Genomes and Genes
pii nitrogen regulatory proteins
Summary: A family of signal transducing adaptor proteins that control the METABOLISM of NITROGEN. They are primarily found in prokaryotes.
- Martinez Argudo I, Contreras A. PII T-loop mutations affecting signal transduction to NtrB also abolish yeast two-hybrid interactions. J Bacteriol. 2002;184:3746-8 pubmed..The reported results underline the strength of two-hybrid assays for analysis of interactions involving the T loop of PII proteins. ..
- Jiang P, Peliska J, Ninfa A. The regulation of Escherichia coli glutamine synthetase revisited: role of 2-ketoglutarate in the regulation of glutamine synthetase adenylylation state. Biochemistry. 1998;37:12802-10 pubmed..The possible biological implications of this regulatory arrangement are discussed. ..
- Leigh J, Dodsworth J. Nitrogen regulation in bacteria and archaea. Annu Rev Microbiol. 2007;61:349-77 pubmed..NifI(1) and NifI(2) comprise a second widespread family of PII proteins (NifI) that are heteromultimeric, respond to 2OG and ATP, and bind and regulate dinitrogenase in Euryarchaeota and many Bacteria. ..
- Lei M, Velos J, Gardino A, Kivenson A, Karplus M, Kern D. Segmented transition pathway of the signaling protein nitrogen regulatory protein C. J Mol Biol. 2009;392:823-36 pubmed publisher..The targeted molecular dynamics pathway suggests that several transient nonnative hydrogen bonds may facilitate the transition. ..
- Kamberov E, Atkinson M, Chandran P, Ninfa A. Effect of mutations in Escherichia coli glnL (ntrB), encoding nitrogen regulator II (NRII or NtrB), on the phosphatase activity involved in bacterial nitrogen regulation. J Biol Chem. 1994;269:28294-9 pubmed..Thus, while the kinase and phosphatase activities of NRII could be genetically separated, some of the highly conserved residues in the C-terminal domain of NRII (Asp-287, Gly-289, Gly-291) are apparently important for both activities. ..
- Commichau F, Forchhammer K, Stülke J. Regulatory links between carbon and nitrogen metabolism. Curr Opin Microbiol. 2006;9:167-72 pubmed..The regulatory networks enable the bacteria to make the appropriate metabolic responses to changing nutrient availabilities in the environment. ..
- Aldehni M, Forchhammer K. Analysis of a non-canonical NtcA-dependent promoter in Synechococcus elongatus and its regulation by NtcA and PII. Arch Microbiol. 2006;184:378-86 pubmed..Furthermore, sequences upstream of the NtcA-binding site have repressive effect on glnN promoter activity. ..
- Mao X, Huo Y, Buck M, Kolb A, Wang Y. Interplay between CRP-cAMP and PII-Ntr systems forms novel regulatory network between carbon metabolism and nitrogen assimilation in Escherichia coli. Nucleic Acids Res. 2007;35:1432-40 pubmed..Therefore, as the major transcriptional effector of the 'glucose effect', CRP affects both the signal transduction pathway and the overall geometry of the transcriptional machinery of components of the nitrogen regulon. ..
- Pioszak A, Ninfa A. Genetic and biochemical analysis of phosphatase activity of Escherichia coli NRII (NtrB) and its regulation by the PII signal transduction protein. J Bacteriol. 2003;185:1299-315 pubmed
- Jiang P, Peliska J, Ninfa A. Reconstitution of the signal-transduction bicyclic cascade responsible for the regulation of Ntr gene transcription in Escherichia coli. Biochemistry. 1998;37:12795-801 pubmed..Thus, the PII protein transduces the glutamine signal to the NRII-NRI monocycle in the form of its uridylylation state and is also the receptor of the antagonistic 2-ketoglutarate signal, which blocks the activity of unmodified PII. ..
- Forchhammer K, Tandeau de Marsac N. Phosphorylation of the PII protein (glnB gene product) in the cyanobacterium Synechococcus sp. strain PCC 7942: analysis of in vitro kinase activity. J Bacteriol. 1995;177:5812-7 pubmed..Unlike the PII-modifying uridylyltransferase- and uridylyl-removing enzyme characterized in proteobacteria, the activity of the PII kinase from the cyanobacterium did not respond to glutamine. ..
- Jiang P, Ninfa A. Alpha-ketoglutarate controls the ability of the Escherichia coli PII signal transduction protein to regulate the activities of NRII (NrB but does not control the binding of PII to NRII. Biochemistry. 2009;48:11514-21 pubmed publisher..Thus, PII control of NRII activities could be dissected into distinct binding and regulation steps, and when present in its physiological concentration range, alpha-ketoglutarate apparently played a role in only the latter step. ..
- Zhang Y, Pohlmann E, Serate J, Conrad M, Roberts G. Mutagenesis and functional characterization of the four domains of GlnD, a bifunctional nitrogen sensor protein. J Bacteriol. 2010;192:2711-21 pubmed publisher..The deletion of C-terminal ACT domains also dramatically decreased UTase activity under all conditions tested, but some of these effects are due to the competition of UTase activity with unregulated UR activity in these variants...
- Davalos M, Fourment J, Lucas A, Bergès H, Kahn D. Nitrogen regulation in Sinorhizobium meliloti probed with whole genome arrays. FEMS Microbiol Lett. 2004;241:33-40 pubmed..In addition to the nitrogen response, glutamate remodelled expression of carbon metabolism by inhibiting expression of the Entner-Doudoroff and pentose phosphate pathways, and by stimulating gluconeogenetic genes independently of ntrC. ..
- Shetty N, Reddy M, Palaninathan S, Owen J, Sacchettini J. Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein. Protein Sci. 2010;19:1513-24 pubmed publisher..coli. The structural conservation and operon organization suggests that the Mtb PII gene encodes for a GlnK protein and might play a key role in the nitrogen regulatory pathway. ..
- Kern D, Volkman B, Luginbuhl P, Nohaile M, Kustu S, Wemmer D. Structure of a transiently phosphorylated switch in bacterial signal transduction. Nature. 1999;402:894-8 pubmed..This creates an exposed hydrophobic surface that is likely to transmit the signal to the transcriptional activation domain. ..
- Pioszak A, Ninfa A. Mutations altering the N-terminal receiver domain of NRI (NtrC) That prevent dephosphorylation by the NRII-PII complex in Escherichia coli. J Bacteriol. 2004;186:5730-40 pubmed..The properties of these altered proteins are consistent with the hypothesis that the NRII-PII complex is not a true phosphatase but rather collaborates with NRI approximately P to bring about its dephosphorylation. ..
- Atkinson M, Ninfa A. Role of the GlnK signal transduction protein in the regulation of nitrogen assimilation in Escherichia coli. Mol Microbiol. 1998;29:431-47 pubmed..We hypothesize that one role of GlnK is to regulate the expression of the level of NRI-P during conditions of severe nitrogen starvation, and by so doing to contribute to the regulation of certain Ntr genes...
- Xu Y, Cheah E, Carr P, van Heeswijk W, Westerhoff H, Vasudevan S, et al. GlnK, a PII-homologue: structure reveals ATP binding site and indicates how the T-loops may be involved in molecular recognition. J Mol Biol. 1998;282:149-65 pubmed publisher..This sequence is more highly conserved than the functional T-loop, suggesting that ATP has an important role in PII-like proteins...
- Espinosa J, Castells M, Laichoubi K, Forchhammer K, Contreras A. Effects of spontaneous mutations in PipX functions and regulatory complexes on the cyanobacterium Synechococcus elongatus strain PCC 7942. Microbiology. 2010;156:1517-26 pubmed publisher..The implications of these results are discussed. ..
- Sakai H, Wang H, Takemoto Hori C, Kaminishi T, Yamaguchi H, Kamewari Y, et al. Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8. J Struct Biol. 2005;149:99-110 pubmed publisher..ATP and GlnK.ADP, have also been determined. ATP/ADP binding within a cleft at the interface of two adjacent T. thermophilus GlnK monomers might affect the conformation of the T-loop...
- Arsene F, Kaminski P, Elmerich C. Modulation of NifA activity by PII in Azospirillum brasilense: evidence for a regulatory role of the NifA N-terminal domain. J Bacteriol. 1996;178:4830-8 pubmed..We propose a model for the regulation of NifA activity in A. brasilense. ..
- Fokina O, Chellamuthu V, Forchhammer K, Zeth K. Mechanism of 2-oxoglutarate signaling by the Synechococcus elongatus PII signal transduction protein. Proc Natl Acad Sci U S A. 2010;107:19760-5 pubmed publisher..Structures of P(II) trimers with one or two bound 2-OG molecules reveal the basis for anticooperative 2-OG binding and shed light on the intersubunit signaling mechanism by which P(II) senses effectors in a wide range of concentrations...
- Espinosa J, Forchhammer K, Burillo S, Contreras A. Interaction network in cyanobacterial nitrogen regulation: PipX, a protein that interacts in a 2-oxoglutarate dependent manner with PII and NtcA. Mol Microbiol. 2006;61:457-69 pubmed..PipX is required for NtcA-dependent transcriptional activation in vivo, thus implying that PipX may function as a prokaryotic transcriptional coactivator. ..
- Jiang P, Ninfa A. Regulation of autophosphorylation of Escherichia coli nitrogen regulator II by the PII signal transduction protein. J Bacteriol. 1999;181:1906-11 pubmed
- Rudnick P, Arcond guy T, Kennedy C, Kahn D. glnD and mviN are genes of an essential operon in Sinorhizobium meliloti. J Bacteriol. 2001;183:2682-5 pubmed publisher..glnD1::Omega or mviN1::Omega mutants could not be isolated by a powerful sucrose counterselection procedure unless a complementing cosmid was provided, indicating that glnD and mviN are members of an indispensable operon in S. meliloti...
- Forchhammer K. Global carbon/nitrogen control by PII signal transduction in cyanobacteria: from signals to targets. FEMS Microbiol Rev. 2004;28:319-33 pubmed
- Bonatto A, Couto G, Souza E, Araujo L, Pedrosa F, Noindorf L, et al. Purification and characterization of the bifunctional uridylyltransferase and the signal transducing proteins GlnB and GlnK from Herbaspirillum seropedicae. Protein Expr Purif. 2007;55:293-9 pubmed..The quantification of these PII forms indicates that GlnB was more efficiently uridylylated than GlnK in the system used...
- Fadi Aldehni M, Sauer J, Spielhaupter C, Schmid R, Forchhammer K. Signal transduction protein P(II) is required for NtcA-regulated gene expression during nitrogen deprivation in the cyanobacterium Synechococcus elongatus strain PCC 7942. J Bacteriol. 2003;185:2582-91 pubmed..Together, these results suggest that under conditions of combined-nitrogen deprivation, the regulation of NtcA-dependent gene expression requires the P(II) signal transduction protein. ..
- Clancy P, Xu Y, van Heeswijk W, Vasudevan S, Ollis D. The domains carrying the opposing activities in adenylyltransferase are separated by a central regulatory domain. FEBS J. 2007;274:2865-77 pubmed..In the light of these results, intramolecular signaling within adenylyltransferase is discussed. ..
- Teixeira P, Jonsson A, Frank M, Wang H, Nordlund S. Interaction of the signal transduction protein GlnJ with the cellular targets AmtB1, GlnE and GlnD in Rhodospirillum rubrum: dependence on manganese, 2-oxoglutarate and the ADP/ATP ratio. Microbiology. 2008;154:2336-47 pubmed publisher..rubrum, a photosynthetic bacterium in which the nitrogen fixation process and its intricate control mechanisms make the regulation of nitrogen metabolism even more complex than in other studied bacteria...
- Sant Anna F, Trentini D, de Souto Weber S, Cecagno R, da Silva S, Schrank I. The PII superfamily revised: a novel group and evolutionary insights. J Mol Evol. 2009;68:322-36 pubmed publisher..Our analysis reveals that horizontal gene transfer could have played an important role in PII evolution. Thus, new insights into PII evolution, a new PII group, and more comprehensive PROSITE signatures are proposed. ..
- Bandyopadhyay A, Arora A, Jain S, Laskar A, Mandal C, Ivanisenko V, et al. Expression and molecular characterization of the Mycobacterium tuberculosis PII protein. J Biochem. 2010;147:279-89 pubmed publisher..Glutaraldehyde crosslinking showed that Mtb PII exists in homotrimeric state which is consistent with other PII proteins. Phylogenetic analysis showed that Mtb PII consistently grouped with other actinobacterial PII proteins. ..
- Huo Y, Tian Z, Rappas M, Wen J, Chen Y, You C, et al. Protein-induced DNA bending clarifies the architectural organization of the sigma54-dependent glnAp2 promoter. Mol Microbiol. 2006;59:168-80 pubmed..This proposal is further supported by the modelling of activator-promoter DNA-Esigma54 complex. ..
- Hastings C, Lee S, Cho H, Yan D, Kustu S, Wemmer D. High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain. Biochemistry. 2003;42:9081-90 pubmed..Analysis of the active structure also suggests that His84 may play a role in controlling the phosphate hydrolysis rate. ..
- Atkinson M, Blauwkamp T, Bondarenko V, Studitsky V, Ninfa A. Activation of the glnA, glnK, and nac promoters as Escherichia coli undergoes the transition from nitrogen excess growth to nitrogen starvation. J Bacteriol. 2002;184:5358-63 pubmed..coli was grown on a low concentration of ammonia in combination with arginine as a nitrogen source, consistent with the hypothesis that Ntr genes other than glnA become activated only upon amplification of the NRI concentration. ..
- Weiss V, Claverie Martin F, Magasanik B. Phosphorylation of nitrogen regulator I of Escherichia coli induces strong cooperative binding to DNA essential for activation of transcription. Proc Natl Acad Sci U S A. 1992;89:5088-92 pubmed..We propose that not the phosphorylation of NRI itself but rather the tetramerization of NRI-phosphate on DNA binding induces the conformational change of the central domain to the active conformation. ..
- Radchenko M, Merrick M. The role of effector molecules in signal transduction by PII proteins. Biochem Soc Trans. 2011;39:189-94 pubmed publisher..The effector molecules appear to play a key role in modulating the conformation of the T-loops and thereby regulating the interactions between PII and its targets. ..
- Jonsson A, Teixeira P, Nordlund S. The activity of adenylyltransferase in Rhodospirillum rubrum is only affected by alpha-ketoglutarate and unmodified PII proteins, but not by glutamine, in vitro. FEBS J. 2007;274:2449-60 pubmed..We propose that in R. rubrum and possibly other diazotrophs alpha-ketoglutarate plays the central role in the regulation of ATase and thus glutamine synthetase activity...
- Jiang P, Mayo A, Ninfa A. Escherichia coli glutamine synthetase adenylyltransferase (ATase, EC 18.104.22.168): kinetic characterization of regulation by PII, PII-UMP, glutamine, and alpha-ketoglutarate. Biochemistry. 2007;46:4133-46 pubmed..Rather, alpha-ketoglutarate dramatically affected the extent of activation or inhibition of the enzyme by PII or PII-UMP. A working hypothesis for the regulation of the AT and AR activities, consistent with all data, is presented. ..
- Zhang Y, Wolfe D, Pohlmann E, Conrad M, Roberts G. Effect of AmtB homologues on the post-translational regulation of nitrogenase activity in response to ammonium and energy signals in Rhodospirillum rubrum. Microbiology. 2006;152:2075-89 pubmed..rubrum. Such interaction specificity might be important in explaining the way in which P(II) proteins regulate processes involved in nitrogen acquisition and utilization...
- Zhang Y, Pohlmann E, Roberts G. Identification of critical residues in GlnB for its activation of NifA activity in the photosynthetic bacterium Rhodospirillum rubrum. Proc Natl Acad Sci U S A. 2004;101:2782-7 pubmed..Finally, the results show that the level of P(II) accumulation is also an important factor for NifA activation...
- Paz Yepes J, Flores E, Herrero A. Transcriptional effects of the signal transduction protein P(II) (glnB gene product) on NtcA-dependent genes in Synechococcus sp. PCC 7942. FEBS Lett. 2003;543:42-6 pubmed..However, strains carrying the GlnB(S49D) and GlnB(S49E) mutant proteins exhibited higher levels of expression of nitrogen-regulated genes than the strains carrying the wild-type P(II) or the GlnB(S49A) protein. ..
- Garcia Dominguez M, Florencio F. Nitrogen availability and electron transport control the expression of glnB gene (encoding PII protein) in the cyanobacterium Synechocystis sp. PCC 6803. Plant Mol Biol. 1997;35:723-34 pubmed
- Atkinson M, Kamberov E, Weiss R, Ninfa A. Reversible uridylylation of the Escherichia coli PII signal transduction protein regulates its ability to stimulate the dephosphorylation of the transcription factor nitrogen regulator I (NRI or NtrC). J Biol Chem. 1994;269:28288-93 pubmed..Thus, both the PII-UTase/UR and PII-NRII interactions display the continuous variability characteristic of rheostats as opposed to the binary variability characteristic of toggle switches. ..
- Espinosa J, Castells M, Laichoubi K, Contreras A. Mutations at pipX suppress lethality of PII-deficient mutants of Synechococcus elongatus PCC 7942. J Bacteriol. 2009;191:4863-9 pubmed publisher..Consistent with the idea that P(II) is essential to counteract the activity of PipX, four different spontaneous mutations in the pipX gene were found in cultures in which glnB had been genetically inactivated. ..
- Conroy M, Durand A, Lupo D, Li X, Bullough P, Winkler F, et al. The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel. Proc Natl Acad Sci U S A. 2007;104:1213-8 pubmed..Y51 of GlnK is also buried in the pore exit, explaining why uridylylation of this residue prevents complex formation. ..
- Noindorf L, Rego F, Baura V, Monteiro R, Wassem R, Cruz L, et al. Characterization of the orf1glnKamtB operon of Herbaspirillum seropedicae. Arch Microbiol. 2006;185:55-62 pubmed..This result suggests that the AmtB protein is involved in the signaling pathway for the reversible inactivation of nitrogenase in H. seropedicae...
- Ninfa A, Atkinson M. PII signal transduction proteins. Trends Microbiol. 2000;8:172-9 pubmed
- Llácer J, Espinosa J, Castells M, Contreras A, Forchhammer K, Rubio V. Structural basis for the regulation of NtcA-dependent transcription by proteins PipX and PII. Proc Natl Acad Sci U S A. 2010;107:15397-402 pubmed publisher..The PipX-NtcA complex consists of one active NtcA dimer and two PipX monomers. PipX coactivates NtcA by stabilizing its active conformation and by possibly helping recruit RNA polymerase but not by providing extra DNA contacts...
- Yurgel S, Kahn M. A mutant GlnD nitrogen sensor protein leads to a nitrogen-fixing but ineffective Sinorhizobium meliloti symbiosis with alfalfa. Proc Natl Acad Sci U S A. 2008;105:18958-63 pubmed publisher..These results indicate that bacterial nitrogen stress regulation is important to symbiotic productivity and suggest that GlnD may act in a novel way to influence symbiotic behavior...
- Pioszak A, Jiang P, Ninfa A. The Escherichia coli PII signal transduction protein regulates the activities of the two-component system transmitter protein NRII by direct interaction with the kinase domain of the transmitter module. Biochemistry. 2000;39:13450-61 pubmed..These results indicate that PII controls NRII by interaction with the conserved kinase domain of the transmitter module. ..