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PubMed1993

The nia gene of Fusarium oxysporum: isolation, sequence and development of a homologous transformation system.

The Fusarium oxysporum gene nia, encoding nitrate reductase (NR), was isolated from a cosmid library by direct complementation of an F. oxysporum nia- mutant. The gene specifies a protein of 905 amino acids and contains a 57-bp intron. Comparison of the deduced aa sequence with NR of other fungi revealed a high degree of similarity and conservation in the intron position. The cloned nia made it possible to develop the first homologous transformation system for this fungus. Transformation frequencies of up to 600 transformants per microgram of DNA were achieved. Gene replacement, single-copy homologous integrations and integrations at non-homologous sites were observed. Direct comparison between plasmids and cosmids carrying the same gene showed a higher frequency of targeted transformation using cosmid vectors. Gene replacement events were observed in about 50% of the transformants analysed with each type of vector used. This high frequency of substitution offers new applications for the transformation system in F. oxysporum.

Amino Acid Sequence↗
PubMed2006

SmPKC1, a new protein kinase C identified in the platyhelminth parasite Schistosoma mansoni.

Schistosoma mansoni signal transduction pathways are promising sources of target molecules for the development of novel control strategies against this platyhelminth parasite of humans. Members of the protein kinase C (PKC) family play key roles in such pathways activated by both receptor tyrosine kinases and other receptors, controlling a variety of physiological processes. Here, we report the cloning and molecular characterization of the first PKC identified in S. mansoni. Structural analysis indicated that SmPKC1 exhibits all the features typical of the conventional PKC subfamily. The gene structure was determined in silico and found to comprise a total of 15 exons and 14 introns. This structure is highly conserved; all intron positions are also present in the human PKCbeta gene and most of the exon sizes are identical. Using PCR on genomic DNA we were able to show that putative orthologues of SmPKC1 are present in 9 Schistosoma species. SmPKC1 expression is developmentally regulated with the highest level of transcripts in miracidia, whereas SmPKC1 protein expression is higher in the sporocyst. The localization of SmPKC1 on the sporocyst ridge cyton and in schistosomula acetabular glands suggests that the enzyme plays a role in signal transduction pathways associated with larval transformation.

Amino Acid Sequence↗
PubMed2006

A novel ethylene receptor homolog gene isolated from ethylene-insensitive flowers of gladiolus (Gladiolus grandiflora hort.).

Gladiolus is an ethylene insensitive flower whose exogenous ethylene and ethylene inhibitors have no effect on the petal senescence process. To study which processes in gladiolus are associated with changes in ethylene perception, two types of gladiolus genes, named GgERS1a and GgERS1b, respectively, homologous to the Arabidopsis ethylene receptor gene ERS1 were isolated. GgERS1a is conserved in terms of exon numbers and intron positions, whereas GgERS1b is almost same with GgERS1a except lacking 636 nucleotide encoding first and second histidine kinase (HisKA) motifs. The sequence data on full length genomic DNA indicated that both GgERS1a and b were spliced from different genomic DNA. As the result of mRNA expression study, in spite of lacking the two significant motifs, the expression of GgERS1b dramatically changed with advance in petal senescence, whereas the level of GgERS1a expressed highly and constitutively. The result suggests that both the genes possess a significant role for the subfunctionalization process to provide ethylene insensitivity in gladiolus flowers.

Amino Acid Sequence↗
PubMed2005

Determination of vhl gene mutations in sporadic renal cell carcinoma.

OBJECTIVE: Characterization of the molecular status of the vhl gene and its relationship to the usual prognostic factors could help establish new diagnostic and therapeutic strategies. This study determines the presence of vhl gene mutations in tumor tissue from patients with sporadic renal cell carcinoma, the relationship between the mutations and classic prognostic factors, and the possible impact on protein function. MATERIALS AND METHOD: Cross-sectional analytical study investigating vhl gene mutations in tumor tissue by PCR testing of the gene exons and automatic sequencing in 96 patients with sporadic renal cell carcinoma. The characteristics of the mutations detected, as well as their relationship with various clinical and pathological parameters and the possible impact on protein function, were analyzed. RESULTS: Twenty-two mutations were found in 21 patients (21.9%); 68.2% were point mutations. The mutations were associated only with tumor histotype and were located in protein functional domains. Three mutations were detected in the intron position; 73.7% were considered relevant to protein function. CONCLUSION: The percentage of vhl gene mutations in sporadic renal cell carcinoma was relatively low, mutations were seen more often in clear cell carcinoma and were not related to the classic clinical prognostic factors. Mutations of the vhl gene produce important changes in the protein, causing it to lose its tumor suppressor function.

Carcinoma, Renal Cell↗
PubMed2005

Characterization of the SCP/TAPS gene family in Drosophila melanogaster.

The SCP/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) gene family encodes proteins found in many eukaryotes. SCP/TAPS proteins are defined by the presence of an SCP/TAPS domain, and many participate in important physiological processes. Five SCP/TAPS genes were previously identified in Drosophila melanogaster and are expressed in the digestive tract or in the testes. Sequence databases were searched to determine if other SCP/TAPS genes were present in D. melanogaster, and an additional 21 SCP/TAPS genes were identified. To further define the roles of these genes, the structures of each gene and protein were analyzed. Based on these analyses, 25 SCP/TAPS genes could be placed into one of two groups. Each group contained conserved intron positions that were not shared with the other group. Proteins encoded by group 1 genes also shared additional sequence motifs and conserved cysteines not found in group 2 proteins. To determine if the two groups were expressed differently, reverse transcriptase (RT)-polymerase chain reaction (PCR) was used to examine expression in adult flies. The results indicated that most genes were preferentially expressed in adult males, suggesting a role for these genes in male reproduction. Members of both groups displayed this preferential expression, so it was not group-specific. The two groups may differ in localization rather than function.

Amino Acid Sequence↗
PubMed2005

The RecQ gene family in plants.

RecQ helicases are conserved throughout all kingdoms of life regarding their overall structure and function. They are 3'-5' DNA helicases resolving different recombinogenic DNA structures. The RecQ helicases are key factors in a number of DNA repair and recombination pathways involved in the maintenance of genome integrity. In eukaryotes the number of RecQ genes and the structure of RecQ proteins vary strongly between organisms. Therefore, they have been named RecQ-like genes. Knockouts of several RecQ-like genes cause severe diseases in animals or harmful cellular phenotypes in yeast. Until now the largest number of RecQ-like genes per organism has been found in plants. Arabidopsis and rice possess seven different RecQ-like genes each. In the almost completely sequenced genome of the moss Physcomitrella patens at least five RecQ-like genes are present. One of the major present and future research aims is to define putative plant-specific functions and to assign their roles in DNA repair and recombination pathways in relation to RecQ genes from other eukaryotes. Regarding their intron positions, the structures of six RecQ-like genes of dicots and monocots are virtually identical indicating a conservation over a time scale of 150 million years. In contrast to other eukaryotes one gene (RecQsim) exists exclusively in plants. It possesses an interrupted helicase domain but nevertheless seems to have maintained the RecQ function. Owing to a recent gene duplication besides the AtRecQl4A gene an additional RecQ-like gene (AtRecQl4B) exists in the Brassicaceae only. Genetic studies indicate that a AtRecQl4A knockout results in sensitivity to mutagens as well as an hyper-recombination phenotype. Since AtRecQl4B was still present, both genes must have non-redundant roles. Analysis of plant RecQ-like genes will not only increase the knowledge on DNA repair and recombination, but also on the evolution and radiation of protein families.

Adenosine Triphosphatases↗
PubMed2004

Proteomic identification, nucleotide sequence, heterologous expression and immunological reactivity of the triosephosphate isomerase of Paracoccidioides brasiliensis.

An antigen of Paracoccidioides brasiliensis (Pb) was gel isolated and characterized. Endoproteinase Lys-C-digested peptides of the purified protein, which presented a molecular mass of 29 kDa and pI of 5.8, were subjected to sequence analysis of their amino acids. Searches at databases comparing the sequence of amino acids from the three peptides of the native protein revealed strong homology to triosephosphate isomerase (TPI: E.C. 5.3.1.1) from several sources. The complete cDNA and gene encoding PbTPI were obtained and both contained an open reading frame predicted to encode a 249-amino acid protein that presented all the peptides characterized in the native PbTPI. The Pbtpi gene contained six exons interrupted by five introns. Analysis performed with the deduced PbTPI suggested its usefulness in providing phylogenetic relatedness, as well as evidencing the correlation between the phylogeny provided by the deduced protein and intron positions in the cognate genes. The immunological reactivity of PbTPI was examined. The complete coding cDNA of PbTPI was overexpressed in an Escherichia coli host to produce high levels of recombinant fusion protein with glutathione S-transferase (GST) that had been purified by affinity chromatography. The purified recombinant TPI was recognized by sera of patients with confirmed paracoccidioidomycosis and not by sera of healthy individuals. Thus, recombinant PbTPI can be a valuable addition to the still small arsenal of P. brasiliensis immunoreactive proteins, which could be tested for incorporation into assays for serodiagnosis of the disease.

Amino Acid Sequence↗
PubMed2006

Overlapping genes as rare genomic markers: the phylogeny of gamma-Proteobacteria as a case study.

Phylogenies can be constructed in many ways, including using shared complex characters known as rare genomic changes (RGCs), such as insertions and deletions (indels), retroposon integrations and intron positions. Here, we demonstrate that distance-based phylogenies, which were determined by shared overlapping genes from 13 completely sequenced gamma-Proteobacteria genomes, are consistent with phylogenies based on 16S rRNAs and other robust markers. These findings suggest that overlapping genes could provide interesting additional insights into the phylogenomics of completely sequenced microbial genomes.

Algorithms↗
PubMed2000

Rose MADS-box genes 'MASAKO C1 and D1' homologous to class C floral identity genes.

We isolated AGAMOUS-like cDNA clones called MASAKO C1-C6 (C4-C6 are 3' or 5' partial cDNA clones) and MASAKO D1 from wild rose (Rosa rugosa Thunb. ex Murray). We found that MASAKO C1 was a homologue of AGAMOUS on the basis of sequence similarity, conservation of intron positions, and stamen- and carpel-specific expression within reproductive organs. MASAKO C1-C6 seem to have arisen via alternative splicing, and a possible function of one of the different mRNAs 'MASAKO C6' is discussed in view of similarities between it and the ag-4 variant 2 within Arabidopsis thaliana. MASAKO D1 was also thought to be a homologue of AGAMOUS based on similarity of their sequences, and on the tissue specific expression pattern with GAG2, which is an AGAMOUS homologue in ginseng. Two types of AGAMOUS homologue genes are possibly present in wild rose, as has been observed in tobacco, petunia, cucumber, and maize.

Journal Article↗
PubMed1998

Molecular characterization, pharmacological properties and chromosomal localization of the human GALR2 galanin receptor.

The neuropeptide galanin mediates a diverse spectrum of biological activities by interacting with specific G protein-coupled receptors. We have used homology genomic library screening and polymerase chain reaction (PCR) techniques to isolate both genomic and cDNA clones encoding the human homolog of the recently cloned rat GALR2 galanin receptor. By fluorescence in situ hybridization, the gene encoding human GALR2 (GALNR2) has been localized to chromosome 17q25.3. The two coding exons of the human GALNR2 gene, interrupted by an intron positioned at the end of transmembrane domain III, encode a 387 amino acid G protein-coupled receptor with 87% overall amino acid identity with rat GALR2. In HEK-293 cells stably expressing human GALR2, binding of [125I]porcine galanin is saturable and can be displaced by galanin, amino-terminal galanin fragments and chimeric galanin peptides but not by carboxy-terminal galanin fragments. In HEK-293 cells, human GALR2 couples both to Galphaq/11 to stimulate phospholipase C and increase intracellular calcium levels and to Galphai/o to inhibit forskolin-stimulated intracellular cAMP accumulation. A wide tissue distribution is observed by reverse transcriptase (RT)-PCR analysis, with human GALR2 mRNA being detected in many areas of the human central nervous system as well as in peripheral tissues.

Amino Acid Sequence↗
PubMed2003

Early divergence of the FtsZ1 and FtsZ2 plastid division gene families in photosynthetic eukaryotes.

Homologues of the bacterial cell division protein FtsZ are found in higher plants where they function as key components of the chloroplast division complex. In contrast to most bacteria that encode a single FtsZ protein, plants encode multiple proteins that group into two families, FtsZ1 and FtsZ2. Using new sequence data from a broad range photosynthetic organisms, we performed a series of analyses to better understand the evolutionary history of the plant FtsZ families. Multiple phylogenetic analyses strongly support the grouping of the plant FtsZ genes and proteins into distinct FtsZ1 and FtsZ2 clades. Protein features representing potentially significant functional differences between FtsZ1 and FtsZ2 are identified. Genomic structure comparisons show that exon length and intron position are conserved within each clade, but differ between the clades except at one position. Our data indicate that the divergence of the FtsZ1 and FtsZ2 families occurred long before the evolution of land plants, preceding the emergence of the green algae. The results are consistent with proposals that the two FtsZ families evolved distinct functions during evolution of the chloroplast division apparatus, and indicate that genetic and functional differentiation occurred much earlier than previously hypothesized.

Amino Acid Sequence↗
PubMed1998

The Arabidopsis SHAGGY-related protein kinase (ASK) gene family: structure, organization and evolution.

Higher plants contain a multigene family encoding proteins that share a highly conserved catalytic protein kinase domain about 70% identical to SHAGGY protein kinase (SGG) and glycogen synthase kinase-3 (GSK-3), respectively, from Drosophila and mammals. In this study we have characterized the structure and evolution of the Arabidopsis SHAGGY-related protein kinase (ASK) gene family. At least ten ASK genes are present per haploid genome of Arabidopsis. The genomic sequences of five ASK genes show a strikingly high conservation of intron positions and exon lengths. Phylogenetic analyses suggested that the Arabidopsis gene family contains at least three ancient classes of genes that diverged early in land plant evolution. The different classes may reflect specificity of substrates and/or biological functions. Eight out of the ten predicted ASK genes were mapped and shown to be dispersed over the five Arabidopsis chromosomes. A tentative model for the organization and evolution of the Arabidopsis ASK genes is presented.

Arabidopsis↗
PubMed1998

Analysis of eight cDNAs and six genes for intermediate filament (IF) proteins in the cephalochordate Branchiostoma reveals differences in the IF multigene families of lower chordates and the vertebrates.

We report the sequences of seven new cytoplasmic intermediate filament (IF) proteins of the cephalochordate Branchiostoma. The eight sequences currently known describe four subfamilies (A, B, C and D). All eight IF proteins show the short-length version of the coil 1b subdomain found in vertebrates and lack the additional 42 residues present in all nuclear lamins and the protostomic IF proteins. Although the lancelet is considered to be the closest relative of the vertebrates, it is difficult to relate its IF subfamilies unambiguously to a particular type I-IV subfamily of vertebrates. C1 and C2 have tail domains with two 64 residue repeats of coiled coil-forming ability, a structural feature unknown for IF proteins from vertebrates or protostomia. The epidermal protein D1 shows only a slightly better identity score with vertebrate type II keratins than with type III proteins, but the D1 gene organization is that of type III proteins. The same holds for A1, A2, B1, B2 and C2 genes, although the latter has an additional and uniquely positioned intron. Antibodies (Ab) raised against recombinant C2 and D1 proteins reveal these proteins in epidermis, some internal epithelia and parts of the spinal cord. The results on exonic sequences, gene organization and expression suggest that Branchiostoma IF proteins may retain a largely archetypal condition, whereas the vertebrates have established the well-known type I-IV IF system.

Amino Acid Sequence↗
PubMed1999

Characterization of the glyceraldehyde-3-phosphate dehydrogenase gene [correction of glyceraldehyde-3-phosphate gene] and the use of its promoter for heterologous expression in Cryptococcus neoformans, a human pathogen.

The GPD gene encoding glyceraldehyde-3-phosphate dehydrogenase was isolated from Cryptococcus neoformans, a heterobasidiomycetous yeast that is pathogenic to humans. The gene contains 11 introns, differing from the conserved intron positions found in the GPD genes of Basidiomycetes. The predicted amino-acid sequence of this gene is extremely similar to that reported from GPD proteins of other basidiomycetes. The promoter region of the C. neoformans GPD gene was similar to those of other basidiomycetes. Plasmid constructs containing up to 1600 base pairs upstream of the native GPD open reading frame were used to express either the native URA5 gene in a ura5 mutant or the heterologous hphI gene (a bacterial gene that confers resistance to the aminoglycoside hygromycin) in a wild-type strain of C. neoformans. Transformation frequencies resulting from the plasmid-borne Gpdp::URA5 gene were at levels similar to those of the native URA5, which suggested that all the sequences necessary for proper expression were present. Transformation frequencies using the Gpdp::hphI gene constructs were poor. However, addition of DNA sequences flanking the 3'-end of an native C. neoformans gene significantly improved the transformation frequencies resulting from the expression of the heterologous hphI gene.

Amino Acid Sequence↗
PubMed2002

Characterization of manganese-dependent peroxidase isoenzymes from the ligninolytic fungus Phanerochaete flavido-alba.

Phanerochaete flavido-alba is able to decolorize and detoxify olive oil wastewater (OMW) in a process in which simple and polymeric phenols are removed. An unusual acidic MnP is accumulated during the degradation course. This microorganism produces two families of MnPs. MnP1 has an apparent molecular weight of 45 kDa and is secreted as a mixture of isoenzymes with pI ranging from 5.6 to 4.75. MnP2, which is produced as an unique isoenzyme, has an apparent molecular weight of 55.6 Mr and an unusual acidic pI lower than 2.8. The higher specific peroxidase activity for purified MnP2 was for Mn2+ oxidation. Hydroquinone and methylhydroquinone oxidation by MnP2 was Mn2+ dependent, in reaction mixtures without exogenous H2O2. Conversely, ABTS oxidation was Mn2+ independent. Two different DNA fragments (mnpA and mnpB), amplified by PCR, using MnP2 N-terminal sequence and oligonucleotides deduced from two conserved sequences of other MnPs, code for MnPs that belong to the P. chrysosporium mnp2 subfamily on the basis of intron position. The structure of mnpA and mnpB seems to be related to known manganese peroxidase genes, but mnpA encodes an Alanine instead of a Serine (Ser168) regarded as invariant within typical MnPs.

Amino Acid Sequence↗
PubMed1998

The crystal structure of a complement-1q family protein suggests an evolutionary link to tumor necrosis factor.

ACRP30--adipocyte complement-related protein of 30 kDa or AdipoQ--is an abundant serum protein, secreted exclusively from fat cells, which is implicated in energy homeostasis and obesity [1,2]. ACRP30 is a close homologue of the complement protein C1q, which is involved in the recognition of microbial surfaces [3-5] and antibody-antigen complexes [6,7] in the classical pathway of complement. We have determined the crystal structure of a homotrimeric fragment from ACRP30 at 2.1 A resolution. The structure reveals an unexpected homology to the tumor necrosis factor (TNF) family. Identical folding topologies, key residue conservations, and similarity of trimer interfaces and intron positions firmly establish an evolutionary link between the TNF and C1q families. We suggest that TNFs--which control many aspects of inflammation, adaptive immunity, apoptosis and energy homeostasis--arose by divergence from a primordial recognition molecule of the innate immune system. The evolutionary connection between C1q-like proteins and TNFs illuminates the shared functions of these two important groups of proteins.

Complement C1q↗
PubMed2001

Structural and functional conservation and divergence among acyl-CoA desaturases of two noctuid species, the corn earworm, Helicoverpa zea, and the cabbage looper, Trichoplusia ni.

In this report, we describe the structural and functional analyses of four acyl-CoA desaturase-encoding cDNAs that we isolated from RNA expressed in the pheromone gland of the corn earworm, Helicoverpa zea. We deduced the homology relationships of the encoded proteins, designated HzPGDs1, HzPGDs2, HzPGDs3 and HzFBDs, to each other and to previously described desaturases of the cabbage looper moth, Trichoplusia ni, the fly, Drosophila melanogaster, and other more distantly related organisms. We also isolated genomic DNA fragments of the four H. zea desaturase-encoding genes, determined the locations of introns present in them, and compared them to conserved intron positions in reported desaturase genes of other species. We measured the levels of the four desaturase mRNAs in H. zea pheromone glands and larval fat bodies by RT-PCR. We established the functional identities of the deduced proteins HzPGDs1 and HzPGDs2, encoded by the two desaturase mRNAs that are differentially and abundantly expressed in pheromone glands of sexually mature adult H. zea females, by functional expression of their encoding cDNAs in a desaturase-deficient mutant, ole1, of the yeast Saccharomyces cerevisiae. We compared the unique unsaturated fatty acid profiles of HzPGDs1- and HzPGDs2-expressing transformants to those of strains expressing previously described Delta11 and Delta9 desaturases of T. ni.

Amino Acid Sequence↗
PubMed2003

Molecular characterization of a nuclear topoisomerase II from Nicotiana tabacum that functionally complements a temperature-sensitive topoisomerase II yeast mutant.

We have successfully expressed enzymatically active plant topoisomerase II in Escherichia coli for the first time, which has enabled its biochemical characterization. Using a PCR-based strategy, we obtained a full-length cDNA and the corresponding genomic clone of tobacco topoisomerase II. The genomic clone has 18 exons interrupted by 17 introns. Most of the 5' and 3' splice junctions follow the typical canonical consensus dinucleotide sequence GU-AG present in other plant introns. The position of introns and phasing with respect to primary amino acid sequence in tobacco TopII and Arabidopsis TopII are highly conserved, suggesting that the two genes are evolved from the common ancestral type II topoisomerase gene. The cDNA encodes a polypeptide of 1482 amino acids. The primary amino acid sequence shows a striking sequence similarity, preserving all the structural domains that are conserved among eukaryotic type II topoisomerases in an identical spatial order. We have expressed the full-length polypeptide in E. coli and purified the recombinant protein to homogeneity. The full-length polypeptide relaxed supercoiled DNA and decatenated the catenated DNA in a Mg(2+)- and ATP-dependent manner, and this activity was inhibited by 4'-(9-acridinylamino)-3'-methoxymethanesulfonanilide (m-AMSA). The immunofluorescence and confocal microscopic studies, with antibodies developed against the N-terminal region of tobacco recombinant topoisomerase II, established the nuclear localization of topoisomerase II in tobacco BY2 cells. The regulated expression of tobacco topoisomerase II gene under the GAL1 promoter functionally complemented a temperature-sensitive TopII(ts) yeast mutant.

Amino Acid Sequence↗