Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLαs/ALEX Relay

XLαs and ALEX are structurally unrelated mammalian proteins translated from alternative overlapping reading frames of a single transcript. Not only are they encoded by the same locus, but a specific XLαs/ALEX interaction is essential for G-protein signaling in neuroendocrine cells. A disruption of this interaction leads to abnormal human phenotypes, including mental retardation and growth deficiency. The region of overlap between the two reading frames evolves at a remarkable speed: the divergence between human and mouse ALEX polypeptides makes them virtually unalignable. To trace the evolution of this puzzling locus, we sequenced it in apes, Old World monkeys, and a New World monkey. We show that the overlap between the two reading frames and the physical interaction between the two proteins force the locus to evolve in an unprecedented way. Namely, to maintain two overlapping protein-coding regions the locus is forced to have high GC content, which significantly elevates its intrinsic evolutionary rate. However, the two encoded proteins cannot afford to change too quickly relative to each other as this may impair their interaction and lead to severe physiological consequences. As a result XLαs and ALEX evolve in an oscillating fashion constantly balancing the rates of amino acid replacements. This is the first example of a rapidly evolving locus encoding interacting proteins via overlapping reading frames, with a possible link to the origin of species-specific neurological differences.

[1]  D. Bonthron,et al.  The human GNAS1 gene is imprinted and encodes distinct paternally and biallelically expressed G proteins. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[2]  W. Huttner,et al.  XL alpha s is a new type of G protein. , 1994, Nature.

[3]  D. Bonthron,et al.  Bidirectional imprinting of a single gene: GNAS1 encodes maternally, paternally, and biallelically derived proteins. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Z. Yang,et al.  Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. , 1998, Molecular biology and evolution.

[5]  F. Giannelli,et al.  Mutation rates in humans. II. Sporadic mutation-specific rates and rate of detrimental human mutations inferred from hemophilia B. , 1999, American journal of human genetics.

[6]  W. Huttner,et al.  Two overlapping reading frames in a single exon encode interacting proteins—a novel way of gene usage , 2001, The EMBO journal.

[7]  G. Schultz,et al.  Characterization of the extra-large G protein alpha-subunit XLalphas. II. Signal transduction properties. , 2000, The Journal of biological chemistry.

[8]  N. Goldman,et al.  A codon-based model of nucleotide substitution for protein-coding DNA sequences. , 1994, Molecular biology and evolution.

[9]  W. Huttner,et al.  XLαs is a new type of G protein , 1994, Nature.

[10]  D. Labie,et al.  Molecular Evolution , 1991, Nature.

[11]  L. Birnbaumer,et al.  XLαs, the extra-long form of the α-subunit of the Gs G protein, is significantly longer than suspected, and so is its companion Alex , 2004 .

[12]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

[13]  G. Schultz,et al.  Characterization of the Extra-large G Protein α-Subunit XLαs , 2000, The Journal of Biological Chemistry.

[14]  Adam Eyre-Walker,et al.  Molecular Evolution by Wen-Hsiung Li. Published by Sinauer Associates, Sunderland, MA, USA. ISBN: 0-87893-463-4 (cloth). , 1997 .

[15]  F. Zindy,et al.  Alternative reading frames of the INK4a tumor suppressor gene encode two unrelated proteins capable of inducing cell cycle arrest , 1995, Cell.

[16]  M. Nei,et al.  Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. , 1986, Molecular biology and evolution.

[17]  Stevan R. Hubbard,et al.  IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA , 2002, Nature.

[18]  D. Krakauer,et al.  STABILITY AND EVOLUTION OF OVERLAPPING GENES , 2000, Evolution; international journal of organic evolution.

[19]  H. Pasolli,et al.  Characterization of the Extra-large G Protein α-Subunit XLαs , 2000, The Journal of Biological Chemistry.

[20]  L. Birnbaumer,et al.  XLalphas, the extra-long form of the alpha-subunit of the Gs G protein, is significantly longer than suspected, and so is its companion Alex. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[21]  W. Huttner,et al.  CORRECTIONS: XLαs is a new type of G protein , 1995, Nature.

[22]  J. Vermylen,et al.  Functional polymorphisms in the paternally expressed XLalphas and its cofactor ALEX decrease their mutual interaction and enhance receptor-mediated cAMP formation. , 2003, Human molecular genetics.

[23]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[24]  M Krawczak,et al.  Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes. , 1998, American journal of human genetics.

[25]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[26]  Eugene V Koonin,et al.  Purifying and directional selection in overlapping prokaryotic genes. , 2002, Trends in genetics : TIG.

[27]  H. Pasolli,et al.  Characterization of the extra-large G protein alpha-subunit XLalphas. I. Tissue distribution and subcellular localization. , 2000, The Journal of biological chemistry.

[28]  S. O’Brien,et al.  Mapping of the gene encoding the alpha subunit of the stimulatory G protein of adenylyl cyclase (GNAS1) to 20q13.2----q13.3 in human by in situ hybridization. , 1991, Genomics.

[29]  Z. Yang,et al.  Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. , 2000, Molecular biology and evolution.

[30]  H. Soreq,et al.  Acetylcholinesterase and butyrylcholinesterase genes coamplify in primary ovarian carcinomas. , 1990, The Journal of clinical investigation.

[31]  Mouse Genome Sequencing Consortium.  Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[32]  Nahum Sonenberg,et al.  Gene Fusion and Overlapping Reading Frames in the Mammalian Genes for 4E-BP3 and MASK* , 2003, Journal of Biological Chemistry.

[33]  J. L. Jensen,et al.  A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames. , 2001, Molecular biology and evolution.

[34]  S. Sunyaev,et al.  Dobzhansky–Muller incompatibilities in protein evolution , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Carsten Schwarz,et al.  Genomewide comparison of DNA sequences between humans and chimpanzees. , 2002, American journal of human genetics.

[36]  J. Vermylen,et al.  Genetic Variation of the Extra-large Stimulatory G Protein α-Subunit Leads to Gs Hyperfunction in Platelets and Is a Risk Factor for Bleeding , 2001, Thrombosis and Haemostasis.

[37]  G. Kelsey,et al.  The imprinted signaling protein XLαs is required for postnatal adaptation to feeding , 2004, Nature Genetics.

[38]  Ziheng Yang,et al.  Statistical methods for detecting molecular adaptation , 2000, Trends in Ecology & Evolution.

[39]  Y. Kaziro,et al.  Isolation and characterization of the human Gs alpha gene. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[40]  G. Kelsey,et al.  The imprinted signaling protein XL alpha s is required for postnatal adaptation to feeding. , 2004, Nature genetics.