3’UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells

Most mammalian genes often feature alternative polyadenylation (APA) sites and hence diverse 3’UTR lengths. Proliferating cells were reported to favor APA sites that result in shorter 3’UTRs. One consequence of such shortening is escape of mRNAs from targeting by microRNAs (miRNAs) whose binding sites are eliminated. Such a mechanism might provide proliferation-related genes with an expression gain during normal or cancerous proliferation. Notably, miRNA sites tend to be more active when located near both ends of the 3’UTR compared to those located more centrally. Accordingly, miRNA sites located near the center of the full 3’UTR might become more active upon 3''UTR shortening. To address this conjecture we performed 3'' sequencing to determine the 3'' ends of all human UTRs in several cell lines. Remarkably, we found that conserved miRNA binding sites are preferentially enriched immediately upstream to APA sites, and this enrichment is more prominent in pro-differentiation/anti-proliferative genes. Binding sites of the miR17-92 cluster, upregulated in rapidly proliferating cells, are particularly enriched just upstream to APA sites, presumably conferring stronger inhibitory activity upon shortening. Thus 3’UTR shortening appears not only to enable escape from inhibition of growth promoting genes but also to potentiate repression of anti-proliferative genes.     

Fine structure of the cell surface and Golgi apparatus of Ochromonas

Ochromonas danica has an unusually flexible cell surface capable of producing projections of varying sizes and shapes: large projections, 340-360 nm long, and small projections, 50-110 nm long. These projections have been demonstrated by transmission and scanning electron microscopy; some of them may break off into the medium and be the source of extracellular membranes and vesicles reported in the cell-free O. danica growth medium. Ruthernium red stained the acid mucopolysaccharide layer just outside the cell surface as well as small blebs at the cell surface. The Golgi complex of O. danica, Ochromonas malhamensis, Ochromonas sociabilis and Ochromonas sp. produced small coated vesicles which may move toward and fuse with the plasma membrane. The role of the several vesicles is unknown but possible functions are discussed.     

Halobacterium salinarum strain MMD047-A low-salt adapted member of the Halobacteriaceae?

In a paper recently in Biotechnology and Bioprocess Engineering (vol. 14, pp. 67–75), Shanmughapriya and coworkers described a prokaryote (strain MMD047) isolated from a marine sponge, which they classified as a strain of Halobacterium salinarum. As the strain grows at low salinity only, its behavior is greatly different from that of other Halobacterium isolates. In spite of multiple requests, the strain has not been made available for further studies and we therefore call upon the authors of the paper to release their interesting isolate for an in-depth taxonomic characterization.     

Polar lipids and pigments as biomarkers for the study of the microbial community structure of solar salterns

Whole community lipids and pigments have been examined over a 3–5-year period in commercial salterns located in the United States, Israel, and Spain. There were significant differences in the types of lipids and pigments within the California saltern system during the 5-year period. These patterns differed seasonally despite examination of ponds with approximately the same salinities. The solar saltern in Eilat, Israel had fewer lipids on the thin-layer chromatography plates and confirmed previous analyses. The biota in the crystallizer pond in Alicante, Spain, resembled the microbial community in Israel. In the crystallizers at all three locations, phosphatidyl glycerol, methyl-phosphatidyl glycerophosphate, phosphatidyl glycerosulfate, and the sulfated diglycosyldiether lipid were identified regardless of season. This was not true for pans with salinities below 25% where no distinctive pattern was observed. Thus, we hypothesize that the more eutrophic inlet waters of the California saltern and the cooler temperatures, which result in longer retention times of water in the different pans, allow for the more diverse microbial community to develop. This is reflected then in more complex lipid and pigment patterns. However, the oligotrophic inlet waters to the Eilat saltern coupled with a drier and warmer climate result in a shorter retention time of water in the pans and a less diverse microbial community as evidenced by fewer extractable lipids and pigments.