|
| |
|
|
|
|
||||
| Home Help Feedback Subscriptions Archive Search Table of Contents | ||||
Journal of Experimental Biology, Vol 201, Issue 8 1099-1117, Copyright © 1998 by Company of Biologists
JOURNAL ARTICLES |
R Hardison
Department of Biochemistry, Pennsylvania State University, University Park, PA 16802, USA. rch8@psu.edu
The discovery of hemoglobins in virtually all kingdoms of organisms has shown (1) that the ancestral gene for hemoglobin is ancient, and (2) that hemoglobins can serve additional functions besides transport of oxygen between tissues, ranging from intracellular oxygen transport to catalysis of redox reactions. These different functions of the hemoglobins illustrate the acquisition of new roles by a pre-existing structural gene, which requires changes not only in the coding regions but also in the regulatory elements of the genes. The evolution of different regulated functions within an ancient gene family allows an examination of the types of biosequence data that are informative for various types of issues. Alignment of amino acid sequences is informative for the phylogenetic relationships among the hemoglobins in bacteria, fungi, protists, plants and animals. Although many of these diverse hemoglobins are induced by low oxygen concentrations, to date none of the molecular mechanisms for their hypoxic induction shows common regulatory proteins; hence, a search for matches in non-coding DNA sequences would not be expected to be fruitful. Indeed, alignments of non-coding DNA sequences do not reveal significant matches even between mammalian alpha- and beta-globin gene clusters, which diverged approximately 450 million years ago and are still expressed in a coordinated and balanced manner. They are in very different genomic contexts that show pronounced differences in regulatory mechanisms. The alpha-globin gene is in constitutively active chromatin and is encompassed by a CpG island, which is a dominant determinant of its regulation, whereas the beta-globin gene is in A+T-rich genomic DNA. Non-coding sequence matches are not seen between avian and mammalian beta-globin gene clusters, which diverged approximately 250 million years ago, despite the fact that regulation of both gene clusters requires tissue-specific activation of a chromatin domain regulated by a locus control region. The cis-regulatory sequences needed for domain opening and enhancement do show common binding sites for transcription factors. In contrast, alignments of non-coding sequences from species representing multiple eutherian mammalian orders, some of which diverged as long as 135 million years ago, are reliable predictors of novel cis-regulatory elements, both proximal and distal to the genes. Examples include a potential target for the hematopoietic transcription factor TAL1.
This article has been cited by other articles:
|
|
 |
|
  J. C. Opazo, F. G. Hoffmann, and J. F. Storz Differential loss of embryonic globin genes during the radiation of placental mammals PNAS, September 2, 2008; 105(35): 12950 - 12955. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Nishi, R. Inagi, H. Kato, M. Tanemoto, I. Kojima, D. Son, T. Fujita, and M. Nangaku Hemoglobin Is Expressed by Mesangial Cells and Reduces Oxidant Stress J. Am. Soc. Nephrol., August 1, 2008; 19(8): 1500 - 1508. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. F. Storz, F. G. Hoffmann, J. C. Opazo, and H. Moriyama Adaptive Functional Divergence Among Triplicated {alpha}-Globin Genes in Rodents Genetics, March 1, 2008; 178(3): 1623 - 1638. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. C. Opazo, F. G. Hoffmann, and J. F. Storz Genomic evidence for independent origins of {beta}-like globin genes in monotremes and therian mammals PNAS, February 5, 2008; 105(5): 1590 - 1595. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. G. Hoffmann and J. F. Storz The {alpha}D-Globin Gene Originated via Duplication of an Embryonic {alpha}-Like Globin Gene in the Ancestor of Tetrapod Vertebrates Mol. Biol. Evol., September 1, 2007; 24(9): 1982 - 1990. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G.-L. Zhou, L. Xin, W. Song, L.-J. Di, G. Liu, X.-S. Wu, D.-P. Liu, and C.-C. Liang Active Chromatin Hub of the Mouse {alpha}-Globin Locus Forms in a Transcription Factory of Clustered Housekeeping Genes. Mol. Cell. Biol., July 1, 2006; 26(13): 5096 - 5105. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Roesner, T. Hankeln, and T. Burmester Hypoxia induces a complex response of globin expression in zebrafish (Danio rerio) J. Exp. Biol., June 1, 2006; 209(11): 2129 - 2137. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. K. Das, S. Dewilde, J. M. Friedman, L. Moens, and D. L. Rousseau Multiple Active Site Conformers in the Carbon Monoxide Complexes of Trematode Hemoglobins J. Biol. Chem., April 28, 2006; 281(17): 11471 - 11479. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. D. Kingsley, J. Malik, R. L. Emerson, T. P. Bushnell, K. E. McGrath, L. A. Bloedorn, M. Bulger, and J. Palis "Maturational" globin switching in primary primitive erythroid cells Blood, February 15, 2006; 107(4): 1665 - 1672. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Ahituv, S. Prabhakar, F. Poulin, E. M. Rubin, and O. Couronne Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny Hum. Mol. Genet., October 15, 2005; 14(20): 3057 - 3063. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. N. Vinogradov, D. Hoogewijs, X. Bailly, R. Arredondo-Peter, M. Guertin, J. Gough, S. Dewilde, L. Moens, and J. R. Vanfleteren Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life PNAS, August 9, 2005; 102(32): 11385 - 11389. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Cassanova, K. M. O'Brien, B. T. Stahl, T. McClure, and R. O. Poyton Yeast Flavohemoglobin, a Nitric Oxide Oxidoreductase, Is Located in Both the Cytosol and the Mitochondrial Matrix: EFFECTS OF RESPIRATION, ANOXIA, AND THE MITOCHONDRIAL GENOME ON ITS INTRACELLULAR LEVEL AND DISTRIBUTION J. Biol. Chem., March 4, 2005; 280(9): 7645 - 7653. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-D. Song, X.-J. Sun, M. Deng, G.-W. Zhang, Y. Zhou, X.-Y. Wu, Y. Sheng, Y. Chen, Z. Ruan, C.-L. Jiang, et al. Hematopoietic gene expression profile in zebrafish kidney marrow PNAS, November 16, 2004; 101(46): 16240 - 16245. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Schmidt, F. Gerlach, A. Avivi, T. Laufs, S. Wystub, J. C. Simpson, E. Nevo, S. Saaler-Reinhardt, S. Reuss, T. Hankeln, et al. Cytoglobin Is a Respiratory Protein in Connective Tissue and Neurons, Which Is Up-regulated by Hypoxia J. Biol. Chem., February 27, 2004; 279(9): 8063 - 8069. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Geuens, I. Brouns, D. Flamez, S. Dewilde, J.-P. Timmermans, and L. Moens A Globin in the Nucleus! J. Biol. Chem., August 15, 2003; 278(33): 30417 - 30420. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Bailly, R. Leroy, S. Carney, O. Collin, F. Zal, A. Toulmond, and D. Jollivet The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection PNAS, May 13, 2003; 100(10): 5885 - 5890. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Gillemans, T. McMorrow, R. Tewari, A. W. K. Wai, C. Burgtorf, D. Drabek, N. Ventress, A. Langeveld, D. Higgs, K. Tan-Un, et al. Functional and comparative analysis of globin loci in pufferfish and humans Blood, April 1, 2003; 101(7): 2842 - 2849. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Harju, K. J. McQueen, and K. R. Peterson Chromatin Structure and Control of {beta}-Like Globin Gene Switching Experimental Biology and Medicine, October 1, 2002; 227(9): 683 - 700. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Bailly, D. Jollivet, S. Vanin, J. Deutsch, F. Zal, F. Lallier, and A. Toulmond Evolution of the Sulfide-Binding Function Within the Globin Multigenic Family of the Deep-Sea Hydrothermal Vent Tubeworm Riftia pachyptila Mol. Biol. Evol., September 1, 2002; 19(9): 1421 - 1433. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Hausladen, A. Gow, and J. S. Stamler Flavohemoglobin denitrosylase catalyzes the reaction of a nitroxyl equivalent with molecular oxygen PNAS, August 17, 2001; (2001) 181199698. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. H. Broyles, V. Belegu, C. R. DeWitt, S. N. Shah, C. A. Stewart, Q. N. Pye, and R. A. Floyd Specific repression of beta -globin promoter activity by nuclear ferritin PNAS, July 31, 2001; 98(16): 9145 - 9150. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. C. Hardison New views of evolution and regulation of vertebrate beta -like globin gene clusters from an orphaned gene in marsupials PNAS, February 13, 2001; 98(4): 1327 - 1329. [Full Text] [PDF]
|
|
|
|
 |
|
 D. T. Lau, A. Saeed-Kothe, S. K. Parker, and H. William Detrich III Adaptive Evolution of Gene Expression in Antarctic Fishes: Divergent Transcription of the 5'-to-5' Linked Adult {alpha}1- and {beta}-Globin Genes of the Antarctic Teleost Notothenia coriiceps is Controlled by Dual Promoters and Intergenic Enhancers Integr. Comp. Biol., February 1, 2001; 41(1): 113 - 132. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Wheeler, R. Hope, S. J. B. Cooper, G. Dolman, G. C. Webb, C. D. K. Bottema, A. A. Gooley, M. Goodman, and R. A. B. Holland An orphaned mammalian beta -globin gene of ancient evolutionary origin PNAS, January 30, 2001; 98(3): 1101 - 1106. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. K. Das, M. Couture, Y. Ouellet, M. Guertin, and D. L. Rousseau Simultaneous observation of the O---O and Fe---O2 stretching modes in oxyhemoglobins PNAS, January 16, 2001; 98(2): 479 - 484. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. H. J. Burr, P. Hunt, D. R. Wagar, S. Dewilde, M. L. Blaxter, J. R. Vanfleteren, and L. Moens A Hemoglobin with an Optical Function J. Biol. Chem., February 18, 2000; 275(7): 4810 - 4815. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Durner, A. J. Gow, J. S. Stamler, and J. Glazebrook Ancient origins of nitric oxide signaling in biological systems PNAS, December 7, 1999; 96(25): 14206 - 14207. [Full Text] [PDF]
|
|
|
|
|
|
S. S. Gross and P. Lane Physiological reactions of nitric oxide and hemoglobin: A radical rethink PNAS, August 31, 1999; 96(18): 9967 - 9969. [Full Text] [PDF]
|
|
|
|
|
|
L. Liu, M. Zeng, and J. S. Stamler Hemoglobin induction in mouse macrophages PNAS, June 8, 1999; 96(12): 6643 - 6647. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Membrillo-Hernandez, M. D. Coopamah, M. F. Anjum, T. M. Stevanin, A. Kelly, M. N. Hughes, and R. K. Poole The Flavohemoglobin of Escherichia coli Confers Resistance to a Nitrosating Agent, a "Nitric Oxide Releaser," and Paraquat and Is Essential for Transcriptional Responses to Oxidative Stress J. Biol. Chem., January 8, 1999; 274(2): 748 - 754. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Liu, M. Zeng, A. Hausladen, J. Heitman, and J. S. Stamler Protection from nitrosative stress by yeast flavohemoglobin PNAS, April 25, 2000; 97(9): 4672 - 4676. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Hausladen, A. Gow, and J. S. Stamler Flavohemoglobin denitrosylase catalyzes the reaction of a nitroxyl equivalent with molecular oxygen PNAS, August 28, 2001; 98(18): 10108 - 10112. [Abstract] [Full Text] [PDF]
|
|
