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Results for “gene expression evolution”

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PubMed2005

Directed evolution of metabolic pathways.

The modification of cellular metabolism is of biotechnological and commercial significance because naturally occurring metabolic pathways are the source of diverse compounds used in fields ranging from medicine to bioremediation. Directed evolution is the experimental improvement of biocatalysts or cellular properties through iterative genetic diversification and selection procedures. The creation of novel metabolic functions without disrupting the balanced intracellular pool of metabolites is the primary challenge of pathway manipulation. The introduction of coordinated changes across multiple genetic elements, in conjunction with functional selection, presents an integrated approach for the modification of metabolism with benign physiological consequences. Directed evolution formats take advantage of the dynamic structures of genomes and genomic sub-structures and their ability to evolve in multiple directions in response to external stimuli. The elucidation, design and application of genome-restructuring mechanisms are key elements in the directed evolution of cellular metabolic pathways.

Biotechnology↗
PubMed2004

Divide et Impera--the midbrain-hindbrain boundary and its organizer.

The midbrain-hindbrain organizer (MHO) is a signalling centre that orchestrates development of the mesencephalic and anterior metencephalic primordia. In recent years, details have been revealed about the molecular nature of these signals, their transmission and reception, and the regulatory processes associated with MHO function. This article reviews recent progress in understanding the genetic and molecular components of the MHO, and how they synergize to control brain development.

Animals↗
PubMed2005

MYB-bHLH-WD40 protein complex and the evolution of cellular diversity.

A protein complex composed of MYB and bHLH transcription factors associated with a WD40 repeat protein initiates multiple cellular differentiation pathways in a range of plants. Recent reports have provided the first coherent models of the network of interactions that lead to diverse cell fates through the activity of this protein complex. The resulting flexibility in plant morphology is likely to have played a major role in angiosperm evolution and success. The complex appears to have arisen in the land plant lineage, although its component parts are considerably more ancient. Here, we review the evolutionary history of the MYB-bHLH-WD40 protein complex and its role in generating plant epidermal cellular diversity.

Biological Evolution↗
PubMed2005

Semi-synthetic DNA shuffling of aveC leads to improved industrial scale production of doramectin by Streptomyces avermitilis.

The avermectin analog doramectin (CHC-B1), sold commercially as Dectomax, is biosynthesized by Streptomyces avermitilis. aveC, a gene encoding an unknown mechanistic function, plays an essential role in the production of doramectin (avermectin CHC-B1), modulating the production ratio of CHC-B1 to other avermectins, most notably the undesirable analog CHC-B2. To improve the production ratio for doramectin, the aveC gene was subjected to iterative rounds of semi-synthetic DNA shuffling. Libraries of shuffled aveC gene variants were transformed into S. avermitilis, screened using a miniaturized 96-well growth and production format, and analyzed by high throughput mass spectrometry to determine CHC-B2:CHC-B1 ratios. Several improved aveC variants were identified; the best shuffled gene encoded 10 amino acid mutations, and conferred a final CHC-B2:CHC-B1 ratio of 0.07:1, a 23-fold improvement over the starting gene (aveC wild type). Chromosomal insertion of an improved aveC shuffled gene into a high titer S. avermitilis strain yielded an improved doramectin production strain. This strain is under development to be used commercially, and is expected to provide considerable cost savings in large-scale manufacture, as well as significantly reducing by-product levels of CHC-B2 requiring disposal.

DNA Shuffling↗
PubMed2004

Engineered protein function by selective amino acid diversification.

Almost all protein engineering methods rely upon making changes to naturally occurring proteins that already possess some of the desired properties. This will probably remain the case as long as we lack a complete understanding of the way that an amino acid sequence gives rise to a protein with a precisely defined biological function. Common to all methods for altering an existing protein is the selection of a subset of amino acids in the protein for variation and a choice of which substitutions to make at each position. Variants are then tested empirically and further variants are created based upon their performance. Differences between protein engineering methods are the ways in which amino acids are chosen for variation, the protocols followed for creating the variants, and how information regarding variant properties is used in creating subsequent variants. In this article, we describe these differences and provide examples of how the experimental parameters of specific projects determine which method is most suitable.

Amino Acids↗
PubMed2001

Intrinsic and extrinsic factors that shape neocortical specification.

Increasing evidence points to the importance of intrinsic molecular cues in specifying the regional identity of mammalian neocortex. Few such cues, however, have been found to be restricted to individual functionally defined cortical areas before the arrival of afferent information. In contrast, thalamocortical axons are specifically targeted to individual cortical areas, raising the possibility that they can instruct some aspects of cortical areal identity. Cortical structure and function can be altered by modifying the source or pattern of activity in thalamocortical afferents. In particular, studies of cross-modal plasticity have shown that in many respects, one sensory cortical area can substitute for another after a switch of input modality during development. Afferent inputs might therefore direct the formation of their own processing circuitry, a possibility that has important implications for brain development, plasticity and evolution.

Animals↗
PubMed2002

Microbial technologies for the discovery of novel bioactive metabolites.

Soil microbes represent an important source of biologically active compounds. These molecules present original and unexpected structure and are selective inhibitors of their molecular targets. At Biosearch Italia, discovery of new bioactive molecules is mostly carried out through the exploitation of a proprietary strain collection of over 50000 strains, mostly unusual genera of actinomycetes and uncommon filamentous fungi. A critical element in a drug discovery based on microbial extracts is the isolation of unexploited groups of microorganisms that are at the same time good producers of secondary metabolites. Molecular genetics can assist in these efforts. We will review the development and application of molecular methods for the detection of uncommon genera of actinomycetes in soil DNA and for the rapid dereplication of actinomycete isolates. The results indicate a substantial presence in many soils of the uncommon genera and a large diversity of isolated actinomycetes. However, while uncommon actinomycete strains may provide an increased chance of yielding novel structures, their genetics and physiology are poorly understood. To speed up their manipulation, we have developed vectors capable of stably maintaining large segments of actinomycete DNA in Escherichia coli and of integrating site specifically in the Streptomyces genome. These vectors are suitable for the reconstruction of gene clusters from smaller segment of cloned DNA, the preparation of large-insert libraries from unusual actinomycete strains and the construction of environmental libraries.

Actinobacteria↗
PubMed1995

Shoot development in plants: time for a change.

The shoot system in plants progresses through several discrete phases during its development. Changes in the timing of these phases have important consequences for the morphogenesis of the shoot and are likely to be important in plant evolution. Genetic analysis of phase change in herbaceous plants, such as maize and Arabidopsis, has defined some of the genes involved in this phenomenon and has suggested a model for the regulation of this key feature of plant development.

Biological Evolution↗
PubMed1997

Genome organization, natural genetic engineering and adaptive mutation.

Bacterial evolution is considered in the light of molecular discoveries about genome organization, biochemical mechanisms of genetic change, and cellular control networks. Prokaryotic genetic determinants are organized as modular composites of coding sequences and protein-factor binding sites joined together during evolution. Studies of genetic change have revealed the existence of biochemical functions capable of restructuring the bacterial genome at various levels and joining together different sequence elements. These natural genetic engineering systems can be subject to regulation by signal transduction networks conveying information about the extracellular and intracellular environments. Mu-mediated araB-lacZ coding sequence fusions provide one example of adaptive mutation (increased formation of useful mutations under selection) and illustrate how physiological regulation can modulate the activity of a natural genetic engineering system under specific conditions.

Bacteria↗
PubMed1999

RNA-triggered gene silencing.

Double-stranded RNA (dsRNA) has recently been shown to trigger sequence-specific gene silencing in a wide variety of organisms, including nematodes, plants, trypanosomes, fruit flies and planaria; meanwhile an as yet uncharacterized RNA trigger has been shown to induce DNA methylation in several different plant systems. In addition to providing a surprisingly effective set of tools to interfere selectively with gene function, these observations are spurring new inquiries to understand RNA-triggered genetic-control mechanisms and their biological roles.

Animals↗
PubMed1997

Isomorphism between cell and human languages: molecular biological, bioinformatic and linguistic implications.

The concept of cell language has been defined in molecular terms. The molecule-based cell language is shown to be isomorphic with the sound- and visual signal-based human language with respect to ten out of the 13 design features of human language characterized by Hockett. Biocybernetics, a general molecular theory of living systems developed over the past two and a half decades, is found to provide a physical theory underlying the phenomenon of cell language. The concept of cell language integrates bioenergetics and bioinformatics on the one hand and reductionistic and holistic experimental data on the other to account for living processes on the molecular level. The isomorphism between cell and human languages suggests that the DNA of higher eucaryotes contains two classes of genes--structural genes corresponding to the lexicon and 'spatiotemporal genes' corresponding to the grammar of cell language. The former is located in coding regions of DNA and the latter is predicted to reside primarily in noncoding regions. The grammar of cell language is identified with the mapping of the nucleotide sequences of DNA onto its 4-dimensional folding patterns that control the spatiotemporal evolution of gene expression. Such a mapping has been referred to as the second genetic code, in contrast to the first genetic code which maps nucleotide triplets onto amino acids. The cell language theory introduces into biology the linguistic principle of 'rule-governed creativity,' leading to the formulation of the concept of 'rule-governed creative molecules' or 'creations.' This concept sheds new light on molecular biology, bioinformatics, protein folding, and developmental biology. In addition, the cell language theory suggests that human language is ultimately founded on cell language.

Cell Biology↗
PubMed2002

The evolution of developmental regulatory pathways.

Evolutionary analysis of the content of developmental regulatory pathways has been advanced by the publication of pairs of complete genome sequences from representative taxonomic groups. Annotation of the fission yeast, rice, and mouse genomes confirms that most regulatory families are shared among eukaryotes but also shows that certain gene families have restricted distributions. Theoretical advances in the past few years include development of the theory of scale-free networks, which provides a new framework in which to consider the connectivity and evolution of regulatory systems, and introduction of algorithms that use comparative data to enhance detection of transcriptional regulatory motifs.

Animals↗
PubMed2001

Angiotensin receptors--evolutionary overview and perspectives.

The structure of the angiotensin molecule has been well preserved throughout the vertebrate scale with some amino acid variations. Specific angiotensin receptors (AT receptors) that mediate important physiological functions have been noted in a variety of tissues and species. Physiological and pharmacological characterization of AT receptors and, more recently, molecular cloning studies have elucidated the presence of AT receptor subtypes. Comparative studies suggest that an AT receptor subtype homologous to the mammalian type 1 receptor subtype (AT(1)), though pharmacologically distinct, is present in amphibians and birds, whereas AT receptors cloned from teleosts show low homology to both AT(1) and AT(2) receptor subtypes. Furthermore, receptors differing from both the AT(1)-homologue receptor and AT(2) receptor exist in some non-mammalian species. This may suggest that the prototype AT receptor evolved in primitive vertebrates and diverged to more than one type of AT receptor subtype during phylogeny. Furthermore, phenotypic modulation of AT receptors appears to occur during individual development/maturation.

Animals↗
PubMed2004

Analyzing the biology on the system level.

Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology, and summarizes the analysis methods, experimental technologies, research developments, and so on in the four key fields of systems biology--systemic structures, dynamics, control methods, and design principles.

Biological Evolution↗