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PubMed2005

Profiling the expression of genes controlling rice grain quality.

Rice provides a staple source of energy, protein and other nutrients to half of the world population. Over 90 of the rice seeds consists of starch and protein by dry weight. The quantity and property of starch and protein thus play a dominant role in the yield and quality of rice. The amylase content of starch is a determining factor in the eating and cooking quality while the amount and essential amino acids balance of storage proteins affect the nutritional quality of rice. In China, the super-hybrid rice currently under the last phase of development has a 35 yield advantage over the best inbred rice varieties. However, its grain quality needs further improvement. This study reported the expression patterns of 44 genes participating in starch, storage protein, and lysine synthesis in the developing rice grain. Field grown rice cultivar 9311, the paternal line of an elite super-hybrid rice LYP9 with its draft genomic sequence released, was used as plant material. Results revealed diverse yet coordinated expression profiles of the genes involved in the three pathways which lead to the final composition and property of starch, protein and lysine that determine the quality of rice, providing useful information for rice quality improvement.

Aspartic Acid↗
PubMed2004

On the origins of the adaptive immune system: novel insights from invertebrates and cold-blooded vertebrates.

When and how adaptive immunity emerged is one of the fundamental questions in immunology. Accumulated evidence suggests that the key components of adaptive immunity, rearranging receptor genes and the MHC, are unique to jawed vertebrates. Recent studies in protochordates, in particular, the draft genome sequence of the ascidian Ciona intestinalis, are providing important clues for understanding the origin of antigen receptors and the MHC. We discuss a group of newly identified protochordate genes along with some cold-blooded vertebrate genes, the ancestors of which might have provided key elements of antigen receptors. The organization of the proto-MHCs in protochordates provides convincing evidence that the MHC regions of jawed vertebrates emerged as a result of two rounds of chromosomal duplication.

Animals↗
PubMed2006

Optimization of RNA isolation from the archaebacterium Methanosarcina barkeri and validation for oligonucleotide microarray analysis.

The recent completion of a draft genome sequence for Methanosarcina barkeri has allowed the application of various high throughput post-genomics technologies, such as nucleic acid microarrays and mass spectrometry of proteins to detect global changes in transcription and translation that occur in response to experimental treatments. However, due to the production of a thick heteropolysaccharide outer layer, M. barkeri usually grows in large aggregates of cells rather than as individual, planktonic cells. Complete disruption of these aggregates and lysis of the released cells presents technical difficulties in ensuring the isolation of intact RNA from the entire population of cells. Initial attempts at isolating RNA from M. barkeri using several standard extraction protocols gave incomplete lysis of cells and resulted in low yields of poor quality RNA. In this study, we tested several chemical and mechanical disruption modifications of standard RNA extraction methods to optimize the extraction efficiency and minimize the number of unlysed cells remaining after extraction. As a further test of the quality of the resulting RNAs, their performance in replicate microarray analyses were determined. The results showed that inclusion of a liquid nitrogen grinding step prior to Trizol extraction, combined with moderate bead beating, yielded the most complete cell lysis, the highest yield of RNA and the most reproducible microarray results for M. barkeri. From these results it is clear that the methods used to isolate RNA can have a significant impact on the variability, trend and, presumably, the accuracy of microarray data. In addition, functional analysis of the microarray results obtained with RNA from the optimized protocol showed that, as expected, the genes involved in methanogenesis were among the most highly expressed genes in M. barkeri.

Gene Expression↗
PubMed2006

Role of defense/stress-related marker genes, proteins and secondary metabolites in defining rice self-defense mechanisms.

Rice, a first cereal crop whose draft genome sequence from two subspecies (japonica-type cv. Nipponbare and indica-type 93-11) was available in 2002, along with its almost complete genome sequence in 2005, has drawn the attention of researchers worldwide because of its immense impact on human existence. One of the most critical research areas in rice is to discern the self-defense mechanism(s), an innate property of all living organisms. The last few decades have seen scattered research into rice responses to diverse environmental stimuli and stress factors. Our understanding on rice self-defense mechanism has increased considerably with accelerated research during recent years mainly due to identification and characterization of several defense/stress-related components, genes, proteins and secondary metabolites. As these identified components have been used to study the defense/stress pathways, their compilation in this review will undoubtedly help rice (and others) researchers to effectively use them as a potential marker for better understanding, and ultimately, in defining rice (and plant) self-defense response pathways.

Gene Expression Regulation, Plant↗
PubMed2005

TnXO1, a germination-associated class II transposon from Bacillus anthracis.

Bacillus anthracis harbours two virulence plasmids, pXO1 (182 kb) and pXO2 (95 kb). Whereas pXO2 harbours the cap operon coding for the capsule, pXO1 contains the pag, lef, and cya genes coding for protective antigen, lethal, and oedema factors, respectively, as well as the atxA regulatory gene. These genes are located within a 44.8 kb long pathogenicity island flanked by insertion sequences. Here, we describe the presence in the same plasmid region of an 8679 bp genetic element displaying the structural features of a class II cointegrative transposon. This element, named TnXO1, bears a transposase and a site-specific recombinase and is delineated by 38 bp terminal inverted repeats sequences similar to those of other members of this group of transposons. A putative res site has been identified in the 200 bp region between these genes. Interestingly, TnXO1 also contains the gerX operon involved in the germination of B. anthracis spores within phagocytic cells. Such close association of a mobile DNA structure with known virulence determinants in a pathogen further prompted us to look for the presence of this transposable element in other members of the Bacillus cereus sensu lato group. No instance of TnXO1 was detected outside of B. anthracis in PCR experiments, although it was found to be present in the genome sequence draft of one strain of B. cereus which has recently been shown to harbour a plasmid almost identical to pXO1.

Antigens, Bacterial↗
PubMed2005

Extracting meaning from functional genomics experiments.

The completion of draft genome sequences for human, mouse, rat, and an increasing number of other species, has provided us with preliminary gene catalogues for many organisms of medical and scientific interests. Interpreting these gene lists in the context of the organism's underlying biology, however, remains difficult. The development of DNA microarrays provided one potential source of data to help interpret gene function; by profiling global patterns of gene expression across diverse conditions, it was hoped that we might be able to develop insight into biological function. But the power of these functional genomics assays, as well as assays in proteomics and metabolomics, is that they primarily give us lists of differentially expressed genes that can be correlated with particular phenotypic states, but which remain difficult to link mechanistically to the biology driving the phenotype.

Animals↗
PubMed2002

Mutation analyses of the NFAT1 gene in chondrosarcomas and enchondromas.

Mice lacking nuclear factor of activated T cell 1 (NFAT1) showed an abnormal proliferation of chondrocytes in articular cartilage and formed an extraosseous cartilaginous mass resembling a neoplastic lesion, suggesting that the NFAT1 gene is a tumor suppressor gene in cartilaginous neoplasms. Here we performed mutation analyses of the NFAT1 gene in human cartilaginous tumors including 30 chondrosarcomas and 15 enchondromas. Reverse transcription-polymerase chain reaction (PCR) analysis revealed the expression of the NFAT1 gene in 15/15 chondrosarcomas and 12/13 enchondromas. To find subtle alterations, the genomic structure of the NFAT1 gene was determined using human genome draft sequences, and a mutation analysis was performed using the exon-by-exon PCR-single-strand conformation polymorphism method. Two heterozygous missense mutations, A1557T (His446Leu) and C2859T (Pro880Leu), were found in eight tumor samples, but the same mutation was also present in the constitutional cells of corresponding patients. The incidence of the mutant alleles in the patient and control groups showed no significant difference, suggesting that these mutations are rare single nucleotide polymorphisms unrelated with tumorigenesis. These results suggest that the NFAT1 gene is not likely to be a tumor suppressor gene in human cartilaginous tumors.

Adolescent↗
PubMed2004

Bovine genomics update: making a cow jump over the moon.

Recent research in bovine genetics has focused on characterization of the biological differences underlying phenotypic variation for qualitative and quantitative traits of economic value in existing cattle populations. The much-anticipated benefits of DNA-based tools to routinely guide selection decisions for more efficient genetic gain and widened profit margins have not been fully met since the origin of this premise over two decades ago. However, the impending release of a high-quality draft genome sequence in 2005 should mark a turning point in these efforts. The following discussion summarizes how the bovine genetics research community has positioned itself to fully utilize a genome sequence resource and frames how genome sequence information can not only be applied to better implement marker-assisted selection, but also address rising consumer concerns relative to animal well-being and food safety.

Animals↗
PubMed2004

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.

Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.

Animals↗
PubMed2002

A high-resolution recombination map of the human genome.

Determination of recombination rates across the human genome has been constrained by the limited resolution and accuracy of existing genetic maps and the draft genome sequence. We have genotyped 5,136 microsatellite markers for 146 families, with a total of 1,257 meiotic events, to build a high-resolution genetic map meant to: (i) improve the genetic order of polymorphic markers; (ii) improve the precision of estimates of genetic distances; (iii) correct portions of the sequence assembly and SNP map of the human genome; and (iv) build a map of recombination rates. Recombination rates are significantly correlated with both cytogenetic structures (staining intensity of G bands) and sequence (GC content, CpG motifs and poly(A)/poly(T) stretches). Maternal and paternal chromosomes show many differences in locations of recombination maxima. We detected systematic differences in recombination rates between mothers and between gametes from the same mother, suggesting that there is some underlying component determined by both genetic and environmental factors that affects maternal recombination rates.

Base Sequence↗
PubMed2004

Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax.

Bacillus anthracis is the etiologic agent of anthrax, an acute fatal disease among mammals. It was thought to differ from Bacillus cereus, an opportunistic pathogen and cause of food poisoning, by the presence of plasmids pXO1 and pXO2, which encode the lethal toxin complex and the poly-gamma-d-glutamic acid capsule, respectively. This work describes a non-B. anthracis isolate that possesses the anthrax toxin genes and is capable of causing a severe inhalation anthrax-like illness. Although initial phenotypic and 16S rRNA analysis identified this isolate as B. cereus, the rapid generation and analysis of a high-coverage draft genome sequence revealed the presence of a circular plasmid, named pBCXO1, with 99.6% similarity with the B. anthracis toxin-encoding plasmid, pXO1. Although homologues of the pXO2 encoded capsule genes were not found, a polysaccharide capsule cluster is encoded on a second, previously unidentified plasmid, pBC218. A/J mice challenged with B. cereus G9241 confirmed the virulence of this strain. These findings represent an example of how genomics could rapidly assist public health experts responding not only to clearly identified select agents but also to novel agents with similar pathogenic potentials. In this study, we combined a public health approach with genome analysis to provide insight into the correlation of phenotypic characteristics and their genetic basis.

Animals↗
PubMed2005

Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals.

Pheromones are chemicals emitted and sensed by conspecifics to elicit social and sexual responses and are perceived in terrestrial vertebrates primarily by the vomeronasal organ (VNO). Pheromone receptors in the mammalian VNO are encoded by the V1R and V2R gene superfamilies. The V1R superfamily contains 187 and 102 putatively functional genes in the mouse and rat, respectively. To investigate whether this large repertoire size is typical among mammals with functional VNOs, we here describe the V1R repertoires of dog, cow, and opossum based on their draft genome sequences. The dog and cow have only 8 and 32 intact V1R genes, respectively. Thus, the intact V1R repertoire size varies by at least 23-fold among placental mammals with functional VNOs. To our knowledge, this size ratio represents the greatest among-species variation in gene family size of all mammalian gene families. Phylogenetic analysis of placental V1R genes suggests multiple losses of ancestral genes in carnivores and artiodactyls and gains of many new genes by gene duplication in rodents, manifesting massive gene births and deaths. We also identify 49 intact opossum V1R genes and discover independent expansions of the repertoire in placentals and marsupials. We further show a concordance between the V1R repertoire size and the complexity of VNO morphology, suggesting that the latter could indicate the sophistication of pheromone communications within species. In sum, our results demonstrate tremendous diversity and rapid evolution of mammalian V1R gene inventories and caution the generalization of VNO biology from rodents to all mammals.

Animals↗
PubMed2003

A novel two-pore domain K+ channel, TRESK, is localized in the spinal cord.

To find a novel human ion channel gene we have executed an extensive search by using a human genome draft sequencing data base. Here we report a novel two-pore domain K+ channel, TRESK (TWIK-related spinal cord K+ channel). TRESK is coded by 385 amino acids and shows low homology (19%) with previously characterized two-pore domain K+ channels. However, the most similar channel is TREK-2 (two-pore domain K+ channel), and TRESK also has two pore-forming domains and four transmembrane domains that are evolutionarily conserved in the two-pore domain K+ channel family. Moreover, we confirmed that TRESK is expressed in the spinal cord. Electrophysiological analysis demonstrated that TRESK induced outward rectification and functioned as a background K+ channel. Pharmacological analysis showed TRESK to be inhibited by previously reported K+ channel inhibitors Ba2+, propafenone, glyburide, lidocaine, quinine, quinidine, and triethanolamine. Functional analysis demonstrated TRESK to be inhibited by unsaturated free fatty acids such as arachidonic acid and docosahexaenoic acid. TRESK is also sensitive to extreme changes in extracellular and intracellular pH. These results indicate that TRESK is a novel two-pore domain K+ channel that may set the resting membrane potential of cells in the spinal cord.

Amino Acid Sequence↗
PubMed2001

A millennial myosin census.

The past decade has seen a remarkable explosion in our knowledge of the size and diversity of the myosin superfamily. Since these actin-based motors are candidates to provide the molecular basis for many cellular movements, it is essential that motility researchers be aware of the complete set of myosins in a given organism. The availability of cDNA and/or draft genomic sequences from humans, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Dictyostelium discoideum has allowed us to tentatively define and compare the sets of myosin genes in these organisms. This analysis has also led to the identification of several putative myosin genes that may be of general interest. In humans, for example, we find a total of 40 known or predicted myosin genes including two new myosins-I, three new class II (conventional) myosins, a second member of the class III/ninaC myosins, a gene similar to the class XV deafness myosin, and a novel myosin sharing at most 33% identity with other members of the superfamily. These myosins are in addition to the recently discovered class XVI myosin with N-terminal ankyrin repeats and two human genes with similarity to the class XVIII PDZ-myosin from mouse. We briefly describe these newly recognized myosins and extend our previous phylogenetic analysis of the myosin superfamily to include a comparison of the complete or nearly complete inventories of myosin genes from several experimentally important organisms.

Animals↗
PubMed2004

Molecular evolution of PAS domain-containing proteins of filamentous cyanobacteria through domain shuffling and domain duplication.

When the entire genome of a filamentous heterocyst-forming N2-fixing cyanobacterium, Anabaena sp. PCC 7120 (Anabaena) was determined in 2001, a large number of PAS domains were detected in signal-transducing proteins. The draft genome sequence is also available for the cyanobacterium, Nostoc punctiforme strain ATCC 29133 (Nostoc), that is closely related to Anabaena. In this study, we extracted all PAS domains from the Nostoc genome sequence and analyzed them together with those of Anabaena. Clustering analysis of all the PAS domains gave many specific pairings, indicative of evolutionary conservations. Ortholog analysis of PAS-containing proteins showed composite multidomain architecture in some cases of conserved domains and domains of disagreement between the two species. Further inspection of the domains of disagreement allowed us to trace them back in evolution. Thus, multidomain proteins could have been generated by duplication or shuffling in these cyanobacteria. The conserved PAS domains in the orthologous proteins were analyzed by structural fitting to the known PAS domains. We detected several subclasses with unique sequence features, which will be the target of experimental analysis.

Amino Acid Sequence↗
PubMed2006

Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.).

Intron length polymorphisms (ILPs) have been used as genetic markers in some studies. However, a systematic investigation and large-scale exploitation of ILP markers has not been reported. In this study, we performed a genome-wide search of ILPs between two subspecies (indica and japonica) in rice using the draft genomic sequences of cultivars 93-11 (indica) and Nipponbare (japonica) and 32,127 full-length cDNA sequences of Nipponbare obtained from public databases. We identified 13,308 putative ILPs. Based on these putative ILPs, we developed 5811 candidate ILP markers via electronic-PCR with primers designed in flanking exons. We further conducted experiment to verify the candidate ILP markers. Out of 215 candidate ILP markers tested on 93-11, Nipponbare and their hybrid, we successfully exploited 173 codominant ILP markers. Further analyses on 10 rice accessions showed that these ILP markers were widely applicable and most (71.1%) exhibited subspecies specificity. This feature suggests that ILPs would be useful for the studies of genome evolution and inter-subspecies heterosis and for cross-subspecies marker-assisted selection in rice. In addition, by testing 51 pairs of the ILP primers on five Gramineae plants and three dicot plants, we found another desirable characteristic of rice ILP markers that they have high transferability to other plants.

Base Sequence↗
PubMed2025

The genome of the polyextremophilic yeast, Naganishia friedmannii, reveals adaptations involved in stress response pathways, carbohydrate metabolism expansion, and a limited DNA repair repertoire.

Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derived carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.

Carbohydrate Metabolism↗