Evolution of Conditional Cooperativity Between HOXA11 and FOXO1 Through Allosteric Regulation

Evolution of Conditional Cooperativity Between HOXA11 and FOXO1 Through Allosteric Regulation

Mauris C. Nnamani, Soumya Ganguly, Vincent J. Lynch, Laura S. Mizoue, Yingchun Tong, Heather Darling, Monika Fuxreiter, Jens Meiler, Gunter P. Wagner
doi: http://dx.doi.org/10.1101/014381

Transcription factors (TFs) play multiple roles in different cells and stages of development. Given this multitude of functional roles it has been assumed that TFs are evolutionarily highly constrained. Here we investigate the molecular mechanisms for the origin of a derived functional interaction between two TFs that play a key role in mammalian pregnancy, HOXA11 and FOXO1. We have previously shown that the regulatory role of HOXA11 in mammalian endometrial stromal cells requires an interaction with FOXO1, and that the physical interaction between these proteins evolved long before their functional cooperativity. Through a combination of functional, biochemical, and structural approaches, we demonstrate that the derived functional cooperativity between HOXA11 and FOXO1 is due to derived allosteric regulation of HOXA11 by FOXO1. This study shows that TF function can evolve through changes affecting the functional output of a pre-existing protein complex.

Geometric constraints dominate the antigenic evolution of influenza H3N2 hemagglutinin

Geometric constraints dominate the antigenic evolution of influenza H3N2 hemagglutinin

Austin G Meyer, Claus O Wilke
doi: http://dx.doi.org/10.1101/014183

We have carried out a comprehensive analysis of the determinants of human influenza A H3 hemagglutinin evolution, considering three distinct predictors of evolutionary variation at in- dividual sites: solvent accessibility (as a proxy for protein fold stability and/or conservation), experimental epitope sites (as a proxy for host immune bias), and proximity to the receptor- binding region (as a proxy for protein function). We have found that these three predictors individually explain approximately 15% of the variation in site-wise dN/dS. However, the sol- vent accessibility and proximity predictors seem largely independent of each other, while the epitope sites are not. In combination, solvent accessibility and proximity explain 32% of the variation in dN/dS. Incorporating experimental epitope sites into the model adds only an ad- ditional 2 percentage points. We have also found that the historical H3 epitope sites, which date back to the 1980s and 1990s, show only weak overlap with the latest experimental epi- tope data, and we have defined a novel set of four epitope groups which are experimentally supported and cluster in 3D space. Finally, sites with dN/dS > 1, i.e., the sites most likely driving seasonal immune escape, are not correctly predicted by either historical or experimental epitope sites, but only by proximity to the receptor-binding region. In summary, proximity to the receptor-binding region, rather than host immune bias, seems to be the primary determinant of H3 immune-escape evolution.

Rates of karyotypic evolution in Estrildid finches differ between island and continental clades

Rates of karyotypic evolution in Estrildid finches differ between island and continental clades
Daniel M Hooper, Trevor D Price
doi: http://dx.doi.org/10.1101/013987

Reasons why chromosomal rearrangements spread to fixation and frequently distinguish related taxa remain poorly understood. We used cytological descriptions of karyotype to identify large pericentric inversions between species of Estrildid finches (family Estrildidae) and a time-dated phylogeny to assess the genomic, geographic, and phylogenetic context of karyotype evolution in this group. Inversions between finch species fixed at an average rate of one every 2.26 My. Inversions were twice as likely to fix on the sex chromosomes compared to the autosomes, possibly a result of their repeat density, and inversion fixation rate for all chromosomes scales with range size. Alternative mutagenic input explanations are not supported, as the number of inversions on a chromosome does not correlate with its length or map size. Inversions have fixed 3.3× faster in three continental clades than in two island chain clades, and fixation rate correlates with both range size and the number of sympatric species pairs. These results point to adaptation as the dominant mechanism driving fixation and suggest a role for gene flow in karyotype divergence. A review shows that the rapid karyotype evolution observed in the Estrildid finches appears to be more general across birds, and by implication other understudied taxa.

Ecological patterns of genome size variation in salamanders

Ecological patterns of genome size variation in salamanders
Bianca Sclavi, John Herrick
Comments: 19 Pages, 4 figures, 1 supplementary figure
Subjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)

Salamanders (urodela) have among the largest vertebrate genomes, ranging in size from 10 to over 80 pg. The urodela are divided into ten extant families each with a characteristic range in genome size. Although changes in genome size often occur randomly and in the absence of selection pressure, non-random patterns of genome size variation are evident among specific vertebrate lineages. Here we report that genome size in salamander families varies inversely with species richness and other ecological factors: clades that began radiating earlier (older crown age) tend to have smaller genomes, higher levels of diversity and larger geographical ranges. These observations support the hypothesis that urodel families with larger genomes either have a lower propensity to diversify or are more vulnerable to extinction than families with smaller genomes.

Reconstructing gene content in the last common ancestor of cellular life: is it possible, should it be done, and are we making any progress?

Reconstructing gene content in the last common ancestor of cellular life: is it possible, should it be done, and are we making any progress?

Arcady Mushegian
doi: http://dx.doi.org/10.1101/013326

I review recent literature on the reconstruction of gene repertoire of the Last Universal Common Ancestor of cellular life (LUCA). The form of the phylogenetic record of cellular life on Earth is important to know in order to reconstruct any ancestral state; therefore I also discuss the emerging understanding that this record does not take the form of a tree. I argue that despite this, “tree-thinking” remains an essential component in evolutionary thinking and that “pattern pluralism” in evolutionary biology can be only epistemological, but not ontological.

A FISH-based chromosome map for the European corn borers yields insights into ancient chromosomal fusions in the silkworm.

A FISH-based chromosome map for the European corn borers yields insights into ancient chromosomal fusions in the silkworm.

Yuji Yasukochi, Mizuki Ohno, Fukashi Shibata, Akiya Jouraku, Ryo Nakano, Yukio Ishikawa, Ken Sahara
doi: http://dx.doi.org/10.1101/013284

A significant feature of the genomes of Lepidoptera, butterflies and moths, is the high conservation of chromosome organization. Recent remarkable progress in genome sequencing of Lepidoptera has revealed that syntenic gene order is extensively conserved across phylogenetically distant species. The ancestral karyotype of Lepidoptera is thought to be n = 31; however, that of the most well studied moth, Bombyx mori, is n = 28, suggesting that three chromosomal fusion events occurred in this lineage. To identify the boundaries between predicted ancient fusions involving B. mori chromosomes 11, 23 and 24, we constructed FISH-based chromosome maps of the European corn borer, Ostrinia nubilalis (n = 31). We first determined 511 Mb genomic sequence of the Asian corn borer, Ostrinia furnacalis, a congener of O. nubilalis, and isolated BAC and fosmid clones that were expected to localize in candidate regions for the boundaries using these sequences. Combined with FISH and genetic analysis, we narrowed down the candidate regions to 40kb ??? 1.5Mb, in strong agreement with a previous estimate based on the genome of a butterfly, Melitaea cinxia. The significant difference in the lengths of the candidate regions where no functional genes were observed may reflect the evolutionary time after fusion events.

Expansion of the HSFY gene family in pig lineages

Expansion of the HSFY gene family in pig lineages

Benjamin M Skinner, Kim Lachani, Carole A Sargent, Fengtang Yang, Peter JI Ellis, Toby Hunt, Beiyuan Fu, Sandra Louzada, Carol Churcher, Chris Tyler-Smith, Nabeel A Affara
doi: http://dx.doi.org/10.1101/012906

Amplified gene families on sex chromosomes can harbour genes with important biological functions, especially relating to fertility. The HSFY family has amplified on the Y chromosome of the domestic pig (Sus scrofa), in an apparently independent event to an HSFY expansion on the Y chromosome of cattle (Bos taurus). Although the biological functions of HSFY genes are poorly understood, they appear to be involved in gametogenesis in a number of mammalian species, and, in cattle, HSFY gene copy number correlates with levels of fertility. We have investigated the HSFY family in domestic pigs, and other suid species including warthogs, bushpigs, babirusas and peccaries. The domestic pig contains at least two amplified variants of HSFY, distinguished predominantly by presence or absence of a SINE within the intron. Both these variants are expressed in testis, and both are present in approximately 50 copies each in a single cluster on the short arm of the Y. The longer form has multiple nonsense mutations rendering it likely non-functional, but many of the shorter forms still have coding potential. Other suid species also have these two variants of HSFY, and estimates of copy number suggest the HSFY family may have amplified independently twice during suid evolution. Given the association of HSFY gene copy number with fertility in cattle, HSFY is likely to play an important role in spermatogenesis in pigs also.