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Genome Organization (genome + organization)
Selected AbstractsGenome Organization of an Infectious Clone of Tomato Leaf Curl Virus (Philippines), a New Monopartite Begomovirus*JOURNAL OF PHYTOPATHOLOGY, Issue 11-12 2002Tatsuya Kon Abstract Complete nucleotide sequence of infectious cloned DNA of Tomato leaf curl virus from Philippines (ToLCV-Ph) was determined. The single circular DNA molecule comprises 2755 nucleotides. ToLCV-Ph DNA contains six open reading frames (ORFs) each capable of encoding proteins with a molecular weight greater than 10 kDa. A partial dimeric ToLCV-Ph DNA clone was constructed in a binary vector and used to agroinoculate tomato plants (Lycopersicon esculentum Mill. cv. Zuikou 102). Typical leaf curl symptoms were observed, showing that the single DNA component is sufficient for infectivity. In total nucleotide sequence comparisons with other geminiviruses, ToLCV-Ph was most closely related to Ageratum yellow vein virus (AYVV) (79% identity), ToLCV-Laos (78%), Soyabean crinkle leaf virus -Thailand (78%) and ToLCV-Taiwan (77%). The significant but relatively low sequence identity in the genomic DNA between ToLCV-Ph and other geminiviruses suggests that it is a distinct geminivirus in the genus Begomovirus. [source] Modulation of oat arginine decarboxylase gene expression and genome organization in transgenic Trypanosoma cruzi epimastigotesFEBS JOURNAL, Issue 3 2006Marķa P. Serra We have previously demonstrated that wild-type Trypanosoma cruzi epimastigotes lack arginine decarboxylase (ADC) enzymatic activity as well as its encoding gene. A foreign ADC has recently been expressed in T. cruzi after transformation with a recombinant plasmid containing the complete coding region of the oat ADC gene. In the present study, upon modulation of exogenous ADC expression, we found that ADC activity was detected early after transfection; subsequently it decreased to negligible levels between 2 and 3 weeks after electroporation and was again detected ,,4 weeks after electroporation. After this period, the ADC activity increased markedly and became expressed permanently. These changes of enzymatic activity showed a close correlation with the corresponding levels of ADC transcripts. To investigate whether the genome organization of the transgenic T. cruzi underwent any modification related to the expression of the heterologous gene, we performed PCR amplification assays, restriction mapping and pulse-field gel electrophoresis with DNA samples or chromosomes obtained from parasites collected at different time-points after transfection. The results indicated that the transforming plasmid remained as free episomes during the transient expression of the foreign gene. Afterwards, the free plasmid disappeared almost completely for several weeks and, finally, when the expression of the ADC gene became stable, two or more copies of the transforming plasmid arranged in tandem were integrated into a parasite chromosome (1.4 Mbp) bearing a ribosomal RNA locus. The sensitivity of transcription to ,-amanitin strongly suggests involvement of the protozoan RNA polymerase I in the transcription of the exogenous ADC gene. [source] The mitochondrial genome of the wine yeast Hanseniaspora uvarum: a unique genome organization among yeast/fungal counterpartsFEMS YEAST RESEARCH, Issue 1 2006Paraskevi V. Pramateftaki Abstract The complete sequence of the apiculate wine yeast Hanseniaspora uvarum mtDNA has been determined and analysed. It is an extremely compact linear molecule containing the shortest functional region ever found in fungi (11 094 bp long), flanked by Type 2 telomeric inverted repeats. The latter contained a 2704-bp-long subterminal region and tandem repeats of 839-bp units. In consequence, a population of mtDNA molecules that differed at the number of their telomeric reiterations was detected. The functional region of the mitochondrial genome coded for 32 genes, which included seven subunits of respiratory complexes and ATP synthase (the genes encoding for NADH oxidoreductase subunits were absent), two rRNAs and 23 tRNA genes which recognized codons for all amino acids. A single intron interrupted the cytochrome oxidase subunit 1 gene. A number of reasons contributed towards its strikingly small size, namely: (1) the remarkable size reduction (by >40%) of the rns and rnl genes; (2) that most tRNA genes and five of the seven protein-coding genes were the shortest among known yeast homologs; and (3) that the noncoding regions were restricted to 5.1% of the genome. In addition, the genome showed multiple changes in the orientation of transcription and the gene order differed drastically from other yeasts. When all protein coding gene sequences were considered as one unit and were compared with the corresponding molecules from all other complete mtDNAs of yeasts, the phylogenetic trees constructed robustly supported its placement basal to the yeast species of the ,Saccharomyces complex', demonstrating the advantage of this approach over single-gene or multigene approaches of unlinked genes. [source] The complete mitochondrial genome sequence of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variabilityINSECT MOLECULAR BIOLOGY, Issue 2 2007J. D. Fenn Abstract The Anabrus simplex is a swarming plague orthopteran found in western North America. The genome is 15 766 bp in length and genome organization follows the ancestral insect gene arrangement. atp6 lacked any readily identifiable stop codon. Examination of mRNA secondary structure for this gene suggested a stem/loop-mediated mRNA post-transcriptional processing to liberate a mature atp6 mRNA with a complete stop codon produced by polyadenylation. Comparison of similar protein with protein gene boundaries in other insect species reveal a general mechanism for mRNA excision and provide further supporting evidence for post-transcriptional mRNA processing in mitochondrial genomes. The A + T-rich region, or control region, was sequenced for 55 A. simplex individuals from 12 different populations. Variance studies between these individuals show that the A + T-rich region contains significant phylogenetic signal to be used in population studies. [source] The highly compact structure of the mitochondrial DNA polymerase genomic region of Drosophila melanogaster: functional and evolutionary implicationsINSECT MOLECULAR BIOLOGY, Issue 3 2000E. Lefai Abstract The structure of a Drosophila melanogaster genomic region containing five tightly clustered genes has been determined and evaluated with regard to its functional and evolutionary relationships. In addition to the genes encoding the two subunits (, and ,) of the DNA polymerase , holoenzyme, the key enzyme for mitochondrial DNA replication, other genes contained in the cluster may be also involved in the cellular distribution of mitochondria and in the coordination of mitochondrial and nuclear DNA replication. The gene cluster is extremely compact, with very little intergenic space. It contains two bidirectional promoter regions, and particularly notable is the 5, end overlap detected in two of its genes, an exceptional situation in both prokaryotic and eukaryotic genome organization. [source] Chromosome organization and gene control: It is difficult to see the picture when you are inside the frameJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 1 2006Pernette J. Verschure Abstract The organization of the genome in the nucleus is related to its function. The functional compartmentalization of the genome is described at the nuclear, chromosomal, subchromosomal, nucleosomal, and DNA sequence level. These descriptions originate from the techniques that were used for analysis. The different levels of compartmentalization are not easily reconciled, because the techniques applied to identify genome compartmentalization generally cannot be performed in combination. We have obtained a large body of information on individual "actors" and "scenes" in the nucleus regarding genome compartmentalization, but we still do not understand how and by what pieces of equipment the "actors" play their game. The next challenge is to understand the combined operation of the various levels of functional genome organization in the nucleus, that is, how do the epigenetic and genetic levels act together. In this paper, I will highlight some of the general features and observations of functional organization of the eukaryotic genome in interphase nuclei and discuss the concepts and views based on observed correlations between genome organization and function. I will reflect on what is to be expected from this field of research when the functional levels of genome compartmentalization are integrated. In this context I will draw attention to what might be needed to improve our understanding. J. Cell. Biochem. © 2006 Wiley-Liss, Inc. [source] Biological and Molecular Characterization of Melon-Infecting Kyuri Green Mottle Mosaic Virus in IndonesiaJOURNAL OF PHYTOPATHOLOGY, Issue 10 2005B. S. Daryono Abstract Melon (Cucumis melo L.) plants showing fruit deformation and mosaic symptoms were found in Java, Indonesia, in 2001. Leaf dips of the symptomatic melon tissue revealed rod-shaped viral particles 300 × 18 nm in size. Biological and serological data described in this study indicate that the virus belonged to the genus tobamovirus and was related to the kyuri green mottle mosaic virus (KGMMV). The genome of the virus has been completely sequenced, consisting of 6512 nucleotides and was compared in detail with KGMMV-C1 and KGMMV-Y. The sequence of their 5,- and 3,- non-coding regions (NCRs) were 91% and 94% identical to KGMMV-C1, and only 82% and 95% identical to KGMMV-Y respectively. The amino acid sequence of the shorter and longer RNA replicase components, movement protein and coat protein were 94%, 91%, 95% and 94% identical to KGMMV-C1 and 93%, 89%, 91% and 85% identical of KGMMV-Y respectively. The results from phylogenetic analysis of the coding regions revealed that KGMMV-YM is a new strain of KGMMV. This is the first report of the complete nucleotide sequence and analysis of genome organization for KGMMV isolated in anywhere in South-East Asia. [source] Genomic mutation rates: what high-throughput methods can tell usBIOESSAYS, Issue 9 2009Koodali T. Nishant Abstract High-throughput DNA analyses are increasingly being used to detect rare mutations in moderately sized genomes. These methods have yielded genome mutation rates that are markedly higher than those obtained using pre-genomic strategies. Recent work in a variety of organisms has shown that mutation rate is strongly affected by sequence context and genome position. These observations suggest that high-throughput DNA analyses will ultimately allow researchers to identify trans -acting factors and cis sequences that underlie mutation rate variation. Such work should provide insights on how mutation rate variability can impact genome organization and disease progression. [source] Dinoflagellate mitochondrial genomes: stretching the rules of molecular biologyBIOESSAYS, Issue 2 2009Ross F. Waller Abstract Mitochondrial genomes represent relict bacterial genomes derived from a progenitor ,-proteobacterium that gave rise to all mitochondria through an ancient endosymbiosis. Evolution has massively reduced these genomes, yet despite relative simplicity their organization and expression has developed considerable novelty throughout eukaryotic evolution. Few organisms have reengineered their mitochondrial genomes as thoroughly as the protist lineage of dinoflagellates. Recent work reveals dinoflagellate mitochondrial genomes as likely the most gene-impoverished of any free-living eukaryote, encoding only two to three proteins. The organization and expression of these genomes, however, is far from the simplicity their gene content would suggest. Gene duplication, fragmentation, and scrambling have resulted in an inflated and complex genome organization. Extensive RNA editing then recodes gene transcripts, and trans-splicing is required to assemble full-length transcripts for at least one fragmented gene. Even after these processes, messenger RNAs (mRNAs) lack canonical start codons and most transcripts have abandoned stop codons altogether. [source] Decoding the rice genomeBIOESSAYS, Issue 4 2006Shubha Vij Rice cultivation is one of the most important agricultural activities on earth, with nearly 90% of it being produced in Asia. It belongs to the family of crops that includes wheat, maize and barley, and it supplies more than 50% of calories consumed by the world population. Its immense economic value and a relatively small genome size makes it a focal point for scientific investigations, so much so that four whole genome sequence drafts with varying qualities have been generated by both public and privately funded ventures. The availability of a complete and high-quality map-based sequence has provided the opportunity to study genome organization and evolution. Most importantly, the order and identity of 37,544 genes of rice have been unraveled. The sequence provides the required ingredients for functional genomics and molecular breeding programs aimed at unraveling intricate cellular processes and improving rice productivity. BioEssays 28: 421,432, 2006. © 2006 Wiley Periodicals, Inc. [source] Chromatin dynamics of unfolding and refolding controlled by the nucleosome repeat length and the linker and core histonesBIOPOLYMERS, Issue 4 2007Toshiro Kobori Abstract Chromatin is composed of genomic DNA and histones, forming a hierarchical architecture in the nucleus. The chromatin hierarchy is common among eukaryotes despite different intrinsic properties of the genome. To investigate an effect of the differences in genome organization, chromatin unfolding processes were comparatively analyzed using Schizosaccaromyces pombe, Saccharomyces cerevisiae, and chicken erythrocyte. NaCl titration showed dynamic changes of the chromatin. 400,1000 mM NaCl facilitated beads with ,115 nm in diameter in S. pombe chromatin. A similar transition was also observed in S. cerevisiae chromatin. This process did not involve core histone dissociation from the chromatin, and the persistence length after the transition was ,26 nm for S. pombe and ,28 nm for S. cerevisiae, indicating a salt-induced unfolding to "beads-on-a-string" fibers. Reduced salt concentration recovered the original structure, suggesting that electrostatic interaction would regulate this discrete folding-unfolding process. On the other hand, the linker histone was extracted from chicken chromatin at 400 mM NaCl, and AFM observed the "beads-on-a-string" fibers around a nucleus. Unlike yeast chromatin, therefore, this unfolding was irreversible because of linker histone dissociation. These results indicate that the chromatin unfolding and refolding depend on the presence and absence of the linker histone, and the length of the linker DNA. © 2007 Wiley Periodicals, Inc. Biopolymers 85:295,307, 2007. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] DNA Microarrays: Experimental Issues, Data Analysis, and Application to Bacterial SystemsBIOTECHNOLOGY PROGRESS, Issue 5 2004Yandi Dharmadi DNA microarrays are currently used to study the transcriptional response of many organisms to genetic and environmental perturbations. Although there is much room for improvement of this technology, its potential has been clearly demonstrated in the past 5 years. The general consensus is that the bottleneck is now located in the processing and analysis of transcriptome data and its use for purposes other than the quantification of changes in gene expression levels. In this article we discuss technological aspects of DNA microarrays, statistical and biological issues pertinent to the design of microarray experiments, and statistical tools for microarray data analysis. A review on applications of DNA microarrays in the study of bacterial systems is presented. Special attention is given to studies in the following areas: (1) bacterial response to environmental changes; (2) gene identification, genome organization, and transcriptional regulation; and (3) genetic and metabolic engineering. Soon, the use of DNA microarray technologies in conjunction with other genome/system-wide analyses (e.g., proteomics, metabolomics, fluxomics, phenomics, etc.) will provide a better assessment of genotype-phenotype relationships in bacteria, which serve as a basis for understanding similar processes in more complex organisms. [source] | |||||||||||||