Unraveling the Secret Lives of Bacteria: Use of In Vivo Expression Technology and Differential Fluorescence Induction Promoter Traps as Tools for Exploring Niche-Specific Gene Expression

A major challenge for microbiologists is to elucidate the strategies deployed by microorganisms to adapt to and thrive in highly complex and dynamic environments. In vitro studies, including those monitoring genomewide changes, have proven their value, but they can, at best, mimic only a subset of the ensemble of abiotic and biotic stimuli that microorganisms experience in their natural habitats. The widely used gene-to-phenotype approach involves the identification of altered niche-related phenotypes on the basis of gene inactivation. However, many traits contributing to ecological performance that, upon inactivation, result in only subtle or difficult to score phenotypic changes are likely to be overlooked by this otherwise powerful approach. Based on the premise that many, if not most, of the corresponding genes will be induced or upregulated in the environment under study, ecologically significant genes can alternatively be traced using the promoter trap techniques differential fluorescence induction and in vivo expression technology (IVET). The potential and limitations are discussed for the different IVET selection strategies and system-specific variants thereof. Based on a compendium of genes that have emerged from these promoter-trapping studies, several functional groups have been distinguished, and their physiological relevance is illustrated with follow-up studies of selected genes. In addition to confirming results from largely complementary approaches such as signature-tagged mutagenesis, some unexpected parallels as well as distinguishing features of microbial phenotypic acclimation in diverse environmental niches have surfaced. On the other hand, by the identification of a large proportion of genes with unknown function, these promoter-trapping studies underscore how little we know about the secret lives of bacteria and other microorganisms.     

Population trends of European common birds are predicted by characteristics of their climatic niche

Temperate species are projected to experience the greatest temperature increases across a range of modelled climate change scenarios, and climate warming has been linked to geographical range and population changes of individual species at such latitudes. However, beyond the multiple modelling approaches, we lack empirical evidence of contemporary climate change impacts on populations in broad taxonomic groups and at continental scales. Identifying reliable predictors of species resilience or susceptibility to climate warming is of critical importance in assessing potential risks to species, ecosystems and ecosystem services. Here we analysed long‐term trends of 110 common breeding birds across Europe (20 countries), to identify climate niche characteristics, adjusted to other environmental and life history traits, that predict large‐scale population changes accounting for phylogenetic relatedness among species. Beyond the now well‐documented decline of farmland specialists, we found that species with the lowest thermal maxima (as the mean spring and summer temperature of the hottest part of the breeding distribution in Europe) showed the sharpest declines between 1980 and 2005. Thermal maximum predicted the recent trends independently of other potential predictors. This study emphasizes the need to account for both land‐use and climate changes to assess the fate of species. Moreover, we highlight that thermal maximum appears as a reliable and simple predictor of the long‐term trends of such endothermic species facing climate change.     

Molecular studies resolve Nyholmiella (Orthotrichaceae) as separated genus

Two Orthotrichum species of the subgenus Orthophyllum were compared with other representatives of this genus using the internally transcribed spacer regions 1 and 2, the chloroplast trnH-psbA region and ISSR and ISJ DNA markers. The applied DNA markers revealed many bands and mutations specific only to O. gymnostomum and O. obtusifolium. A phylogenetic analysis clearly supported the previous concepts postulating that species of the subgenus Orthophyllum should be recognized as separate genus Nyholmiella.     

Endocytic recycling proteins EHD1 and EHD2 interact with fer-1-like-5 (Fer1L5) and mediate myoblast fusion

The mammalian ferlins are calcium-sensing, C2 domain-containing proteins involved in vesicle trafficking. Myoferlin and dysferlin regulate myoblast fusion and muscle membrane resealing, respectively. Correspondingly, myoferlin is most highly expressed in singly nucleated myoblasts, whereas dysferlin expression is increased in mature, multinucleated myotubes. Myoferlin also mediates endocytic recycling and participates in trafficking the insulin-like growth factor receptor. We have now characterized a novel member of the ferlin family, Fer1L5, because of its high homology to dysferlin and myoferlin. We found that Fer1L5 protein is expressed in small myotubes that contain only two to four nuclei. We also found that Fer1L5 protein binds directly to the endocytic recycling proteins EHD1 and EHD2 and that the second C2 domain in Fer1L5 mediates this interaction. Reduction of EHD1 and/or EHD2 inhibits myoblast fusion, and EHD2 is required for normal translocation of Fer1L5 to the plasma membrane. The characterization of Fer1L5 and its interaction with EHD1 and EHD2 underscores the complex requirement of ferlin proteins and mediators of endocytic recycling for membrane trafficking events during myotube formation.     

The phylogenetic structure of the genus Acinetobacter

Abstract A N-acetyl-D-galactosamine (GalNAc) specific bacterial lectin-like substance from Eikenella corrodens 1073 (EcLS) was found to have potent mitogenic activity when cultured with splenocytes from BALB/c mice. The results indicated that B lymphocytes are the major cell type responding to EcLS. The mitogenic activity of EcLS was dose-dependent, and the optimal concentration was around 5 μg/ml. The mitogenic activity did not appear to be due to a bacterial endotoxin, as GalNAc inhibited the mitogenic activity of EcLS, but did not inhibit the activity of lipopolysaccharide isolated from E. corrodens . EcLS stimulated murine B lymphocytes not only to proliferate, but also to differentiate into antibody-secreting cells, as demonstrated by the production of immunoglobulin by B lymphocytes stimulated with EcLS. These findings suggest that EcLS is a novel lectin that not only induces B lymphocyte proliferation, but also differentiation.     

The role of bovine lipoproteins in the regulation of steroidogenesis and HMG-CoA reductase in bovine adrenocortical cells.

The sources of cholesterol for steroid hormone production were examined using bovine adrenocortical (BAC) cells in primary culture. The experiments were designed to determine the effects of lipoproteins on cortisol production and the level of BAC cell 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase. Most studies on BAC cell lipoprotein requirements have been conducted using human low-density lipoprotein (hHDL); none have used the homologous bovine lipoproteins. BAC cells treated with corticotropin (ACTH) in a medium devoid of lipoproteins increased and maintained cortisol production 7- to 20-fold above basal levels. Under such conditions ACTH also increased the rate of HMG-CoA reductase activity. Inhibition of HMG-CoA reductase with mevinolin inhibited cortisol production by 85%, indicating that the cells were using cholesterol synthesized de novo for steroid production. Cortisol production was increased almost 40-fold above basal levels if hLDL (100 micrograms/ml) was included in the incubation medium. Human LDL also suppressed the levels of HMG-CoA reductase in a concentration-dependent fashion. Human HDL was without effect on either BAC cell steroidogenesis of HMG-CoA reductase. Addition of bovine LDL (bLDL) to the incubation medium also caused an increase in cortisol production and inhibited cholesterol synthesis. By contrast to hHDL, bHDL (100 micrograms/ml) increased the ability of BAC cells to produce cortisol production. Bovine HDL (bHDL) also was able to decrease HMG-CoA reductase, but not to the extent caused by hLDL or bLDL. These data demonstrate that bovine adrenal cells can use bHDL as a source of cholesterol for steroid hormone production. These findings may be of particular importance when one considers that in vivo, the bHDL content of bovine serum greatly surpasses the level of bLDL.