Fast and sensitive multiple sequence alignments on a microcomputer

Higgins, Desmond G.; Sharp, Paul M.

doi:10.1093/bioinformatics/5.2.151

Cited by 891 publications

(677 citation statements)

References 10 publications

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“…Predicted amino acid sequence of caspase 9 from X. tropicalis was aligned with the amino-acid sequences of caspase 9 from X. laevis (GI: 7619908), mouse (GI: 33990597), and human (GI: 28558771), using Clustal V Method (Higgins and Sharp, 1989). Indication of the CARD domain, the catalytic domain, the Asp cleavage sites, and the phosphorylation sites are indicated as described in previously published reports (Li et al, 1997;Cardone et al, 1998;Nakajima et al, 2000).…”

Section: Comparison Of Caspase 9 Sequencesmentioning

confidence: 99%

Apoptosis of tail muscle during amphibian metamorphosis involves a caspase 9-dependent mechanism

et al. 2005

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The climax of amphibian metamorphosis is marked by thyroid hormone-dependent tadpole tail resorption, implicating apoptosis of multiple cell types, including epidermal cells, fibroblasts, nerve cells, and muscles. The molecular cascades leading to and coordinating the death of different cell types are not fully elucidated. It is known that the mitochondrial pathway, and in particular the Bax and XR11 genes, regulates the balance between apoptosis and survival in muscle. However, the down-stream factors modulated by changes in mitochondrial permeability have not been studied in a functional context. To investigate further the mitochondrial-dependent pathway, we analyzed the regulation and the role of caspase 9 in Xenopus tadpoles. We report that caspase 9 mRNA is expressed in the tail before metamorphosis and increases before and during climax. Similarly, at the protein level, the production of active forms of caspase 9 increases in muscle tissue as metamorphosis progresses. To assess the functional role of caspase 9, we designed a dominant-negative protein. Overexpression of this dominant-negative abrogates both Bax-induced cell death in vitro and muscle apoptosis in vivo during natural metamorphosis. These findings consolidate a model of metamorphic muscle death that directly implicates the mitochondrial pathway and the apoptosome. Developmental Dynamics 233:76 -87, 2005.

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Section: Comparison Of Caspase 9 Sequencesmentioning

confidence: 99%

Apoptosis of tail muscle during amphibian metamorphosis involves a caspase 9-dependent mechanism

et al. 2005

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“…The programs CLUSTALV (Higgins & Sharp, 1989) and Predictprotein (Rost & Sander, 1993; send an e-mail message with "help" to PredictProtein@EMBL-Heidelbergde) were used. The PredictProtein server generated a multiple sequence alignment and a secondary structure prediction for the P. aerophilum protein.…”

Section: Multiple Sequence Alignmentsmentioning

confidence: 99%

The sequence of a subtilisin‐type protease (aerolysin) from the hyperthermophilic archaeum Pyrobaculum aerophilum reveals sites important to thermostability

et al. 1994

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The hyperthermophilic archaeum Pyrobaculum aerophilum grows optimally at 100 "C and pH 7.0. Cell homogenates exhibit strong proteolytic activity within a temperature range of 80-130 "C. During an analysis of cDNA and genomic sequence tags, a genomic clone was recovered showing strong sequence homology to alkaline subtilisins of Bacihs sp. The total DNA sequence of the gene encoding the protease (named "aerolysin") was determined. Multiple sequence alignment with 15 different serine-type proteases showed greatest homology with subtilisins from gram-positive bacteria rather than archaeal or eukaryal serine proteases.Models of secondary and tertiary structure based on sequence alignments and the tertiary structures of subtilisin Carlsberg, BPN', thermitase, and protease K were generated for P. aerophilurn subtilisin. This allowed identification of sites potentially contributing to the thermostability of the protein. One common transition put alanines at the beginning and end of surface alpha-helices. Aspartic acids were found at the N-terminus of several surface helices, possibly increasing stability by interacting with the helix dipole. Several of the substitutions in regions expected to form surface loops were adjacent to each other in the tertiary structure model.

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“…Alignment and phylogenetic tree construction of new and full-length Cx43 sequences from GenBank was performed with Lasergene software (DNASTAR, Madison, Wis.), operating with ClustalW and Joint Neighbour algorithms (Saitou and Nei 1987;Higgins and Sharp 1990).…”

Section: Methodsmentioning

confidence: 99%

Connexin43 orthologues in vertebrates: phylogeny from fish to man

et al. 2004

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The gap junction protein connexin43 (Cx43) is widely expressed in all vertebrate species; however, in ventricular myocardium, Cx43 expression is restricted to mammalian species only, where it provides the molecular correlate for both electrical conduction and synchronization of the repolarization process. The evolutionarily "late" appearance of Cx43 in the heart suggests physiological adaptation to euthermia with its concomitant demands related to increased cardiovascular output. We tested to what extent mammalian Cx43 differs from that of non-mammalian vertebrates and whether Cx43 from hibernating species contains specific sequence characteristics which could be attributed to their non-isothermal life cycle. We cloned the complete coding region of Cx43 from the African green monkey, European hedgehog (hibernator), Russian dwarf hamster, rabbit, European ground squirrel (hibernator) and pig. After sequencing, these were compared to 12 full-length Cx43 sequences present in GenBank (3 fish, 2 frogs, chicken and 6 mammals amongst which there was one other hibernator). Overall identity ranged from 68.7% to 97.7% at the nucleotide level and from 71.6% to 99.7% at the amino acid level. The phylogeny of Cx43 mirrors the general phylogenetic histories of the investigated species to a large extent. From 382 amino acids there were only 6 specific for mammals. There were no substitutions specific for hibernators. In conclusion, mammalian Cx43 is characterized by 6 specific amino acids, and no obvious differences between non-hibernating and hibernating mammals were observed.

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Fast and sensitive multiple sequence alignments on a microcomputer

Cited by 891 publications

References 10 publications

Apoptosis of tail muscle during amphibian metamorphosis involves a caspase 9-dependent mechanism

Apoptosis of tail muscle during amphibian metamorphosis involves a caspase 9-dependent mechanism

The sequence of a subtilisin‐type protease (aerolysin) from the hyperthermophilic archaeum Pyrobaculum aerophilum reveals sites important to thermostability

Connexin43 orthologues in vertebrates: phylogeny from fish to man

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