Search results for "Sequence analysis"
showing 10 items of 1349 documents
Acetyltransfer in natural product biosynthesis--functional cloning and molecular analysis of vinorine synthase.
2004
Vinorine synthase (EC 2.3.1.160) catalyses the acetyl-CoA- or CoA-dependent reversible formation of the alkaloids vinorine (or 11-methoxy-vinorine) and 16-epi-vellosimine (or gardneral). The forward reaction leads to vinorine, which is a direct biosynthetic precursor along the complex pathway to the monoterpenoid indole alkaloid ajmaline, an antiarrhythmic drug from the Indian medicinal plant Rauvolfia serpentina. Based on partial peptide sequences a cDNA clone was isolated and functionally expressed in Escherichia coli. The Km values of the native enzyme for gardneral and acetyl-CoA were determined to be 7.5 and 57 microM. The amino acid sequence of vinorine synthase has highest level of i…
Isolation and characterization of five Fox (Forkhead) genes from the sponge Suberites domuncula.
2003
Fox or Forkhead genes constitute a subgroup of the helix-turn-helix class of transcription factors with a characteristic and highly conserved DNA binding domain. To date, around 100 different Fox genes have been reported ranging from yeast to humans; these have been classified into 18 subclasses (A to P). Fox proteins are responsible for a wide range of functions and key roles in early developmental processes, during organogenesis and also for the function of the major organs and tissues in the adult. Here, we report the isolation and phylogenetic characterization of five members of the Fox family from the sponge Suberites domuncula. Four of them (Sd-FoxL2, Sd-FoxP, Sd-FoxD and Sd-FoxF) fal…
Characterization of a cDNA encoding RP43, a CUB-domain-containing protein from the tube of Riftia pachyptila (Vestimentifera), and distribution of it…
2000
A major 43kDa protein from the protective tube of Riftiapachyptila (Vestimentifera), named RP43, was partly microsequenced after isolation by SDS/PAGE from the protein fraction of tubes collected around the hydrothermal vents at the East Pacific Rise. On the basis of the partial peptide sequences obtained, experiments using reverse-transcriptase-mediated PCR and rapid amplification of cDNA ends led to the complete cDNA sequence. Analysis of deduced amino acid sequence of RP43 showed the presence of CUB domains (100–110-residue-spanning domains first reported in the complement subcomponents C1r/C1s, epidermal-growth-factor-related sea urchin protein and bone morphogenetic protein 1) that se…
A heterochromatic P sequence in the D. subobscura genome.
1994
The study of a heterochromatic P sequence of D. subobscura reveals that it is a degraded element, located at the centromeric region of the A chromosome (X chromosome in this species), and that it is strongly diverged from the euchromatic P sequences previously described in this species. This heterochromatic sequence is composed of some P element fragments embedded in undefined beta-heterochromatic sequences. These mosaic P sequences do not show any transcriptional activity and seem to be ancient parasites of the D. subobscura genome. Phylogenetic analyses indicate that both the euchromatic and heterochromatic P sequences of D. subobscura could come from an ancestral element which was presen…
Characterization and phylogenetic analysis of a cDNA encoding the Fes/FER related, non-receptor protein-tyrosine kinase in the marine sponge Sycon ra…
1998
Abstract In search of ancient versions of phylogenetically conserved genes/proteins, which are typical for multicellular animals, we have decided to analyse marine sponges (Porifera), the most ancient and most primitive metazoan organisms. We report here the complete nucleotide sequence of Sycon raphanus cDNA coding for a 879 aa long protein (100 kDa), which displays high overall similarity in primary structure and organization of domains with non-receptor tyrosine kinases (TKs) from the Fes/FER family. The encoded protein, which we named Fes/FER_SR, has a highly conserved, 260 aa long tyrosine kinase domain at the C-terminus. Amino-terminal to the catalytic domain is an 85 aa long SH2 doma…
Src proteins/src genes: from sponges to mammals
2004
The genome of marine sponge Suberites domuncula, a member of the most ancient and most simple metazoan phylum Porifera, encodes at least five genes for Src-type proteins, more than, i.e., Caenorhabditis elegans or Drosophila melanogaster (two in each). Three proteins, SRC1SD, SRC2SD and SRC3SD, were fully characterized. The overall homology (identity+similarity) among the three S. domuncula Srcs (68-71%) is much lower than the sequence conservation between orthologous Src proteins from freshwater sponges (82-85%). It is therefore very likely that several src genes/proteins were already present in the genome of Urmetazoa, the hypothetical metazoan ancestor. We have identified in the S. domun…
Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota
2011
The human gut is the natural habitat for a large and dynamic bacterial community that has a great relevance for health. Metagenomics is increasing our knowledge of gene content as well as of functional and genetic variability in this microbiome. However, little is known about the active bacteria and their function(s) in the gastrointestinal tract. We performed a metatranscriptomic study on ten healthy volunteers to elucidate the active members of the gut microbiome and their functionality under conditions of health. First, the microbial cDNAs obtained from each sample were sequenced using 454 technology. The analysis of 16S transcripts showed the phylogenetic structure of the active microbi…
An AFLP clock for the absolute dating of shallow-time evolutionary history based on the intraspecific divergence of southwestern European alpine plan…
2009
The dating of recent events in the history of organisms needs divergence rates based on molecular fingerprint markers. Here, we used amplified fragment length polymorphisms (AFLPs) of three distantly related alpine plant species co-occurring in the Spanish Sierra Nevada, the Pyrenees and the southwestern Alps/Massif Central to establish divergence rates. Within each of these species (Gentiana alpina, Kernera saxatilis and Silene rupestris), we found that the degree of AFLP divergence (D(N72)) between mountain phylogroups was significantly correlated with their time of divergence (as inferred from palaeoclimatic/palynological data), indicating constant AFLP divergence rates. As these rates d…
Computational annotation of genes differentially expressed along olive fruit development
2009
Abstract Background Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software. Results mRNA from fruits of the cv. Leccino sampled at three different stages [i.e., initial fruit set (stage 1), completed pit hardening (stage 2) a…
Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.
2000
Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the rough…