Conserved Subgroups and Developmental Regulation in the Monocot rop Gene Family

Plant Physiology

Volumn 133, Issue 4, 2003, Pages 1791-1808

  Christensen, Todd M ^a   Vejlupkova, Zuzana ^a   Sharma, Yogesh K ^b,d   Arthur, Kirstin M ^a   Spatafora, Joseph W ^a   Albright, Carol A ^c   Meeley, Robert B ^b   Duvick, Jon P ^b   Quatrano, Ralph S ^c,e   Fowler, John E ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b PIONEER HI BRED INTERNATIONAL INC   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

^e WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLIC ACIDS; CROPS; GENES; PROTEINS; RNA; SIGNALING; TISSUE;

SIGNAL TRANSDUCTION;

PLANTS (BOTANY);

DICOTYLEDONEAE; EMBRYOPHYTA; LILIOPSIDA; MAGNOLIOPHYTA; ORYZA SATIVA; ZEA; ZEA MAYS;

EID: 9144227526     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.103.029900     Document Type: Article

References (65)

1. Abdul-Manan N, Aghazadeh B, Liu GA, Majumdar A, Ouerfelli O, Siminovitch KA, Rosen MK (1999) Structure of Cdc42 in complex with the GTPase-binding domain of the "Wiskott-Aldrich syndrome" protein. Nature 399: 379-383
2. Ahn S, Tanksley SD (1993) Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90: 7980-7984
3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
4. Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7: 986-995
5. Baxter-Burrell A, Yang Z, Springer PS, Bailey-Serres J (2002) RopGAP4-dependent Rop GTPase rheostat control of Arabidopsis oxygen deprivation tolerance. Science 296: 2026-2028
6. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M et al. (2000a) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18: 630-634
7. Brenner S, Williams SR, Vermaas EH, Storck T, Moon K, McCollum C, Mao JI, Luo S, Kirchner JJ, Eletr S et al. (2000b) In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci USA 97: 1665-1670
8. Dong Q, Roy L, Freeling M, Walbot V, Brendel V (2003) ZmDB, an integrated database for maize genome research. Nucleic Acids Res 31: 244-247
9. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868
10. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791
11. Fernandes J, Brendel V, Gai X, Lal S, Chandler VL, Elumalai RP, Galbraith DW, Pierson EA, Walbot V (2002) Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization. Plant Physiol 128: 896-910
12. Fowler JE, Quatrano RS (1997) Plant cell morphogenesis: plasma membrane interactions with the cytoskeleton and cell wall. Annu Rev Cell Dev Biol 13: 697-743
13. Freeling M (2001) Grasses as a single genetic system: reassessment 2001. Plant Physiol 125: 1191-1197
14. Fu Y, Li H, Yang Z (2002) The ROP2 GTPase controls the formation of cortical fine F-actin and the early phase of directional cell expansion during Arabidopsis organogenesis. Plant Cell 14: 777-794
15. Fu Y, Wu G, Yang Z (2001) Rop GTPase-dependent dynamics of tip-localized F-actin controls tip growth in pollen tubes. J Cell Biol 152: 1019-1032
16. Fu Y, Yang Z (2001) Rop GTPase: a master switch of cell polarity development in plants. Trends Plant Sci 6: 545-547
17. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95: 1971-1974
18. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Vanna H et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100
19. Guo H, Moose SP (2003) Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15: 1143-1158
20. Hall A (1998) Rho GTPases and the actin cytoskeleton. Science 279: 509-514
21. Hall A, Nobes CD (2000) Rho GTPases: molecular switches that control the organization and dynamics of the actin cytoskeleton. Philos Trans R Soc Lond B Biol Sci 355: 965-970
22. Hassanain HH, Sharma YK, Moldovan L, Khramtsov V, Berliner LJ, Duvick JP, Goldschmidt-Clermont PJ (2000) Plant rac proteins induce superoxide production in mammalian cells. Biochem Biophys Res Commun 272: 783-788
23. Helentjaris T, Weber D, Wright S (1988) Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118: 353-363
24. Hirshberg M, Stockley RW, Dodson G, Webb MR (1997) The crystal structure of human rac1, a member of the rho-family complexed with a GTP analogue. Nat Struct Biol 4: 147-152
25. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755
26. Huelsenbeck JP, Ronquist F, Nielsen R, Rollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314
27. Ivanchenko M, Vejlupkova Z, Quatrano RS, Fowler JE (2000) Maize ROP7 GTPase contains a unique, CaaX box-independent plasma membrane targeting signal. Plant J 24: 79-90
28. Johnson DI (1999) Cdc42: an essential Rho-type GTPase controlling eukaryotic cell polarity. Microbiol Mol Biol Rev 63: 54-105
29. Kaplinsky NJ, Braun DM, Penterman J, Goff SA, Freeling M (2002) Utility and distribution of conserved noncoding sequences in the grasses. Proc Natl Acad Sci USA 99: 6147-6151
30. Kawasaki T, Henmi K, Ono E, Hatakeyama S, Iwano M, Satoh H, Shimamoto K (1999) The small GTP-binding protein Rac is a regulator of cell death in plants. Proc Natl Acad Sci USA 96: 10922-10926
31. Kost B, Lemichez E, Spielhofer P, Hong Y, Tolias K, Carpenter C, Chua N-H (1999a) Rac homologues and compartmentalized phosphatidylinositol 4,5-bisphosphate act in a common pathway to regulate polar pollen tube growth. J Cell Biol 145: 317-330
32. Kost B, Mathur J, Chua NH (1999b) Cytoskeleton in plant development. Curr Opin Plant Biol 2: 462-470
33. Lapouge K, Smith SJ, Walker PA, Gamblin SJ, Smerdon SJ, Rittinger K (2000) Structure of the TPR domain of p67phox in complex with Rac GTP. Mol Cell 6: 899-907
34. Lavy M, Bracha-Drori K, Sternberg H, Yalovsky S (2002) A cell-specific, prenylation-independent mechanism regulates targeting of type II RACs. Plant Cell 14: 2431-2450
35. Lemichez E, Wu Y, Sanchez JP, Mettouchi A, Mathur J, Chua NH (2001) Inactivation of AtRac1 by abscisic acid is essential for stomatal closure. Genes Dev 15: 1808-1816
36. Li H, Lin Y, Heath RM, Zhu MX, Yang Z (1999) Control of pollen tube tip growth by a Rop GTPase-dependent pathway that leads to tip-localized calcium influx. Plant Cell 11: 1731-1742
37. Li H, Shen JJ, Zheng ZL, Lin Y, Yang Z (2001) The Rop GTPase switch controls multiple developmental processes in Arabidopsis. Plant Physiol 126: 670-684
38. Li H, Wu G, Ware D, Davis KR, Yang Z (1998) Arabidopsis Rho-related GTPases: differential gene expression in pollen and polar localization in fission yeast. Plant Physiol 118: 407-417
39. Lin Y, Yang Z (1997) Inhibition of pollen tube elongation by microinjected anti-Rop1Ps antibodies suggests a crucial role for Rho-type GTPases in the control of tip growth. Plant Cell 9: 1647-1659
40. Lu Y, Settleman J (1999) The role of rho family GTPases in development: lessons from Drosophila melanogaster. Mol Cell Biol Res Commun 1: 87-94
41. Mott HR, Owen D, Nietlispach D, Lowe PN, Manser E, Lim L, Laue ED (1999) Structure of the small G protein Cdc42 bound to the GTPase-binding domain of ACK. Nature 399: 384-388
42. Nebenführ A, Lomax TL (1998) Multiplex titration RT-PCR: rapid determination of gene expression patterns for a large number of genes. Plant Mol Biol Rep 16: 323-339
43. Ono E, Wong HL, Kawasaki T, Hasegawa M, Kodama O, Shimamoto K (2001) Essential role of the small GTPase Rac in disease resistance of rice. Proc Natl Acad Sci USA 98: 759-764
44. Ostermeier C, Brunger AT (1999) Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A. Cell 96: 363-374
45. Owen D, Mott HR, Laue ED, Lowe PN (2000) Residues in Cdc42 that specify binding to individual CRIB effector proteins. Biochemistry 39: 1243-1250
46. Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358
47. Pereira-Leal JB, Seabra MC (2000) The mammalian Rab family of small GTPases: definition of family and subfamily sequence motifs suggests a mechanism for functional specificity in the Ras superfamily. J Mol Biol 301: 1077-1087
48. Pereira-Leal JB, Seabra MC (2001) Evolution of the Rab family of small GTP-binding proteins. J Mol Biol 313: 889-901
49. Perou CM, Jeffrey SS, van de Rijn M, Rees CA, Eisen MB, Ross DT, Pergamenschikov A, Williams CF, Zhu SX, Lee JC et al. (1999) Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA 96: 9212-9217
50. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J (2001) The TIGR gene indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 29: 159-164
51. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual, Ed 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
52. Sentoku N, Sato Y, Kurata N, Ito Y, Kitano H, Matsuoka M (1999) Regional expression of the rice KN1-type homeobox gene family during embryo, shoot, and flower development. Plant Cell 11: 1651-1664
53. Settleman J (2001) Rac 'n Rho: the music that shapes a developing embryo. Dev Cell 1: 321-331
54. Tatusova TA, Madden TL (1999) BLAST 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174: 247-250
55. Usuka J, Zhu W, Brendel V (2000) Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics 16: 203-211
56. Valster AH, Hepler PK, Chernoff J (2000) Plant GTPases: the rhos in bloom. Trends Cell Biol 10: 141-146
57. Vernoud V, Horton AC, Yang Z, Nielsen E (2003) Analysis of the small GTPase gene superfamily of Arabidopsis. Plant Physiol 131: 1191-1208
58. Vetter IR, Wittinghofer A (2001) The guanine nucleotide-binding switch in three dimensions. Science 294: 1299-1304
59. Wilson WA, Harrington SE, Woodman WL, Lee M, Sorrells ME, McCouch SR (1999) Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids. Genetics 153: 453-473
60. Winge P, Brembu T, Bones AM (1997) Cloning and characterization of rac-like cDNAs from Arabidopsis thaliana. Plant Mol Biol 35: 483-495
61. Winge P, Brembu T, Kristensen R, Bones AM (2000) Genetic structure and evolution of RAC-GTPases in Arabidopsis thaliana. Genetics 156: 1959-1971
62. Wu G, Gu Y, Li S, Yang Z (2001) A genome-wide analysis of Arabidopsis Rop-interactive CRIB motif-containing proteins that act as Rop GTPase targets. Plant Cell 13: 2841-2856
63. Yang Z (2002) Small GTPases: versatile signaling switches in plants. Plant Cell Suppl 14: S375-S388
64. Zheng ZL, Nafisi M, Tam A, Li H, Crowell DN, Chary SN, Schroeder JI, Shen J, Yang Z (2002) Plasma membrane-associated ROP10 small GTPase is a specific negative regulator of abscisic acid responses in Arabidopsis. Plant Cell 14: 2787-2797
65. Zheng ZL, Yang Z (2000) The Rop GTPase: an emerging signaling switch in plants. Plant Mol Biol 44: 1-9