Sex in the postgenomic era

The possible existence of ancient asexual lineages has long puzzled evolutionary biologists because a lack of recombination should, in theory, cause such lineages to be short lived. Recent research on what was considered to be a classic example of a such a lineage, an all-female polyploid hybrid complex of Ambystoma salamanders, not only refutes previous allegations of sexual abstinence in this complex, but also provides insights into unprecedented flexibility in interactions between genomes residing within individuals. These studies have important implications for understanding mechanisms for maintaining a functional balance between hybridizing genomes. They also demonstrate how combining genomic tools with older techniques can change current views on the rules governing genetic exchange.     

Plasmodium research in the postgenomic era

The complete genomic sequence of Plasmodium falciparum strain 3D7 was published in October 2002. At the Next Steps in Malaria Research meeting in April 2005, the next practical steps were considered and the priorities ranked for postgenomic research in Plasmodium. The high-throughput approaches that will help to answer the major biological questions regarding Plasmodium should, like the genome project itself, build community-shared resources, and efforts must be made to help researchers ready themselves to use the tools that will become available.     

Functional screening revisited in the postgenomic era

Functional screening can reveal a hidden function of a gene. cDNA library-based functional screening has flourished in various fields of biology so far, such as cancer biology, developmental biology and neuroscience. In the postgenomic era, however, various sequence database and public full-length cDNA resources are available, which now allow us to perform more straightforward, gene-oriented screening. Furthermore, the advent of RNA interference techniques has made it possible to perform effective loss-of-function screening. Gene-based functional screening is able to bridge the gap between genes and biological phenomena and raise important biological questions which should be tackled by integration of 'omic' datasets. These possible roles of functional screening will become more and more important in modern molecular biology moving toward the system level understanding of living organisms.     

Strain improvement in actinomycetes in the postgenomic era

With the recent advances in DNA sequencing technologies, it is now feasible to sequence multiple actinomycete genomes rapidly and inexpensively. An important observation that emerged from early Streptomyces genome sequencing projects was that each strain contains genes that encode 20 or more potential secondary metabolites, only a fraction of which are expressed during fermentation. More recently, this observation has been extended to many other actinomycetes with large genomes. The discovery of a wealth of orphan or cryptic secondary metabolite biosynthetic gene clusters has suggested that sequencing large numbers of actinomycete genomes may provide the starting materials for a productive new approach to discover novel secondary metabolites. The key issue for this approach to be successful is to find ways to turn on or turn up the expression of cryptic or poorly expressed pathways to provide material for structure elucidation and biological testing. In this review, I discuss several genetic approaches that are potentially applicable to many actinomycetes for this application.     

The yeast genome and the first steps toward the postgenomic era

Data on the structure and function of the yeastSaccharomyces cerevisiae genome are summarized. Hypotheses of the evolution of the yeast genome are considered. The methods used to establish the function of earlier uncharacterized genes, to study the expression of the entire genome, and to analyze the yeast proteome are described along with the first results of this work. The prospects of further development of yeast genetics in the postgenomic era are discussed.     

Microalgae in the postgenomic era: a blooming reservoir for new natural products

Bacteria, fungi, algae and higher plants are the most prolific producers of natural products (secondary metabolites). Compared to macroalgae, considerably fewer natural products have been isolated from microalgae, which offer the possibility of obtaining sufficient and well-defined biological material from laboratory cultures. Interest in microalgae is reinforced by large-scale data sets from genome sequencing projects and the development of genetic tools such as transformation protocols. This review highlights what is currently known about the biosynthesis and biological role of natural products in microalgae, with examples from isoprenoids, complex polyketides, nonribosomal peptides, polyunsaturated fatty acids and oxylipins, alkaloids, and aromatic secondary metabolites. In addition, we introduce a bioinformatic analysis of available genome sequences from totally 16 microalgae, belonging to the green and red algae, heterokonts and haptophytes. The results suggest that the biosynthetic potential of microalgae is underestimated and many microalgal natural products remain to be discovered.     

High-throughput proteomics: protein expression and purification in the postgenomic world.

Proteomics has become a major focus as researchers attempt to understand the vast amount of genomic information. Protein complexity makes identifying and understanding gene function inherently difficult. The challenge of studying proteins in a global way is driving the development of new technologies for systematic and comprehensive analysis of protein structure and function. Protein expression and purification are key processes in these studies, but have typically only been applied on a case-by-case basis to proteins of interest. Researchers are addressing the challenge of parallel expression and purification of large numbers of gene products through the principles of high-throughput screening technologies commonly used in pharmaceutical development. Some of the issues relevant to these approaches are discussed here.     

Assignment of the disulfide bonds in the sweet protein brazzein

The thermostable sweet protein brazzein consists of 54 amino acid residues and has four intramolecular disulfide bonds, the location of which is unknown. We found that brazzein resists enzymatic hydrolysis at enzyme/substrate ratios (w/w) of 1:100-1:10 at 35–40°C for 24–48 h. Brazzein was hydrolyzed using thermolysin at an enzyme/substrate ratio of 1:1 (w/w) in water, pH 5.5. for 6 h and at 50°C. The disulfide bonds were determined, by a combination of mass spectrometric analysis and amino acid sequencing of cystine-containing peptides, to be between Cys4-Cys52, Cys16-Cys37, Cys22-Cys47, and Cys26-Cys49. These disulfide bonds contribute to its thermostability. © 1996 John Wiley & Sons, Inc.     

A postgenomic view of the heat shock proteins in kinetoplastids

The kinetoplastids Leishmania major, Trypanosoma brucei and Trypanosoma cruzi are causative agents of a diverse spectrum of human diseases: leishmaniasis, sleeping sickness and Chagas' disease, respectively. These protozoa possess digenetic life cycles that involve development in mammalian and insect hosts. It is generally accepted that temperature is a triggering factor of the developmental programme allowing the adaptation of the parasite to the mammalian conditions. The heat shock response is a general homeostatic mechanism that protects cells from the deleterious effects of environmental stresses, such as heat. This response is universal and includes the synthesis of the heat-shock proteins (HSPs). In this review, we summarize the salient features of the different HSP families and describe their main cellular functions. In parallel, we analyse the composition of these families in kinetoplastids according to literature data and our understanding of genome sequence data. The genome sequences of these parasites have been recently completed. The HSP families described here are: HSP110, HSP104, group I chaperonins, HSP90, HSP70, HSP40 and small HSPs. All these families are widely represented in these parasites. In particular, kinetoplastids possess an unprecedented number of members of the HSP70, HSP60 and HSP40 families, suggesting key roles for these HSPs in their biology.     

Egb 761 in the postgenomic era: new tools from molecular biology for the study of complex products such as Ginkgo biloba extract.

The decoding of the human genome has completely changed our views on medicine. Beyond sequencing, tools of the postgenomic era may lead to a better understanding of various therapies, especially those with a complex effect on numerous cellular components and functions. The development of high-density oligonucleotide microarrays led to pioneer studies on the multiple gene expression effects exhibited by Ginkgo biloba extract EGb 761, changing traditional pharmacology and medicine concepts. Instead of studying a simple gene or protein, a global investigation of all genes or proteins at once can give insights of the complexity of biological systems.     

REALIS: postgenomic analysis of Listeria Monocytogenes

Listeria monocytogenes is a remarkably successful food-borne pathogen. It is capable a) of surviving and proliferating under conditions that exist within the food chain, such as at low temperatures, high salt and low pH and b) of colonizing animal host tissues after ingestion of contaminated food, causing opportunistic infections mainly, but not exclusively, in immunocompromised hosts. The ultimate goals of REALIS are two fold: Firstly, it aims to completely decipher all genes required for survival in and adaptation of Listeria monocytogenes to two very different environments, ie., the infected host and the external environment. Secondly, using genomics and postgenomic tools, REALIS seeks to precisely address fundamental questions regarding evolutionary relationships between pathogenic and non-pathogenic Listeria and to define qualities of particularly successful clonal pathovariants in causing disease. This project will provide both industry and health care managers with rational approaches to curbing food-borne contamination, minimising risks of infection and providing novel pharmacological approaches for halting the fulminant course of infection.