Home About us Contact
|
Home About us Contact | ||
|
|
||
Sequenced Genomes (sequenced + genome)
Selected AbstractsGenotype and time of day shape the Populus drought responseTHE PLANT JOURNAL, Issue 4 2009Olivia Wilkins Summary As exposure to episodic drought can impinge significantly on forest health and the establishment of productive tree plantations, there is great interest in understanding the mechanisms of drought response in trees. The ecologically dominant and economically important genus Populus, with its sequenced genome, provides an ideal opportunity to examine transcriptome level changes in trees in response to a drought stimulus. The transcriptome level drought response of two commercially important Populus clones (P. deltoides × P. nigra, DN34, and P. nigra × P. maximowiczii, NM6) was characterized over a diurnal period using a 4 × 2 × 2 complete randomized factorial anova experimental design (four time points, two genotypes and two treatment conditions), using Affymetrix Poplar GeneChip microarrays. Notably, the specific genes that exhibited changes in transcript abundance in response to drought differed between the genotypes and/or the time of day that they exhibited their greatest differences. This study emphasizes the fact that it is not possible to draw simple, generalized conclusions about the drought response of the genus Populus on the basis of one species, nor on the basis of results collected at a single time point. The data derived from our studies provide insights into the variety of genetic mechanisms underpinning the Populus drought response, and provide candidates for future experiments aimed at understanding this response across this economically and ecologically important genus. [source] Natural transformation of Vibrio fischeri requires tfoX and tfoYENVIRONMENTAL MICROBIOLOGY, Issue 8 2010Amber Pollack-Berti Summary Recent evidence has indicated that natural genetic transformation occurs in Vibrio cholerae, and that it requires both induction by chitin oligosaccharides, like chitohexaose, and expression of a putative regulatory gene designated tfoX. Using sequence and phylogenetic analyses we have found two tfoX paralogues in all sequenced genomes of the genus Vibrio. Like V. cholerae, when grown in chitohexaose, cells of V. fischeri are able to take up and incorporate exogenous DNA. Chitohexaose-independent transformation by V. fischeri was observed when tfoX was present in multicopy. The second tfoX paralogue, designated tfoY, is also required for efficient transformation in V. fischeri, but is not functionally identical to tfoX. Natural transformation of V. fischeri facilitates rapid transfer of mutations across strains, and provides a highly useful tool for experimental genetic manipulation in this species. The presence of chitin-induced competence in several vibrios highlights the potential for a conserved mechanism of genetic exchange across this family of environmentally important marine bacteria. [source] Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxideENVIRONMENTAL MICROBIOLOGY, Issue 5 2009Axel W. Strittmatter Summary Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp,1) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood,Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO2 but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII- c3, Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2. [source] Characterization of acetyl-CoA/propionyl-CoA carboxylase in Metallosphaera sedulaFEBS JOURNAL, Issue 4 2003Carboxylating enzyme in the 3-hydroxypropionate cycle for autotrophic carbon fixation Autotrophic Archaea of the family Sulfolobaceae (Crenarchaeota) use a modified 3-hydroxypropionate cycle for carbon dioxide assimilation. In this cycle the ATP-dependent carboxylations of acetyl-CoA and propionyl-CoA to malonyl-CoA and methylmalonyl-CoA, respectively, represent the key CO2 fixation reactions. These reactions were studied in the thermophilic and acidophilic Metallosphaera sedula and are shown to be catalyzed by one single large enzyme, which acts equally well on acetyl-CoA and propionyl-CoA. The carboxylase was purified and characterized and the genes were cloned and sequenced. In contrast to the carboxylase of most other organisms, acetyl-CoA/propionyl-CoA carboxylase from M. sedula is active at 75 °C and is isolated as a stabile functional protein complex of 560 ± 50 kDa. The enzyme consists of two large subunits of 57 kDa each representing biotin carboxylase (,) and carboxytransferase (,), respectively, and a small 18.6 kDa biotin carrier protein (,). These subunits probably form an (,,,)4 holoenzyme. It has a catalytic number of 28 s,1 at 65 °C and at the optimal pH of 7.5. The apparent Km values were 0.06 mm for acetyl-CoA, 0.07 mm for propionyl-CoA, 0.04 mm for ATP and 0.3 mm for bicarbonate. Acetyl-CoA/propionyl-CoA carboxylase is considered the main CO2 fixation enzyme of autotrophic members of Sulfolobaceae and the sequenced genomes of these Archaea contain the respective genes. Due to its stability the archaeal carboxylase may prove an ideal subject for further structural studies. [source] Helicobacter pylori HP1034 (ylxH) is required for motilityHELICOBACTER, Issue 5 2004Karin Van Amsterdam ABSTRACT Background.,Helicobacter pylori motility is essential for the colonization and persistence in the human gastric mucosa. So far, more than 50 genes have been described to play a role in flagellar biosynthesis. H. pylori YlxH (HP1034) is annotated as an ATP-binding protein. However, H. pylori YlxH shows similarity to proteins involved in the flagellar biosynthesis of other bacterial species. Moreover, H. pylori ylxH is found adjacent to genes involved in flagellar biosynthesis in the sequenced genomes of H. pylori 26695 and J99. We therefore aimed to determine the role of YlxH in H. pylori motility. Materials and methods., Motility, flagellar biosynthesis and transcriptional regulation of genes encoding flagellar proteins was compared between H. pylori 11A and a knockout of ylxH in H. pylori 11A. Results., The ylxH knockout in H. pylori 11A was nonmotile on soft agar plates, whereas H. pylori 11A was motile. Furthermore, the H. pylori 11A ylxH knockout lacked flagella, while H. pylori 11A possessed two to three flagella. Transcription of H. pylori flaG (HP0751), fliM (HP1031) and fliA (HP1032) was reduced in the H. pylori 11A ylxH¯ knockout, whereas transcription of flaA (HP0601) was not altered. However, Western blot analysis showed substantially reduced amounts of the major flagellin subunit FlaA in the H. pylori 11A ylxH knockout compared to H. pylori 11A. Conclusions.,H. pylori YlxH is essential for the assembly of flagella and hence for the motility of H. pylori. [source] Protein folding in the post-genomic eraJOURNAL OF CELLULAR AND MOLECULAR MEDICINE, Issue 3 2002Jeannine M. Yon Abstract Protein folding is a topic of fundamental interest since it concerns the mechanisms by which the genetic message is translated into the three-dimensional and functional structure of proteins. In these post-genomic times, the knowledge of the fundamental principles are required in the exploitation of the information contained in the increasing number of sequenced genomes. Protein folding also has practical applications in the understanding of different pathologies and the development of novel therapeutics to prevent diseases associated with protein misfolding and aggregation. Significant advances have been made ranging from the Anfinsen postulate to the "new view" which describes the folding process in terms of an energy landscape. These new insights arise from both theoretical and experimental studies. The problem of folding in the cellular environment is briefly discussed. The modern view of misfolding and aggregation processes that are involved in several pathologies such as prion and Alzheimer diseases. Several approaches of structure prediction, which is a very active field of research, are described. [source] Nature versus nurture in two highly enantioselective esterases from Bacillus cereus and Thermoanaerobacter tengcongensisMICROBIAL BIOTECHNOLOGY, Issue 1 2010Stephan Grosse Summary There is an increasing need for the use of biocatalysis to obtain enantiopure compounds as chiral building blocks for drug synthesis such as antibiotics. The principal findings of this study are: (i) the complete sequenced genomes of Bacillus cereus ATCC 14579 and Thermoanaerobacter tengcongensis MB4 contain a hitherto undescribed enantioselective and alkaliphilic esterase (BcEST and TtEST respectively) that is specific for the production of (R)-2-benzyloxy-propionic acid ethyl ester, a key intermediate in the synthesis of levofloxacin, a potent antibiotic; and (ii) directed evolution targeted for increased thermostability of BcEST produced two improved variants, but in either case the 3,5°C increase in the apparent melting temperature (Tm) of the mutants over the native BcEST that has a Tm of 50°C was outperformed by TtEST, a naturally occurring homologue with a Tm of 65°C. Protein modelling of BcEST mapped the S148C and K272R mutations at protein surface and the I88T and Q110L mutations at more buried locations. This work expands the repertoire of characterized members of the ,/,-fold hydrolase superfamily. Further, it shows that genome mining is an economical option for new biocatalyst discovery and we provide a rare example of a naturally occurring thermostable biocatalyst that outperforms experimentally evolved homologues that carry out the same hydrolysis. [source] Three monophyletic superfamilies account for the majority of the known glycosyltransferasesPROTEIN SCIENCE, Issue 7 2003Jing Liu Abstract Sixty-five families of glycosyltransferases (EC 2.4.x.y) have been recognized on the basis of high-sequence similarity to a founding member with experimentally demonstrated enzymatic activity. Although distant sequence relationships between some of these families have been reported, the natural history of glycosyltransferases is poorly understood. We used iterative searches of sequence databases, motif extraction, structural comparison, and analysis of completely sequenced genomes to track the origins of modern-type glycosyltransferases. We show that >75% of recognized glycosyltransferase families belong to one of only three monophyletic superfamilies of proteins, namely, (1) a recently described GPGTF/GT-B superfamily; (2) a nucleoside-diphosphosugar transferase (GT-A) superfamily, which is characterized by a DxD sequence signature and also includes nucleotidyltransferases; and (3) a GT-C superfamily of integral membrane glycosyltransferases with a modified DxD signature in the first extracellular loop. Several developmental regulators in Metazoans, including Fringe and Egghead homologs, belong to the second superfamily. Interestingly, Tout-velu/Exostosin family of developmental proteins found in all multicellular eukaryotes, contains separate domains belonging to the first and the second superfamilies, explaining multiple glycosyltransferase activities in one protein. [source] The 1.4,Å resolution structure of Paracoccus pantotrophus pseudoazurinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010Shabir Najmudin Pseudoazurins are small type 1 copper proteins that are involved in the flow of electrons between various electron donors and acceptors in the bacterial periplasm, mostly under denitrifying conditions. The previously determined structure of Paracoccus pantotrophus pseudoazurin in the oxidized form was improved to a nominal resolution of 1.4,Å, with R and Rfree values of 0.188 and 0.206, respectively. This high-resolution structure makes it possible to analyze the interactions between the monomers and the solvent structure in detail. Analysis of the high-resolution structure revealed the structural regions that are responsible for monomer,monomer recognition during dimer formation and for protein,protein interaction and that are important for partner recognition. The pseudoazurin structure was compared with other structures of various type 1 copper proteins and these were grouped into families according to similarities in their secondary structure; this may be useful in the annotation of copper proteins in newly sequenced genomes and in the identification of novel copper proteins. [source] Visualization of aligned genomic open reading frame data,BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 1 2003Alan P. Boyle Abstract Students can better appreciate the value of genomic data if they are asked to use the data themselves. However, in general the enormous volume of data involved makes detailed examination difficult. Here we present a web site that allows students to study one particular aspect of sequenced genomes. They are able to align the open reading frames (ORFs) of any available genome that is of reasonable size. The ORFs may be aligned using either the start codon or the stop codon as the starting points. Results will readily show the presence of common ribosome binding sites as well as reveal interesting order within the ORFs that is nonexistent outside of them. Students will be able to ask various questions involving comparisons of genomes and see the results presented in both a tabular and graphic format. An example problem is presented under "Results." [source] The life and death of gene familiesBIOESSAYS, Issue 1 2009Jeffery P. Demuth Abstract One of the unique insights provided by the growing number of fully sequenced genomes is the pervasiveness of gene duplication and gene loss. Indeed, several metrics now suggest that rates of gene birth and death per gene are only 10,40% lower than nucleotide substitutions per site, and that per nucleotide, the consequent lineage-specific expansion and contraction of gene families may play at least as large a role in adaptation as changes in orthologous sequences. While gene family evolution is pervasive, it may be especially important in our own evolution since it appears that the "revolving door" of gene duplication and loss has undergone multiple accelerations in the lineage leading to humans. In this paper, we review current understanding of gene family evolution including: methods for inferring copy number change, evidence for adaptive expansion and adaptive contraction of gene families, the origins of new families and deaths of previously established ones, and finally we conclude with a perspective on challenges and promising directions for future research. [source] Polyploidy in vertebrate ancestry: Ohno and beyondBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2004REBECCA F. FURLONG Over 30 years ago, Susumu Ohno proposed that two rounds of polyploidy occurred early in vertebrate evolution. We re-examine this proposal using three recent lines of evidence. First, total gene number estimates from completely sequenced genomes suggest an increase in total gene number somewhere along the vertebrate or prevertebrate lineage, compatible with Ohno's model. Second, analyses of homeobox and other genes from amphioxus reveal very extensive gene duplication specifically on the vertebrate lineage. This refines the timing of putative polyploidy to after the divergence of amphioxus and vertebrates. Third, the existence of four-fold paralogy regions in the human genome is suggestive of two rounds of polyploidy, although other explanations are possible. We propose an experimental test, based on chromosomal localization of genes in amphioxus, that should resolve whether paralogy regions are indeed remnants of duplication in vertebrate ancestry. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82, 425,430. [source] Why repetitive DNA is essential to genome functionBIOLOGICAL REVIEWS, Issue 2 2005James A. Shapiro ABSTRACT There are clear theoretical reasons and many well-documented examples which show that repetitive DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the ,functionalist' perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component. [source] In this issue: Biotechnology Journal 12/2009BIOTECHNOLOGY JOURNAL, Issue 12 2009Article first published online: 14 DEC 200 Genome-scale in silico modeling Milne et al., Biotechnol. J. 2009, 4, 1653,1670 Driven by advancements in high-throughput biological technologies and the growing number of sequenced genomes, the construction of in silico models at the genome scale has provided powerful tools to investigate a vast array of biological systems and applications. Nathan Price and colleagues review comprehensively the use of such models in industrial and medical biotechnology, including biofuel generation, food production, and drug development. As such, genome-scale models can provide a basis for rational genome-scale engineering and synthetic biology. Genome-scale in silico models promise to extend their application and analysis scope to become a transformative tool in biotechnology. From metagenomics to metaproteomics Tuffin et al., Biotechnol. J. 2009, 4, 1671,1683 Metagenomics emerged in the late 1990s as a tool for accessing and studying the collective microbial genetic material in the environment and has been widely predicted to reach new dimensions of the protein sequence space. A decade on, researchers from South Africa see that while several novel enzyme activities and protein structures have been identified the greatest advancement has been made in the isolation of novel protein sequences, some of which have no close relatives, form deeply branched lineages and even represent novel families. However, there is much room for improvement in the methods employed that need to be addressed in order to access novel biocatalytic activities. Recombinant secondary metabolites Schäfer et al., Biotechnol. J. 2009, 4, 1684,1703 Plants produce a high diversity of natural products or secondary metabolites which have interesting biological properties and quite a number are of medicinal importance. Their functions range from the protection against herbivores and/or microbial pathogens to defend against abiotic stress, e.g. UV-B exposure. Because the production of valuable natural products, such as the anticancer drugs paclitaxel, vinblastine or camptothecin in plants is a costly process, biotechnological alternatives to produce these alkaloids more economically become more and more important. This review provides an overview of the state of art to produce alkaloids in recombinant microorganisms, such as bacteria or yeast. In a longterm perspective, it will probably be possible to generate gene cassettes for complete pathways, which could then be used for the production of valuable natural products in bioreactors or for metabolic engineering of crop plants. [source] Accomplishments in genome-scale in silico modeling for industrial and medical biotechnologyBIOTECHNOLOGY JOURNAL, Issue 12 2009Caroline B. Milne Abstract Driven by advancements in high-throughput biological technologies and the growing number of sequenced genomes, the construction of in silico models at the genome scale has provided powerful tools to investigate a vast array of biological systems and applications. Here, we review comprehensively the uses of such models in industrial and medical biotechnology, including biofuel generation, food production, and drug development. While the use of in silico models is still in its early stages for delivering to industry, significant initial successes have been achieved. For the cases presented here, genome-scale models predict engineering strategies to enhance properties of interest in an organism or to inhibit harmful mechanisms of pathogens. Going forward, genome-scale in silico models promise to extend their application and analysis scope to become a transformative tool in biotechnology. [source] Genomic Analyses and the Origin of the EukaryotesCHEMISTRY & BIODIVERSITY, Issue 11 2007Maria Abstract The availability of whole-genome data has created the extraordinary opportunity to reconstruct in fine details the ,tree of life'. The application of such comprehensive effort promises to unravel the enigmatic evolutionary relationships between prokaryotes and eukaryotes. Traditionally, biologists have represented the evolutionary relationships of all organisms by a bifurcating phylogenetic tree. But recent analyses of completely sequenced genomes using conditioned reconstruction (CR), a newly developed gene-content algorithm, suggest that a cycle graph or ,ring' rather than a ,tree' is a better representation of the evolutionary relationships between prokaryotes and eukaryotes. CR is the first phylogenetic-reconstruction method to provide precise evidence about the origin of the eukaryotes. This review summarizes how the CR analyses of complete genomes provide evidence for a fusion origin of the eukaryotes. [source] | ||||||||||||||||