A renaissance of metabolite sensing and signaling: From modular domains to riboswitches

Plant Cell

Volumn 16, Issue 9, 2004, Pages 2252-2257

  Templeton, George W ^a   Moorhead, Greg B G ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 4544357628     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.104.160930     Document Type: Review

References (46)

1. Arcondeguy, T., Jack, R., and Merrick, M. (2001). P(II) signal transduction proteins, pivotal players in microbial nitrogen control. Microbiol. Mol. Biol. Rev. 65, 80-105.
2. Babitzke, P., and Gollnick, P. (2001). Posttranscription initiation control of tryptophan metabolism in Bacillus subtilis by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure. J. Bacteriol. 183, 5795-5802.
3. Barrick, J.E., Corbino, K.A., Winkler, W.C., Nahvi, A., Mandal, M., Collins, J., Lee, M., Roth, A., Sudarsan, N., Jona, I., Wickiser, J.K., and Breaker, R.R. (2004). New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. USA 101, 6421-6426.
4. Bedalov, A., and Simon, J.A. (2003). Sir2 flexes its muscle. Dev. Cell 5, 188-189.
5. Berger, F., Ramirez-Hernandez, M.H., and Ziegler, M. (2004). The new life of a centenarian: Signalling functions of NAD(P). Trends Biochem. Sci. 29, 111-118.
6. Brekasis, D., and Paget, M.S. (2003). A novel sensor of NADH/NAD+ redox poise in Streptomyces coelicolor A3(2). EMBO J. 22, 4856-4865.
7. Carling, D. (2004). The AMP-activated protein kinase cascade - A unifying system for energy control. Trends Biochem. Sci. 29, 18-24.
8. Cherkasova, V.A., and Hinnebusch, A.G. (2003). Translational control by TOR and TAP42 through dephosphorylation of elF2alpha kinase GCN2. Genes Dev. 17, 859-872.
9. Crespo, J.L., Powers, T., Fowler, B., and Hall, M.N. (2002). The TOR-controlled transcription activators GLN3, RTG1, and RTG3 are regulated in response to intracellular levels of glutamine. Proc. Natl. Acad. Sci. USA 99, 6784-6789.
10. Fingar, D.C., and Blenis, J. (2004). Target of rapamycin (TOR): An integrator of nutrient and growth factor signals and coordinator of cell growth and cell cycle progression. Oncogene 23, 3151-3171.
11. Fjeld, C.C., Birdsong, W.T., and Goodman, R.H. (2003). Differential binding of NAD+ and NADH allows the transcriptional corepressor carboxyl-terminal binding protein to serve as a metabolic sensor. Proc. Natl. Acad. Sci. USA 100, 9202-9207.
12. Forchhammer, K. (2004). Global carbon/nitrogen control by PII signal transduction in cyanobacteria: From signals to targets. FEMS Microbiol. Rev. 28, 319-333.
13. Forchhammer, K., and Tandeau de Marsac, N. (1995). Phosphorylation of the PII protein (glnB gene product) in the cyanobacterium Synechococcus sp. strain PCC 7942: Analysis of in vitro kinase activity. J. Bacteriol. 177, 5812-5817.
14. Fulco, M., Schiltz, R.L., Iezzi, S., King, M.T., Zhao, P., Kashiwaya, Y., Hoffman, E., Veech, R.L., and Sartorelli, V. (2003). Sir2 regulates skeletal muscle differentiation as a potential sensor of the redox state. Mol. Cell 12, 51-62.
15. Gaussin, V., Hue, L., Stalmans, W., and Bollen, M. (1996). Activation of hepatic acetyl-CoA carboxylase by glutamate and Mg2+ is mediated by protein phosphatase-2A. Biochem. J. 316, 217-224.
16. Halford, N.G., Hey, S., Jhurreea, D., Laurie, S., McKibbin, R.S., Zhang, Y., and Paul, M.J. (2004). Highly conserved protein kinases involved in the regulation of carbon and amino acid metabolism. J. Exp. Bot. 55, 35-42.
17. Hardie, D.G. (2003). Minireview: The AMP-activated protein kinase cascade: The key sensor of cellular energy status. Endocrinology 144, 5179-5183.
18. Hardie, D.G., Scott, J.W., Pan, D.A., and Hudson, E.R. (2003). Management of cellular energy by the AMP-activated protein kinase system. FEBS Lett. 546, 113-120.
19. Harris, T.E., and Lawrence, J.C., Jr. (2003). TOR signaling. Sci STKE 2003, re15.
20. Hawley, S.A., Boudeau, J., Reid, J.L., Mustard, K.J., Udd, L., Makela, T.P., Alessi, D.R., and Hardie, D.G. (2003). Complexes between the LKB1 tumor suppressor, STRADalpha/beta and MO25alpha/beta are upstream kinases in the AMP-activated protein kinase cascade. J. Biol. 2, 28.
21. Hsieh, M.H., Lam, H.M., van de Loo, F.J., and Coruzzi, G. (1998). A PII-like protein in Arabidopsis: Putative role in nitrogen sensing. Proc. Natl. Acad. Sci. USA 95, 13965-13970.
22. Hudson, E.R., Pan, D.A., James, J., Lucocq, J.M., Hawley, S.A., Green, K.A., Baba, O., Terashima, T., and Hardie, D.G. (2003). A novel domain in AMP-activated protein kinase causes glycogen storage bodies similar to those seen in hereditary cardiac arrhythmias. Curr. Biol. 13, 861-866.
23. Irmler, A., Sanner, S., Dierks, H., and Forchhammer, K. (1997). Dephosphorylation of the phosphoprotein P(II) in Synechococcus PCC 7942: Identification of an ATP and 2-oxoglutarate-regulated phosphatase activity. Mol. Microbiol. 26, 81-90.
24. Kornberg, A. (2003). Ten commandments of enzymology, amended. Trends Biochem. Sci. 28, 515-517.
25. Kubodera, T., Watanabe, M., Yoshiuchi, K., Yamashita, N., Nishimura, A., Nakai, S., Gomi, K., and Hanamoto, H. (2003). Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR. FEBS Lett. 555, 516-520.
26. Lamb, H.K., Leslie, K., Dodds, A.L., Nutley, M., Cooper, A., Johnson, C., Thompson, P., Stammers, D.K., and Hawkins, A.R. (2003). The negative transcriptional regulator NmrA discriminates between oxidized and reduced dinucleotides. J. Biol. Chem. 278, 32107-32114.
27. Mandal, M., and Breaker, R.R. (2004). Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol. 5, 451-463.
28. Menand, B., Desnos, T., Nussaume, L., Berger, F., Bouchez, D., Meyer, C., and Robaglia, C. (2002). Expression and disruption of the Arabidopsis TOR (target of rapamycin) gene. Proc. Natl. Acad. Sci. USA 99, 6422-6427.
29. Miranda-Rios, J., Navarro, M., and Soberon, M. (2001). A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc. Natl. Acad. Sci. USA 98, 9736-9741.
30. Moorhead, G.B., and Smith, C.S. (2003). Interpreting the plastid carbon, nitrogen, and energy status. A role for PII? Plant Physiol. 133, 492-498.
31. Nishimura, M., Fedorov, S., and Uyeda, K. (1994). Glucose-stimulated synthesis of fructose 2,6-bisphosphate in rat liver. Dephosphorylation of fructose 6-phosphate, 2-kinase:fructose 2,6-bisphosphatase and activation by a sugar phosphate. J. Biol. Chem. 269, 26100-26106.
32. Pan, D., Dong, J., Zhang, Y., and Gao, X. (2004). Tuberous sclerosis complex: From Drosophila to human disease. Trends Cell Biol. 14, 78-85.
33. Polekhina, G., Gupta, A., Michell, B.J., van Denderen, B., Murthy, S., Feil, S.C., Jennings, I.G., Campbell, D.J., Witters, L.A., Parker, M.W., Kemp, B.E., and Stapleton, D. (2003). AMPK beta subunit targets metabolic stress sensing to glycogen. Curr. Biol. 13, 867-871.
34. Rolland, F., Moore, B., and Sheen, J. (2002). Sugar sensing and signaling in plants. Plant Cell 14 (suppl.), S185-S205.
35. Schalm, S.S., and Blenis, J. (2002). Identification of a conserved motif required for mTOR signaling. Curr. Biol. 12, 632-639.
36. Scott, J.W., Hawley, S.A., Green, K.A., Anis, M., Stewart, G., Scullion, G.A., Norman, D.G., and Hardie, D.G. (2004). CBS domains form energy-sensing modules whose binding of adenosine ligands is disrupted by disease mutations. J. Clin. Invest. 113, 274-284.
37. Smith, C.S., Morrice, N.A., and Moorhead, G.B. (2004). Lack of evidence for phosphorylation of Arabidopsis thaliana PII: Implications for plastid carbon and nitrogen signaling. Biochim. Biophys. Acta 1699, 145-154.
38. Smith, C.S., Weljie, A.M., and Moorhead, G.B. (2003). Molecular properties of the putative nitrogen sensor PII from Arabidopsis thaliana. Plant J. 33, 353-360.
39. Smith, C.S., Zaplachinski, S.T., Muench, D.G., and Moorhead, G.B. (2002). Expression and purification of the chloroplast putative nitrogen sensor, PII, of Arabidopsis thaliana. Protein Expr. Purif. 25, 342-347.
40. Sudarsan, N., Barrick, J.E., and Breaker, R.R. (2003). Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9, 644-647.
41. Tanigawa, R., Shirokane, M., Maeda Si, S., Omata, T., Tanaka, K., and Takahashi, H. (2002). Transcriptional activation of NtcA-dependent promoters of Synechococcus sp. PCC 7942 by 2-oxoglutarate in vitro. Proc. Natl. Acad. Sci. USA 99, 4251-4255.
42. Trauner, D., and Kramer, R.H. (2004). Metabolic modulation of potassium channels. Sci STKE 2004, PE22.
43. Vazquez-Bermudez, M.F., Herrero, A., and Flores, E. (2002). 2-Oxoglutarate increases the binding affinity of the NtcA (nitrogen control) transcription factor for the Synechococcus glnA promoter. FEBS Lett. 512, 71-74.
44. Vitreschak, A.G., Rodionov, D.A., Mironov, A.A., and Gelfand, M.S. (2004). Riboswitches: The oldest mechanism for the regulation of gene expression? Trends Genet. 20, 44-50.
45. Wilson, W.A., and Roach, P.J. (2002). Nutrient-regulated protein kinases in budding yeast. Cell 111, 155-158.
46. Winkler, W., Nahvi, A., and Breaker, R.R. (2002). Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952-956.