Comparative genomic analysis of eutherian interferon-γ-inducible GTPases

Functional and Integrative Genomics

Volumn 12, Issue 4, 2012, Pages 599-607

  Premzl, Marko ^a  

^a Laboratory of Genomics   (Croatia)

Author keywords

Comparative genomic analysis; Gene annotations; Interferon inducible GTPases; Molecular evolution; Phylogenetic analysis

Indexed keywords

GAMMA INTERFERON INDUCIBLE GUANOSINE TRIPHOSPHATASE; GUANOSINE TRIPHOSPHATASE; UNCLASSIFIED DRUG; GAMMA INTERFERON;

ENZYME INDUCTION; GENE CLUSTER; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PLACENTAL MAMMALS; PRIORITY JOURNAL; PROMOTER REGION; RELIABILITY; REVIEW; ANIMAL; CLASSIFICATION; GENETICS; GENOME; MAMMAL; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY;

EUTHERIA;

ANIMALS; CLASSIFICATION; EVOLUTION, MOLECULAR; GENOME; GTP PHOSPHOHYDROLASES; INTERFERON-GAMMA; MAMMALS; MOLECULAR SEQUENCE ANNOTATION; MULTIGENE FAMILY; PHYLOGENY;

EID: 84877077267     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-012-0291-2     Document Type: Review

References (31)

1. Bekpen C, Hunn JP, Rohde C, Parvanova I, Guethlein L, Dunn DM, Glowalla E, Leptin M, Howard JC (2005) The interferon-inducible p47 (IRG) GTPases in vertebrates: loss of the cell autonomous resistance mechanism in the human lineage. Genome Biol 6:R92
2. Bekpen C, Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB, Ventura M, Kidd JM, Siswara P, Howard JC, Eichler EE (2009) Death and resurrection of the human IRGM gene. PLoS Genet 5:e1000403
3. Boehm U, Guethlein L, Klamp T, Ozbek K, Schaub A, Fütterer A, Pfeffer K, Howard JC (1998) Two families of GTPases dominate the complex cellular response to IFN-γ. J Immunol 161:6715-6723
4. Carlow DA, Marth J, Clark-Lewis I, Teh HS (1995) Isolation of a gene encoding a developmentally regulated T cell-specific protein with a guanine nucleotide triphosphate-binding motif. J Immunol 154:1724-1734
5. Carlow DA, Teh SJ, Teh HS (1998) Specific antiviral activity demonstrated by TGTP, a member of a new family of interferon-induced GTPases. J Immunol 161:2348-2355
6. Colicelli J (2004) Human RAS superfamily proteins and related GTPases. Sci STKE 2004:RE13
7. Collazo CM, Yap GS, Sempowski GD, Lusby KC, Tessarollo L, Woude GF, Sher A, Taylor GA (2001) Inactivation of LRG-47 and IRG-47 reveals a family of interferon γ-inducible genes with essential, pathogen-specific roles in resistance to infection. J Exp Med 194:181-188
8. Feng CG, Collazo-Custodio CM, Eckhaus M, Hieny S, Belkaid Y, Elkins K, Jankovic D, Taylor GA, Sher A (2004) Mice deficient in LRG-47 display increased susceptibility to mycobacterial infection associated with the induction of lymphopenia. J Immunol 172:1163-1168
9. Feng CG, Weksberg DC, Taylor GA, Sher A, Goodell MA (2008) The p47 GTPase Lrg-47 (Irgm1) links host defense and hematopoietic stem cell proliferation. Cell Stem Cell 2:83-89
10. Ghosh A, Uthaiah R, Howard J, Herrmann C, Wolf E (2004) Crystal structure of IIGP1: a paradigm for interferon-inducible p47 resistance GTPases. Mol Cell 15:727-739
11. Gilly M, Wall R (1992) The IRG-47 gene is IFN-γ induced in B cells and encodes a protein with GTP-binding motifs. J Immunol 148:3275-3281
12. Gilly M, Damore MA, Wall R (1996) A promoter ISRE and dual 5′ YY1 motifs control IFN-γ induction of the IRG-47 G-protein gene. Gene 179:237-244
13. Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C, Antonarakis SE, Brent MR (2003) Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci U S A 100:1140-1145
14. Henry SC, Daniell XG, Burroughs AR, Indaram M, Howell DN, Coers J, Starnbach MN, Hunn JP, Howard JC, Feng CG, Sher A, Taylor GA (2009) Balance of Irgm protein activities determines IFN-γ-induced host defense. J Leukoc Biol 85:877-885
15. Henry SC, Traver M, Daniell X, Indaram M, Oliver T, Taylor GA (2010) Regulation of macrophage motility by Irgm1. J Leukoc Biol 87:333-343
16. Howard J (2008) The IRG proteins: a function in search of a mechanism. Immunobiology 213:367-375
17. Khaminets A, Hunn JP, Könen-Waisman S, Zhao YO, Preukschat D, Coers J, Boyle JP, Ong YC, Boothroyd JC, Reichmann G, Howard JC (2010) Coordinated loading of IRG resistance GTPases on to the Toxoplasma gondii parasitophorous vacuole. Cell Microbiol 12:939-961
18. Klamp T, Boehm U, Schenk D, Pfeffer K, Howard JC (2003) A giant GTPase, very large inducible GTPase-1, is inducible by IFNs. J Immunol 171:1255-1265
19. Lafuse WP, Brown D, Castle L, Zwilling BS (1995) Cloning and characterization of a novel cDNA that is IFN-γ-induced in mouse peritoneal macrophages and encodes a putative GTP-binding protein. J Leukoc Biol 57:477-483
20. Li G, Zhang J, Sun Y, Wang H, Wang Y (2009) The evolutionarily dynamic IFN-inducible GTPase proteins play conserved immune functions in vertebrates and cephalochordates. Mol Biol Evol 26:1619-1630
21. MacMicking JD (2004) IFN-inducible GTPases and immunity to intracellular pathogens. Trends Immunol 25:601-609
22. Margulies EH, Vinson JP, Comparative Sequencing Program NISC, Miller W, Jaffe DB, Lindblad-Toh K, Chang JL, Green ED, Lander ES, Mullikin JC, Clamp M (2005) An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proc Natl Acad Sci USA 102:4795-4800
23. Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ (2001) Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618
24. Prescott NJ, Dominy KM, Kubo M, Lewis CM, Fisher SA, Redon R, Huang N, Stranger BE, Blaszczyk K, Hudspith B, Parkes G, Hosono N, Yamazaki K, Onnie CM, Forbes A, Dermitzakis ET, Nakamura Y, Mansfield JC, Sanderson J, Hurles ME, Roberts RG, Mathew CG (2010) Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease. Hum Mol Genet 19:1828-1839
25. Singh SB, Davis AS, Taylor GA, Deretic V (2006) Human IRGM induces autophagy to eliminate intracellular mycobacteria. Science 313:1438-1441
26. Sorace JM, Johnson RJ, Howard DL, Drysdale BE (1995) Identification of an endotoxin and IFN-inducible cDNA: possible identification of a novel protein family. J Leukoc Biol 58:477-484
27. Taylor GA (2007) IRG proteins: key mediators of interferon-regulated host resistance to intracellular pathogens. Cell Microbiol 9:1099-1107
28. Taylor GA, Jeffers M, Largaespada DA, Jenkins NA, Copeland NG, Woude GF (1996) Identification of a novel GTPase, the inducibly expressed GTPase, that accumulates in response to interferon γ. J Biol Chem 271:20399-20405
29. Taylor GA, Collazo CM, Yap GS, Nguyen K, Gregorio TA, Taylor LS, Eagleson B, Secrest L, Southon EA, Reid SW, Tessarollo L, Bray M, McVicar DW, Komschlies KL, Young HA, Biron CA, Sher A, Vande Woude GF (2000) Pathogen-specific loss of host resistance in mice lacking the IFN-γ-inducible gene IGTP. Proc Natl Acad Sci USA 97:751-755
30. Zeng J, Parvanova IA, Howard JC (2009) A dedicated promoter drives constitutive expression of the cell-autonomous immune resistance GTPase, Irga6 (IIGP1) in mouse liver. PLoS One 4:e6787
31. Zhao YO, Könen-Waisman S, Taylor GA, Martens S, Howard JC (2010) Localisation and mislocalisation of the interferon-inducible immunity-related GTPase, Irgm1 (LRG-47) in mouse cells. PLoS One 5:e8648