Genome sequencing and informatics: new tools for biochemical discoveries

Bioinformatic analyses of transmembrane transport: novel software for deducing protein phylogeny, topology, and evolution

During the past decade, we have experienced a revolution in the biological sciences resulting from the flux of information generated by genome-sequencing efforts. Our understanding of living organisms, the metabolic processes they catalyze, the genetic systems encoding cellular protein and stable RNA constituents, and the pathological conditions caused by some of these organisms has greatly benefited from the availability of complete genomic sequences and the establishment of comprehensive databases. Many research institutes around the world are now devoting their efforts largely to genome sequencing, data collection and data analysis. In this review, we summarize tools that are in routine use in our laboratory for characterizing transmembrane transport systems. Applications of these tools to specific transporter families are presented. Many of the computational approaches described should be applicable to virtually all classes of proteins and RNA molecules.

Phylogeny as a guide to structure and function of membrane transport proteins

Protein phylogeny, based on primary amino acid sequence relatedness, reflects the evolutionary process and therefore provides a guide to structure, mechanism and function. Any two proteins that are related by common descent are expected to exhibit similar structures and functions to a degree proportional to the degree of their sequence similarity; but two independently evolving proteins should not. This principle provides the impetus to define protein phylogenetic relationships and interrelate families when possible. In this mini-review, we summarize the computational approaches and criteria we use to establish common evolutionary origin. We apply these tools to define distant superfamily relationships between several previously recognized transport protein families. In some cases, available structural and functional data are evaluated in order to substantiate our claim that molecular phylogeny provides a reliable guide to protein structure and function.

Metabolic modeling of microbial strains in silico

The large volume of genome-scale data that is being produced and made available in databases on the World Wide Web is demanding the development of integrated mathematical models of cellular processes. The analysis of reconstructed metabolic networks as systems leads to the development of an in silico or computer representation of collections of cellular metabolic constituents, their interactions and their integrated function as a whole. The use of quantitative analysis methods to generate testable hypotheses and drive experimentation at a whole-genome level signals the advent of a systemic modeling approach to cellular and molecular biology.

Physiologic processes affecting the content and distribution of phytonutrients in plants

Plant physiologists and biochemists are unraveling the transport mechanisms and biosynthetic pathways that determine each plant's unique phytonutrient composition so that crop plants can be modified to improve their nutrition quality. However, before this goal can be achieved, more information is needed on various plant and human phytonutrient-related processes, and some new technical capabilities are required. The current status of our knowledge base and recommendations for technical improvements and research priorities will be discussed.

IMPROVING THE NUTRIENT COMPOSITION OF PLANTS TO ENHANCE HUMAN NUTRITION AND HEALTH

Plant foods contain almost all of the mineral and organic nutrients established as essential for human nutrition, as well as a number of unique organic phytochemicals that have been linked to the promotion of good health. Because the concentrations of many of these dietary constituents are often low in edible plant sources, research is under way to understand the physiological, biochemical, and molecular mechanisms that contribute to their transport, synthesis and accumulation in plants. This knowledge can be used to develop strategies with which to manipulate crop plants, and thereby improve their nutritional quality. Improvement strategies will differ between various nutrients, but generalizations can be made for mineral or organic nutrients. This review focuses on the plant nutritional physiology and biochemistry of two essential human nutrients, iron and vitamin E, to provide examples of the type of information that is needed, and the strategies that can be used, to improve the mineral or organic nutrient composition of plants.