Computational sequence analysis revisited: new databases, software tools, and the research opportunities they engender

Diethylstilbestrol regulates expression of avian apolipoprotein D during regression and recrudescence of the oviduct and epithelial-derived ovarian carcinogenesis

Apolipoprotein D (APOD) is a glycoprotein which is widely expressed in mammalian tissues. It is structurally and functionally similar to the lipocalins which are multiple lipid-binding proteins that transport hydrophobic ligands and other small hydrophobic molecules, including cholesterol and several steroid hormones. Although multiple functions for APOD in various tissues have been reported, its expression, biological function, and hormonal regulation in the female reproductive system are not known. Thus, in this study, we focused on correlations between APOD and estrogen during development, differentiation, regression, and regeneration of the oviduct in chickens and in the development of ovarian carcinogenesis in laying hens. Results of the present study indicated that APOD messenger RNA (mRNA) expression increased (P < 0.001) in the luminal and glandular (GE) epithelia of the chicken oviduct in response to diethylstilbestrol (a nonsteroidal synthetic estrogen). In addition, the expression of APOD mRNA and protein decreased (P < 0.001) as the oviduct regressed during induced molting, and gradually increased (P < 0.001) with abundant expression in GE of the oviduct during recrudescence after molting. Furthermore, APOD mRNA and protein were predominantly localized in GE of cancerous, but not normal ovaries from laying hens. Collectively, results of the present study suggest that APOD is a novel estrogen-stimulated gene in the chicken oviduct which likely regulates growth, differentiation, and remodeling of the oviduct during oviposition cycles. Moreover, up-regulated expression of APOD in epithelial cell-derived ovarian cancerous tissue suggests that it could be a candidate biomarker for early detection and treatment of ovarian cancer in laying hens and in women.

Comparative 17beta-estradiol response and lipoprotein interactions of an avian apolipoprotein

Apolipoprotein D (apo D), a member of the lipocalin protein family, has been identified and cloned in several mammalian species; its physiological functions, however, remain poorly understood. As with other lipocalins, apo D can bind small hydrophobic ligands. Lipids and hormones, such as cholesterol, arachidonic acid, and progesterone can bind to apo D; but the physiological significance of these interactions is not clear. We previously reported the existence of an avian (Gallus domesticus) apo D-like protein, and indicated a possible role for it in reproduction. This report provides a further comparative characterization of this avian protein. Evidence is presented that the putative avian apo D, like some (e.g., human) but not other (e.g., rat) mammalian apo Ds, preferentially associates with high density lipoproteins (HDL) in the circulation. These results confirm the apolipoprotein nature of the avian apo D-like protein, and indicate that it has conserved the HDL-interaction property of some mammalian apo Ds. The response of circulatory levels of the avian protein to 17beta-estradiol treatment is also examined. Large estrogen-dependent increases are known to occur in the circulatory levels of some avian apolipoproteins, such as apo B and vitellogenins, that represent major yolk precursors and nutrient sources for the embryo. Although the avian apo D-like protein is also a known yolk precursor, the minor estrogen-dependent increase observed for this apolipoprotein (less than 7% that of apo B) distinguishes it from the major yolk-precursor apolipoproteins. The response of the avian apo D-like protein to 17beta-estradiol is more like that of other yolk precursor proteins that transport regulatory molecules such as vitamin A and thyroid hormones.

The bacterial lipocalins

The lipocalins were once regarded as a eukaryotic protein family, but new members have been recently discovered in bacteria. The first bacterial lipocalin (Blc) was identified in Escherichia coli as an outer membrane lipoprotein expressed under conditions of environmental stress. Blc is distinguished from most lipocalins by the absence of intramolecular disulfide bonds, but the presence of a membrane anchor is shared with two of its closest homologues, apolipoprotein D and lazarillo. Several common features of the membrane-anchored lipocalins suggest that each may play an important role in membrane biogenesis and repair. Additionally, Blc proteins are implicated in the dissemination of antibiotic resistance genes and in the activation of immunity. Recent genome sequencing efforts reveal the existence of at least 20 bacterial lipocalins. The lipocalins appear to have originated in Gram-negative bacteria and were probably transferred horizontally to eukaryotes from the endosymbiotic alpha-proteobacterial ancestor of the mitochondrion. The genome sequences also reveal that some bacterial lipocalins exhibit disulfide bonds and alternative modes of subcellular localization, which include targeting to the periplasmic space, the cytoplasmic membrane, and the cytosol. The relationships between bacterial lipocalin structure and function further illuminate the common biochemistry of bacterial and eukaryotic cells.

Cloning of the Arabidopsis WIGGUM gene identifies a role for farnesylation in meristem development

Control of cellular proliferation in plant meristems is important for maintaining the correct number and position of developing organs. One of the genes identified in the control of floral and apical meristem size and floral organ number in Arabidopsis thaliana is WIGGUM. In wiggum mutants, one of the most striking phenotypes is an increase in floral organ number, particularly in the sepals and petals, correlating with an increase in the width of young floral meristems. Additional phenotypes include reduced and delayed germination, delayed flowering, maturation, and senescence, decreased internode elongation, shortened roots, aberrant phyllotaxy of flowers, aberrant sepal development, floral buds that open precociously, and occasional apical meristem fasciation. As a first step in determining a molecular function for WIGGUM, we used positional cloning to identify the gene. DNA sequencing revealed that WIGGUM is identical to ERA1 (enhanced response to abscisic acid), a previously identified farnesyltransferase beta-subunit gene of Arabidopsis. This finding provides a link between protein modification by farnesylation and the control of meristem size. Using in situ hybridization, we examined the expression of ERA1 throughout development and found it to be nearly ubiquitous. This extensive expression domain is consistent with the pleiotropic nature of wiggum mutants and highlights a broad utility for farnesylation in plant growth and development.

Radioimmunoassay for serum apolipoprotein D, an atypical apolipoprotein: validation and clinical application

Apolipoprotein D (apoD) is an atypical apolipoprotein in terms of its structure, synthesis and probable function. It is the most abundant protein in breast cyst fluids of patients suffering from macrocystic disease of the breast, a disease associated with an increased risk of developing breast cancer. We have developed and optimized a competitive radioimmunoassay for the measurement of apoD in human serum. The assay uses a solid phase separation method and with a 4 h incubation period, it can be completed in a single working day. The within and between run coefficients of variation were < 8.5% and < 12.2%, respectively, and quantitative recovery of apoD was obtained over the range 250-5000 micrograms/L. There was no difference in the serum concentrations of apoD between female controls, patients with benign breast disease and early breast cancer. However, serum apoD was significantly lower in breast cancer patients with bone metastasis.

Identification and structure of activated-platelet protein-1, a protein with RNA-binding domain motifs that is expressed by activated platelets

Beyond their critical role in thrombosis, platelets perform important functions in vascular remodeling, inflammation, and wound repair. Many of these functions are executed by molecules expressed by activated platelets. A novel molecule, activated-platelet protein-1 (APP-1), was identified by a monoclonal antibody against activated rabbit platelets. When platelets were stimulated by thrombin, A23187 or ADP, APP-I was expressed on the platelet surface. APP-1 was also detected in whole cell lysates of platelets, but not on the external surfaces of resting platelets. With maximal activation by thrombin, 15 900 +/- 2800 molecules APP-1 were expressed/platelet. A 2.3-kb cDNA fragment containing a partial coding sequence for APP-1 was isolated from a rabbit bone marrow library by expression cloning with the anti-APP-1 monoclonal antibody. When expressed as a recombinant fusion protein in bacteria, APP-1 bound specifically to poly(A)-Sepharose. The full-length cDNA coding for human APP-1, obtained by DNA hybridization techniques, showed 98.7% amino acid sequence identity with the rabbit protein. Northern analysis with human APP-1 identified a 3.7-kb mRNA transcript in megakaryocytic lines that express transcripts for platelet proteins. Human APP-1 has four ribonucleotide binding domains with ribonucleoprotein 1 and 2 motifs. By virtue of its ribonucleotide binding domains, APP-1 is structurally related to polyadenylate-binding protein, which regulates translation initiation and polyadenylate shortening, and to nucleolysin, a specific effector molecule found in the granules of cytotoxic T lymphocytes.

BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web

The BCM Search Launcher is an integrated set of World Wide Web (WWW) pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to (1) nucleic acid sequence searches, (2) multiple and pair-wise sequence alignments, (3) gene feature searches, (4) protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http:@gc.bcm.tmc.edu:8088/search-launcher.html.

New approaches in molecular structure prediction

In the past years, much effort has been put on the development of new methodologies and algorithms for the prediction of protein secondary and tertiary structures from (sequence) data; this is reviewed in detail. New approaches for these predictions such as neural network methods, genetic algorithms, machine learning, and graph theoretical methods are discussed. Secondary structure prediction algorithms were improved mostly by considering families of related proteins; however, for the reliable tertiary structure modeling of proteins, knowledge-based techniques are still preferred. Methods and examples with more or less successful results are described. Also, programs and parameterizations for energy minimisations, molecular dynamics, and electrostatic interactions have been improved, especially with respect to their former limits of applicability. Other topics discussed in this review include the use of traditional and on-line databases, the docking problem and surface properties of biomolecules, packing of protein cores, de novo design and protein engineering, prediction of membrane protein structures, the verification and reliability of model structures, and progress made with currently available software and computer hardware. In summary, the prediction of the structure, function, and other properties of a protein is still possible only within limits, but these limits continue to be moved.

Identification of a circulatory and oocytic avian apolipoprotein D

Apolipoprotein D (apo D) is an unusual apolipoprotein with respect to structure and sites of synthesis. It has been identified in the circulatory system of certain mammals, but its physiological role remains poorly understood. In this report, it is shown that apo D is not exclusively a mammalian apolipoprotein, and evidence is presented which suggests a novel function for this protein during oogenesis in the chicken. The avian apo D which we identify has the same molecular mass (29 kDa) as the human protein and also associates preferentially with the plasma lipoprotein fraction. In addition to the 29 kDa avian apo D species, an immunoreactive 24 kDa protein is observed in chicken serum. The chicken apo D (along with the 24 kDa species) is also demonstrated to be present in the yolk of the rapidly growing chicken oocyte, a cell with high endocytic activity. Clathrin-coated vesicles from chicken oocytes, which we have previously shown to contain specific lipoproteins along with their oocytic receptors (Bujo et al., 1994: EMBO J 13:5165-5175), also contain chicken apo D. Thus, apo D represents a novel candidate for plasma-to-oocyte transport of lipids and/or their mobilization during embryogenesis in oviparous species.

Proteins regulating Ras and its relatives

GTPases of the Ras superfamily regulate many aspects of cell growth, differentiation and action. Their functions depend on their ability to alternate between inactive and active forms, and on their cellular localization. Numerous proteins affecting the GTPase activity, nucleotide exchange rates and membrane localization of Ras superfamily members have now been identified. Many of these proteins are much larger and more complex than their targets, containing multiple domains capable of interacting with an intricate network of cellular enzymes and structures.