Identification of physicochemical selective pressure on protein encoding nucleotide sequences

Background  

Statistical methods for identifying positively selected sites in protein coding regions are one of the most commonly used tools in evolutionary bioinformatics. However, they have been limited by not taking the physiochemical properties of amino acids into account.     

MicroRNA miR-155 Inhibits Bone Morphogenetic Protein (BMP) Signaling and BMP-Mediated Epstein-Barr Virus Reactivation

MicroRNA miR-155 is expressed at elevated levels in human cancers including cancers of the lung, breast, colon, and a subset of lymphoid malignancies. In B cells, miR-155 is induced by the oncogenic latency gene expression program of the human herpesvirus Epstein-Barr virus (EBV). Two other oncogenic herpesviruses, Kaposi''s sarcoma-associated herpesvirus and Marek''s disease virus, encode functional homologues of miR-155, suggesting a role for this microRNA in the biology and pathogenesis of these viruses. Bone morphogenetic protein (BMP) signaling is involved in an array of cellular processes, including differentiation, growth inhibition, and senescence, through context-dependent interactions with multiple signaling pathways. Alteration of this pathway contributes to a number of disease states including cancer. Here, we show that miR-155 targets the 3′ untranslated region of multiple components of the BMP signaling cascade, including SMAD1, SMAD5, HIVEP2, CEBPB, RUNX2, and MYO10. Targeting of these mediators results in the inhibition of BMP2-, BMP6-, and BMP7-induced ID3 expression as well as BMP-mediated EBV reactivation in the EBV-positive B-cell line, Mutu I. Further, miR-155 inhibits SMAD1 and SMAD5 expression in the lung epithelial cell line A549, it inhibits BMP-mediated induction of the cyclin-dependent kinase inhibitor p21, and it reverses BMP-mediated cell growth inhibition. These results suggest a role for miR-155 in controlling BMP-mediated cellular processes, in regulating BMP-induced EBV reactivation, and in the inhibition of antitumor effects of BMP signaling in normal and virus-infected cells.Despite the limited genetic content of microRNAs, their pervasive role in controlling normal and pathology-associated cellular processes has become firmly established in recent years. The importance of microRNA dysregulation in cancer is well appreciated, and a number of oncomirs and tumor suppressor microRNAs have been identified (15). As a member of the oncomir class of microRNAs, miR-155 is implicated in lymphomagenesis and a wide array of nonlymphoid tumors including breast, colon, and lung (7, 16, 24, 39, 42, 43). Despite strong evidence implicating miR-155 in cancer etiology, the mechanisms through which miR-155 supports the tumor phenotype are unclear, possibly due to limited knowledge of how predicted targets may be involved in the phenotypic properties of cancer. On the other hand, miR-155''s roles in normal immune cell development and the adaptive immune response are much better understood (33, 41). These studies have demonstrated a critical role for miR-155 in immune cell activation and maturation. This evidence and other work (8, 40) have identified critical miR-155 targets whose downregulation is required for these processes.The Epstein-Barr virus (EBV) is a human DNA tumor virus that contributes to lymphoid and epithelial cell malignancies. As a herpesvirus, a unique aspect of the EBV infection cycle is the ability to exist in either a lytic replicative state or in a latent state in which no virus is produced. Depending in part on cell background, EBV utilizes multiple forms of latency gene expression programs. True latency and type I latency are defined by the expression of no protein coding genes or by expression of the episomal replication factor EBNA1 only. Type II latency is defined by the expression of EBNA1 and the latent membrane proteins, LMP1 and/or LMP2, and is the predominant form observed in epithelial tissues. Type III latency refers to expression of the full repertoire of latency genes, which are highly tumorigenic and are capable of growth-transforming naïve resting B cells. While this form of latency is not well tolerated in immunocompetent individuals except during early stages of infection (prior to the development of adaptive immunity to these proteins), type III latency-associated lymphoid malignancies are common in immunocompromised individuals. Expression of type III latency genes in B cells mimics antigen-dependent B-cell activation, and accompanying this activation is a substantial induction of miR-155 expression (17, 20, 23, 29, 44). While it is reasonable to assume that induction of miR-155 by the type III latency program plays a role in EBV-mediated B-cell activation and oncogenesis, little is known regarding the role of miR-155 in the virus life cycle or its tumor-promoting activities.Originally identified as cytokines critically involved in the regulation of osteogenic differentiation, bone morphogenetic proteins (BMPs) are now appreciated as having critical functions in a vast number of developmental processes. Dysregulation of BMP signaling is also implicated in disease states including cancer (1). The canonical signaling pathway stimulated by BMP receptor engagement is the phosphorylation of the SMADs (mothers against decapentaplegic homologs), SMAD1, SMAD5, and SMAD9, which facilitates active transport of these mediators from the cytoplasm to the nucleus, where they bind and activate cellular promoters. While these signaling mediators are considered to have fairly redundant activities, the influence of BMP activation can have widely distinct outcomes on a particular cell depending on cellular context (3, 27). These distinctions arise from the innate low-affinity DNA binding properties of SMADs and the concordant requirement for any of a broad range of cofactors that facilitate high-affinity binding to specific sets of promoters. Using this signaling mechanism, the phenotypic outcome of BMP receptor engagement is controlled by the level of activation of other signaling pathways and SMAD binding cofactors. While activation of BMP signaling appears to contribute to some cancer types, it inhibits other cancer types by promoting growth arrest and differentiation and by inducing senescence (1). In immune cells, BMP signaling has been shown by multiple groups to inhibit lymphocyte activation, maturation, and growth (2, 6, 13, 18, 19, 37). Here, we show that miR-155 inhibits BMP signaling by targeting multiple factors in the BMP signal transduction cascade. This function may be important during immune cell activation by preventing BMP from impeding this process, it may be important for the survival of EBV type III latency associated tumors by preventing BMP-mediated viral reactivation and cell death, and it may be relevant to other cancer types by blocking growth arrest properties of BMPs.     

Foraging energetics of the ant,Paraponera clavata

The energy currencies used by foraging animals are expected to relate to the energy costs and benefits of resource collection. However, actual costs of foraging are rarely measured. We measured the ratio of energetic benefit relative to cost (B/C) during foraging for the giant tropical ant, Paraponera clavata. The B/C ratio was 3.9 for nectar-foragers and 67 for insect prey foragers. In contrast, the B/C ratio during foraging for seed harvester ants (Pogonomyrmex occidentalis) is over 1000, demonstrating that the B/C ratio can vary widely among ants. The B/C ratio was 300 times lower for nectar-foraging Paraponera than for the seed-harvesting Pogonomyrmex because of: (1) a 5-fold lower energetic benefit per trip, (2) a 10-fold greater cost due to longer foraging distances, and (3) a 6-fold greater energy cost per meter due to larger body size. For Paraponera daily colonial energy intake rates are similar to expeditures and may limit colony growth and reproduction. In contrast, for Pogonomyrmex energy intake rates are an order of magnitude higher than estimated costs, suggesting that Pogonomyrmex colonies are unlikely to be limited by short-term energy intake. We suggest that variation in individual B/C ratios may explain why the foraging behavior of Paraponera but not Pogonomyrmex appears sensitive to foraging costs.     

In vitro methylation inhibits the promotor activity of a cloned intracisternal A-particle LTR.

We studied the relation between LTR methylation and expression of the family of endogenous retrovirus-like elements related to mouse intracisternal A-particles (IAP). Comparative HpaII/MspI and HhaI restriction analysis of genomic DNA's showed that in cells and tissues with a low level of IAP gene expression, HpaII and HhaI sites within the 5' LTR were heavily methylated, while in cells abundantly expressing IAP's 20 to 30% of the 5' LTRs were demethylated at these sites. The effects of methylation on the promoter activity of a cloned IAP 5' LTR was studied directly, using the plasmid pMIA5' L-cat in which this LTR was linked to the chloramphenicol acetyl transferase (CAT) gene. In vitro methylation of three HhaI sites located between -137 and -205 bp from the RNA start site of this LTR completely inactivated the promoter activity of pMIA5' L-cat transfected into COS7 cells. Methylation of a HpaII site located 94 bp downstream from the RNA start site reduced the promoter activity by 75%. The results show that methylation at sites both upstream and downstream from the RNA start site profoundly effects the promoter activity of this LTR and suggest that methylation within the 5' LTR can serve to regulate IAP gene expression in vivo.     

Autonomic and behavioral thermoregulation in guinea pigs during postnatal maturation

Fewell, James E., Maria Kang, and Heather L. Eliason.Autonomic and behavioral thermoregulation in guinea pigs during postnatal maturation. J. Appl.Physiol. 83(3): 830-836, 1997.Serial experimentswere carried out on seven chronically instrumented Hartley-strainguinea pigs at 1, 3, and 5 wk of age to define their autonomic andbehavioral thermoregulatory profiles and to test the hypothesis thatthey have the mechanisms in place shortly after birth that allow themto optimize their energy expenditure for thermoregulation by selectinga thermal environment that requires the lowest metabolic oxygenrequirements. Each animal was studied in both a thermocline todetermine selected ambient temperature and in a metabolic chamberto determine the thermoregulatory response to forced changes in ambienttemperature. In the thermocline, the guinea pigs at all postnatal agesselected an ambient temperature that placed core temperature, oxygenconsumption, thermal conductance, heart rate, and respiratory rate atlevels comparable to those observed at ambient temperatures in whichminimal oxygen consumption occurred in the metabolic chamber. Thus ourexperiments provide evidence that guinea pigs have theneurophysiological mechanisms in place shortly after birth that allowthem to optimize their energy expenditure for thermoregulation byselecting a thermal environment that corresponds to the lowestmetabolic oxygen requirements.