humans. This strategy requires one to undertake expensive and time-consuming genome sequencing projects to study the function of just a particular set of genes. This is a genuinely tedious task if we want to apply this approach to those bacterial strains isolated from the environment. Here we use a shotgun DNA microarray strategy (2) for gene expression analysis in environmental isolates, bypassing the need for previous knowledge of the genome sequence.The Gram-negative bacterium Leptospirillum ferrooxidans is one of the most abundant bacteria in mineral-processing bioreactors, as well as in certain natural environments like the extremely acidic Tinto River (in the southwestern region of Spain), which has pH values between 0.8 and 2.4 and high metal concentrations along the entire 90 km of its length (3, 4). L. ferrooxidans is a strict iron-oxidizing acidophile considered one of the main responsible agents for maintaining the pH balance and hence the physicochemical properties of the ecosystem. This process is achieved by accelerating the limiting step for pyrite (FeS 2 ) leaching: the production of ferric iron (Fe 3ϩ ) (5, 6). L. ferrooxidans is also very important because of its capacity to extract heavy metals from minerals or contamina...

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“…Structurally, this region shows a very high complexity. It has two potential NtrC-binding sites, three NifA sites and one IHF (integration host factor) -binding site localized upstream of an σ N type promoter (-24/-12) (Souza et al 1991b, Wassem et al 2000. In summarizing, the studies showed that NtrC and RpoN are essential for expression from the nifA promoter and that IHF positively modulates activation by NtrC and acts negatively for activation by NifA (Souza et al 1991a, b, 1999, Wassem et al 2000.…”

Section: Genetics Studiesmentioning

confidence: 99%

History on the biological nitrogen fixation research in graminaceous plants: special emphasis on the Brazilian experience

Baldani

2005

An. Acad. Bras. Ciênc.

229

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This review covers the history on Biological Nitrogen Fixation (BNF) in Graminaceous plants grown in Brazil, and describes research progress made over the last 40 years, most of which was coordinated by Johanna Döbereiner. One notable accomplishment during this period was the discovery of several nitrogen-fixing bacteria such as the rhizospheric (Beijerinckia fluminensis and Azotobacter paspali), associative (Azospirillum lipoferum, A. brasilense, A. amazonense) and the endophytic (Herbaspirillum seropedicae, H. rubrisubalbicans, Gluconacetobacter diazotrophicus, Burkholderia brasilensis and B. tropica). The role of these diazotrophs in association with grasses, mainly with cereal plants, has been studied and a lot of progress has been achieved in the ecological, physiological, biochemical, and genetic aspects. The mechanisms of colonization and infection of the plant tissues are better understood, and the BNF contribution to the soil/plant system has been determined. Inoculation studies with diazotrophs showed that endophytic bacteria have a much higher BNF contribution potential than associative diazotrophs. In addition, it was found that the plant genotype influences the plant/bacteria association. Recent data suggest that more studies should be conducted on the endophytic association to strengthen the BNF potential. The ongoing genome sequencing programs: RIOGENE (Gluconacetobacter diazotrophicus) and GENOPAR (Herbaspirillum seropedicae) reflect the commitment to the BNF study in Brazil and should allow the country to continue in the forefront of research related to the BNF process in Graminaceous plants.

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Sequence and structural organization of a nifA-like gene and part of a nifB-like gene of Herbaspirillum seropedicae strain Z78

Cited by 45 publications

References 42 publications

Expression of the nifA gene of Herbaspirillum seropedicae: role of the NtrC and NifA binding sites and of the −24/−12 promoter element

Expression of the nifA gene of Herbaspirillum seropedicae: role of the NtrC and NifA binding sites and of the −24/−12 promoter element

Gene function analysis in environmental isolates: The nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans

History on the biological nitrogen fixation research in graminaceous plants: special emphasis on the Brazilian experience

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