Occurrence of two distinct types of tissue inhibitor of metalloproteinases-2 in teleost fish

Kubota, Shin; Kinoshita, Masato; Uji, Susumu; Yokoyama, Yoshihiro; Yamamoto, Eiichi; Hirono, Ikuo; Aoki, Takashi; Sakaguchi, Morihiko; Morioka, Katsuji; Itoh, Yoshiaki; Toyohara, Haruhiko

doi:10.1016/j.bbaexp.2003.08.007

Cited by 15 publications

(16 citation statements)

References 32 publications

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“…As we increased the number of top-matching sequences to two top-scoring matches, both the strong and weak components contained all and only the four human TIMP paralogs and no further increase in the number of top-scoring sequences allowed had an influence on the contents of the strong or weak components. Note that the order in which paralogs were identified is consistent with the evolutionary history of TIMPs represented in TreeFam tree TF317409: the most recent gene duplication (in early vertebrates) gave rise to TIMP4/TIMP2 [18]. …”

Section: Resultsmentioning

confidence: 90%

Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by Confusing Paralogs and Epaktologs

Nagy

Bányai

Patthy

2011

Genes

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In the accompanying paper (Nagy, Szláma, Szarka, Trexler, Bányai, Patthy, Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors) we showed that in the case of UniProtKB/TrEMBL, RefSeq, EnsEMBL and NCBI's GNOMON predicted protein sequences of Metazoan species the contribution of erroneous (incomplete, abnormal, mispredicted) sequences to domain architecture (DA) differences of orthologous proteins might be greater than those of true gene rearrangements. Based on these findings, we suggest that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. In this manuscript we examine the impact of confusing paralogous and epaktologous multidomain proteins (i.e., those that are related only through the independent acquisition of the same domain types) on conclusions drawn about DA evolution of multidomain proteins in Metazoa. To estimate the contribution of this type of error we have used as reference UniProtKB/Swiss-Prot sequences from protein families with well-characterized evolutionary histories. We have used two types of paralogy-group construction procedures and monitored the impact of various parameters on the separation of true paralogs from epaktologs on correctly annotated Swiss-Prot entries of multidomain proteins. Our studies have shown that, although public protein family databases are contaminated with epaktologs, analysis of the structure of sequence similarity networks of multidomain proteins provides an efficient means for the separation of epaktologs and paralogs. We have also demonstrated that contamination of protein families with epaktologs increases the apparent rate of DA change and introduces a bias in DA differences in as much as it increases the proportion of terminal over internal DA differences. We have shown that confusing paralogous and epaktologous multidomain proteins significantly increases the apparent rate of DA change in Metazoa and introduces a positional bias in favor of terminal over internal DA changes. Our findings caution that earlier studies based on analysis of datasets of protein families that were contaminated with epaktologs may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. A reassessment of the DA evolution of multidomain proteins is presented in an accompanying paper [1].

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Section: Resultsmentioning

confidence: 90%

Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by Confusing Paralogs and Epaktologs

Nagy

Bányai

Patthy

2011

Genes

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“…These MMPs could be involved in the embryonic development, morphogenesis and tissue remodeling (Kubota et al, 2003). On the other hand, the tissue inhibitors of metalloproteinases (TIMPs) are involved in the downregulation of MMPs activities; therefore, TIMPs play a critical role in the regulation of ECM degradation.…”

Section: Discussionmentioning

confidence: 99%

“…In this context, TIMPs could increase their expression against degradation processes of the larva´s ECM, produced for example, by bacteria present in the gapping condition. Given the importance of these proteins, little information exists on the presence of TIMPs in teleost fish and in the Atlantic halibut, the sequence of TIMP has not been reported (Kubota et al, 2003;Lodemel et al, 2004). In halibut, TIMP was constitutively expressed in normal larvae; the lack of change in the expression of TIMP in gaping larvae may indicate that there is not an activation process of degradation of the ECM by bacterial proteinase.…”

Section: Discussionmentioning

confidence: 99%

Characterization of culturable bacterial flora in yolk sac larvae of Atlantic halibut (Hippoglossus hippoglossus L.) with

Urtubia¹,

Gallardo²,

Lavín³

et al. 2014

lajar

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ABSTRACT.One of the main problems facing Atlantic halibut hatcheries is the high mortality in the early stages of larval development. Several factors could be involved, for example: water quality, diseases or abnormalities, such as deformities occurring in the yolk sac larvae prior to exogenous feeding. The aim of this study was to identify differences in bacterial flora associated with yolk sac larvae with oral deformity. We also aimed to establish whether there is any relationship between bacterial strains and the "gaping jaws" syndrome. During our study, 74 bacterial isolates were obtained using three different nutrient media: Marine Agar, R2A and TCBS. Some of these bacteria were characterized using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and 16S rRNA sequencing. The immune response in larvae exhibiting the "gaping jaws" condition was measured by real time PCR. Our results showed significant differences in bacterial flora between normal and gaping larvae. The gaping yolk sac larvae were predominantly colonized by members of the families Vibrionaceae and Flavobacteriaceae. Bacteria belonging to the Bacillus and Pseudoalteromonas genera were also present but less frequent. It was not possible to associate a type or group of bacteria directly related to "gaping". Strikingly, larvae with gaping jaws had an increase in the expression of two immune related genes, like hepcidin and chemokine (MIP-1ß). These results indicate activation of the immune response in larvae with "gaping jaws" syndrome and this response could be related to bacteria isolated from gaping condition. Keywords: Atlantic halibut, Hippoglossus hippoglossus, bacterial flora, "gaping jaws", immune genes.Caracterización de la flora cultivable y la respuesta inmune en larvas con saco vitelino del halibut del Atlántico (Hippoglossus hippoglossus L.) con el síndrome de "gaping jaws" RESUMEN. Uno de los mayores problemas que enfrentan los criaderos de halibut del Atlántico es la alta mortalidad en estados tempranos del desarrollo larval. Distintos factores pueden estar involucrados, e.g., calidad del agua, enfermedades o anormalidades tales como deformidades que ocurren en las larvas en estado de saco vitelino antes de la alimentación exógena. El objetivo de este estudio fue identificar diferencias en la flora bacteriana asociada a larvas con saco vitelino con deformidad oral. Además se buscó establecer si existió relación entre alguna cepa bacteriana y el síndrome de "gaping jaws". Durante el estudio, 74 cepas bacterianas fueron aisladas usando diferentes medios de cultivo: agar marino, R2A y agar TCBS. Algunas de las bacterias fueron caracterizadas usando reacción en cadena de la polimerasa con análisis del polimorfismo de los fragmentos de restricción (PCR-RFLP) y secuenciación del gen ribosomal 16S. La respuesta inmune de larvas con el síndrome de "gaping jaws" fue medida por PCR en tiempo real. Los resultados evidenciaron diferencias significativas en la flora entre larvas normales y "gaping jaws". Las larvas c...

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“…This result indicates that MMP are candidates for factors causing the softening. MMP 14–18 and TIMP 19,20 were cloned in fishes, and some properties were being clarified. Kubota et al 21 .…”

Section: Introductionmentioning

confidence: 99%

“…13 This result indicates that MMP are candidates for factors causing the softening. MMP [14][15][16][17][18] and TIMP 19,20 were cloned in fishes, and some properties were being clarified. Kubota et al 21 have recently demonstrated that MMP-9 exists in Japanese flounder muscle and the recombinant protein is able to solubilize type I collagen, a quantitatively major component of ECM, at a chilled temperature.…”

Section: Introductionmentioning

confidence: 99%

Solubilization of type I and V collagens in Japanese flounder muscle during chilled storage

et al. 2005

Self Cite

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The post-mortem changes of type I and V collagens in Japanese flounder muscle during chilled storage were examined. The muscle softened significantly within 12 h under chilled storage. Both type I and V collagens isolated by ion-exchange chromatographies showed no remarkable changes in band patterns even after 24 h of storage, suggesting that degraded collagen molecules may be removed from the collagen fraction by a conventional preparation method. In contrast, type I and V collagen molecules were detected by Western blotting with each specific antibody in a saline extract and gradually increased during chilled storage. These results suggest that both type I and V collagens may participate in the post-mortem softening of fish muscle.

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Occurrence of two distinct types of tissue inhibitor of metalloproteinases-2 in teleost fish

Cited by 15 publications

References 32 publications

Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by Confusing Paralogs and Epaktologs

Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by Confusing Paralogs and Epaktologs

Characterization of culturable bacterial flora in yolk sac larvae of Atlantic halibut (Hippoglossus hippoglossus L.) with

Solubilization of type I and V collagens in Japanese flounder muscle during chilled storage

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