The NifL-NifA System: a Multidomain Transcriptional Regulatory Complex That Integrates Environmental Signals

Martínez‐Argudo, Isabel; Little, Richard; Shearer, Neil; Johnson, Philip E.; Dixon, Ray

doi:10.1128/jb.186.3.601-610.2004

Cited by 140 publications

(128 citation statements)

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“…A first group of genes (from PST1302 to PST1323 in A1501) contained nifB and nifQ involved in synthesis of FeMo-co and nifLA. NifL and NifA were the negative/positive regulatory proteins for nif operon expression (23,24). Four additional genes associated with nifB and nifQ ( Fig.…”

Section: Resultsmentioning

confidence: 96%

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

Yan

Yang

et al. 2008

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

329

263

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The capacity to fix nitrogen is widely distributed in phyla of Bacteria and Archaea but has long been considered to be absent from the Pseudomonas genus. We report here the complete genome sequencing of nitrogen-fixing root-associated Pseudomonas stutzeri A1501. The genome consists of a single circular chromosome with 4,567,418 bp. Comparative genomics revealed that, among 4,146 protein-encoding genes, 1,977 have orthologs in each of the five other Pseudomonas representative species sequenced to date. The genome contains genes involved in broad utilization of carbon sources, nitrogen fixation, denitrification, degradation of aromatic compounds, biosynthesis of polyhydroxybutyrate, multiple pathways of protection against environmental stress, and other functions that presumably give A1501 an advantage in root colonization. Genetic information on synthesis, maturation, and functioning of nitrogenase is clustered in a 49-kb island, suggesting that this property was acquired by lateral gene transfer. New genes required for the nitrogen fixation process have been identified within the nif island. The genome sequence offers the genetic basis for further study of the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in the interaction with host plants; moreover, it opens up new perspectives for wider application of root-associated diazotrophs in sustainable agriculture.genome sequencing ͉ root-associated diazotroph

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Section: Resultsmentioning

confidence: 96%

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

Yan

Yang

et al. 2008

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

329

263

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“…The activity of NifLA complexes is modulated by GlnK (a PII parologue protein), ATP/ADP ratio and 2-oxoglutarate, but it is clear that mechanisms of signal communication between NifA and NifL are different in these two species (Martínez-Argudo et al, 2004). In both systems, GlnK, which senses the nitrogen status of the cell, was shown to interact with the NifLA via direct proteinprotein interaction (Stips et al, 2004;Martínez-Argudo et al, 2004). In the case of Azotobacter, when nitrogen is limiting, GlnK, in its uridylylated form, does not interact with NifL, and thus NifL does not antagonize NifA activity Martínez-Argudo et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

“…In both systems, GlnK, which senses the nitrogen status of the cell, was shown to interact with the NifLA via direct proteinprotein interaction (Stips et al, 2004;Martínez-Argudo et al, 2004). In the case of Azotobacter, when nitrogen is limiting, GlnK, in its uridylylated form, does not interact with NifL, and thus NifL does not antagonize NifA activity Martínez-Argudo et al, 2004). In contrast, GlnK is required for the relief of NifL inhibition in K. pneumoniae (He et al, 1998;Stips et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

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Interaction between NifL and NifA in the nitrogen-fixing Pseudomonas stutzeri A1501

et al. 2006

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Pseudomonas stutzeri strain A1501 isolated from rice fixes nitrogen under microaerobic conditions in the free-living state. This paper describes the properties of nifL and nifA mutants as well as the physical interaction between NifL and NifA proteins. A nifL mutant strain that carried a mutation nonpolar on nifA expression retained nitrogenase activity. Complementation with a plasmid containing only nifL led to a decrease in nitrogenase activity in both the wild-type and the nifL mutant, suggesting that NifL acts as an antiactivator of NifA activity. Using the yeast two-hybrid system and purified protein domains of NifA and NifL, an interaction was shown between the C-terminal domain of NifL and the central domain of NifA, suggesting that NifL antiactivator activity is mediated by direct protein interaction with NifA.

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“…NifL is an antiactivator that tightly regulates the activity of its partner protein NifA, a member of the family of 54 -transcriptional activators (1,2), by means of the formation of an inhibitory complex (3)(4)(5). The domain architecture of NifL is similar to that of some HPKs, with an N-terminal Per-ArntSim (PAS) domain (6, 7) containing a flavin adenine dinucleotide (FAD) cofactor that senses the redox status (8,9) and a C-terminal domain containing conserved residues corresponding to the N, G1, F, and G2 boxes that constitute the ATPbinding domain of the GHKL superfamily of ATPases (10-14) (Fig.…”

mentioning

confidence: 99%

A crucial arginine residue is required for a conformational switch in NifL to regulate nitrogen fixation in Azotobacter vinelandii

Martínez‐Argudo

Little

Dixon

2004

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

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NifL is an antiactivator that tightly regulates transcription of genes required for nitrogen fixation in Azotobacter vinelandii by controlling the activity of its partner protein NifA, a member of the family of 54 -dependent transcriptional activators. Although the C-terminal region of A. vinelandii NifL shows homology to the transmitter domains of histidine protein kinases, signal transduction between NifL and NifA is conveyed by means of proteinprotein interactions rather than by phosphorylation. Binding of the ligand 2-oxoglutarate to NifA plays a crucial role in preventing inhibition by NifL under conditions appropriate for nitrogen fixation. We have used a suppressor screen to identify a critical arginine residue (R306) in NifL that is required to release NifA from inhibition under appropriate environmental conditions. Amino acid substitutions at position 306 result in constitutive inhibition of NifA activity by NifL, thus preventing nitrogen fixation. Biochemical studies with one of the mutant proteins demonstrate that the substitution alters the conformation of NifL significantly and prevents the response of NifA to 2-oxoglutarate. We propose that arginine 306 is critical for the propagation of signals perceived by A. vinelandii NifL in response to the redox and fixed-nitrogen status and is required for a conformational switch that inactivates the inhibitory function of NifL under conditions appropriate for nitrogen fixation.2-oxoglutarate ͉ signal transduction ͉ antiactivator ͉ redox control ͉ nitrogen regulation S tructural rearrangements of sensor proteins in response to environmental cues provide a fundamental mechanism for signal propagation within cells. However, although conformational changes have been well characterized in isolated signaling domains, mechanisms for signal transmission by means of interdomain interactions are frequently less well understood. For example, structural studies have identified ligand-induced conformational changes in the sensor domains of histidine protein kinases (HPKs), but it is not known how these changes are communicated to the kinase domain to control phosphoryl transfer.The Azotobacter vinelandii NifL regulatory protein is a histidine kinase-like protein that controls the expression of the genes required for nitrogen fixation in response to the redox, nitrogen, and carbon status. NifL is an antiactivator that tightly regulates the activity of its partner protein NifA, a member of the family of 54 -transcriptional activators (1, 2), by means of the formation of an inhibitory complex (3-5). The domain architecture of NifL is similar to that of some HPKs, with an N-terminal Per-ArntSim (PAS) domain (6, 7) containing a flavin adenine dinucleotide (FAD) cofactor that senses the redox status (8, 9) and a C-terminal domain containing conserved residues corresponding to the N, G1, F, and G2 boxes that constitute the ATPbinding domain of the GHKL superfamily of ATPases (10-14) (Fig. 1). Unlike the HPKs, the GHKL domain of NifL does not exhibit ATP hydrolysis or transphos...

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The NifL-NifA System: a Multidomain Transcriptional Regulatory Complex That Integrates Environmental Signals

Cited by 140 publications

References 104 publications

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

Interaction between NifL and NifA in the nitrogen-fixing Pseudomonas stutzeri A1501

A crucial arginine residue is required for a conformational switch in NifL to regulate nitrogen fixation in Azotobacter vinelandii

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