Mutational dynamics of murine angiogenin duplicates

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Codõer, Francisco M ^b   Alfonso Loeches, Silvia ^c   Fares, Mario A ^a,d  

^a TRINITY COLLEGE DUBLIN   (Ireland)

^b HOSPITAL UNIVERSITARI GERMANS TRIAS I PUJOL   (Spain)

^c CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

^d Ciudad Politécnica de la Innovación   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BLOOD; CANCER; DIVERGENCE; EVOLUTIONARY BIOLOGY; GENE; MUTATION; NEUROLOGY; PHYLOGENETICS; PROTEIN;

MAMMALIA; MURINAE; RATTUS; VERTEBRATA;

ANGIOGENIN; PANCREATIC RIBONUCLEASE;

ANIMAL; ARTICLE; CHEMISTRY; GENE DUPLICATION; GENETICS; MOLECULAR EVOLUTION; MOUSE; MUTATION; PHYLOGENY; PROTEIN SECONDARY STRUCTURE; RAT;

ANIMALS; EVOLUTION, MOLECULAR; GENE DUPLICATION; MICE; MUTATION; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; RATS; RIBONUCLEASE, PANCREATIC;

EID: 77957924791     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-310     Document Type: Article

References (78)

1. Amino acid sequence of human tumor derived angiogenin. DJ Strydom JW Fett RR Lobb EM Alderman JL Bethune JF Riordan BL Vallee, Biochemistry 1985 24 20 5486 5494 10.1021/bi00341a031 2866794
2. Evolution of vertebrates. JJ Beintema HJ Breukelman A Carsana A Furia, Ribonucleases: Structure and Function New York: Academic Press New York 1997
3. The angiogenins: an emerging family of ribonuclease related proteins with diverse cellular functions. SA Adams V Subramanian, Angiogenesis 1999 3 3 189 199 10.1023/A:1009015512200 14517418
4. Structure and function of angiogenin. JF Riordan, Ribonucleases: Structure and Function New York: Academic Press New York 1997
5. Angiogenin: a review of the pathophysiology and potential clinical applications. A Tello-Montoliu JV Patel GY Lip, J Thromb Haemost 2006 4 9 1864 1874 10.1111/j.1538-7836.2006.01995.x 16961595
6. A monoclonal antibody to human angiogenin. Inhibition of ribonucleolytic and angiogenic activities and localization of the antigenic epitope. JW Fett KA Olson SM Rybak, Biochemistry 1994 33 18 5421 5427 10.1021/bi00184a010 7514035
7. A monoclonal antibody to human angiogenin suppresses tumor growth in athymic mice. KA Olson TC French BL Vallee JW Fett, Cancer Res 1994 54 17 4576 4579 8062244
8. Angiogenin antagonists prevent tumor growth in vivo. KA Olson JW Fett TC French ME Key BL Vallee, Proc Natl Acad Sci USA 1995 92 2 442 446 10.1073/pnas.92.2.442 7831307
9. Prevention of human prostate tumor metastasis in athymic mice by antisense targeting of human angiogenin. KA Olson HR Byers ME Key JW Fett, Clin Cancer Res 2001 7 11 3598 3605 11705882
10. Chimeric anti-angiogenin antibody cAb 26-2F inhibits the formation of human breast cancer xenografts in athymic mice. R Piccoli KA Olson BL Vallee JW Fett, Proc Natl Acad Sci USA 1998 95 8 4579 4583 10.1073/pnas.95.8.4579 9539780
11. A small-molecule inhibitor of the ribonucleolytic activity of human angiogenin that possesses antitumor activity. RY Kao JL Jenkins KA Olson ME Key JW Fett R Shapiro, Proc Natl Acad Sci USA 2002 99 15 10066 10071 10.1073/pnas.152342999 12118120
12. ANG mutations segregate with familial and 'sporadic' amyotrophic lateral sclerosis. MJ Greenway PM Andersen C Russ S Ennis S Cashman C Donaghy V Patterson R Swingler D Kieran J Prehn, et al. Nat Genet 2006 38 4 411 413 10.1038/ng1742 16501576
13. Characterization of human angiogenin variants implicated in amyotrophic lateral sclerosis. B Crabtree N Thiyagarajan SH Prior P Wilson S Iyer T Ferns R Shapiro K Brew V Subramanian KR Acharya, Biochemistry 2007 46 42 11810 11818 10.1021/bi701333h 17900154 (Pubitemid 47623749)
14. Angiogenin loss-of-function mutations in amyotrophic lateral sclerosis. D Wu W Yu H Kishikawa RD Folkerth AJ Iafrate Y Shen W Xin K Sims GF Hu, Ann Neurol 2007 62 6 609 617 10.1002/ana.21221 17886298
15. Isolation and characterization of angiogenin, an angiogenic protein from human carcinoma cells. JW Fett DJ Strydom RR Lobb EM Alderman JL Bethune JF Riordan BL Vallee, Biochemistry 1985 24 20 5480 5486 10.1021/bi00341a030 4074709
16. Crystal structure of human angiogenin reveals the structural basis for its functional divergence from ribonuclease. KR Acharya R Shapiro SC Allen JF Riordan BL Vallee, Proc Natl Acad Sci USA 1994 91 8 2915 2919 10.1073/pnas.91.8.2915 8159679
17. Characteristic ribonucleolytic activity of human angiogenin. R Shapiro JF Riordan BL Vallee, Biochemistry 1986 25 12 3527 3532 10.1021/bi00360a008 2424496
18. Sites of modification of human angiogenin by bromoacetate at pH 5.5. R Shapiro DJ Strydom S Weremowicz BL Vallee, Biochem Biophys Res Commun 1988 156 1 530 536 10.1016/S0006-291X(88)80874-X 3178849
19. A covalent angiogenin/ribonuclease hybrid with a fourth disulfide bond generated by regional mutagenesis. JW Harper BL Vallee, Biochemistry 1989 28 4 1875 1884 10.1021/bi00430a067 2719939
20. Role of glutamine-117 in the ribonucleolytic activity of human angiogenin. N Russo R Shapiro KR Acharya JF Riordan BL Vallee, Proc Natl Acad Sci USA 1994 91 8 2920 2924 10.1073/pnas.91.8.2920 8159680
21. Structural features that determine the enzymatic potency and specificity of human angiogenin: threonine-80 and residues 58-70 and 116-123. R Shapiro, Biochemistry 1998 37 19 6847 6856 10.1021/bi9800146 9578571
22. Crystallographic studies on structural features that determine the enzymatic specificity and potency of human angiogenin: Thr44, Thr80, and residues 38-41. DE Holloway GB Chavali MC Hares MD Baker GV Subbarao R Shapiro KR Acharya, Biochemistry 2004 43 5 1230 1241 10.1021/bi035654+ 14756559
23. Crystallographic studies on the role of the C-terminal segment of human angiogenin in defining enzymatic potency. DD Leonidas R Shapiro GV Subbarao A Russo KR Acharya, Biochemistry 2002 41 8 2552 2562 10.1021/bi015768q 11851402
24. Role of lysines in human angiogenin: chemical modification and site-directed mutagenesis. R Shapiro EA Fox JF Riordan, Biochemistry 1989 28 4 1726 1732 10.1021/bi00430a045 2497770
25. Site-directed mutagenesis of histidine-13 and histidine-114 of human angiogenin. Alanine derivatives inhibit angiogenin-induced angiogenesis. R Shapiro BL Vallee, Biochemistry 1989 28 18 7401 7408 10.1021/bi00444a038 2479414
26. Alteration of the enzymatic specificity of human angiogenin by site-directed mutagenesis. TP Curran R Shapiro JF Riordan, Biochemistry 1993 32 9 2307 2313 10.1021/bi00060a023 8095159
27. A combined kinetic and modeling study of the catalytic center subsites of human angiogenin. N Russo KR Acharya BL Vallee R Shapiro, Proc Natl Acad Sci USA 1996 93 2 804 808 10.1073/pnas.93.2.804 8570639
28. Dual site model for the organogenic activity of angiogenin. TW Hallahan R Shapiro BL Vallee, Proc Natl Acad Sci USA 1991 88 6 2222 2226 10.1073/pnas.88.6.2222 2006161
29. Importance of asparagine-61 and asparagine-109 to the angiogenic activity of human angiogenin. TW Hallahan R Shapiro DJ Strydom BL Vallee, Biochemistry 1992 31 34 8022 8029 10.1021/bi00149a036 1380830
30. Identification of the nucleolar targeting signal of human angiogenin. J Moroianu JF Riordan, Biochem Biophys Res Commun 1994 203 3 1765 1772 10.1006/bbrc.1994.2391 7945327
31. Characterization of mouse angiogenin-related protein: implications for functional studies on angiogenin. V Nobile BL Vallee R Shapiro, Proc Natl Acad Sci USA 1996 93 9 4331 4335 10.1073/pnas.93.9.4331 8633065
32. mAngiogenin-3, a target gene of oncoprotein E2a-Pbx1, encodes a new angiogenic member of the angiogenin family. X Fu WG Roberts V Nobile R Shapiro MP Kamps, Growth Factors 1999 17 2 125 137 10.3109/08977199909103521 10595312
33. Biological and structural features of murine angiogenin-4, an angiogenic protein. B Crabtree DE Holloway MD Baker KR Acharya V Subramanian, Biochemistry 2007 46 9 2431 2443 10.1021/bi062158n 17279775
34. The mouse angiogenin gene family: structures of an angiogenin-related protein gene and two pseudogenes. WE Brown V Nobile V Subramanian R Shapiro, Genomics 1995 29 1 200 206 10.1006/geno.1995.1232 8530072
35. The angiogenins. DJ Strydom, Cell Mol Life Sci 1998 54 8 811 824 10.1007/s000180050210 9760990
36. Rapid evolution of the ribonuclease A superfamily: adaptive expansion of independent gene clusters in rats and mice. NA Singhania KD Dyer J Zhang MS Deming CA Bonville JB Domachowske HF Rosenberg, J Mol Evol 1999 49 6 721 728 10.1007/PL00006594 10594173
37. The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories. S Cho JJ Beintema J Zhang, Genomics 2005 85 2 208 220 10.1016/j.ygeno.2004.10.008 15676279
38. Structural and functional implications of positive selection at the primate angiogenin gene. DS Osorio A Antunes MJ Ramos, BMC Evol Biol 2007 7 167 10.1186/1471-2148-7-167 17883850
39. Diversifying selection of the tumor-growth promoter angiogenin in primate evolution. J Zhang HF Rosenberg, Mol Biol Evol 2002 19 4 438 445 11919285
40. Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo. DE Wildman M Uddin G Liu LI Grossman M Goodman, Proc Natl Acad Sci USA 2003 100 12 7181 7188 10.1073/pnas.1232172100 12766228
41. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. H Shimodaira M Hasegawa, Mol Biol Evol 1999 16 1114 1116
42. The probability of preservation of a newly arisen gene duplicate. M Lynch M O'Hely B Walsh A Force, Genetics 2001 159 4 1789 1804 11779815
43. Nuclear translocation of angiogenin in proliferating endothelial cells is essential to its angiogenic activity. J Moroianu JF Riordan, Proc Natl Acad Sci USA 1994 91 5 1677 1681 10.1073/pnas.91.5.1677 8127865
44. Maximum-likelihood approach for gene family evolution under functional divergence. X Gu, Mol Biol Evol 2001 18 4 453 464 11264396
45. Statistical methods for testing functional divergence after gene duplication. X Gu, Mol Biol Evol 1999 16 12 1664 1674 10605109
46. Evolution by Gene duplication. S Ohno, Berlin: Springer-Verlag 1970
47. Evolution of genetic redundancy. MA Nowak MC Boerlijst J Cooke JM Smith, Nature 1997 388 6638 167 171 10.1038/40618 9217155
48. The evolutionary fate and consequences of duplicate genes. M Lynch JS Conery, Science 2000 290 5494 1151 1155 10.1126/science.290.5494.1151 11073452
49. The evolution of gene duplication: classifying and distinguishing between models. H Innan F Kondrashov, Nat Rev Genet 2010 11 97 108 10.1038/nrg2689 20051986
50. Shifts in the selection-drift balance drive the evolution and epidemiology of foot-and-mouth disease virus. DC Tully MA Fares, J Virol 2009 83 2 781 790 10.1128/JVI.01500-08 19004952
51. Model building by comparison at CASP3: using expert knowledge and computer automation. PA Bates MJ Sternberg, Proteins 1999 3 47 54 10.1002/(SICI)1097-0134(1999)37:3+<47::AID-PROT73.0.CO;2-F 10526351
52. Domain fishing: a first step in protein comparative modelling. B Contreras-Moreira PA Bates, Bioinformatics 2002 18 8 1141 1142 10.1093/bioinformatics/18.8.1141 12176841
53. Computational analysis of the active sites in binary and ternary complexes of the vitamin D receptor. W Sicinska P Rotkiewicz, J Steroid Biochem Mol Biol 2007 103 3-5 305 309 10.1016/j.jsbmb.2006.12.077 17267206
54. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. RC Edgar, BMC Bioinformatics 2004 5 113 10.1186/1471-2105-5-113 15318951
55. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucleic Acids Res 2004 32 5 1792 1797 10.1093/nar/gkh340 15034147
56. ProtTest: selection of best-fit models of protein evolution. F Abascal R Zardoya D Posada, Bioinformatics 2005 21 9 2104 2105 10.1093/bioinformatics/ bti263 15647292
57. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 5 696 704 10.1080/10635150390235520 14530136
58. Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination. H Akashi, Genetics 1999 151 1 221 238 9872962
59. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. KA Crandall CR Kelsey H Imamichi HC Lane NP Salzman, Mol Biol Evol 1999 16 3 372 382 10331263
60. In search of molecular darwinism. PM Sharp, Nature 1997 385 6612 111 112 10.1038/385111a0 8990106
61. Hearing silence: non-neutral evolution at synonymous sites in mammals. JV Chamary JL Parmley LD Hurst, Nat Rev Genet 2006 7 2 98 108 10.1038/nrg1770 16418745
62. Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. I Mayrose A Doron-Faigenboim E Bacharach T Pupko, Bioinformatics 2007 23 13 319 327 10.1093/bioinformatics/btm176 17646313
63. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. JL Parmley JV Chamary LD Hurst, Mol Biol Evol 2006 23 2 301 309 10.1093/molbev/msj035 16221894
64. Widespread positive selection in synonymous sites of mammalian genes. AM Resch L Carmel L Marino-Ramirez AY Ogurtsov SA Shabalina IB Rogozin EV Koonin, Mol Biol Evol 2007 24 8 1821 1831 10.1093/molbev/msm100 17522087
65. PAML 4: phylogenetic analysis by maximum likelihood. Z Yang, Mol Biol Evol 2007 24 8 1586 1591 10.1093/molbev/msm088 17483113
66. Variance to mean ratio, R(t), for poisson processes on phylogenetic trees. N Goldman, Mol Phylogenet Evol 1994 3 3 230 239 10.1006/mpev.1994.1025 7820287
67. Statistical properties of a DNA sample under the finite-sites model. Z Yang, Genetics 1996 144 4 1941 1950 8978077
68. A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. MA Fares SF Elena J Ortiz A Moya E Barrio, J Mol Evol 2002 55 5 509 521 10.1007/s00239-002-2346-9 12399925
69. SWAPSC: sliding window analysis procedure to detect selective constraints. MA Fares, Bioinformatics 2004 20 16 2867 2868 10.1093/ bioinformatics/bth303 15130925
70. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. WH Li, J Mol Evol 1993 36 1 96 99 10.1007/BF02407308 8433381
71. A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. MA Fares SA Travers, Genetics 2006 173 1 9 23 10.1534/genetics.105.053249 16547113
72. CAPS: coevolution analysis using protein sequences. MA Fares D McNally, Bioinformatics 2006 22 22 2821 2822 10.1093/bioinformatics/btl493 17005535
73. Functional coevolutionary networks of the Hsp70-Hop-Hsp90 system revealed through computational analyses. SA Travers MA Fares, Mol Biol Evol 2007 24 4 1032 1044 10.1093/molbev/msm022 17267421
74. A study of the coevolutionary patterns operating within the env gene of the HIV-1 group M subtypes. SA Travers DC Tully GP McCormack MA Fares, Mol Biol Evol 2007 24 12 2787 2801 10.1093/molbev/msm213 17921487
75. Amino acid substitution matrices from protein blocks. S Henikoff JG Henikoff, Proc Natl Acad Sci USA 1992 89 22 10915 10919 10.1073/pnas.89.22.10915 1438297
76. Resampling-based multiple testing. P Westfall S Young, New York: John Wiley & Sons 1993
77. Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. WR Atchley KR Wollenberg WM Fitch W Terhalle AW Dress, Mol Biol Evol 2000 17 1 164 178 10666716
78. Inferred Biomolecular Interaction Server - a web server to analyze and predict protein interacting partners and binding sites. BA Shoemaker D Zhang RR Thangudu M Tyagi JH Fong A Marchler-Bauer SH Bryant T Madej AR Panchenko, Nucleic Acids Res 2010 38 D 518 24 10.1093/nar/gkp842