Sydney G Kustu

Professor
Ph.D.  University of California, Davis
  

481A Koshland Hall
Berkeley, California 94720-3102
kustu@berkeley.edu
office: 510-643-9308   lab: 510-643-9307   fax:  510-642-4995

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Our major focus is on membrane channels for ammonium¹ and carbon dioxide (probably the hydrated forms in both cases). The Amt and Rh proteins are the only two members of their protein superfamily². Amt proteins, also called Mep in some organisms, are membrane channels for ammonium, whereas Rhesus (Rh) proteins appear to be channels for carbon dioxide. Although the Rh blood group substance is one of the most abundant proteins in red cell membranes (~10⁵ copies/cell), its function has been unknown for over six decades.

We have studied Amt proteins in E. coli, S. cerevisiae, N. crassa and most recently the green alga Chlamydomonas reinhardtii. Genetic and physiological evidence in all indicated that Amt proteins are channels for ammonium, and Khademi et al.³ recently confirmed this by determining the structure of the E. coli AmtB protein to an extraordinary resolution of 1.35 Å. Amt channels are required for optimal growth of E. coli at low external concentrations of NH₃.

Unlike Amt proteins, which are widespread among microbes and apparently ancient, Rh proteins appear to be rare in microbes. C. reinhardtii has two RH genes and four AMT genes. The Rh1 protein of C. reinhardtii is expressed at high levels only under conditions of CO₂ excess and is required for rapid growth at high CO₂ concentrations (3%). By contrast, the AMT genes of this organism are expressed under nitrogen-limiting conditions and its Amt4 protein plays a major role in uptake of the ammonium analogue, methylammonium. Contrasting the substrates of Rh and Amt proteins in the same organism was important because it is widely believed by others⁴ that ammonium is the physiological substrate for both. Until recently, it was thought that both were active transporters for ammonium.

Human geneticists have evidence that the red cell proteins carrying the classical Rh antigens are evolving a new function⁵. Along with Band 3, the bicarbonate exchanger, these proteins help to maintain the flexible, flattened shape of the red cell⁶. Knowing that the ancestral function of Rh proteins is as carbon dioxide channels, one can infer that their structural role in helping to maintain the shape of the red cell is newly evolving. Like their primary role, this secondary role increases the rate of gas exchange across red cell membranes.



1Soupene, He, Yan and Kustu 1998. Ammonia acquisition in enteric bacteria: physiological role of the ammonium/methylammonium transport B (AmtB) protein. Proc. Natl. Acad. Sci. USA 95:7030-7034 [PNAS]

2Marini et al. 1997. The Rh (rhesus) blood group polypeptides are related to NH4+ transporters. Trends Biochem. Sci. 22:460-461 [PubMed]

3Khademi et al. 2004. Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 Å. Science 305:1587-1594 [Science (abstract)]

4Marini et al. 1997. A family of ammonium transporters in Saccharomyces cerevisiae. Mol. Cell. Biol. 17:4282-4293 [MCB];
von Wiren et al. 2000. The molecular physiology of ammonium uptake and retrieval. Curr. Opin. Plant Biol. 3:254-261 [PubMed];
von Wiren and Merrick 2004. Regulation and function of ammonium carriers in bacteria, fungi, and plants. Top. Curr. Genet. 9:95-120

5Huang et al. 2000. Sequence, organization, and evolution of Rh50 glycoprotein genes in nonhuman primates. J. Mol. Evol. 51:76-87 [PubMed];
Kitano and Saitou 2000. Evolutionary history of the Rh blood group-related genes in vertebrates. Immunogenet. 51:856-862 [PubMed];
Matassi et al. 1999. The members of the RH gene family (RH50 and RH30) followed different evolutionary pathways. J. Mol. Evol. 48:151-159 [PubMed]

6Beckmann et al. 2001. Coexpression of band 3 mutants and Rh polypeptides: differential effects of band 3 on the expression of the Rh complex containing D polypeptide and the Rh complex containing CcEe polypeptide. Blood 97:2496-2505 [Blood]

K.-S. Kim, S. Kustu, and W. Inwood. 2006. Natural history of transposition in the green alga Chlamydomonas reinhardtii: Use of the AMT4 locus as an experimental system. Genetics 173:2005-2019. [Genetics]

S. Kustu and W. Inwood. 2006. Biological gas channels for NH₃ and CO₂: evidence that Rh (Rhesus) proteins are CO₂ channels. Transfus. Clin. Biol. 13:103-10. [TCB (abstract)]

K. D. Loh, P. Gyaneshwar, E. Markenscoff Papadimitriou, R. Fong, K.-S. Kim, R. Parales, Z. Zhou, W. Inwood, and S. Kustu. 2006. A previously undescribed pathway for pyrimidine catabolism. Proc. Natl. Acad. Sci. USA 103:5114-9. [PNAS] [commentary]

K.-S. Kim, E. Feild, N. King, T. Yaoi, S. Kustu, and W. Inwood. 2005. Spontaneous mutations in the ammonium transport gene AMT4 of Chlamydomonas reinhardtii. Genetics 170:631-644. [Genetics]

P. Gyaneshwar, O. Paliy, J. McAuliffe, A. Jones, M. I. Jordan, and S. Kustu. 2005. Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation. Proc. Natl. Acad. Sci. USA 102:3453-3458. [PNAS]

P. Gyaneshwar, O. Paliy, J. McAuliffe, D. L. Popham, M. I. Jordan, and S. Kustu. 2005. Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses. J. Bacteriol. 187:1074-1090. [JB]

D. P. Zimmer, O. Paliy, B. Thomas, P. Gyaneshwar, and S. Kustu. 2004. Genome image programs: Visualization and interpretation of Escherichia coli microarray experiments. Genetics 167:2111-2119. [Genetics]

E. Soupene, W. Inwood, and S. Kustu. 2004. Lack of the Rhesus protein Rh1 impairs growth of the green alga Chlamydomonas reinhardtii at high CO₂. Proc. Natl. Acad. Sci. USA 101:7787-7792. [PNAS]

S. Y. Lee, A. De La Torre, D. Yan, S. Kustu, B. T. Nixon, and D. E. Wemmer. 2003. Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. Genes Dev. 17:2552-2563. [Genes Dev]

E. Soupene, W. C. van Heeswijk, J. Plumbridge, V. Stewart, D. Bertenthal, H. Lee, G. Prasad, O. Paliy, P. Charernnoppakul, and S. Kustu. 2003. Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J. Bacteriol. 185:5611-5626. [JB]

C. A. Hastings, S. Y. Lee, H. S. Cho, D. Yan, S. Kustu, and D. E. Wemmer. 2003. High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain. Biochemistry 42:9081-9090. [Biochemistry (abstract)]

Corbin, R. W., O. Paliy, F. Yang, J. Shabanowitz, M. Platt, C. E. Lyons, Jr., K. Root, J. McAuliffe, M. I. Jordan, S. Kustu, E. Soupene, and D. F. Hunt. 2003. Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc. Natl. Acad. Sci. USA 100:9232-9237. [PNAS]

E. Soupene, N. King, H. Lee, and S. Kustu. 2002. Aquaporin Z of Escherichia coli: Reassessment of its regulation and physiological role. J. Bacteriol. 184:4304-4307. [JB]

E. Soupene, T. Chu, R. W. Corbin, D. F. Hunt, and S. Kustu. 2002. Gas channels for NH₃: Proteins from hyperthermophiles complement an Escherichia coli mutant. J. Bacteriol. 184:3396-3400. [JB]

E. Soupene, N. King, E. Feild, P. Liu, K. K. Niyogi, C.-H. Huang, and S. Kustu. 2002. Rhesus expression in a green alga is regulated by CO₂. Proc. Natl. Acad. Sci. USA 99:7769-7773. [PNAS]

E. Soupene, H. Lee, and S. Kustu. 2002. Ammonium/methylammonium transport (Amt) proteins facilitate diffusion of NH₃ bidirectionally. Proc. Natl. Acad. Sci. USA 99:3926-3931. [PNAS]

H. S. Cho, J. G. Pelton, D. Yan, S. Kustu, and D. E. Wemmer. 2001. Phosphoaspartates in bacterial signal transduction. Curr. Opin. Struct. Biol. 11:679-684. [Curr Opin Struct Biol (abstract)]

E. Soupene, R. M. Ramirez, and S. Kustu. 2001. Evidence that fungal MEP proteins mediate diffusion of the uncharged species NH₃ across the cytoplasmic membrane. Mol. Cell. Biol. 21:5733-5741. [MCB]

H. Cho, W. Wang, R. Kim, H. Yokota, S. Damo, S.-H. Kim, D. Wemmer, S. Kustu, and D. Yan. 2001. BeF₃^- acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a BeF₃^- complex with phosphoserine phosphatase. Proc. Natl. Acad. Sci. USA 98:8525-8530. [PNAS] [commentary]

V. F. Wendisch, D. P. Zimmer, A. Khodursky, B. Peter, N. Cozzarelli, and S. Kustu. 2001. Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Anal. Biochem. 290:205-213. [Anal Biochem (abstract)]

S.-Y. Lee, H. S. Cho, J. G. Pelton, D. Yan, R. K. Henderson, D. S. King, L.-s. Huang, S. Kustu, E. A. Berry, and D. E. Wemmer. 2001. Crystal structure of an activated response regulator bound to its target. Nat. Struct. Biol. 8:52-56. [Nat Struct Biol]

D. P. Zimmer, E. Soupene, H. L. Lee, V. F. Wendisch, A. B. Khodursky, B. J. Peter, R. A. Bender, and S. Kustu. 2000. Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc. Natl. Acad. Sci. USA 97:14674-14679. [PNAS] [commentary]

J. Lee, J. T. Owens, I. Hwang, C. Meares, and S. Kustu. 2000. Phosphorylation-induced signal propagation in the response regulator NtrC. J. Bacteriol. 182:5188-5195. [JB]

H. S. Cho, S.-Y. Lee, D. Yan, X. Pan, J. S. Parkinson, S. Kustu, D. E. Wemmer, and J. G. Pelton. 2000. NMR Structure of Activated CheY. J. Mol. Biol. 297:543-551. [JMB (abstract)]

D. Yan, H. S. Cho, C. A. Hastings, M. M. Igo, S.-L. Lee, J. G. Pelton, V. Stewart, D. E. Wemmer, and S. Kustu. 1999. Beryllofluoride mimics phosphorylation of NtrC and other bacterial response regulators. Proc. Natl. Acad. Sci. USA 96:14789-14794. [PNAS] [commentary]

D. Kern, B. F. Volkman, P. Luginbuhl, M. J. Nohaile, S. Kustu, and D. Wemmer. 1999. Structure of a transiently phosphorylated switch in bacterial signal transduction. Nature 402:894-898. [Nature (abstract)]