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At least 847 records · Page 47Linked to original sources
PubMed2004

Genome sequence and characterization of a virus (HaRNAV) related to picorna-like viruses that infects the marine toxic bloom-forming alga Heterosigma akashiwo.

Heterosigma akashiwo (Rhaphidophyceae) is a unicellular, flagellated, bloom-forming, toxic alga of ecological and economic importance. Here, we report the results of sequencing and analyzing the genome of an 8.6-kb single-stranded RNA virus (HaRNAV-SOG263) that infects H. akashiwo. Our results show that HaRNAV is related to picorna-like viruses, but does not belong within any currently defined virus family. This is based on the genome organization and sequence comparisons of putative RNA-dependent RNA polymerase (RdRp), helicase, and capsid protein sequences. The genome sequence predicts a single open reading frame (orf) encoding a polyprotein that contains conserved picorna-like protein domains, with putative nonstructural protein domains present in the N-terminus and the structural proteins in the C-terminus of the polyprotein. We have analyzed and compared the virus structural proteins from infectious and noninfectious particles. In this way, we identified structural protein cleavage sites as well as protein processing events that are presumably important for maturation of virus particles. The combination of genome structure and sequence relationships to other viruses suggests that HaRNAV is the first member of a proposed new virus family (Marnaviridae), related to picorna-like viruses.

Amino Acid Sequence↗
PubMed2003

Genomic structure and characterization of the promoter region of the human NAK gene.

NAK has been identified as an IkappaB-kinase activating-kinase that plays an important role in NF-kappaB activation in response to several pro-inflammatory cytokines such as TNF-alpha. We describe here the genomic structure of the human NAK gene and analysis of the promoter. The gene spanned 40.5 kb and contained 21 exons with lengths ranging from 39 to 196 bp. Comparison of the phase and position of intron insertions within the human NAK gene with those within IKKalpha, IKKbeta and IKK epsilon indicated that the exon/intron organization of IKK epsilon is more highly conserved than that of IKKalpha or IKKbeta. The transcriptional start site was mapped at a position about 98 bp upstream from the translation start site by means of both an RNase protection assay and a primer extension method. Fluorescence in situ hybridization using full-length human NAK cDNA as a probe showed that the human NAK gene is localized to human chromosome 13q14.2-3, a region in which the loss of heterozygosity is associated with squamous cell carcinoma and leukemia. By using a series of deletion constructs in performing a reporter assay, a minimal 77 bp upstream of the transcriptional initiation site was shown to contribute to the major promoter activity.

5' Flanking Region↗
PubMed2004

Fkbp8: novel isoforms, genomic organization, and characterization of a forebrain promoter in transgenic mice.

The immunophilin homolog FKBP8 has been implicated in the regulation of apoptosis. Here we show that the 38-kDa form of FKBP8 (FKBP38) derives from a truncated ORF. The extended FKBP8 ORFs are 46 and 44 kDa in mouse and 45 kDa in human. Although the genomic organization of mouse and human FKBP8 is evolutionarily conserved, additional first exons are encoded by the murine locus. A 4.4-kb murine Fkbp8 gene fragment, containing a GC-rich potential promoter, directed expression of a LacZ reporter gene to forebrain neurons in transgenic mice. Expression of the transgene was observed in CA1 pyramidal neurons of the hippocampus in transgenic mice from three lines. One transgenic founder mouse exhibited widespread forebrain expression of the LacZ transgene that resembles the pattern for the endogenous Fkbp8 gene. Thus promoter/enhancer elements for forebrain expression are located around the first exons of the mouse Fkbp8 gene.

Alternative Splicing↗
PubMed1977

Characterization of Allomyces genome.

Allomyces arbuscula DNA isolated from whole cells (bulk DNA) is composed of a major (alpha) and two minor components (beta & gamma) with buoyant densities in neutral CsCl corresponding to 1.721, 1.710 and 1.702 g/cm3, respectively. The DNA obtained from purified nuclei contains alpha component only. The beta component corresponds to mitochondrial DNA. The gamma component is also extra-nuclear but has not been characterized. The reassociation kinetics of sheared, bulk and nuclear DNA show that (i) 25 % bulk and 10% of nuclear DNA reanneal very rapidly and contain highly repeated sequences; (ii) moderately repeated sequences, accounting for 15% of both bulk and nuclear DNA, have a sequence complexity of approximately 7.2-10(6) daltons and are repeated about 320 times; (iii) the slow reannealing fraction accounts for about 60% of the genome and has kinetic properties similar to single copy sequences. The sequence complexity of this fraction was determined in relation to that of Escherichia coli. After a correction for the size of the repeated sequences the genome size of A. arbuscula was calculated to be 1.7-10(10) daltons.

Base Sequence↗
PubMed2000

Genomic and functional characterization of the oas gene family encoding O-acetylserine (thiol) lyases, enzymes catalyzing the final step in cysteine biosynthesis in Arabidopsis thaliana.

The final step of cysteine biosynthesis in plants is catalyzed by O-acetylserine (thiol) lyase (OAS-TL), which occurs as several isoforms found in the cytosol, the plastids and the mitochondria. Genomic DNA blot hybridization and isolation of genomic clones indicate single copy genes (oasA1, oasA2, oasB and oasC) that encode the activities of OAS-TL A, B and C found in separate subcellular compartments in the model plant Arabidopsis thaliana. Sequence analysis reveals that the newly discovered oasA2 gene represents a pseudogene that is still transcribed, but is not functionally translated. The comparison of gene structures suggests that oasA1/oasA2 and oasB/oasC are closely related and may be derived from a common ancestor by subsequent duplications. OAS-TL A, B and C were overexpressed in an Escherichia coli mutant lacking cysteine synthesis and exhibited bifunctional OAS-TL and beta-cyanoalanine synthase (CAS) activities. However, all three proteins represent true OAS-TLs according to kinetic analysis and are unlikely to function in cyanide detoxification or secondary metabolism. In addition, it was demonstrated that the mitochondrial OAS-TL C exhibits in vivo protein-protein interaction capabilities with respect to cysteine synthase complex formation similar to cytosolic OAS-TL A and plastid OAS-TL B. Multiple database accessions for each of the A. thaliana OAS-TL isoforms can thus be attributed to a specified number of oas genes to which functionally defined gene products are assigned, and which are responsible for compartment-specific cysteine synthesis.

Arabidopsis↗
PubMed2004

Genomic structure and characterization of the 5'-flanking region of the human ghrelin gene.

Ghrelin, an endogenous ligand for the GH secretagogue receptor, induces GH secretion, food intake, and positive energy balance. Although ghrelin exhibits a variety of hormonal actions, the mechanisms regulating ghrelin expression and secretion remain unclear. To understand regulation of human ghrelin gene expression, we examined the genomic structure of approximately 5,000 bp of the 5'-flanking region of the human ghrelin gene. We performed rapid amplification of cDNA ends to estimate transcriptional start sites, indicating that there are two transcriptional initiation sites within the human ghrelin gene. Both transcripts were equally expressed in the human stomach, whereas the longer transcript was mainly expressed in a human medullary thyroid carcinoma (TT) cell line. Functional analysis using promoter-reporter constructs containing the 5'-flanking region of the gene indicated that the sequence residing within the -349 to -193 region is necessary for human ghrelin promoter function in TT cells. Within this region existed several consensus sequences for a number of transactivating regulatory proteins, including an E-box site. Destruction of this site decreased to 40% of the promoter activity. The upstream region of the promoter has two additional putative E-box sites, and site-directed mutagenesis suggested that these are also involved in promoter activation. Electrophoretic mobility shift assays demonstrated that the upstream stimulatory factor specifically bound to these E-box elements. These results suggest a potential role for upstream stimulatory factor transcription factors in the regulation of human ghrelin expression.

5' Flanking Region↗
PubMed2001

Characterization of the genomic structure of the human neuronal nicotinic acetylcholine receptor CHRNA5/A3/B4 gene cluster and identification of novel intragenic polymorphisms.

Genes coding for the alpha5, alpha3, and beta4 subunits (CHRNA5, CHRNA3, and CHRNB4) of the neuronal nicotinic acetylcholine receptors (nAChRs) are clustered on chromosome 15q24. Linkage of this chromosomal region to autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), an idiopathic partial epilepsy, was reported in one family. Moreover, mutations in other neuronal nAChR subunit genes coding for the alpha4 (CHRNA4) and the beta2 (CHRNB2) subunits were associated with ADNFLE. Apart from the exon-intron structure of CHRNA3, the genomic organization of this gene cluster was unknown, making comprehensive mutational analyses impossible. The genomic structure of CHRNA5 and CHRNB4 is here reported. Moreover, two hitherto unknown introns were identified within the 3' untranslated region of CHRNA3, causing a partial tail-to-tail overlap with CHRNA5. Four novel intragenic polymorphisms were identified and characterized in the cluster.

Amino Acid Sequence↗
PubMed1988

EIAV genomic organization: further characterization by sequencing of purified glycoproteins and cDNA.

Nucleotide sequence analyses of two different proviral clones of equine infectious anemia virus (EIAV), designated lambda 12 (K. Rushlow et al., 1986, Virology 155, 309-321) and 1369 (T. Kawakami et al., 1987, Virology 158, 300-312), indicate significant differences in the organization of two critical regions of the viral genome, i.e., in the short open reading frames in the pol-env intergenic region and in the 5'-end of the env gene. To determine the correct structure of the EIAV genome, we have performed nucleotide sequence analyses of cDNA clones produced from viral RNA and direct sequencing of purified EIAV envelope glycoproteins (gp90 and gp45). The results of the cDNA sequencing confirm the presence of two short open reading frames in the pol-env intergenic region, as reported previously for the lambda 12 clone. The protein sequencing data correlated exactly with the amino-terminal sequences of gp90 and gp45 deduced from lambda 12 nucleotide sequences. However, the protein sequencing also revealed that the putative signal sequence of EIAV gp90 is not removed during processing. Thus, EIAV apparently contains short open reading frames analogous to human immunodeficiency virus, but differs in its mode of env polyprotein processing.

Amino Acid Sequence↗
PubMed2006

The complete mitochondrial genome sequence and characterization of single-nucleotide polymorphisms in the control region of the Asian seabass (Lates calcarifer).

We determined the complete mtDNA nucleotide sequence of Lates calcarifer using the shotgun sequencing method. The mitochondrial DNA (mtDNA) was 16,535 base pairs (bp) in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major noncoding control region (CR). The CR was unusually short at only 768 bp. A striking feature of the mitochondrial genome was the high G+C content (46.1%), which is among the highest in fish. The gene order was identical to that of a typical vertebrate. Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes of 30 fish species representing 14 suborders clearly showed Lates calcarifer was located in the cluster of fish species from the order Perciformes, supporting the traditional systematic classification. We characterized single-nucleotide polymorphisms (SNPs) in the CR by sequencing the complete CR of 25 individuals obtained from Australia and Singapore. A total of 68 SNPs were detected. Eighteen SNPs were fixed with alternative nucleotides in Australian and Singapore seabass, and these SNPs could be used for differentiating fish from the two countries.

Animals↗
PubMed2026

Genomic and transcriptomic characterization of genes expressed at 20 MPa by the marine actinobacterium Kocuria flava.

A marine hydrocarbonoclastic actinobacterium Kocuria flava IOS11 was isolated from 3500 m deep-sea water of the Indian Ocean. The isolate efficiently degraded phenanthrene (250 mg/L) achieving 82 and 98% of degradation at 0.1 MPa and 20 MPa, respectively within a period of 5 days. Whole genome, transcriptomee and metabolomic analysis elucidated its phenanthrene biodegradation efficiency under in situ deep-sea conditions. The genome sequence comprises 3.47 Mb distributed across 88 scaffolds with a high GC content of 74.30%. The genome analysis encoded 3126 genes including 3052 protein coding sequences with functional annotation identifying a broad array of genes associated with PAHs degradation, environmental stress adaptation, biosurfactant and siderophore synthesis. Transcriptome profiling under 0.1 and 20 MPa conditions with phenanthrene as a sole carbon source revealed enhanced expression of hydrocarbon degrading genes, transporters, biosurfactant associated enzymes and stress responsive genes including integrases, DNA repair protein Rad, alanine ligase, heat and cold shock proteins under high pressure conditions underscoring the deep-sea adaptation capabilities of the strain. The degradation pathway of phenanthrene was proposed through integrated genome, transcriptome and metabolomic analysis. These studies provided K. flava IOS11 as a metabolically versatile and pressure adapted bacterium with promising potential for bioremediation application in extreme marine environment.

Transcriptome↗
PubMed2001

Detection of chromosomal alterations in bladder cancer by comparative genomic hybridization.

OBJECTIVES: To characterize which genomic alterations occur in bladder cancers of different grades and stages, and to evaluate the prognostic implication of chromosomal imbalances. Materials and methods Twelve transitional cell carcinoma cell lines were used to study chromosomal aberrations, using comparative genomic hybridization to examine metaphase cells. RESULTS: There was a mean of 6.0 aberrations per tumour with 4.9 gains and 1.08 deletions per tumour cell line. The mean number of aberrations was the same in grade 2 and 3 tumours. High-stage (>/= T2) carcinomas had markedly more genomic gains than had low-stage (T1) tumours, with 7.2 gains and 1.3 deletions per >/= T2 tumour, and 2.7 gains and 0.8 deletions per T1 tumour, although the difference was not statistically significant. The most frequent changes were gains of chromosome 1 (seven), 9 and 16 (six), and losses of chromosomes 14 (three), 21 and Y (two). The changes 1p+, 3p+, 9q+, 14p-, 16q+ and Yp- were significantly more frequent in low-grade tumours, with 1p+, 3p+ and Yq- the most frequent in stage T1 tumours, and 16p+, 9q+ and 13q- the most frequent in stage >/= T2 tumours. Conclusion These findings indicate several genomic regions in chromosomes 1, 9, 14 and 16 that may carry genes for the development and progression of bladder cancers.

Carcinoma, Transitional Cell↗
PubMed2026

Genome-wide identification, characterization, evolutionary analysis, and expression profiling of the FCS-like zinc finger (FLZ) gene family in soybean (Glycine max L.) under abiotic stresses.

Drought and salinity limit soybean yield. Despite their role in the SnRK1 energy-sensing complex, a systematic study of FCS-Like Zinc Finger (FLZ) proteins in soybean has not been reported. We performed a genome-wide identification of the GmFLZ gene family, identifying 40 members distributed across 18 of the 20 soybean chromosomes. Phylogenetic analysis of 87 FLZ proteins from Glycine max, Arabidopsis thaliana, and Oryza sativa revealed four major evolutionary clades, suggesting that diversification predates the separation of monocots and dicots. Structural analysis identified ten conserved motifs, with Motifs 1 and 2 present in all family members. Gene duplication analysis identified 304 paralogous pairs, most arising from segmental duplication. Ka/Ks analysis indicated localized positive selection in six gene pairs and purifying selection in 97.9% of pairs. Tissue-specific expression profiling across nine tissues showed that GmFLZ5, GmFLZ15, GmFLZ25, and GmFLZ34 had the highest expression levels detected across the GmFLZ family, with GmFLZ5 the most highly expressed member in leaves, nodules, and stem and showing moderate expression in pod, root, and root hairs, whereas GmFLZ18, GmFLZ23, and GmFLZ37 showed root-preferential expression. RT-qPCR validation under drought (20% PEG-6000) and salt (200 mM NaCl) treatments in the Giza 5 cultivar showed that 36 and 34 of the 40 GmFLZ genes, respectively, exhibited at least a two-fold change in expression, with GmFLZ21 and GmFLZ35 among the most strongly induced under salt stress. These findings provide an evolutionary and functional framework for the GmFLZ family and identify candidate genes for future functional studies in soybean stress tolerance.

Glycine max↗
PubMed2026

Genomic and Clinicopathological Characterization of a Reassortant HPAI H5N1 (Clade 2.3.4.4b) in an Endangered Cinereous Vulture (Aegypius monachus) in South Korea, 2026.

Clade 2.3.4.4b highly pathogenic avian influenza viruses (HPAIVs) continue to circulate widely in East Asia and undergo frequent reassortment in wild birds. Raptors are regarded as spillover hosts that may be exposed through predation or scavenging, yet integrated clinicopathologic and genomic investigations in cinereous vultures remain limited. Here, we describe a fatal H5N1 HPAIV infection in a cinereous vulture (Aegypius monachus) found in South Korea on January 17, 2026. On presentation, the cinereous vulture showed severe neurologic dysfunction, including inability to stand, right-sided head tilt with pathologic nystagmus, reduced oculocephalic and palpebral reflexes, and intermittent bilateral leg tremors. The cinereous vulture died within 2 days after rescue, and a complete necropsy was performed. Hematologic and biochemical testing revealed marked heterophil predominance, severe lymphopenia, mild monocytosis, and globulin values near the upper end of the reference interval. An oropharyngeal swab tested positive for influenza A virus, and a virus isolate, designated A/Cinereous_Vulture/Korea/26-JBN47/2026(H5N1), was recovered in embryonated chicken eggs. Histopathology showed nonsuppurative encephalitis and necrotizing myocarditis, and influenza A nucleoprotein was detected immunohistochemically in neurons and cardiomyocytes. Tissue real-time RT-PCR showed the lowest cycle threshold value in the brain. Whole-genome sequencing demonstrated that 26-JBN47 belonged to clade 2.3.4.4b and contained a polybasic HA cleavage site (PLREKRRKR/GLF). Segment-level phylogenetic analysis revealed a reassortant genome constellation comprising a maintained H5N1 backbone in HA, NA, and M; low PAIV (LPAIV)-associated but H5N1-incorporated PA and NP segments; flyway-associated PB2 and NS segments; and a PB1 segment phylogenetically linked to regional LPAIV lineages. Molecular marker analysis identified multiple substitutions previously reported to be associated with receptor-binding properties, polymerase-related fitness, virulence, and host-response modulation, whereas canonical PB2 mammalian-adaptive markers were absent. These findings show that 26-JBN47 was a reassortant clade 2.3.4.4b H5N1 HPAIV associated with systemic disease and clinicopathological findings consistent with neurotropic and cardiotropic infection in a cinereous vulture. They also support the potential value of scavenging raptors as sentinels of local or regional HPAIV circulation involving reassortant viruses in East Asia.

Animals↗
PubMed2000

Genomic organization and characterization of the promoter of the human ATP-binding cassette transporter-G1 (ABCG1) gene.

The ATP-binding cassette transporter G1 (ABCG1) was recently identified as a regulator of macrophage cholesterol and phospholipid transport. This transporter together with ABCA1 belongs to a group of sterol-sensitive ABC proteins which are induced by lipid loading or specific oxysterols. We report here the genomic structure of ABCG1 along with the 5' flanking sequence using library screening and BLAST search analysis. The ABCG1 gene spans more than 70 kb and contains 15 exons. The exon size is between 30 and 1081 bp and the introns range in size from 137 bp to more than 45 kb. All exon-intron boundaries display the canonical GT/AG sequences. Using promoter-luciferase reporter assays in the myeloid cell lines THP-1 and RAW246.7 and the hepatoma cell line HepG2 we could demonstrate the functionality of the ABCG1 promoter and the minimal sequence requirements for gene expression. The TATA-less proximal promoter contains multiple Sp1 binding sites and a consensus sequence for sterol regulatory element binding protein.

ATP-Binding Cassette Transporters↗
PubMed1999

Cloning of the cyclin A1 genomic structure and characterization of the promoter region. GC boxes are essential for cell cycle-regulated transcription of the cyclin A1 gene.

Cyclin A1 is a recently cloned cyclin with high level expression in meiotic cells in the testis. However, it is also frequently expressed at high levels in acute myeloid leukemia. To elucidate the regulation of cyclin A1 gene expression, we cloned and analyzed the genomic structure of cyclin A1. It consists of 9 exons within 13 kilobase pairs. The TATA-less promoter initiates transcription from several start sites with the majority of transcripts beginning within a 4-base pair stretch. A construct containing a fragment from -190 to +145 showed the highest transcriptional activity. Transfection of cyclin A1 promoter constructs into S2 Drosophila cells demonstrated that Sp1 is essential for the activity of the promoter. Sp1, as well as Sp3, bound to four GC boxes between nucleotides -130 and -80 as observed by gel shift analysis. Mutations in two or more of the four GC boxes decreased promoter activity by >80%. The promoter was found to be cell cycle-regulated with highest activities found in late S and G2/M phase. Further analyses suggested that cell cycle regulation was accomplished by periodic repression of the GC boxes in G1 phase. Taken together, our data show that cyclin A1 promoter activity critically depends on four GC boxes, and members of the Sp1 family appear to be involved in directing expression of cyclin A1 in both a tissue- and cell cycle-specific manner.

Base Sequence↗
PubMed1998

The mouse Lect2 gene: cloning of cDNA and genomic DNA, structural characterization and chromosomal localization.

We previously purified bovine leukocyte cell-derived chemotaxin 2 (LECT2) as a 16 kDa-secreted protein with a neutrophil chemotactic activity. LECT2 protein is thought to be multifunctional, since it was recently found to be identical to chondromodulin-II, a growth stimulator of chondrocyte cells. We report here the cloning and structural analysis of mouse Lect2 cDNAs and genomic DNA, and chromosomal mapping. Two types of mouse Lect2 cDNAs were cloned: one encoded the mouse counterpart of human and bovine LECT2 proteins, and the other encoded a queer type LECT2 protein whose amino-acid sequence in the carboxy terminus was different from that of the normal type LECT2 protein. The mouse Lect2 gene spanned approx. 8 kb and consisted of five exons and four introns. The genomic organization revealed that two type transcripts arose by an alternative splicing event involving exon 4. A primer extension analysis revealed that several transcription initiation sites occurred within 60-210 nucleotides upstream from the translation initiation codon. The mouse Lect2 gene was mapped to a region adjacent to D13Mit13, D13Mit21 and Il-9 on chromosome 13 by interspecific backcross mapping.

Amino Acid Sequence↗
PubMed2006

Genome and proteome characterization of the psychrophilic Flavobacterium bacteriophage 11b.

Virion DNA of bacteriophage 11b (Phi11b), which infects a psychrophilic Flavobacterium isolate from Arctic sea-ice, was determined to consist of 36,012 bp. With 30.6% its GC content corresponds to that of host-genus species and is the lowest of all phages of Gram-negative bacteria sequenced so far. Similarities of several of 65 predicted ORFs, genome organization and phylogeny suggest an affiliation to 'mesophilic' nonmarine siphoviruses, e.g. to bacteriophages SPP1 and HK97. Early genes presumably encode an essential recombination factor (ERF), a single strand binding (SSB) protein, an endonuclease, and a DNA methylase. The late gene segment is likely to contain a terminase, portal, minor head, protease and a major capsid gene. Five ORFs exhibited similarities to Bacteroidetes species and seem to reflect the host specificity of the phage. Among PAGE-separated virion proteins that were identified by MALDI-ToF mass spectrometry are the portal, the major capsid, and a putative conserved tail protein. The Phi11b genome is the first to be described of a cultivated virus infecting a psychrophilic host as well as a Bacteroidetes bacterium.

Arctic Regions↗