Timothy C. Hall's Lab

The Dicot Group: Transcriptional Regulation of Gene Expression

Research funded by NSF grant MCB-0801640

Recent Staff Members
Dr. Wang Kit "Danny" Ng - Assistant Research Professor
Dr. Raul Carranco - Visiting Research Scientist
Dr. Mahesh Chandrasekharan - Postdoctoral Research Associate
Dr. Guofu Li - Postdoctoral Research Associate
Dr. Xin Zhou - Graduate Assistant
James Townsend - Research Assistant
Kenneth Bishop - Technician II

Research Outline

Seed storage proteins are vital sources of food for humans and livestock. Their rapid synthesis and accumulation over defined developmental periods in specific tissues makes them excellent targets for basic studies on gene regulation. We have recently reviewed (Hall et al., 1999) our long-term investigation of the ß-phas gene, which encodes one of the polypeptides of the most abundant protein, phaseolin, present in the bean, Phaseolus vulgaris and recent developments are summarized in Li et al. (2001b).

Current studies are directed to an understanding of the role of chromatin in the stringent spatial regulation of expression from the phas promoter, which is silent in vegetative tissues and very active in seed tissues. We found that a tightly (rotationally and translationally) positioned nucleosome is present over the TATA region of the ß-phas promoter in vegetative tissues, precluding binding of TBP ( Li et al., 1998) and have recently shown that expression can be activated in vegetative tissues by a two-step process thatinvolves the transcription factor PvAlf in chromatin remodeling and abscisic acid (ABA) in activation (Li et al., 1999). We are investigating the possibility that domains within the phas promoter are responsible for module-specific expression ( Li and Hall, 1999). The power of Arabidopsis genomics, its short life cycle and ease of transformation, has led to our recent adoption of Arabidopsis in place of tobacco as the model system for most of our studies on expression from the phas promoter. We are also investigating the value of Medicago truncatula as a relatively large-seeded model legume for studies on phas.

Recent findings (Li et al., 2001a) strongly implicate the involvement of a serine/threonine phosphatase as a key regulator of expression from the phas promoter and that phosphorylation of a kinase or a transcription factor is a component of the ABA-mediated activation pathway. We are especially interested in exploring the ability of PvAlf to interact with nucleosomal DNA and the factors that interact with PvAlf to mediate chromatin remodeling.

Dicot Publications

(Click here for a complete listing of lab publications)

Publications related to PHASEOLIN

A. Invited Chapters and Reviews

1. Hall, T. C., Sun, S. M., Buchbinder, B. U. and Belozerskii, M. A. 1977. The translation of mRNA for storage globulin of the bean, Phaseolus vulgaris. In: Translation of Natural and Synthetic Polynucleotides. A. Legocki, Ed. Univ. of Agriculture in Poznan, Poland. pp. 217-223.

2. Hall, T. C. 1979a. Plant messenger RNA. In: Nucleic Acids in Plants. T. C. Hall and J. W. Davies, Eds. CRC Press. I: 217-251.

3. Hall, T. C., Sun, S. M., Ma, Y., McLeester, R. C., Pyne, J. W., Bliss, F. A. and Buchbinder, B. U. 1979. The major storage protein of French bean seeds: Characterization in vivo and translation in vitro. In: The Plant Seed: Development, Preservation, and Germination. Rubenstein, R. L. Phillips, C. E. Green and B. G. Gengenbach, Eds. Academic Press, Inc., New York. I: 3-26.

4. Hall, T. C., Sun, S. M., Buchbinder, B. U., Pyne, J. W., Bliss, F. A. and Kemp, J. D. 1980. Bean seed globulin mRNA: Translation, characterization, and its use as a probe towards genetic engineering of crop plants. In: Genome Organization and Expression in Plants. C. J. Leaver, Ed. Plenum Pub. Corp. pp. 259-272.

5. Hall, T. C. and Kemp, J. D. 1981. Enhancing protein quality and quantity. In: Genetic Engineering. Proceedings of the Batelle Memorial Institute International Conference, V: 36-71.

6. Brown, J. W. S., Ersland, D. R., and Hall, T. C. 1982. Molecular aspects of storage protein synthesis during seed development. In: The Physiology and Biochemistry of Seed Development, Dormancy and Germination. A. A. Khan, Ed. Elsevier/North-Holland Biomedical Press. pp. 3-42.

7. Ersland, D., Brown, J. W. S., Casey, R. and Hall, T. C. 1983. The storage proteins of Phaseolus vulgaris L., Vicia faba L., and Pisum sativum L. In: Seed Proteins: Biochemistry, Genetics, Nutritive Value. W. Gottschalk and H. P. Muller, Eds. Martinus Nijhoff: The Hague. pp. 355-375.

8. Hall, T. C. 1983. Workshop summary: From test tube to farm. In: Plant Molecular Biology. U.C.L.A. Symposia on Molecular and Cellular Biology. R. B. Goldberg, Ed. Alan R. Liss, Inc., New York, New Series. 12: 481-484.

9. Hall, T. C., Slightom, J. L., Ersland, D. R., Murray, M. G., Hoffman, L. M., Adang, M. J., Brown, J. W. S., Ma, Y., Matthews, J. A., Cramer, J. H., Barker, R. F., Sutton, D. W., and Kemp, J. D. 1983. Phaseolin: Nucleotide sequence explains molecular weight and charge heterogeneity of a small multigene family and also assists vector construction for gene expression in alien tissue. In: Structure and Function of Plant Genomes. O. Ciferri and L. Dure, Eds. Plenum Press. pp. 123-142.

10. Hall, T. C., Slightom, J. L. Ersland, D. R., Scharf, P., Barker, R. F., Murray, M. G., Brown, J. W. S. and Kemp, J. D. 1983. The phaseolin family of seed protein genes: Sequences and properties. In: Advances in Gene Technology: Molecular Genetics of Plants and Animals. K. Downey, R. W. Voellmy, F. Ahmad and J. Schultz, Eds. Academic Press. pp. 349-367.

11. Kemp, J. D., Sutton, D. W., Fink, C., Barker, R. F., and Hall, T. C. 1983. Agrobacterium-mediated transfer of foreign genes into plants. In: Beltsville Symposia in Agriculture 7: Genetic Engineering Applications to Agriculture. L. D. Owens, Ed. Rowman & Allenheld, Totowa. pp. 215-228.

12. Slightom, J. L., Adang, M. J., Ersland, D. R., Hoffman, L. M., Murray, M. J. and Hall, T. C. 1983. French bean storage protein gene family: Organization, nucleotide sequence and expression. In: Manipulation and Expression of Genes in Eukaryotes. P. Nagley, A. W. Linnane, W. J. Peacock and J. A. Pateman, Eds. Academic Press, Inc., Sydney, Australia. pp.203-211.

13. Hall, T.C. 1985. Expression of plant genes in alien cellular environments. In: Oxford Surveys of Plant Molecular and Cell Biology. B. J. Miflin, Ed. Oxford University Press, N.Y. 2: 329-338.

14. Hall, T. C., Reichert, N. A., Sengupta-Gopalan, C., Cramer, J. H., Lea, K., Barker, R. F., Slightom, J. L., Klassy, R., Kemp, J. D. 1985. Regulation of bean ß-phaseolin gene expression in yeast and tobacco seed. In: Molecular Form and Function of the Plant Genome. L. van Vloten-Doting, G. S. P. Groot and T. C. Hall, Eds. Plenum Press, New York. pp. 517-529.

15. van Vloten-Doting, L., Groot, G. S. P. and Hall, T. C., Eds. 1985. Molecular Form and Function of the Plant Genome. Plenum Press, New York.

16. Bustos, M. M., Kalkan, F. A., Begum, D., Battraw, M. J. and Hall, T. C. 1992. Transcriptional and targeting determinants affecting phaseolin accumulation. In: Biotechnology and Nutrition. D. D. Bills and S.-D. Kung, eds. Butterworth-Heinemann, Boston. 215-235.

17. Hall, T. C. 1993. Revolutionary evolution. In: Transgenic Plants. S.-D. Kung and R. Wu, eds. Academic Press, Inc., Orlando. 247-255.

18. Hall, T. C., Chandrasekharan, M. B. and Li, G. 1999. Phaseolin: its past, properties, regulation and future. In: Seed Proteins. Casey, R. and Shewry, P. R., eds. Kluwer, Dordrecht, The Netherlands. 209-240.

19. Li, G., Chandrasekharan, M.B., Wolffe, A.P. and Hall, T.C. 2001. Chromatin structure and phaseolin gene regulation. Plant Mol. Biol. 46:121-129.

20. Li, G., Hall, T. C., and Holmes-Davis, R. 2002. Plant chromatin: development and gene control. Bioessays 24, 234-243.

B. Reviewed Papers

21. Hall, T. C., McLeester, R. C. and Bliss, F. A. 1972. Electrophoretic analysis of protein changes during the development of the French bean fruit. Phytochemistry 11: 647-649.

22. Bliss, F. A., Barker, L. N., Franckowiak, J. D. and Hall, T. C. 1973. Genetic and environmental variation of seed yield, yield components, and seed protein quantity and quality of cowpea. Crop Sci. 13: 656-660.

23. McLeester, R. C., Hall, T. C., Sun, S. M. and Bliss, F. A. 1973. Comparison of globulin proteins from Phaseolus vulgaris with those from Vicia faba. Phytochemistry 2: 85-93.

24. Sun, S. M., McLeester, R. C., Bliss, F. A. and Hall, T. C. 1974. Reversible and irreversible dissociation of globulins from Phaseolus vulgaris seed. J. Biol. Chem. 249: 2118-2121.

25. Romero, J., Sun, S. M., McLeester, R. C., Bliss, F. A. and Hall, T. C. 1975. Heritable variation in a polypeptide subunit of the major storage protein of the bean, Phaseolus vulgaris L. Plant Physiol. 56: 776-779.

26. Sun, S. M., Buchbinder, B. U., and Hall, T. C. 1975. Cell-free synthesis of the major storage protein of the bean, Phaseolus vulgaris L. Plant Physiol. 56: 780-785.

27. Sun, S. M., and Hall, T. C. 1975. Solubility characteristics of globulins from Phaseolus seeds in regard to their isolation and characterization. Agr. and Food Chem. 23: 184-189.

28. Stockman, D. R., Hall T. C. and Ryan, D. S. 1976. Affinity chromatography of the major seed protein of the bean (Phaseolus vulgaris L.) Plant Physiol. 58: 272-275.

29. Bliss, F. A. and Hall, T. C. 1977. Food legumes -- Compositional and nutritional changes induced by breeding. Cereal Foods World 22: 106-113.

30. Hall, T. C., Bliss, F. A., Ryan, D. S., and Sun, S. M. 1977. The subunit structure and cell-free synthesis of the major storage protein from bean (Phaseolus vulgaris L.) seeds. Colloques Internationaux du C.N.R.S. 261: 335-343.

31. Hall, T. C., McLeester, R. C. and Bliss, F. A. 1977. Equal expression of the maternal and paternal alleles for the polypeptide subunits of the major storage protein of the bean Phaseolus vulgaris L. Plant Physiol. 59: 1122-1124.

32. Hall, T. C., Ma, Y., Buchbinder, B. U., Pyne, J. W., Sun, S. M. and Bliss, F. A. 1978. Messenger RNA for G1 protein of French bean seeds: Cell-free translation and product characterization. Proc. Natl. Acad. Sci. USA 75: 3196-3200.

33. Sun, S. M., Mutschler, M. A., Bliss, F. A., and Hall, T. C. 1978. Protein synthesis and accumulation in bean cotyledons during growth. Plant Physiol. 61: 918-923.

34. Brown, J. W. S., Bliss, F. A. and Hall, T. C. 1980. Microheterogeneity of globulin-1 storage protein from French bean with isoelectrofocusing. Plant Physiol. 66: 838-840.

35. Ma, Y., Bliss, F. A. and Hall, T. C. 1980. Peptide mapping reveals considerable sequence homology among the three polypeptide subunits of G1 storage protein from French bean seed. Plant Physiol. 66: 897-902.

36. Mutschler, M. A., Bliss, F. A. and Hall, T. C. 1980. Variation in the accumulation of seed storage protein among genotypes of Phaseolus vulgaris (L.) Plant Physiol. 65: 627-630.

37. Brown, J. W. S., Bliss, F. A. and Hall, T. C. 1981. Linkage relationships between genes controlling seed proteins in French bean. Theoret. Appl. Genet. 60: 251-259.

38. Brown, J. W. S., Ma, Y., Bliss, F. A. and Hall, T. C. 1981. Genetic variation in the subunits of globulin-1 storage protein of French bean. Theoret. Appl. Genet. 59: 83-88.

39. Brown, J. W. S., Osborn, T. C., Bliss, F. A. and Hall, T. C. 1981. Genetic variation in the subunits of globulin-2 and albumin seed proteins of French bean. Theoret. Appl. Genet. 60: 245-250.

40. Matthews, J. A., Brown, J. W. S., and Hall, T. C. 1981. Phaseolin mRNA is translated to yield glycosylated polypeptides by Xenopus oocytes. Nature 294: 175-176.

41. Sun, S. M., Slightom, J. L. and Hall, T. C. 1981. Intervening sequences in a plant gene -- Comparison of the partial sequence of cDNA and genomic DNA of French bean phaseolin. Nature 289: 37-41.

42. Brown, J. W. S., McFerson, J. R., Bliss, F. A. and Hall, T. C. 1982. Genetic divergence among commercial classes of Phaseolus vulgaris in relation to phaseolin pattern. HortScience 17: 752-754.

43. Brown, J. W. S., Osborn, T. C., Bliss, F. A., and Hall, T. C. 1982a. Bean lectins I: Relationships between agglutinating activity and electrophoretic variation in the lectin-containing G2/albumin seed proteins of French bean (Phaseolus vulgaris L.) Theoret. Appl. Genet. 62: 263-271.

44. Brown, J. W. S., Osborn, T. C., Bliss, F. A., and Hall, T. C. 1982b. Bean lectins II: Relationship between qualitative lectin variation in Phaseolus vulgaris L. and previous observations on purified bean lectins. Theoret. Appl. Genet. 62: 361-367.

45. Murai, N., Sutton, D. W., Murray, M. G., Slightom, J. L., Merlo, D. J., Reichert, N. A., Sengupta-Gopalan, C., Stock, C. A., Barker, R. F., Kemp, J. D. and Hall, T. C. 1983. Phaseolin gene from bean is expressed after transfer to sunflower via tumor-inducing plasmid vectors. Science 222: 476-482.

46. Slightom, J. L., Sun, S. M. and Hall, T. C. 1983. Complete nucleotide sequence of a French bean storage protein gene: Phaseolin. Proc. Natl. Acad. Sci. USA 80: 1897-1901.

47. Blagrove, R. J., Lilley, G. G., Van Donkelaar, A., Sun, S. M. and Hall, T. C. 1984. Structural studies of a French bean storage protein: phaseolin. Int. J. Biol. Macromol. 6: 137-141.

48. Talbot, D.R., Adang, M.J., Slightom, J.L. and Hall, T.C. 1984. Size and organization of a multigene family encoding phaseolin, the major seed storage protein of Phaseolus vulgaris L. Mol. Gen. Genet. 198: 42-49.

49. Sengupta-Gopalan, C., Reichert, N. A., Barker, R. F., Hall, T. C., and Kemp, J. D. 1985. Developmentally regulated expression of the bean ß-phaseolin gene in tobacco seed. Proc. Natl. Acad. Sci. USA 82: 3320-3324.

50. Paaren, H. E., Slightom, J. L., Hall, T. C., Inglis, A. S. and Blagrove, R. J. 1987. Purification of a seed glycoprotein: N-terminal and deglycosylation analysis of phaseolin. Phytochemistry 26: 335-343.

51. Thomas, T. L. and Hall, T. C. 1987. Gene transfer and expression in plants: Implications and potential. Bioessays 3: 149-153.

52. Bustos, M. M., Luckow, V. A., Griffing, L. R., Summers, M. D. and Hall, T. C. 1988. Expression, glycosylation and secretion of phaseolin in a baculovirus system. Plant Mol. Biol. 10: 475-488.

53. Bustos, M. M., Guiltinan, M. J., Jordano, J., Begum, D., Kalkan F. A. and Hall, T. C. 1989. Regulation of ß-Glucuronidase expression in transgenic tobacco plants by an A/T rich, cis-acting sequence found upstream of a French bean ß-phaseolin gene. Plant Cell 1: 839-853.

54. Anthony, J. L., Vonder Haar, R. A. and Hall, T. C. 1990. Nucleotide sequence of an ß-phaseolin gene from Phaseolus vulgaris. Nucl. Acids Res. 18: 3396.

55. Yang, L., Domoney, C., Casey, R. and Hall, T. C. 1990. Processing Pisum sativum seed storage protein precursors in vitro. Cell Research 2: 153-162.

56. Anthony, J. L., Vonder Haar, R. A. and Hall, T. C. 1991. Nucleotide sequence of a genomic clone encoding arcelin, a lectin-like seed protein from Phaseolus vulgaris. Plant Physiol. 97: 839-840.

57. Bustos, M. M., Battraw, M. J., Kalkan, F. A., and Hall, T. C. 1991. Transient gene expression in electroporated bean cotyledon protoplasts. Plant Mol. Biol. Reporter 9: 322-332.

58. Bustos, M. M., Begum, D., Kalkan, F. A., Battraw, M. J. and Hall, T. C. 1991. Positive and negative cis-acting DNA domains are required for spatial and temporal regulation of gene expression by a seed storage protein promoter. EMBO J. 10: 1469-1479.

59. Bustos, M. M., Kalkan, F. A., VandenBosch, K. A. and Hall, T. C. 1991. Differential accumulation of four phaseolin glycoforms in transgenic tobacco. Plant Mol. Biol. 16: 381-395.

60. van der Geest, A. H. M., Hall, G. E., Spiker, S. and Hall, T. C. 1994. The ß-phaseolin gene is flanked by matrix attachment regions. Plant J. 6: 413-423.

61. Frisch, D. A., van der Geest, A. H. M., Dias, K. and Hall, T. C. 1995. Chromosomal integration is required for spatial regulation of expression from the ß-phaseolin promoter. Plant J. 7: 503-512.

62. van der Geest, A. H. M., Frisch, D. A., Kemp, J. D. and Hall, T. C. 1995. Cell ablation reveals that expression from the phaseolin promoter is confined to embryogenesis and microsporogenesis. Plant Physiol. 109: 1151-1158.

63. van der Geest, A. H. M. and Hall, T. C. 1996. A 68 bp element of the ß-phaseolin promoter functions as a seed-specific enhancer. Plant Mol. Biol. 32: 579-588.

64. van der Geest, A. H. M. and Hall, T. C. 1997. The ß-phaseolin 5' matrix attachment region acts as an enhancer facilitator. Plant Mol. Biol. 33: 553-557.

65. Li, G., Chandler, S. P., Wolffe, A. and Hall, T. C. 1998. Architectural specificity in chromatin structure at the TATA box in vivo: Nucleosome displacement upon ß-phaseolin gene activation. Proc. Natl. Acad. Sci. USA. 95: 4772-4777.

66. Vaucheret, H., Elmayan, T., Thierry, D., van der Geest, A., Hall, T., Conner, A. J., Mlynarova, L. and Nap, J. P. 1998. Flank matrix attachment regions (MARs) from chicken, bean, yeast or tobacco do not prevent homology-dependent trans-silencing in transgenic tobacco plants. Mol. Gen. Genet. 259: 388-392.

67. Hall, T.C., Li, G., and Chandrasekharan, M. 1998. Participation of chromatin in the regulation of phaseolin gene expression. J. Plant Physiol. 152: 614-620.

68. Li, G., Bishop, K. J., Chandrasekharan, M. B. and Hall, T. C. 1999. ß-phaseolin gene activation is a two-step process: PvAlf-facilitated chromatin modification followed by abscisic acid-mediated gene activation. Proc. Natl. Acad. Sci., U.S.A. 96: 7104-7109.

69. Li, G. and Hall, T. C. 1999. Footprinting in vivo reveals changing profiles of multiple factor interactions with the ß-phaseolin promoter during embryogenesis. Plant J. 18: 633-642.

70. Li, G., Bishop, K.J. and Hall, T.C. 2001. De novo activation of the ß-phaseolin promoter by phosphatase or protein synthesis inhibitors. J. Biol. Chem. 276: 2062-2068.

71. Chandrasekharan, M.B., Bishop, K.J. and Hall, T.C. 2003. Module-specific expression of the ß-phaseolin promoter during embryogenesis. Plant J. 33: 853-866.

72. Chandrasekharan, M.B., Li, G., Bishop, K.J. and Hall, T.C. 2003. S-phase progression is required for PvALF and ABA-mediated transcriptional activation. J. Biol. Chem. 278: 45397-45045.

73. Grace, M.L., Chandrasekharan, M.B., Hall, T.C. and Crowe, A.J. 2004. Sequence and spacing of TATA box elements are critical for accurate initiation of the ß-phaseolin promoter. J. Biol. Chem. 279: 8102-8110.

74. Ng, D. W-K, Chandrasekharan, M.B., Hall, T.C. 2004. The 5' UTR negatively regulates expression from the ABI3 promoter. Plant Mol. Biol. 54: 25-38.

75. Zhou, X, Chandrasekharan, M.B. Hall, T.C. 2004. High rooting frequency and functional analysis of GUS and GFP expression in transgenic Medicago truncatula A17. New Phytol. 162: 813-822.

76. Carranco, R., Chandrasekharan, M.B. Townsend, J.C. and Hall, T.C. 2004. Interaction of PvALF and VP1 B3 domains with the ß-phaseolin promoter. Plant Mol. Biol. 55: 221-237.

77. Ng, D. W-K, Chandrasekharan, M.B. and Hall, T.C. 2006. Ordered histone modifications are associated with transcriptional poising and activation of the Phaseolin promoter. Plant Cell 18: 119-132.

78. Ng, D.W.-K., and Hall, T.C. (2008). PvALF and FUS3 activate expression from the phaseolin promoter by different mechanisms. Plant Mol. Biol. 66: 233-244.

79. Emani, C., and Hall, T. C. (2008). Phaseolin: Structure and evolution. Open Evol. J. 2: 66-74.

Other Dicot Publications

1. Frisch, D. A., Harris-Haller, L., Yokubaitis, N. T., Thomas, T. L., Hardin, S. H., and Hall, T. C. 1995. Complete sequence of the binary vector Bin 19. Plant Mol. Biol. 27: 405-409.

2. Wang, T., Iyer, L.M, Pancholy, R., Shi, X and Hall, T. C. 2005.Assessment of penetrance and expressivity of RNAi-mediated silencing of the Arabidopsis phytoene desaturase gene. New Phytol. 167: 751-760.

3. Zhou, X, Carranco, R., Vitha, S, and Hall, T.C. 2005. The dark side of GFP. New Phytol. 168: 313-322.

4. Yang, G., and Hall T.C. 2006. HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana. Bioinformatics 22: 523-526.