Hidden Homology Research Articles

Evolution: Hidden homologies may underpin the diversity of arthropods

Arthropods are remarkable for the diversity of their exoskeletons. A new study shows that these structures, from crustacean carapaces to insect wings, may be homologous and derived from hidden developmental structures preserved through arthropod evolution.

Evolution of alpha-amylases: architectural features and key residues in the stabilization of the (beta/alpha)(8) scaffold.

We provide a comprehensive analysis of the current enzymes with alpha-amylase activity (AAMYs) that belong to family 13 glycoside hydrolase (GH-13; 144 Archaea, Bacteria, and Eukaryota sequences from 87 different species). This study aims to further knowledge of the evolutionary molecular relationships among the sequences of their A and B domains with special emphasis on the correlation between what is observed in the structures and protein evolution. Multialignments for the A domain distinguish two clusters for sequences from Archaea organisms, eight for sequences from Bacteria organisms, and three for sequences from Eukaryota organisms. The clusters for Bacteria do not follow any strict taxonomic pathway; in fact, they are rather scattered. When we compared the A domains of sequences belonging to different kingdoms, we found that various pairs of clusters were significantly similar. Using either sequence similarity with crystallized structures or secondary-structure prediction methods, we identified in all AAMYs the eight putative beta-strands that constitute the beta-sheet in the TIM barrel of the A domain and studied the packing in its interior. We also discovered a "hidden homology" in the TIM barrel, an invariant Gly located upstream in the sequence before the conserved Asp in beta-strand 3. This Gly precedes an alpha-helix and is actively involved in capping its N-terminal end with a capping box. In all cases, a Schellman motif caps the C-terminal end of this helix.

Invariant glycines and prolines flanking in loops the strand β2 of various (α/β)8‐barrel enzymes: A hidden homology?

The question of parallel (alpha/beta)8-barrel fold evolution remains unclear, owing mainly to the lack of sequence homology throughout the amino acid sequences of (alpha/beta)8-barrel enzymes. The "classical" approaches used in the search for homologies among (alpha/beta)8-barrels (e.g., production of structurally based alignments) have yielded alignments perfect from the structural point of view, but the approaches have been unable to reveal the homologies. These are proposed to be "hidden" in (alpha/beta)8-barrel enzymes. The term "hidden homology" means that the alignment of sequence stretches proposed to be homologous need not be structurally fully satisfactory. This is due to the very long evolutionary history of all (alpha/beta)8-barrels. This work identifies so-called hidden homology around the strand beta 2 that is flanked by loops containing invariant glycines and prolines in 17 different (alpha/beta)8-barrel enzymes, i.e., roughly in half of all currently known (alpha/beta)8-barrel proteins. The search was based on the idea that a conserved sequence region of an (alpha/beta)8-barrel enzyme should be more or less conserved also in the equivalent part of the structure of the other enzymes with this folding motif, given their mutual evolutionary relatedness. For this purpose, the sequence region around the well-conserved second beta-strand of alpha-amylase flanked by the invariant glycine and proline (56_GFTAIWITP, Aspergillus oryzae alpha-amylase numbering), was used as the sequence-structural template. The proposal that the second beta-strand of (alpha/beta)8-barrel fold is important from the evolutionary point of view is strongly supported by the increasing trend of the observed beta 2-strand structural similarity for the pairs of (alpha/beta)8-barrel enzymes: alpha-amylase and the alpha-subunit of tryptophan synthase, alpha-amylase and mandelate racemase, and alpha-amylase and cyclodextrin glycosyltransferase. This trend is also in agreement with the existing evolutionary division of the entire family of (alpha/beta)8-barrel proteins.

Lionel Rothkrug, Religious Practices and Collective Perceptions: Hidden Homologies in the Renaissance and Reformation, constituting tome VII, No. 1 (Spring 1980) of Historical Reflexions, Univ. of Waterloo, Ontario. $ 16

Lionel Rothkrug, <i>Religious Practices and Collective Perceptions: Hidden Homologies in the Renaissance and Reformation,</i> constituting tome VII, No. 1 (Spring 1980) of <i>Historical Reflexions,</i> Univ. of Waterloo, Ontario. $ 16

Religious Practices and Collective Perceptions: Hidden Homologies in the Renaissance and Reformation. Lionel Rothkrug

Religious Practices and Collective Perceptions: Hidden Homologies in the Renaissance and Reformation. Lionel Rothkrug

Comptes rendus / Reviews of books: Religious Practices and Collective Perceptions: Hidden Homologies in the Renaissance and Reformation Lionel Rothkrug Historical Reflections, 7/1 Waterloo, Ontario: Department of History, University of Waterloo, 1980. Pp. xiv + 266

Comptes rendus / Reviews of books: Religious Practices and Collective Perceptions: Hidden Homologies in the Renaissance and Reformation Lionel Rothkrug Historical Reflections, 7/1 Waterloo, Ontario: Department of History, University of Waterloo, 1980. Pp. xiv + 266

:Religious Practices and Collective Perceptions: Hidden Homologies in the Renaissance and Reformation

:<i>Religious Practices and Collective Perceptions: Hidden Homologies in the Renaissance and Reformation</i>

Religious Practices and Collective Perceptions: Hidden Homologies in the Renaissance and Reformation

Religious Practices and Collective Perceptions: Hidden Homologies in the Renaissance and Reformation

Religious Practices and Collective Perceptions, Hidden Homologies in the Renaissance and Reformation, by Lionel Rothkrug. Foreword by John New. Commentary by Erik Midelfort and George Williams. Historical Reflections/Réflexions Historiques, vol. 7, no. 1 (Spring 1980)

<i>Religious Practices and Collective Perceptions, Hidden Homologies in the Renaissance and Reformation</i>, by Lionel Rothkrug. Foreword by John New. Commentary by Erik Midelfort and George Williams. <i>Historical Reflections/Réflexions Historiques</i>, vol. 7, no. 1 (Spring 1980)