Current Genomics - Volume 2, Issue 4, 2001

Helicases are enzymes that unwind DNA-DNA and RNA-DNA duplexes play important roles in many DNA metabolic activities like replication, transcription, recombination and repair. The molecular link between helicases and genomic stability has become stronger by recent studies indicating that the genes responsible for certain human degenerative disorders such as Werner syndrome (WS), Bloom syndrome (BS) and Rothmund-Thomson syndrome (RTS) encode for helicase domain containing proteins (HDPs) homologous to bacterial RecQ super family of helicases. The patients suffering from these disorders show many signs that are suggestive of accelerated aging at an early adulthood. Some of the features include atrophy of the skin, graying of the hair, cataracts, diabetes and osteoporosis. Additionally, symptoms of accelerated aging and genomic instability have also been noticed in xeroderma pigmentosum (XP) and Cockayne syndrome (complementation group B) patients. The gene products of XP complementation groups B and D are helicases and they play dual roles both in nucleotide excision repair and RNA polymerase II transcription. The CSB protein with a remarkably conserved helicase domain is homologous to yeast SWI / SNF family of proteins that have regulatory roles in transcription, chromosome stability and DNA repair. Although genomic instability is a common feature of helicase disorders, elucidation of precise biological function(s) of helicases is critical for defining the molecular basis for diverse clinical symptoms of these patients. Recent studies have characterized the preferred DNA substrates for RecQ helicases and also identified the interaction of HDPs with a number of proteins involved in DNA replication, transcription, recombination and repair. These interactions have given great insights into functional complexities of helicases. This review deals with our current knowledge on the diverse biological functions of HDPs and their collective role in the maintenance of genomic stability.

Comparative genomic in situ hybridization (CGH) studies have marked regions of unbalanced genomic alterations in a variety of human solid and hematological malignancies. Subsequent molecular analysis helped to pinpoint genes contributing to tumorigenic development and progression. CGH has since become a routine tool in molecular diagnostics and cancer research. Since mice and rats represent major model systems for human malignancies, CGH was soon adapted for tracing DNA copy number changes in experimental rodent tumor genomes. A stronghold of this approach is the potential transfer of information to the human situation by use of comparative maps of mouse and rat, and the human genome. This allows for an evaluation and validation of rodent tumor models at the genomic level. This review will illuminate the insights obtained by CGH analysis of rodent tumor genomes and the comparative transfer of this information between rodents and human.

The function and the organization of eukaryotic cells require directional transport of vesicles between compartments. This sort of membrane flow relies on the presence of docking and fusion machinery. The core of this machinery is a protein complex composed of syntaxin, SNAP-25 and VAMP, collectively termed SNAREs. A correct interaction among SNARE prototypes is essential for fruitful docking and fusion. Analysis of large-scale sequencing projects reveals that each of the SNARE proteins (syntaxin, SNAP-25 and VAMP) is a member of a large protein family that is represented in every eukaryotic genome. The diversity among the three SNARE prototypes allows an enriched combinatorial make-up to meet a wide range of cellular demands for secretion. Herein, we discuss the diversity in SNARE proteins from a genomic perspective. We combine information from large-scale sequence data with structural and functional classifications of SNAREs. Using a sequence-based automated protein classification tool, we expose weak but significant connections among all three SNARE protein clusters. These connections define a local evolutionary network within the protein universe. Genomic data allows us to identify classical SNAREs as well as their remote evolutionary relatives. We focus on the SNARE representatives from human and plant genomes to discuss the source of complexity and specificity for docking and fusion in a eukaryotic cell. How many of the potential SNARE combinations are indeed valid in vivo, and to what extent does each combination specify a biochemical and biophysical unique entity, is yet to be experimentally determined.

Free radicals and their sequelae figure prominently in cellular and organismal aging. Generated primarily in mitochondria as unwanted products of oxidative phosphorylation, free radicals induce a wide variety of damage that compromises molecular, cellular and organismal integrity. The free-living nematode Caenorhabditis elegans has been employed widely to explore the genetics of aging. One extremely successful approach has been to isolate mutants that extend life span. Conversely, genetic analyses of mutants that shorten life span have also provided insights into aging as it occurs in wild type. In this review we focus on three such “aging” mutants of C. elegans (mev-1, gas-1 and clk-1). Although isolated in different laboratories and using different selection criteria, all three affect aging by perturbing mitochondrial structure and / or function. gas-1 encodes a subunit of complex I, one of the five membrane-bound mitochondrial complexes that comprise the electron transport system. Originally isolated because they are hypersensitive to volatile anesthetics, gas-1 mutants were subsequently found to be hypersensitive to oxidative stress, presented in the form of either hyperoxia or methyl viologen. mev-1 encodes a subunit of complex II and was initially studied on the basis of its hypersensitivity to oxidative stress. Mutations in this gene confer a variety of interesting phenotypes, including precocious aging, hypermutability, abnormal mitochondrial structure, compromised DNA repair capacity and increased endogenous levels of free radicals. clk-1 encodes a protein homologous to the yeast coq7 / cat5 gene product. clk-1 mutations result in reduced rates of certain developmental and behavioral phenomena as well as in an extended life span. In yeast, coq7 / cat5 mutants were reported to be defective in respiration due to a deficiency in the biosynthesis of ubiquinone. It has been hypothesized that the involvement of clk-1 / coq7 / cat5 in ubiquinone biosynthesis is regulatory because clk-1 mutants show normal rates of mitochondrial respiration. The phenotypes of each of these three mutants will be presented, with emphasis on how they provide information about the normal aging process.

Turner syndrome is a well defined sex chromosomal disorder characterized by short stature, characteristic somatic stigmata, and gonadal dysgenesis. In this review, I summarize recent progress in the clarification of genetic mechanisms involved in the development of clinical features. The essence is as follows: (1) Short stature is primarily ascribed to loss of SHOX cloned from the short arm pseudoautosomal region and GCY postulated between DYZ3 and DYS11 in the proximal part of Yq, in addition to non-specific growth disadvantage caused by chromosome imbalance. (2) Skeletal features such as short matacarpals, cubitus valgus, Madelung deformity, high arched palate, and short neck are primarily attributable to SHOX haploinsufficiency, with expressivity in the limb and faciocervical regions being influenced by gonadal function status and the presence or absence of the lymphogenic gene, respectively. (3) Soft tissue features such as webbed neck and lymphedema and visceral features such as aortic coarctation and horseshoe kidney appear to be due to haploinsufficiency of the lymphogenic gene postulated between DMD and MAOA in the proximal Xp region and between PABY and DYS255 in the distal Yp region. (4) Gonadal dysgenesis is explained by pairing failure of homologous chromosomes in meiocytes that are genetically destined to develop as oocytes, rather than by the dosage effect of an X-linked gene(s). In addition, the underlying factors for the extreme prenatal lethality, cognitive dysfunction, mental retardation, gonadal tumors, and immune-related diseases are discussed.

The pituitary gland is a complex endocrine organ secreting hormones that regulate a wide array of vertebrate physiological processes, including growth, lactation, metabolic homeostasis, reproduction, water balance, and the stress response. In the mature organ, specialized cells that have a common origin in the early ectoderm release their characteristic products into the bloodstream. Together, the embryological processes that commit the hormone-secreting cells to their specific fates and the clinical and agricultural relevance of understanding pituitary function have defined pituitary development as an excellent model system for the study of the genetic cascades that guide cell determination and differentiation. Recently, many genes that regulate pituitary development have been identified. These genes encode transcription factors and signaling proteins and often are expressed in temporally controlled, pituitary-specific or pituitary-restricted patterns. Further, dominant and recessive mutations in these genes are associated with compound pituitary diseases in human patients and animal models. The advance of genome projects will facilitate approaches to understand the genetic mechanisms that regulate the activation of pituitary regulatory genes and to discover how the function of the encoded transcription factors is precisely regulated by intrinsic and extrapituitary signals. Gene array and differential screening approaches will enable the identification of direct and downstream target genes of pituitary transcription factors. Protein interaction screens will identify regulatory proteins required for pituitary gene control. Characterization of the pathways that coordinate pituitary development will direct treatment of pediatric and adult pituitary diseases, guide genetic counseling of families with hereditary conditions affecting the pituitary, and may allow embryonic manipulation to improve productivity in the meat industry.

This report provides an overview of the development and applications of DNA-based microarrays and biochip technology in genomics. DNA microarrays and biochip technologies are having a significant impact on a wide variety of areas in genomic research. Many fields, including gene discovery, drug discovery, toxicological research, and medical diagnostics, will benefit from the use of DNA micro array and biochip technologies. High-density micro array chips with relatively large detection systems are useful in the research laboratory for monitoring the expression of large numbers of genes in parallel. On the other hand, small and inexpensive integrated biochips that combine probe arrays with sensor microchips are most suitable for medical diagnosis at the site-of-care.