Mammalian Database Research Articles

The connexin gene family in mammals

Unannotated mammalian genome databases (dog, cow, opossum) were searched for candidate connexin genes, using sequences from annotated genomes (man, mouse). All 18 'multi-species' connexin genes, i.e., orthologs of connexin26 , 29/31.3 (duplicated in opossum), 30, 30.2/31.9, 30.3, 31, 31.1, 32, 36, 37, 39/40.1, 40, 43, 45, 44/46, 47, 50, and 57/62 , were found in dog, cow and opossum. Connexin25 and 58 have been considered specific for man, but evident orthologs of connexin25 were found in dog, cow and opossum, and orthologs of connexin58 were found in dog and cow. Moreover, a connexin43 -like sequence (approx. 80% identical to connexin43 ) was found in man, chimpanzee, dog and cow. In the three former species, the sequences were located on the X chromosome. In man, chimpanzee and cow, there were stop codons in all reading frames; these sequences are therefore judged as pseudogenes, called here Cx43pX . In the dog, the sequence contained an open reading frame for a protein of 35.7 kDa (connexin35.7). We suggest that these sequences are orthologs of connexin33 , previously considered as a rodent-specific connexin gene. Thus, connexin25 , 33 and 58 are not species-specific genes. However, the opossum may possess a candidate, connexin39.2 , without obvious orthologs in other mammals. Furthermore, pseudogenes of primate connexin31.3 and opossum connexin35 (one of the two orthologs of primate connexin31.3) were detected. These results suggest that the structure of the mammalian connexin gene family should be revised, especially with regard to the so-called 'species-specific' connexins .

Genome-wide promoter extraction and analysis in human, mouse, and rat

An investigation of how to improve mammalian promoter prediction by incorporating both transcript and conservation information leads to the creation of CSHLmpd, a mammalian promoter database.

Quantitative Analysis of Liver Protein Expression During Hibernation in the Golden-mantled Ground Squirrel

Mammals that enter deep hibernation experience extreme reductions in body temperature and in metabolic, respiratory, and heart rates for several weeks at a time. Survival of these extremes likely entails a highly regulated network of tissue- and time-specific gene expression patterns that remain largely unknown. To date, studies to identify differentially-expressed genes have employed a candidate gene approach or in a few cases broader unbiased screens at the RNA level. Here we use a proteomic approach to compare and identify differentially expressed liver proteins from two seasonal stages in the golden-mantled ground squirrel (summer and entrance into torpor) using two-dimensional gels followed by MS/MS. Eighty-four two-dimensional gel spots were found that quantitatively alter with the hibernation season, 68 of which gave unambiguous identifications based on similarity to sequences in the available mammalian database. Based on what is known of these proteins from prior research, they are involved in a variety of cellular processes including protein turnover, detoxification, purine biosynthesis, gluconeogenesis, lipid metabolism and mobility, ketone body formation, cell structure, and redox balance. A number of the enzymes found to change seasonally are known to be either rate-limiting or first enzymes in a metabolic pathway, indicating key roles in metabolic control. Functional roles are proposed to explain the changes seen in protein levels and their potential influence on the phenotype of hibernation.

Identification and expression of alpha cDNA encoding human 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (ACMSD): a key enzyme for the tryptophan-niacine pathway and quinolinate hypothesis.

Quinolinate (quinolinic acid) is a potent endogenous excitotoxin of neuronal cells. Elevation of quinolinate levels in the brain has been implicated in the pathogenesis of various neurodegenerative disorders, the so-called "quinolinate hypothesis." Quinolinate is non-enzymatically derived from 2-amino-3-carboxymuconate-6-semialdehyde (ACMS). 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (ACMSD) is the only known enzyme which can process ACMS to a benign catabolite and thus prevent the accumulation of quinolinate from ACMS. ACMSD seems to be regulated by nutritional and hormonal signals, but its molecular mechanism has, to date, been largely unknown. Utilizing partial amino acid sequences obtained from highly purified porcine kidney ACMSD, a cDNA encoding human ACMSD was cloned and characterized. The cDNA encodes a unique open reading frame of 336 amino acids and displays little homology to any known enzymes or motifs in mammalian databases, suggesting that ACMSD may contain a new kind of protein fold. Real-time PCR-based quantification of ACMSD revealed very low but significant levels of the expression in the brain. Brain ACMSD messages was down- and up-regulated in response to low protein diet and streptozocin-induced diabetes, respectively. Expression of QPRT, another enzyme which catabolizes quinolinate, was also found in the brain. This suggests that a pathway does exist by which the levels of quinolinate in the brain are regulated. In this report, we address the molecular basis underlying quinolinate metabolism and the regulation of ACMSD expression.

Identification and Expression of a cDNA Encoding Human α-Amino-β-carboxymuconate-ε-semialdehyde Decarboxylase (ACMSD): A KEY ENZYME FOR THE TRYPTOPHAN-NIACINE PATHWAY AND “QUINOLINATE HYPOTHESIS”

Quinolinate (quinolinic acid) is a potent endogenous excitotoxin of neuronal cells. Elevation of quinolinate levels in the brain has been implicated in the pathogenesis of various neurodegenerative disorders, the so-called "quinolinate hypothesis." Quinolinate is non-enzymatically derived from alpha-amino-beta-carboxymuconate-epsilon-semialdehyde (ACMS). Alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD) is the only known enzyme that can process ACMS to a benign catabolite and thus prevent the accumulation of quinolinate from ACMS. ACMSD seems to be regulated by nutritional and hormonal signals, but its molecular mechanism has, to date, been largely unknown. Utilizing partial amino acid sequences obtained from highly purified porcine kidney ACMSD, a cDNA encoding human ACMSD was cloned and characterized. The cDNA encodes a unique open reading frame of 336 amino acids and displays little homology to any known enzymes or motifs in mammalian databases, suggesting that ACMSD may contain a new kind of protein fold. Real-time PCR-based quantification of ACMSD revealed very low but significant levels of the expression in the brain. Brain ACMSD messages were down- and up-regulated in response to low protein diet and streptozocin-induced diabetes, respectively. The enzyme activities measured from partially purified brains were closely correlated with the changes in the message levels. Expression of quinolinate phosphoribosyltransferase (QPRT), another enzyme that catabolizes quinolinate, was also found in the brain. This suggests that a pathway does exist by which the levels of quinolinate in the brain are regulated. In this report, we address the molecular basis underlying quinolinate metabolism and the regulation of ACMSD expression.

Internet Comparative Mapping Resources.

Databases accessible over the Internet have become an essential tool in the study of genome organization. Recent growth in the field of genomics has resulted in the study of an increasing number of organisms in addition to a flood of data from the more intensively studied organisms. Although this rapid growth in the quantity of data has greatly increased the likelihood that data useful to an individual researcher will be available, the job of finding that data in the traditional journal publication system is significantly more difficult. To increase the accessibility of these data, several databases have been established and made available via the Internet. This availability allows the rapid access of current, in-depth data not practical for journal publications, with the additional benefit of enabling searchers to extract the data based on their own criteria. Genome databases have been established on an organism-specific basis, usually with a proprietary database structure and delivery system. The largest of these databases are the Human Genome Organization's genome database at Oak Ridge National Laboratory (Oak Ridge, Tennessee) and the Mouse Genome Database at The Jackson Laboratory (Bar Harbor, Maine). Many of the species groups are now migrating to a common database platform; and several species groups including those working on pig, cattle, sheep, horse, chicken, and cat are now using the ARKdb platform developed and run at the Roslin Institute in Edinburgh, Scotland. This usage of a common system holds great promise for the integration and cross-referencing of data for these species. At the time of this writing, the status and direction of the largest genome database—the human genome database—are uncertain due to the termination of funding for its development. The database will be hosted in its current form at Oak Ridge National Laboratory with no additional development, representing a shift in the focus from geneand clone-based information to a model of annotated sequence. This shift is likely to present some difficulties for comparative mapping in the short term. Comparative mapping data are integrated into many of the species-specific databases in several ways. The basic type of comparative linkage comprises shared symbols and names and includes the use of symbols from other species as an alias. This type of linkage has many flaws, including inflexibility with regard to our evolving understanding of gene homologies and sensitivity to nomenclature changes. The more advanced comparative information is obtained from direct links by unique identifiers to entries in other databases and in some cases dedicated detailed comparative databases. The most comprehensive comparative database available as of October 1998 is the Mouse Genome Database (mammalian homology database), which lists homologies in a broad range of species as given in published journal articles (with references) and includes a powerful set of search criteria in a forms interface with tabular or graphical output. The main limitations of all current comparative mapping resources are the manual nature of establishing homology links and the typical absence of database entries that indicate the evidence for the homology. The next wave of genome database innovation will be the development of automated software agents, which will explore databases and create their own database of links between the different species databases based on a defined set of homology criteria. One of these agent systems, under development at the time of this writing at the Roslin Institute and the University of Edinburgh, will hopefully result in the efficient creation of current, robust, and well-defined homology links between species databases. Although comparative gene mapping databases are continuing to evolve, Internet-based resources have become an entrenched and vital tool for the comparative mapper. Use of this tool can only grow in importance as the data sets involved continue to expand and as more sophisticated tools are developed for their exploitation.

A Rosetta stone of mammalian genetics.

The Mammalian Comparative Database provides genetic maps of mammalian species. Comparative maps are valuable aids for predicting linkages, developing animal models and studying genome organization and evolution.