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The Degradome database: expanding roles of mammalian proteases in life and disease

José G. Pérez-Silva, Yaiza Español, Gloria Velasco, Víctor Quesada
2015 Nucleic Acids Research  
This increase reflects the growing interest on the roles of the degradome in multiple diseases, including cancer and ageing.  ...  Since the definition of the degradome as the complete repertoire of proteases in a given organism, the combined effort of numerous laboratories has greatly expanded our knowledge of its roles in biology  ...  In these last years, the field of degradomics has experienced a remarkable expansion, not so much in the number of known proteases as in the biological and pathological roles played by the degradome.  ... 
doi:10.1093/nar/gkv1201 pmid:26553809 pmcid:PMC4702854 fatcat:4imogxun3neh5ezykumnc2jdcy

Matrix Proteases and the Degradome [chapter]

Clara Soria-Valles, Carlos López-Otín, Ana Gutiérrez-Fernández
2012 Matrix Proteases in Health and Disease  
The Instituto Universitario de Oncología is supported by Obra Social Cajastur and Acción Transversal del Cáncer-RTICC.  ...  Acknowledgments Our work is supported by grants from the Ministerio de Ciencia e Innovación-Spain, Fundación ''M. Botín'', and European Union (FP7 MicroEnviMet).  ...  Owing to the extension of these resources, we briefly introduce some remarkable tools and databases that can be useful for the genomic study of proteases: Degradome database (http://degradome.uniovi.es  ... 
doi:10.1002/9783527649327.ch1 fatcat:zaemcplgtjcs3gwxofi5j7u4dm

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

Víctor Quesada, Gloria Velasco, Xose S Puente, Wesley C Warren, Carlos López-Otín
2010 BMC Genomics  
The degradome -the complete repertoire of proteases in an organism-is involved in multiple key biological and pathological processes.  ...  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  ...  The Instituto Universitario de Oncología is supported by Obra Social Cajastur and Acción Transversal del Cáncer-RTICC. Author Details  ... 
doi:10.1186/1471-2164-11-220 pmid:20359326 pmcid:PMC2865498 fatcat:xbqquldiazbg5gxd2ika4wxbcu

Expression Profile of the Schistosoma japonicum Degradome Reveals Differential Protease Expression Patterns and Potential Anti-schistosomal Intervention Targets

Shuai Liu, Pengfei Cai, Xianyu Piao, Nan Hou, Xiaosu Zhou, Chuang Wu, Heng Wang, Qijun Chen, Cynthia Gibas
2014 PLoS Computational Biology  
Blood fluke proteases play pivotal roles in the processes of invasion, nutrition acquisition, immune evasion, and other hostparasite interactions.  ...  The degradomes of the four parasitic organisms and Homo sapiens were then comparatively analyzed.  ...  Acknowledgments We appreciate very much the efforts of technicians at CapitalBio for microarray performance.  ... 
doi:10.1371/journal.pcbi.1003856 pmid:25275570 pmcid:PMC4183426 fatcat:tdrtsffr2nazpp7d5qzybw7hua

Proteases: Multifunctional Enzymes in Life and Disease

Carlos López-Otín, Judith S. Bond
2008 Journal of Biological Chemistry  
Acknowledgments-We thank all members of our laboratories for helpful comments on the manuscript.  ...  Data for human and mouse proteases are from Ref. 17 and the Degradome Database; data for Arabidopsis are from Ref. 13; and data for Drosophila are from the MEROPS Database (merops.sanger.ac.uk).  ...  In relation to the relevance of proteases for human disease, genomic studies will contribute to the elucidation of genetic diseases caused by mutations in protease loci as well as to the identification  ... 
doi:10.1074/jbc.r800035200 pmid:18650443 pmcid:PMC2576539 fatcat:cyet6cqv3zcjbpfgbna53wvtb4

Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel

Rui Kuang, Jianying Gu, Hong Cai, Yufeng Wang
2008 Genetica  
In this study, we focus on the prediction of proteases, which have long been considered attractive drug targets because of their indispensable roles in parasite development and infection.  ...  This catalog of proteases provides a short list of targets for functional characterization and rational inhibitor design.  ...  Diseases or the National Institutes of Health.  ... 
doi:10.1007/s10709-008-9336-9 pmid:19057851 pmcid:PMC2721224 fatcat:v6tbgkncybbm5ahwrxb6tpxho4

Metadegradomics

Alain Doucet, Georgina S. Butler, David Rodríguez, Anna Prudova, Christopher M. Overall
2008 Molecular & Cellular Proteomics  
It is crucial to determine which proteases contribute to the pathology versus their roles in homeostasis and in mitigating cancer.  ...  At the global level, the N terminome analysis of whole communities of proteases in tissues and organs in vivo provides a full scale understanding of the protease web and the web-sculpted proteome, so defining  ...  web can be deciphered, and so the role of the protease or the substrate protein in disease can be understood and validated for drug development.  ... 
doi:10.1074/mcp.r800012-mcp200 pmid:18596063 fatcat:i3iwx4bsibchzkvqcig7zmfntm

Serine peptidases: Classification, structure and function

M. J. Page, E. Di Cera
2008 Cellular and Molecular Life Sciences (CMLS)  
H. and Antalis, T. M. (2003) Mem- brane anchored serine proteases: A rapidly expanding group of cell surface proteolytic enzymes with potential roles in cancer.  ...  Serine peptidases play key roles in human health and disease and their biochemical properties shaped the molecular evolution of these processes.  ... 
doi:10.1007/s00018-008-7565-9 pmid:18259688 fatcat:x7rglc7x2vcn5km2ifrgxhaltq

Matriptase-2 (TMPRSS6): a proteolytic regulator of iron homeostasis

A. J. Ramsay, J. D. Hooper, A. R. Folgueras, G. Velasco, C. Lopez-Otin
2009 Haematologica  
The finding of this regulatory role for matriptase-2 was originally derived from the observation that mice deficient in this protease present with anemia due to elevated levels of hepcidin and impaired  ...  In this review, after overviewing the membrane anchored serine proteases, in particular the TTSP family, we summarize the identification and characterization of matriptase-2 and describe its functional  ...  Authorship and Disclosures All authors equally contributed to this paper. The authors declare they have no conflicts of interest. References  ... 
doi:10.3324/haematol.2008.001867 pmid:19377077 pmcid:PMC2688576 fatcat:dv4uoy2h4fda3aqiwtszd5x36u

Identification and Characterization of Human and Mouse Ovastacin

Víctor Quesada, Luis M. Sánchez, Jesús Álvarez, Carlos López-Otín
2004 Journal of Biological Chemistry  
We have cloned and characterized human and mouse ovary cDNAs encoding a new protein of the astacin family of metalloproteinases, called ovastacin because of its predominant expression in ovarian tissues  ...  On the basis of these results, we suggest that ovastacin could play in mammals a physiological function similar to that performed by hatching proteases in evolutionary distant species from arthropods to  ...  Perales, and A. M. Pendás for helpful comments and support and M. Fernández and C. Garabaya for excellent technical assistance.  ... 
doi:10.1074/jbc.m401588200 pmid:15087446 fatcat:xiqxqwhl5bf4bo4fx65iwindze

Human Autophagins, a Family of Cysteine Proteinases Potentially Implicated in Cell Degradation by Autophagy

Guillermo Mariño, José A. Urı́a, Xose S. Puente, Vı́ctor Quesada, Javier Bordallo, Carlos López-Otı́n
2002 Journal of Biological Chemistry  
Functional and morphological analysis in autophagy-defective yeast strains lacking Apg4/Aut2 revealed that human autophagins-1 and -3 were able to complement the deficiency in the yeast protease, restoring  ...  proteolytic system in the induction, regulation, and execution of autophagy.  ...  of the human degradome, the complete set of proteases produced by human tissues (1) .  ... 
doi:10.1074/jbc.m208247200 pmid:12446702 fatcat:rr5t6dhp5zcfxbmmtqwqsde544

Peptides derived of kunitz-type serine protease inhibitor as potential vaccine against experimental schistosomiasis [article]

Juan Hernandez-Goenaga, Julio Lopez-Aban, Anna V Protasio, Belen Vicente, Esther del Olmo, Magnolia Vanegas, Pedro Fernandez-Soto, Manuel Alfonso Patarroyo, Antonio Muro
2019 bioRxiv   pre-print
Kunitz-type serine protease inhibitors have been identified as important players in the interaction of other flatworm parasites with their mammalian hosts.  ...  Kunitz peptides were highly protective in vaccinated BALB/c mice showing significant reductions in recovery of adult females (89-91%), and in the numbers of eggs trapped in the livers (77-81%) and guts  ...  The Degradome database: 575 expanding roles of mammalian proteases in life and disease. Nucleic Acids Res. 576 2016;44(D1):D351-5. doi: 10.1093/nar/gkv1201. PMID: 26553809 577 21.  ... 
doi:10.1101/634360 fatcat:hwd4lp3dwbejpbj4ainrhyn7v4

Turnip mosaic virus in oilseed rape activates networks of sRNA-mediated interactions between viral and host genomes

Nicolas Pitzalis, Khalid Amari, Stéfanie Graindorge, David Pflieger, Livia Donaire, Michael Wassenegger, César Llave, Manfred Heinlein
2020 Communications Biology  
AbstractVirus-induced plant diseases in cultivated plants cause important damages in yield.  ...  We show that the induction of host-encoded, virus-activated small interfering RNAs (vasiRNAs) observed in virus-infected tissues is accompanied by site-specific cleavage events on both viral and host RNAs  ...  The funding bodies did not participate in the design of the study and collection, analysis, and interpretation of data, and in writing the manuscript.  ... 
doi:10.1038/s42003-020-01425-y pmid:33230160 fatcat:6tdlqfvjm5c3la3jgk5t7n75ki

Peptide-based protease inhibitors from plants

Roland Hellinger, Christian W. Gruber
2019 Drug Discovery Today  
Proteases have an important role in homeostasis, and dysregulation of protease function can lead to pathogenesis.  ...  Therefore, proteases are promising drug targets in cancer, inflammation, and neurodegenerative disease research.  ...  Acknowledgement Work on peptides in the laboratory of C.W.G. was supported by the Austrian Science Fund FWF (I3243).  ... 
doi:10.1016/j.drudis.2019.05.026 pmid:31170506 pmcid:PMC6753016 fatcat:xishozmhyvfhhn7mpqqokdpjda

Mass spectrometry-based proteomics: existing capabilities and future directions

Thomas E. Angel, Uma K. Aryal, Shawna M. Hengel, Erin S. Baker, Ryan T. Kelly, Errol W. Robinson, Richard D. Smith
2012 Chemical Society Reviews  
Characterization of proteins at the proteome and sub-proteome (e.g., the phosphoproteome, proteoglycome, or degradome/peptidome) levels provides a foundation for understanding fundamental aspects of biology  ...  MS-based proteomics is increasingly contribute to our understanding of the dynamics, interactions, and roles that proteins and peptides play, advancing our understanding of biology on a systems wide level  ...  the National Institutes of Health and Laboratory Directed Research and Development program at Pacific Northwest National Laboratory.  ... 
doi:10.1039/c2cs15331a pmid:22498958 pmcid:PMC3375054 fatcat:s3z6cz3pwvdj3n76pkvooyqcgq
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