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PubMed1999

Genomic signature: characterization and classification of species assessed by chaos game representation of sequences.

We explored DNA structures of genomes by means of a new tool derived from the "chaotic dynamical systems" theory (the so-called chaos game representation [CGR]), which allows the depiction of frequencies of oligonucleotides in the form of images. Using CGR, we observe that subsequences of a genome exhibit the main characteristics of the whole genome, attesting to the validity of the genomic signature concept. Base concentrations, stretches (runs of complementary bases or purines/pyrimidines), and patches (over- or underexpressed words of various lengths) are the main factors explaining the variability observed among sequences. The distance between images may be considered a measure of phylogenetic proximity. Eukaryotes and prokaryotes can be identified merely on the basis of their DNA structures.

Algorithms↗
PubMed2004

Genome diversity among regional populations of Francisella tularensis subspecies tularensis and Francisella tularensis subspecies holarctica isolated from the US.

Francisella tularensis is a highly infectious facultative intracellular pathogen that is considered a potential agent of bioterrorism. Four different F. tularensis subspecies have been identified and they appear to display different ecological and virulence characteristics as well as differences in geographical distribution. One simple explanation for the variation in ecological and virulence characteristics is that they are conferred by differences in genome content. To characterize genome content among stains isolated from United States, we have used a DNA microarray designed from a shotgun library of a reference strain. Polymorphisms distributed among polyphyletic sets of strains was the most common pattern of genome alteration observed, indicating that strain-specific genome variability is significant. Nonetheless, 13 different contiguous segments of the genome were found to be missing exclusively in each of the subsp. holarctica strains tested. All 13 are associated with repeat sequences or transposases that could promote insertion/deletion events. Comparison of the live vaccine strain to other holarctica strains also identified three regions that are absent exclusively in the live vaccine strain derived from holarctica.

Bacterial Vaccines↗
PubMed2025

Genome assembly and annotation of the parasitoid jewel wasp Nasonia oneida.

The jewel wasp, Nasonia (Hymenoptera: Pteromalidae), is a well-established model system for evolutionary genetics and host-microbial interactions. Here, we present the genome of N. oneida, a species lacking prior genomic characterization, using 10× Genomics linked-read (400× coverage), Illumina short-read (120× coverage), and transcriptome data (30× coverage). The assembled genome size is 267 Mb, comprising 4,675 scaffolds, with a scaffold N50 of 1 Mb and 98.40% Benchmarking Universal Single-Copy Orthologues (BUSCOs) completeness score. Annotation revealed 32.29% (86.46 Mb) of repetitive sequences and 14,221 protein-coding genes. Comparative genomics of N. oneida with 15 other hymenopteran species validated the presence of 5,939 gene families shared among them, including 3643 single-copy and 2296 multicopy gene families. This study provides the first de novo assembly of N. oneida, providing a significant addition to the growing repertoire of molecular tools for comparative genomics and functional studies to understand the evolution of closely related species as well as the evolution of parasitic wasps.

Animals↗
PubMed2025

Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth.

The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.

Streptomyces↗
PubMed1999

Molecular characterization and genomic mapping of human IPM 200, a second member of a novel family of proteoglycans.

We report herein the characterization of the cDNA for a novel human chondroitin sulfate proteoglycan, designated IPM 200, and the chromosomal location of its gene, designated IMPG2. IPM 200 was isolated from the retinal interphotoreceptor matrix, a unique extracellular matrix that occupies the subretinal space between the apices of the retinal pigment epithelium and the neural retina. The cDNA contains an open reading frame of 3,726 bp that codes for a core protein with a deduced molecular weight of 138.5 kDa. The deduced IPM 200 core protein contains a putative transmembrane domain, two EGF-like repeats, numerous N- and O-linked glycosylation consensus sequences and one consensus sequence for glycosaminoglycan attachment. IMPG2 maps to human chromosome 3q12.2-12.3. Based on homologies within their amino acid sequences we propose that IPM 200 and a previously described human proteoglycan, IPM 150, form a new family of extracellular matrix glycoconjugates.

Amino Acid Sequence↗
PubMed2004

Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes.

Through pattern matching of the cytochrome c heme-binding site (CXXCH) against the genome sequence of Shewanella oneidensis MR-1, we identified 42 possible cytochrome c genes (27 of which should be soluble) out of a total of 4758. However, we found only six soluble cytochromes c in extracts of S. oneidensis grown under several different conditions: (1) a small tetraheme cytochrome c, (2) a tetraheme flavocytochrome c-fumarate reductase, (3) a diheme cytochrome c4, (4) a monoheme cytochrome c5, (5) a monoheme cytochrome c', and (6) a diheme bacterial cytochrome c peroxidase. These cytochromes were identified either through N-terminal or complete amino acid sequence determination combined with mass spectroscopy. All six cytochromes were about 10-fold more abundant when cells were grown at low than at high aeration, whereas the flavocytochrome c-fumarate reductase was specifically induced by anaerobic growth on fumarate. When adjusted for the different heme content, the monoheme cytochrome c5 is as abundant as are the small tetraheme cytochrome and the tetraheme fumarate reductase. Published results on regulation of cytochromes from DNA microarrays and 2D-PAGE differ somewhat from our results, emphasizing the importance of multifaceted analyses in proteomics.

Amino Acid Sequence↗
PubMed1998

A chitinase encoding gene (chit1 gene) from the entomopathogen Metarhizium anisopliae: isolation and characterization of genomic and full-length cDNA.

There are no reports to date of entire gene sequences coding for chitinolytic enzymes from entomopathogenic fungi, even though these enzymes act synergistically with proteolytic enzymes to solubilize insect cuticle during the key step of host penetration, having considerable importance in the biological control of some insect pests. This paper reports the complete nucleotide sequence and analysis of the chromosomal and full-length cDNA copies of the regulated gene (chit1) coding one of the chitinases produced by the biocontrol agent Metarhizium anisopliae. Degenerated primers, encompassing conserved regions of other fungal chitinases, were used to amplify a 650-bp DNA fragment, which was used to isolate genomic and cDNA clones from M. anisopliae. Albeit at least two different chitinases are characterized in this fungus, only one chit gene was isolated. The chit1 gene is interrupted by three short typical fungal introns and has a 1,521-bp ORF, which encodes a protein of 423 amino acids with a stretch of 35 amino acid residues displaying characteristics of signal peptide. The deduced sequence of the mature protein predicts a 42-kDa protein with pI of 5.8. Southern analysis of genomic DNA indicates a single copy of chit1 in the M. anisopliae genome.

Amino Acid Sequence↗
PubMed2000

Nuclear control of mitochondrial genome reorganization characterized using cultured cells of ditelosomic and nullisomic-tetrasomic wheat lines.

In vitro-mediated reorganization of the mitochondrial genome is governed by information contained in the nuclear genome. Here we show, from the study of tissue cultures initiated from an almost complete collection of ditelosomic and nullisomic-tetrasomic wheat lines, that nuclear control of the mitochondrial genome structure is a highly complex process. Whereas information responsible for the amplification of defined molecular configurations has been found to be located in either a single or a few chromosomal arms, other rearrangements such as changes in the relative amounts of interconverting subgenomic structures are governed by a number of genes scattered over most of the wheat chromosomes.

Aneuploidy↗
PubMed2003

Identification and characterization of genomic rearrangements of MSH2 and MLH1 in Lynch syndrome (HNPCC) by novel techniques.

It has recently been suggested that large genomic rearrangements account for 10-20% of all MSH2 mutations, and a lower proportion of all MLH1 mutations, among individuals with Lynch syndrome (hereditary non-polyposis colorectal cancer, HNPCC). These rearrangements are notoriously difficult to detect; moreover, for clinical purposes, simple tests must be devised to screen family members at risk. Here we used the multiplex ligation-dependent probe amplification (MLPA) method to screen for MSH2 and MLH1 deletions in 70 patients whose colorectal or endometrial tumors were MSI positive, yet no mutation had been found by genomic exon-by-exon sequencing of MSH2, MLH1, and MSH6. We identified five candidates with four different MSH2 deletions (exons 1-2, exons 1-6, exons 1-7 and exon 8) and one candidate with an MLH1 deletion (exons 3-6). To confirm the screening results and to characterize the breakpoints of these genomic deletions precisely, we used diploid-to-haploid conversion and inverse PCR as well as long-range PCR. In each case, we were able to pinpoint the breakpoint and design a simple diagnostic PCR. The procedures we used appear to be sensitive, specific, and simple enough for clinical use.

Adaptor Proteins, Signal Transducing↗
PubMed2026

Biological characterization and genome analysis of Bacillus thuringiensis GX0003935 with biocontrol activity against Meloidogyne enterolobii.

Meloidogyne enterolobii is a highly aggressive root-knot nematode, and reduced availability of chemical nematicides increases the need for effective biocontrol alternatives. We characterized Bacillus thuringiensis GX0003935 in terms of nematicidal activity, stability, biocontrol efficacy, and genome features. The culture broth and filtrate caused more than 97% corrected mortality of second-stage juveniles within 48 h, whereas bacterial suspension showed limited activity, suggesting that extracellular factors substantially contribute to nematicidal activity. The culture filtrate retained high nematicidal activity after exposure to UV irradiation, heat treatment, broad pH range, and prolonged storage, and the strain maintained stable activity during serial passaging. Furthermore, protease sensitivity assays, ammonium sulfate precipitation, and polarity characterization collectively suggested a composite active system involving proteinaceous and non-proteinaceous components. In pot trials, culture broth and filtrate reduced galling by approximately 74%. Genome sequencing combined with ANI/dDDH analyses confirmed GX0003935 as B. thuringiensis. Multiple candidates (proteases, chitinases, and toxin proteins) and secondary metabolite biosynthetic gene clusters were revealed, while known nematicidal Cry toxins were not detected. RT-qPCR results confirmed that the expression of these candidate genes at different growth stages. B. thuringiensis GX0003935 exhibits stable, extracellular-factor-associated nematicidal activity and effectively suppresses M. enterolobii in water spinach, indicating its potential as a biocontrol candidate.

Bacillus thuringiensis↗
PubMed2005

Functional characterization and genomic organization of the human Na(+)-sulfate cotransporter hNaS2 gene (SLC13A4).

Sulfate plays an essential role in human growth and development. Here, we characterized the functional properties of the human Na(+)-sulfate cotransporter (hNaS2), determined its tissue distribution, and identified its gene (SLC13A4) structure. Expression of hNaS2 protein in Xenopus oocytes led to a Na(+)-dependent transport of sulfate that was inhibited by thiosulfate, phosphate, molybdate, selenate and tungstate, but not by oxalate, citrate, succinate, phenol red or DIDS. Transport kinetics of hNaS2 determined a K(m) for sulfate of 0.38mM, suggestive of a high affinity sulfate transporter. Na(+) kinetics determined a Hill coefficient of n=1.6+/-0.6, suggesting a Na:SO(4)(2-) stoichiometry of 2:1. hNaS2 mRNA was highly expressed in placenta and testis, with intermediate levels in brain and lower levels found in the heart, thymus, and liver. The SLC13A4 gene contains 16 exons, spanning over 47kb in length. Its 5'-flanking region contains CAAT- and GC-box motifs, and a number of putative transcription factor binding sites, including GATA-1, AP-1, and AP-2 consensus sequences. This is the first study to characterize hNaS2 transport kinetics, define its tissue distribution, and resolve its gene (SLC13A4) structure and 5' flanking region.

Animals↗
PubMed1995

Characterization and genomic mapping of the ZNF80 locus: expression of this zinc-finger gene is driven by a solitary LTR of ERV9 endogenous retroviral family.

ERV9 is a low repeated family of human endogenous retroviral elements, which has close to 50 members, in addition to at least 4000 solitary LTRs. Previous work has shown that randomly selected LTRs can promote transcription of reporter genes, raising the possibility that these sequences may affect the expression of adjacent cellular genes. We describe here the structure of the ZNF80 cDNA clone putatively coding for a zinc-finger protein, whose 5' terminus starts from within an ERV9-LTR. Characterization of the single copy genomic locus indicates that a complete ERV9-LTR element is present upstream of the ZNF80 coding region and that this element acts as a functional promoter in both in vivo and in vitro experiments. A 2.6 kb long transcript is selectively expressed only in some hematopoietic cell lineages. Interestingly we mapped the ZNF80 locus to the 3q13.3 band, a region involved in karyotype rearrangements associated with myelocytic disorders. We have also analyzed the ZNF80 genomic organization in African green monkey and we show that this lower primate does not harbour an ERV9 element at this locus. Our findings strongly suggest that the expression of a zinc finger gene, which is highly conserved during evolution of primates, is regulated in humans by an LTR element of the ERV9 family.

Animals↗
PubMed2026

Molecular characterization and genome sequence analysis of Dichroa emaravirus, a putative novel member of the genus Emaravirus.

Hydrangea febrifuga (syn. Dichroa febrifuga) is a traditional medicinal plant distributed in China and Southeast Asia, and febrifugine, one of its principal bioactive constituents, has served as an important lead compound for antimalarial drug development. Viral infections may adversely affect the quality of medicinal plants; however, no emaravirus has previously been reported from H. febrifuga. Here, high-throughput sequencing was performed on H. febrifuga leaves exhibiting mosaic symptoms collected in Yunnan Province, China. Combined with RT-PCR, Sanger sequencing, and 5'/3' rapid amplification of cDNA ends (RACE), five full-length genomic RNA segments of a putative novel emaravirus, tentatively designated Dichroa emaravirus (DEV), were identified and characterized. The five negative-sense single-stranded RNA (-ssRNA) segments have a combined length of 12,971 nt and encode an RNA-dependent RNA polymerase (RdRp), glycoprotein precursor (GP), nucleocapsid protein (NP), movement protein (MP), and an uncharacterized accessory protein, P5. The maximum amino acid sequence identities of DEV P1-P4 with recognized emaraviruses were 73.90%, 51.82%, 65.60%, and 81.30%, respectively, whereas P5 showed a maximum identity of 49.16% with its closest homolog. Thus, three of the four core proteins had maximum identities below 80%, consistent with the current ICTV species demarcation criterion for the genus Emaravirus. Maximum-likelihood phylogenetic analyses based on the four core proteins further supported the placement of DEV within the genus Emaravirus (family Fimoviridae). These results support DEV as a putative novel emaravirus and represent the first report of an emaravirus associated with H. febrifuga.

Genome, Viral↗
PubMed2005

Acute myeloid leukemia with a complex aberrant karyotype is a distinct biological entity characterized by genomic imbalances and a specific gene expression profile.

Acute myeloid leukemia (AML) with a complex aberrant karyotype is a distinct biological entity. It is characterized by: (1) a sharp increase in incidence above age 50; (2) a characteristic pattern of chromosomal gain and, especially, loss, that is, of 5q14q33, 7q32q35, and 17p13, translating into reduced expression of genes in these regions; (3) a unique gene expression pattern including up-regulation of genes involved in DNA repair; (4) a high incidence of TP53 deletions and/or mutations; and (5) an overall unfavorable prognosis. Further unraveling the biology of AML with a complex aberrant karyotype by gene expression profiling may provide deeper insights into the pathogenesis of as well as the reasons for chemoresistance in this AML subtype. These data may be the basis for developing targeted therapeutic strategies to increase the cure rate in patients with AML and a complex aberrant karyotype.

Acute Disease↗
PubMed2026

Genome-wide characterization of the bZIP gene family in Rattus norvegicus and expression profiling analysis during brain development.

BACKGROUND: The brown rat (Rattus norvegicus) serves as a cornerstone model organism in biomedical research, particularly for understanding physiological homeostasis and stress responses. The basic leucine zipper (bZIP) transcription factor family is a pivotal regulatory network involved in growth, organogenesis, and neurodevelopment. Despite its importance, a systematic characterization of the bZIP gene family in rats has remained elusive. RESULTS: In this study, we performed a genome-wide identification of 61 RnbZIP genes, which were categorized into 10 distinct subfamilies based on phylogenetic relationships and chromosomal localization. Structural analysis revealed conserved motif arrangements within subfamilies, while collinearity analysis identified significant gene duplication events-predominantly tandem and segmental duplications-that have driven the evolutionary expansion of the RnbZIP family. Quantitative analysis showed that members within the same subfamily shared 45%-92% sequence similarity (calculated using the BLOSUM62 scoring matrix), and all duplicated gene pairs underwent strong purifying selection (Ka/Ks&#x2009;<&#x2009;1). Comparative genomics across seven rodent species further underscored the evolutionary conservation and divergence of these factors. Expression profiling across diverse organs and brain developmental stages indicated that RnbZIP genes exhibit high tissue specificity. Notably, 10 candidate genes, including RnbZIP01, RnbZIP02, and RnbZIP08, demonstrated dynamic expression patterns during brain maturation, suggesting their essential roles in neurodevelopmental processes. CONCLUSIONS: Our findings provide a comprehensive structural and evolutionary framework for the RnbZIP gene family, highlighting their potential regulatory functions in rat organogenesis and brain development. This study establishes a valuable resource for further functional characterization of specific bZIP members in mammalian neurological systems.

Animals↗
PubMed2026

Genome-Wide Characterization of &#x3b2;-Glucosidase (TaBGLU) Genes in Bread Wheat and Their Expression Under Drought, Cold, and Combined Stress.

Glycoside hydrolase 1 (GH1) &#x3b2;-glucosidases were known to activate hormone conjugates and defense metabolites, yet their genomic organization and stress-response dynamics in wheat remained incompletely defined. We therefore performed an integrated characterization of TaBGLUs spanning phylogeny, gene structure and conserved motifs, subcellular localization, promoter cis-elements, Gene Ontology enrichment, protein-protein interaction networks, and targeted expression profiling. Wheat TaBGLUs partitioned into well-supported clades that shared canonical GH1 catalytic residues and a largely conserved motif scaffold. Subcellular localization predictions indicated predominant nuclear and chloroplast targeting, with a smaller cohort directed to secretory or endomembrane compartments. Promoters were enriched for light-responsive, hormone-related (ABA, JA/SA, auxin, GA) and stress-associated (MYB/WRKY, heat, low temperature) cis-elements, and functional annotations were consistent with roles in carbohydrate and cell-wall metabolism, hormone homeostasis, and defense. Network analysis revealed a densely connected TaBGLU submodule embedded within broader carbohydrate and defense interaction networks, suggesting coordinated or cooperative functions. Expression profiling under cold, drought, and combined drought and cold demonstrated broad stress inducibility, with early activation detected by 6 h, cold-responsive maxima typically at 12 h, drought-responsive peaks predominating at 24 h, and combined stress eliciting both earlier and more sustained expression maxima between 12-24 h. Representative strongly responsive genes included TaBGLU20, TaBGLU44, TaBGLU6, and TaBGLU23, which showed pronounced late induction under combined stress, TaBGLU30, which exhibited an earlier combined-stress peak, and TaBGLU12, which displayed a marked late drought-specific response. Taken together, this integrated genomic, regulatory, and expression atlas refined the wheat BGLU repertoire relative to previous gene model inventories, highlighted candidate TaBGLUs with central network positions and strong stress inducibility, and provided concrete entry points for functional validation and breeding for improved stress resilience.

Triticum↗
PubMed2001

Promoter characterization and genomic organization of the human breast cancer resistance protein (ATP-binding cassette transporter G2) gene.

The breast cancer resistance protein (BCRP) gene, formally known as ATP-binding cassette transporter G2 (ABCG2) gene, encodes an ABC half transporter that causes resistance to certain cancer chemotherapeutic drugs when transfected and expressed in drug sensitive cancer cells. Here we report the organization of the BCRP gene, and the initial characterization of the BCRP promoter. We identified the genomic sequence of BCRP and its promoter by screening a human genomic lambda phage library, as well as a BAC library, and by searching the human genome database. The BCRP gene spans over 66 kb and consists of 16 exons and 15 introns. The exons range in size from 60 to 532 bp. The translational start site is found in the second exon. The first exon contains the majority of the 5' UTR. Promoter activity was characterized by a luciferase reporter assay using transient transfection of the human breast cancer cell line MCF7, and the human choriocarcinoma cell lines JAR, BeWo and JEG-3, which we find to have high endogenous expression of BCRP. The BCRP gene is transcribed by a TATA-less promoter with several putative Sp1 sites, which are downstream from a putative CpG island. The sequence 312 bp directly upstream from the BCRP transcriptional start site conferred basal promoter activity. The 5' region upstream of the basal promoter is characterized by both positive and negative regulatory domains.

ATP Binding Cassette Transporter, Subfamily G, Mem↗