Search results for "alignment"
showing 10 items of 627 documents
Structural insights into the GTPase domain of Escherichia coli MnmE protein
2007
The Escherichia coli MnmE protein is a 50-kDa multidomain GTPase involved in tRNA modification. Its homologues in eukaryotes are crucial for mitochondrial respiration and, thus, it is thought that the human protein might be involved in mitochondrial diseases. Unlike Ras, MnmE shows a high intrinsic GTPase activity and requires effective GTP hydrolysis, and not simply GTP binding, to be functionally active. The isolated MnmE G-domain (165 residues) conserves the GTPase activity of the entire protein, suggesting that it contains the catalytic residues for GTP hydrolysis. To explore the GTP hydrolysis mechanism of MnmE, we analyzed the effect of low pH on binding and hydrolysis of GTP, as well…
Characterisation, analysis of expression and localisation of the opsin gene repertoire from the perspective of photoperiodism in the aphid Acyrthosip…
2017
Organisms exhibit a wide range of seasonal responses as adaptions to predictable annual changes in their environment. These changes are originally caused by the effect of the Earth's cycles around the sun and its axial tilt. Examples of seasonal responses include floration, migration, reproduction and diapause. In temperate climate zones, the most robust variable to predict seasons is the length of the day (i.e. the photoperiod). The first step to trigger photoperiodic driven responses involves measuring the duration of the light-dark phases, but the molecular clockwork performing this task is poorly characterized. Photopigments such as opsins are known to participate in light perception, b…
Usher syndrome and Leber congenital amaurosis are molecularly linked via a novel isoform of the centrosomal ninein-like protein.
2009
Contains fulltext : 80984.pdf (Publisher’s version ) (Closed access) Usher syndrome (USH) and Leber congenital amaurosis (LCA) are autosomal recessive disorders resulting in syndromic and non-syndromic forms of blindness. In order to gain insight into the pathogenic mechanisms underlying retinal degeneration, we searched for interacting proteins of USH2A isoform B (USH2A(isoB)) and the LCA5-encoded protein lebercilin. We identified a novel isoform of the centrosomal ninein-like protein, hereby named Nlp isoform B (Nlp(isoB)), as a common interactor. Although we identified the capacity of this protein to bind calcium with one of its three EF-hand domains, the interacton with USH2A(isoB) did …
Cloning and sequencing of the dnaK region of Streptomyces coelicolor A3(2)
1993
Abstract The dnaK homologue of Streptomyces coelicolor A3(2) strain M145 has been cloned and sequenced. Nucleotide sequence analysis of a 2.5-kb region revealed an open reading frame (ORF) encoding a predicted DnaK protein of 618 amino acids (Mr = 66 274). The dnaK coding sequence displays extreme codon bias and shows a strong preference for CGY and GGY, for Arg and Gly codons, respectively. The predicted DnaK sequence has a high Lys:Arg ratio which is not typical of streptomycete proteins. The region immediately downstream from dnaK contains an ORF for a GrpE-like protein; the predicted start codon of grpE overlaps the last two codons of dnaK, indicating that the two genes are translationa…
Genes and derived amino acid sequences of S-layer proteins from mesophilic, thermophilic, and extremely thermophilic methanococci
2002
Cells of methanococci are covered by a single layer of protein subunits (S-layer) in hexagonal arrangement, which are directly exposed to the environment and which cannot be stabilized by cellular components. We have isolated S-layer proteins from cells of Methanococcus vannielii ( T(opt.)=37 degrees C), Methanococcus thermolithotrophicus ( T(opt.)=65 degrees C), and Methanococcus jannaschii ( T(opt.)=85 degrees C). The primary structure of the S-layer proteins was determined by sequencing the corresponding genes. According to the predicted amino acid sequence, the molecular masses of the S-layer proteins of the different methanococci are in a small range between 59,064 and 60,547 Da. Compa…
A human CCT5 gene mutation causing distal neuropathy impairs hexadecamer assembly in an archaeal model
2014
Chaperonins mediate protein folding in a cavity formed by multisubunit rings. The human CCT has eight non-identical subunits and the His147Arg mutation in one subunit, CCT5, causes neuropathy. Knowledge is scarce on the impact of this and other mutations upon the chaperone's structure and functions. To make progress, experimental models must be developed. We used an archaeal mutant homolog and demonstrated that the His147Arg mutant has impaired oligomeric assembly, ATPase activity, and defective protein homeostasis functions. These results establish for the first time that a human chaperonin gene defect can be reproduced and studied at the molecular level with an archaeal homolog. The major…
Study of the aminopeptidase N gene family in the lepidopterans Ostrinia nubilalis (Hübner) and Bombyx mori (L.): Sequences, mapping and expression
2010
Aminopeptidases N (APNs) are a class of ectoenzymes present in lepidopteran larvae midguts, involved in the Bacillus thuringiensis (Bt) toxins mode of action. In the present work, seven aminopeptidases have been cloned from the midgut of Ostrinia nubilalis, the major Lepidopteran corn pest in the temperate climates. Six sequences were identified as APNs because of the presence of the HEXXH(X)18E and GAMEN motifs, as well as the signal peptide and the GPI-anchor sequences. The remaining sequence did not contain the two cellular targeting signals, indicating it belonged to the puromycin-sensitive aminopeptidase (PSA) family. An in silico analysis allowed us to find orthologous sequences in Bo…
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.
2018
Abstract Motivation K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability. Results We introduce a novel idea of encoding k-mers as well as their frequency, achieving good memory saving and retrieval efficiency. Specifically, we propose a Bloom filter-like data structure to encode counted k-mers by coupled-bit arrays—one for k-mer representation and the other for frequency encoding. Exper…
A new species of Pythium with filamentous sporangia having pectinolytic activities, isolated in the Burgundy region of France.
2001
A new species, Pythium pectinolyticum (F-83.1), isolated from soil samples taken in the Burgundy region is being described here. This species is characterised by its filamentous non-inflated type of sporangia, smooth-walled mostly catenulate oogonia and very rare antheridia. This fungus is a very slow-growing organism on most of the solid media, but it grows well in liquid media and also on those containing pectin as the sole source of carbon. Morphological features are described here together with the sequences of the internal transcribed spacer 1 region of the nuclear ribosomal DNA of the fungus, its comparison with related species, and its pectinolytic behaviour.
Amino acids in the second transmembrane helix of the Lhca4 subunit are important for formation of stable heterodimeric light-harvesting complex LHCI-…
2007
Photosynthetic light-harvesting complexes (LHCs) are assembled from apoproteins (Lhc proteins) and non-covalently attached pigments. Despite a considerable amino acid sequence identity, these proteins differ in their oligomerization behavior. To identify the amino acid residues determining the heterodimerization of Lhca1 and Lhca4 to form LHCI-730, we mutated the poorly conserved second transmembrane helix of the two subunits. Mutated genes were expressed in Escherichia coli and the resultant proteins were refolded in vitro and subsequently analyzed by gel electrophoresis. Replacement of the entire second helix in Lhca4 by the one of Lhca3 abolished heterodimerization, whereas it had no eff…