Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals

<p>Abstract</p> <p>Background</p> <p>The degradome -the complete repertoire of proteases in an organism- is involved in multiple key biological and pathological processes. Previous studies in several organisms have yielded sets of curated protease sequences which may be used to characterize the degradome in a novel genome by similarity. Differences between degradomes can then be related to physiological traits of the species under study. Therefore, the sequencing of the zebra finch genome allows the comparison between the degradomes of mammals and birds and may help to understand the biological peculiarities of the zebra finch.</p> <p>Results</p> <p>A set of curated protease sequences from humans and chicken was used to predict the sequences of 460 protease and protease-like genes in the zebra finch genome. This analysis revealed important differences in the evolution of mammalian and bird degradomes, including genomic expansions and deletions of caspases, cytotoxic proteases, kallikreins, matrix metalloproteases, and trypsin-like proteases. Furthermore, we found several zebra finch-specific features, such as duplications in <it>CASP3 </it>and <it>BACE</it>, and a large genomic expansion of acrosin.</p> <p>Conclusions</p> <p>We have compared the degradomes of zebra finch, chicken and several mammalian species, with the finding of multiple differences which illustrate the evolution of the protease complement of these organisms. Detailed analysis of these changes in zebra finch proteases has shown that they are mainly related to immunological, developmental, reproductive and neural functions.</p

Molecular cloning and expression of collagenase-3, a novel human matrix metalloproteinase produced by breast carcinomas

Esta publicación detalla los experimentos realizados para la clonación de un ADNc que codifica una nueva metaloproteasa de matriz extracelular a partir de una biblioteca de ADNc procedente de un carcinoma mamario. Este trabajo es de gran interés en la investigación del cáncer, ya que describe la identificación de una nueva colagenasa en los carcinomas mamarios proponiendo un posible papel en el proceso tumoral. Hay evidencia de que las metaloproteasas participan en el proceso de degradación proteolítica de los diferentes componentes de la membrana basal, favoreciendo así la invasión tumoral y las metástasis. El ADNc de la colagenasa-3 se expresó en un sistema de virus vaccinia, y la proteína recombinante fue capaz de degradar los colágenos fibrilares, lo que apoya la hipótesis de que el ADNc aislado codifica para una colagenasa auténtica. El análisis por Northern blot del ARN de tejidos normales y patológicos demostró la existencia de tres especies diferentes de ARNm en los tumores de mama, que parecen ser el resultado de la utilización de distintos sitios de poliadenilación presentes en la región 3'-no codificante del gen. Por el contrario, no se detectó ARNm de la colalagenasa-3 por Northern blot ni por PCR en otros tejidos humanos como mama normal, fibroadenomas mamarios, hígado, placenta, ovario, útero, próstata y glándula parótida. Sobre la base del aumento de la expresión de la colagenasa-3 en los carcinomas de mama y la ausencia de expresión detectable en los tejidos normales, se propone un posible papel de esta metaloproteinasa en el proceso tumoral

Loss of genes implicated in gastric function during platypus evolution

Several genes implicated in food digestion have been deleted or inactivated in platypus. This loss perhaps explains the anatomical and physiological differences in the gastrointestinal tract between monotremes and other vertebrates and provides insights into platypus genome evolution

African swinw fever (ASF) virus: A missing link between poxviruses and iridoviruses

Trabajo presentado en el VII International Congress of Virology, celebrado en Edmonton (Canadá) del 09 al 14 de agosto de 1987

miR-29 is an important driver of aging-related phenotypes

The authors thank Dr. Peter J Havel (UC Davis) for sharing monkey tissue samples. We also thank Dr. Greg Hannon for sending us the mouse embryonic stem cells overexpressing miR‐29b that we used to generate the miR-29TG mice. We appreciate the help of Mervi Eeva, Ying Li, and Bentley Midkiff at the UNC Translational Pathology Laboratory (TPL) for expert technical assistance and Dr. Dale Cowley for assistance in gen- erating the miR-29 transgenic mice. We also thank Janice Weaver and Carolyn Suitt at the UNC Animal Histopathology and the Center for Gas- trointestinal Biology and Disease (CGIBD), respectively, as well as Dr. Andrew Troy for assistance in isolating muscle tissue.Peer reviewe

Pleiotropic functions of the tumor- and metastasis-suppressing Matrix Metalloproteinase-8 in mammary cancer in MMTV-PyMT transgenic mice

Matrix metalloproteinase-8 (MMP-8; neutrophil collagenase) is an important regulator of innate immunity which has onco-suppressive actions in numerous tumor types

POT1 mutations predispose to familial melanoma

Deleterious germline variants in CDKN2A account for around 40% of familial melanoma cases, and rare variants in CDK4, BRCA2, BAP1 and the promoter of TERT have also been linked to the disease. Here we set out to identify new high-penetrance susceptibility genes by sequencing 184 melanoma cases from 105 pedigrees recruited in the UK, The Netherlands and Australia that were negative for variants in known predisposition genes. We identified families where melanoma cosegregates with loss-of-function variants in the protection of telomeres 1 gene (POT1), with a proportion of family members presenting with an early age of onset and multiple primary tumors. We show that these variants either affect POT1 mRNA splicing or alter key residues in the highly conserved oligonucleotide/oligosaccharide-binding (OB) domains of POT1, disrupting protein-telomere binding and leading to increased telomere length. These findings suggest that POT1 variants predispose to melanoma formation via a direct effect on telomeres.D.J.A., C.D.R.-E., Z.D., J.Z.L., J.C.T., M.P. and T.M.K. were supported by Cancer Research UK and the Wellcome Trust (WT098051). C.D.R.-E. was also supported by the Consejo Nacional de Ciencia y Tecnología of Mexico. K.A.P. and A.M.D. were supported by Cancer Research UK (grants C1287/A9540 and C8197/A10123) and by the Isaac Newton Trust. N.K.H. was supported by a fellowship from the National Health and Medical Research Council of Australia (NHMRC). L.G.A. was supported by an Australia and New Zealand Banking Group Limited Trustees PhD scholarship. A.L.P. is supported by Cure Cancer Australia. The work was funded in part by the NHMRC and Cancer Council Queensland. The work of N.A.G. was in part supported by the Dutch Cancer Society (UL 2012-5489). M.H., J.A.N.-B. and D.T.B. were supported by Cancer Research UK (programme awards C588/A4994 and C588/A10589 and the Genomics Initiative). C.L.-O., A.J.R. and V.Q. are funded by the Spanish Ministry of Economy and Competitiveness through the Instituto de Salud Carlos III (ISCIII), the Red Temática de Investigación del Cáncer (RTICC) del ISCIII and the Consolider-Ingenio RNAREG Consortium. C.L.-O. is an investigator with the Botín Foundation.This is the author accepted manuscript. The final version is available from NPG via http://dx.doi.org/10.1038/ng.294