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At least 361 records · Page 20Linked to original sources
PubMed2005

Fertility restorer locus Rf1 [corrected] of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12.

With an aim to clone the sorghum fertility restorer gene Rf1, a high-resolution genetic and physical map of the locus was constructed. The Rf1 locus was resolved to a 32-kb region spanning four open reading frames: a plasma membrane Ca(2+)-ATPase, a cyclin D-1, an unknown protein, and a pentatricopeptide repeat (PPR13) gene family member. An approximately 19-kb region spanning the cyclin D-1 and unknown protein genes was completely conserved between sterile and fertile plants as was the sequence spanning the coding region of the Ca(2+)-ATPase. In contrast, 19 sequence polymorphisms were located in an approximately 7-kb region spanning PPR13, and all markers cosegregated with the fertility restoration phenotype. PPR13 was predicted to encode a mitochondrial-targeted protein containing a single exon with 14 PPR repeats, and the protein is classified as an E-type PPR subfamily member. To permit sequence-based comparison of the sorghum and rice genomes in the Rf1 region, 0.53 Mb of sorghum chromosome 8 was sequenced and compared to the colinear region of rice chromosome 12. Genome comparison revealed a mosaic pattern of colinearity with an approximately 275-kb gene-poor region with little gene conservation and an adjacent, approximately 245-kb gene-rice region that is more highly conserved between rice and sorghum. Despite being located in a region of high gene conservation, sorghum PPR13 was not located in a colinear position on rice chromosome 12. The present results suggest that sorghum PPR13 represents a potential candidate for the sorghum Rf1 gene, and its presence in the sorghum genome indicates a single gene transposition event subsequent to the divergence of rice and sorghum ancestors.

Amino Acid Sequence↗
PubMed2004

Diversification of ftsZ during early land plant evolution.

The plastid division proteins FtsZ are encoded by a small nuclear gene family in land plants. Although it has been shown for some of the gene products that they are imported into plastids and function in plastid division, the evolution and function of this gene family and their products remain to be unraveled. Here we present two new ftsZ genes from the moss Physcomitrella patens and compare the genomic structure of members of the two plant ftsZ gene families. Comparison of sequence features and phylogenetic analyses confirm the presence of two clusters of paralogues in land plants and demonstrate that these genes were duplicated before the divergence of mosses, ferns and seed plants.

Amino Acid Sequence↗
PubMed2005

Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea.

Using a phylogenetic approach, we discovered three putative horizontal transfers between bacterial and archaeal species involving large clusters of genes. One transfer involves an operon of 13 genes, called mbx, which probably was transferred into the genome of Thermotoga maritima from a species belonging or close to the Pyrococcus genus. The two others implied an operon of six genes, called ech, transferred independently to the genomes of Thermoanaerobacter tengcongensis and Desulfovibrio gigas, from a species belonging or close to the Methanosarcina genus. All these transfers affected operons coding for multisubunit membrane-bound (NiFe) hydrogenases involved in the energy metabolism of the donor genomes. The functionality of the transferred operons has not been experimentally demonstrated for T. maritima, whereas in D. gigas and T. tengcongensis the encoded multisubunit hydrogenase could have a role in energy conservation. This report adds several cases of horizontal gene transfers among hydrogenases already described.

Archaea↗
PubMed2005

Structure, evolution, and expression of the two invertase gene families of rice.

Invertases catalyze the irreversible hydrolysis of sucrose to glucose and fructose. Plants contain two unrelated families of these enzymes: acid forms that derive from periplasmic invertases of eubacteria and are found in cell wall and vacuole, and neutral/alkaline forms evolved from the cytosolic invertases of cyanobacteria. Genomes of rice (Oryza sativa) and thale cress (Arabidopsis thaliana) contain multiple genes encoding these two families. Here for rice we identify the member genes of a cell-wall group (designated OsCIN1-9), a vacuolar group (OsVIN1-2), and two ancient neutral/alkaline groups: alpha (OsNIN1-4) and beta (OsNIN5-8). In Arabidopsis these groups contain six, two, four and five members, respectively. It is believed that the vacuolar group evolved from the cell-wall group. We provide evidence that the N-terminal signal peptide that directs cell-wall invertases co-translationally into the endoplasmic reticulum for secretion was replaced in the vacuolar group by a sequence similar to the complex N-terminal motif that targets alkaline phosphatase post-translationally to the vacuolar membrane of yeast. Since the last common ancestor of Arabidopsis and rice, the two invertase families evolved equally rapidly via gene duplication and gene loss, but the acid invertase family underwent approximately 10 events of intron loss compared with a single event of intron gain in the neutral/alkaline invertase family. Transcripts were detected for all rice invertase genes except OsCIN9. The acid invertase genes showed greater spatial and temporal diversity of expression than the neutral/alkaline genes.

Amino Acid Sequence↗
PubMed2004

Evidence for recombination in the microcystin synthetase (mcy) genes of toxic cyanobacteria Microcystis spp.

Recombination has been suggested to be an important factor for the genetic variation of bacterial genes, but few studies have dealt with intragenic recombination between the same or closely related species of cyanobacteria. Here we provide strong evidence for recombination in the microcystin synthetase (mcy) gene cluster of the toxic cyanobacteria Microcystis spp. This gene cluster contains 10 genes (mcyA to J) that encode a mixed polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) complex. mcy gene sequences were determined for four selected regions (within mcyA, D, G, and J) within the mcy gene cluster from 1 Canadian and 10 Asian toxic Microcystis and compared with previously published mcy sequences. Split decomposition analysis indicated a reticulate phylogeny of mcyA, and several potential recombination tracts of mcyA were identified by the RDP analysis and a runs test implemented in GENECONV. In contrast, no recombination was detected in the mcyD, G, and J sequences. However, discrepancies among the four mcy gene genealogies were evident from the results of independent split decomposition analyses, which were further supported by incongruence length difference (ILD) tests. Taken together, these findings suggest that both intragenic and intergenic recombination within the mcy gene cluster contributes to the genetic diversity of the mcy genes of Microcystis spp.

Bacterial Proteins↗
PubMed2004

A plant orthologue of RNase L inhibitor (RLI) is induced in plants showing RNA interference.

RNase L inhibitors (RLIs) correspond to a group of soluble proteins from the large ATP binding cassette (ABC) family of proteins. Structurally, RLIs have an N-terminal Fe-S domain and two nucleotide binding domains. Orthologous RLI sequences with more than 48% identity have been found from Archea to Eukaryota, but have not as yet been identified in Eubacteria. Some organisms, like Arabidopsis thaliana and human, have paralogous genes with differential expression patterns, the function of which remains to be determined. Expression of Arabidopsis RLI2 was slightly increased in transgenic plants showing RNA interference, suggesting a role in this pathway.

ATP-Binding Cassette Transporters↗
PubMed2004

Canonical P elements are transcriptionally active in the saltans group of Drosophila.

Up to now, investigations of expression and regulation of P transposable element have been almost exclusively carried out with the Drosophila melanogaster canonical P element. Analyzing eight species of the saltans group, we detected transposase mRNA in germline tissues of D. saltans and D. prosaltans and repressor mRNA in somatic tissues of D. saltans and D. sturtevanti. Sequencing analysis suggested that these transcripts might belong to the canonical subfamily and that they can be transpositionally active only in D. saltans. d(N) and d(S) values of Adh and the P element suggested that the sequences found in D. saltans and D. prosaltans might have been present in the ancestor of the saltans subgroup and that the sequence found in D. sturtevanti might have been horizontally transferred from D. saltans.

Animals↗
PubMed2003

Genetic organization of genes encoding phenol hydroxylase, benzoate 1,2-dioxygenase alpha subunit and its regulatory proteins in Acinetobacter calcoaceticus PHEA-2.

Acinetobacter calcoaceticus PHEA-2 is a phenol-degrading bacterium isolated from the wastewater from an oil refinery. A 10-kb XhoI fragment consisting of nine complete Open Reading Frames (ORFs) and one partial ORF was screened from a lambda library of PHEA-2 by Southern hybridization. The sequence analyses revealed that ORF2-ORF7, designated mphKLMNOP, are homologous to dmpKLMNOP of Pseudomonas sp. CF600 and mopKLMNOP of Acinetobacter calcoaceticus NCIB8250, sharing 38%-72% and 58.5%-93.5% respectively. The products encoded by dmp and mop genes convert phenol to catechol. The mph-operon and downstream ORFs, ORF9 and ORF10, sharing high identities to benM and benA, which encode ben-operon regulatory protein and benzoate 1,2-dioxygenase alpha subunit respectively, are separated by ORF8, whose function is unknown. The organization of the mph and ben operons is different from that described previously.

Acinetobacter calcoaceticus↗
PubMed2003

Characterisation and expression analysis of a nitrate transporter and nitrite reductase genes, two members of a gene cluster for nitrate assimilation from the symbiotic basidiomycete Hebeloma cylindrosporum.

Symbiotic ectomycorrhizal fungi contribute to the nitrogen nutrition of their host-plants but little information is available on the molecular control of their nitrogen metabolism. We cloned and characterised genes encoding a nitrite reductase and a nitrate transporter in the ectomycorrhizal basidiomycete Hebeloma cylindrosporum. These two genes are divergently transcribed and linked to a previously cloned nitrate reductase gene, thus demonstrating that nitrate assimilation gene clusters occur in homobasidiomycetes. The nitrate transporter polypeptide (NRT2) is characterised by 12 transmembrane domains and presents both a long putative intracellular loop and a short C-terminal tail, two structural features which distinguish fungal high-affinity transporters from their plant homologues. In different wild-type genetic backgrounds, transcription of the two genes was repressed by ammonium and was strongly stimulated not only in the presence of nitrate but also in the presence of organic nitrogen sources or under nitrogen deficiency.

Anion Transport Proteins↗
PubMed2003

A putative mitochondrial fission gene from the ectomycorrhizal ascomycete Tuber borchii Vittad.: cloning, characterisation and phylogeny.

Mitochondrial binary division is a complex process occurring in multiple steps, mediated by several proteins. In Saccharomyces cerevisiae, a mitochondrial membrane protein, Fis1p, is required for the proper assembly of the mitochondrial division apparatus. In this study, we report the cloning, characterisation and phylogenetic analysis of Tbfis1, a gene from the ectomycorrhizal ascomycetous truffle Tuber borchii, encoding for an orthologue of S. cerevisiae Fis1p. The Tbfis1 coding region consists of a 468-nucleotide open reading frame interrupted by four introns, which encodes for a polypeptide of 155 amino acids, having a predicted transmembrane domain structure typical of the Fis1p Family. Southern blot analysis revealed that Tbfis1 is a single-copy gene in the T. borchii genome. Tbfis1 is highly expressed during the first stages of T. borchii fruit body ripening, while its expression decreases during T. borchii mycelium ageing. Also, Virtual Northern blot analysis revealed Tbfis1 expression in the symbiotic phase of the fungus life cycle. Phylogenetic analysis allowed the identification of Tbfis1 orthologues in filamentous fungi, yeasts, plants, worms, flies and mammals, indicating that the function of the protein coded by this gene has been conserved during evolution.

Amino Acid Sequence↗
PubMed2003

The Aa-Pri4 gene, specifically expressed during fruiting initiation in the Agrocybe aegerita complex, contains an unusual CT-rich leader intron within the 5' uncoding region.

The Aa1-Pri4 gene was cloned from the edible mushroom Agrocybe aegerita. The gene, specifically expressed during fruiting initiation, encodes a glycine-rich protein of 116 amino acids, with no homology to already known proteins. Homologous genes were amplified from two other strains belonging to the Agr. aegerita complex and originating from South-East Asia; and a comparison of the three genes revealed a high conservation of the coding sequences (72.8-97.8%). The PRI4 putative protein sequences were highly similar (87.5-100.0%); and all of them contained two protein kinase C sites, suggesting a potential supplementary regulation by phosphorylation at the protein level. The 5' uncoding regions all presented a leader intron, very variable in sequence (45.7% identity), but with a high C+T content (74.5-79.0%). The presence of such CT-rich sequences previously described in the promoter of highly expressed fungal genes suggests that the leader intron of the Aa1-Pri4 gene could be involved in the high-level, stage-specific expression.

Agaricales↗
PubMed2003

The application of PCR for the isolation of a lipase gene from the genomic DNA of an Antarctic microfungus.

We successfully isolated a lipase gene (designated lipPA) directly from the genomic DNA of an Antarctic isolate of Penicillium allii using PCR and a suite of degenerate primers specifically designed to target two conserved regions of fungal lipase genes. We applied the biolistic transformation system to successfully integrate the lipPA gene into a heterologous fungal host, Trichoderma reesei, one of the most powerful secretors of extracellular proteins, and induced the transformant to secrete an active lipase into the growth medium. The recombinant lipase had a temperature optimum of 25 degrees C at pH 7.9 and retained greater than 50% of the maximum activity from 10 degrees C to 35 degrees C and over a pH range from 4.0 to 8.5.

Amino Acid Sequence↗
PubMed2004

The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective.

Land plants exhibit a significant evolutionary plasticity in their mitochondrial DNA (mtDNA), which contrasts with the more conservative evolution of their chloroplast genomes. Frequent genomic rearrangements, the incorporation of foreign DNA from the nuclear and chloroplast genomes, an ongoing transfer of genes to the nucleus in recent evolutionary times and the disruption of gene continuity in introns or exons are the hallmarks of plant mtDNA, at least in flowering plants. Peculiarities of gene expression, most notably RNA editing and trans-splicing, are significantly more pronounced in land plant mitochondria than in chloroplasts. At the same time, mtDNA is generally the most slowly evolving of the three plant cell genomes on the sequence level, with unique exceptions in only some plant lineages. The slow sequence evolution and a variable occurrence of introns in plant mtDNA provide an attractive reservoir of phylogenetic information to trace the phylogeny of older land plant clades, which is as yet not fully resolved. This review attempts to summarize the unique aspects of land plant mitochondrial evolution from a phylogenetic perspective.

DNA, Mitochondrial↗
PubMed2004

Organization and expression of the SLC36 cluster of amino acid transporter genes.

Three closely related genes encoding amino acid transport proteins are clustered on 5q32 in humans, and Chromosome (Chr) 11 in mice. The human SLC36A1 gene, which encodes the lysosomal amino acid transporter LYAAT1/PAT1, generates multiple alternative mRNAs, some of which encode truncated proteins. SLC36A1 is expressed in numerous tissues, whereas expression of SLC36A2, which encodes the glycine transporter tramdorinl/PAT2, is most abundant in kidney and muscle. Expression of a third gene, SLC36A3, is restricted to testis. Mouse Slc36a2 also is expressed in bone and fat tissue. Polymorphisms in human SLC36A2 exclude it as a candidate locus for a peripheral neuropathy that has been mapped to 5q31-33. SLC36A2 is a candidate gene for 5q-myelodysplastic syndrome, on the basis of its chromosomal location and its expression in bone.

Amino Acid Sequence↗
PubMed2005

Transcripts associated with Prdx6 (peroxiredoxin 6) and related genes in mouse.

PRDX6 is a cytosolic member of the peroxiredoxin family of antioxidant proteins, which protect cells from oxidative damage by reducing cellular peroxides. Knockout studies and transgenic overexpression of Prdx6 in mice have demonstrated an important role for this protein in the defense against oxidative stress. Using Northern blotting with various Prdx6 probes, we have revealed the existence of multiple transcripts with distinct tissue distributions and regulation, including the major 1.4-kb transcript highly expressed in liver and lung, and two additional transcripts expressed primarily in liver. We hypothesized that these additional transcripts correspond either to alternative Prdx6 mRNAs or to highly related genes such as the intronless genes Aop2-rs1 and Aop2-rs2. A combination of Northern blotting, RACE, and EST and genomic sequence analysis has determined that all three liver transcripts are derived from the Prdx6 gene, as they are absent in Prdx6-null mice and differ in their 3' UTRs, suggesting the utilization of different transcription termination signal sequences which we have identified by sequence analysis. We found the Aop2-rs1 gene to be exclusively expressed in testis as a 1.2-kb transcript and have identified putative regulatory elements in its promoter. In contrast, Aop2-rs2 appears not to be expressed in any tissues, although we have evidence for the existence of other related genes that are expressed in a tissue-specific manner. Since the Prdx6 transcripts exhibit differential regulation in response to growth and oxidative stress, further investigation may reveal their distinct roles in the cell and mechanism of regulation.

Animals↗
PubMed2005

The rat pink-eyed dilution (p) mutation: an identical intragenic deletion in pink-eye dilute-coat strains and several Wistar-derived albino strains.

We identified the rat pink-eyed dilution (p) and pink eye Mishima (p(m)) mutations. The p(m) mutation, which was isolated from a wild rat caught in Mishima Japan in 1961 and is carried in the NIG-III strain, is a splice donor site mutation in intron 5. The p mutation, which was first described in 1914 and is carried in several p/p rats including the RCS and BDV strains, is an intragenic deletion including exons 17 and 18. In addition to RCS and BDV strains, several albino strains, KHR, KMI and WNA, all descendants of albino stock of the Wistar Institute, are homozygous for the p allele. Analyses revealed that the colored p strains and the Wistar-derived albino p strains had the same marker haplotype spanning approximately 4 Mb around the P locus. This indicates that these p strains share a common ancestor and the p allele did not arise independently via recurrent mutations. The historical relationship among the p strains suggests that the p deletion had been maintained in stock heterogeneous for the C and P loci and then was inherited independently by the ancestor of the Wistar albino stock and the ancestor of the pink-eyed agouti rats in Europe.

Albinism↗
PubMed2003

The ThioredoxinT and deadhead gene pair encode testis- and ovary-specific thioredoxins in Drosophila melanogaster.

So far, two thioredoxin proteins, DHD and Trx-2, have been biochemically characterized in Drosophila melanogaster. Here, with the cloning and characterization of TrxT we describe an additional thioredoxin with testis-specific expression. TrxT and dhd are arranged as a gene pair, transcribed in opposite directions and sharing a 471 bp regulatory region. We show that this regulatory region is sufficient for correct expression of the two genes. This gene pair makes a good model for unraveling how closely spaced promoters are differentially regulated by a short common control region. Both TrxT and DHD proteins are localized within the nuclei in testes and ovaries, respectively. Use of a transgenic construct expressing TrxT fused to Enhanced Yellow Fluorescent Protein reveals a clear association of TrxT with the Y chromosome lampbrush loops ks-1 and kl-5 in primary spermatocytes. The association is lost in the absence of the Y chromosome. Our results suggest that nuclear thioredoxins may have regulatory functions in the germline.

Amino Acid Sequence↗
PubMed2004

Structure and developmental expression of hatching enzyme genes of the Japanese eel Anguilla japonica: an aspect of the evolution of fish hatching enzyme gene.

We isolated seven cDNA clones from embryos of the Japanese eel Anguilla japonica. Each deduced amino acid sequence consisted of a signal peptide, a propeptide and a mature enzyme portion belonging to the astacin protease family. A phylogenetic analysis showed that the eel enzymes resembled the high choriolytic enzyme (HCE) of medaka Oryzias latipes, and the hatching enzymes of the zebra fish Danio rerio and masu salmon Oncorhynchus masou. Hatching enzymes of these teleosts belonged to the group of the medaka HCE, and not the medaka low choriolytic enzyme (LCE), another hatching enzyme of medaka. Southern blot analysis showed that the genes of the eel hatching enzymes were multicopy genes like the medaka HCE genes. However, one of the eel hatching enzyme genes comprised eight exons and seven introns, and the exon-intron organization was similar to the medaka LCE gene, which is a single-copy gene. The molecular evolution of the fish hatching enzyme genes is discussed. In addition, whole-mount in situ hybridization and immunocytochemistry showed that the eel hatching enzyme was first expressed in the pillow anterior to the forebrain of early neurula, and finally in the cell mass on the yolk sac of later stage embryos. The early differentiation profile of eel hatching gland cells was similar to that of medaka, masu salmon and zebrafish, whereas the final location of the gland cells was different among fishes.

Amino Acid Sequence↗