Protein-Binding RNA Aptamers Affect Molecular Interactions Distantly from Their Binding Sites

Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site.     

Polyketide synthase genes and the natural products potential of Dictyostelium discoideum

MOTIVATION: The genome of the social amoeba Dictyostelium discoideum contains an unusually large number of polyketide synthase (PKS) genes. An analysis of the genes is a first step towards understanding the biological roles of their products and exploiting novel products. RESULTS: A total of 45 Type I iterative PKS genes were found, 5 of which are probably pseudogenes. Catalytic domains that are homologous with known PKS sequences as well as possible novel domains were identified. The genes often occurred in clusters of 2-5 genes, where members of the cluster had very similar sequences. The D.discoideum PKS genes formed a clade distinct from fungal and bacterial genes. All nine genes examined by RT-PCR were expressed, although at different developmental stages. The promoters of PKS genes were much more divergent than the structural genes, although we have identified motifs that are unique to some PKS gene promoters.     

Tissue distribution of a human Ca v 1.2 alpha1 subunit splice variant with a 75 bp insertion

Mesenchymal stem cells from human bone marrow (MSC) express mRNA encoding the L-type Ca2+ channel Ca v 1.2 alpha1 subunit (alpha(1)1.2). We now describe a splice variant including an alternative exon of 75 bp in the region between exons 9 and 10, which we identified in MSC by semi-quantitative RT-PCR. With primers specific for variants including (+9*) or excluding the 75 bp insertion (-9*), we found comparable mRNA expression patterns in MSC and in primary cultures of related connective tissue cells (chondrocytes, osteoblasts and fibroblasts). Since culture conditions might have altered variant expression, we investigated mRNA levels in various native human tissue samples (cartilage, bone, fat, liver, kidney, aorta, bladder, cardiac ventricle and atrium, CNS). We found highest levels of the +9* variant in aorta, containing smooth muscle and connective tissue cells, but the variant was expressed in all tissues. We therefore hypothesized that broad expression of +9* might be linked to the presence of vasculature and/or connective tissue structures, rather than to tissue-specific parenchymal cells (e.g. cardiomyocytes). To test this hypothesis we separated human atrium into a cardiomyocyte-enriched fraction and a cardiomyocyte-depleted fraction. RT-PCR demonstrated significantly larger levels of the +9* variant in the non-cardiomyocyte fraction. The result was even more clear in single cell RT-PCR experiments, where the +9* variant was undetectable in cardiomyocytes but present in non-cardiomyocytes. We conclude that the +9* variant is present in all human tissues investigated so far, and suggest that expression in human atrium is associated with vascular smooth muscle and/or connective tissue cells.     

The Agrobacterium DNA Transfer Complex

Agrobacterium tumefaciens elicits tumorous growths on plants by transforming plant cells with a segment of its own DNA. This trait led to development of Agrobacterium as a vector for genetic transformation of flowering plants. The transformation process is a unique mixture of several distinct steps, some of which are evolutionarily and functionally related to bacterial conjugation, and some of which converge with eukaryotic cellular processes. Recent work has advanced our understanding of each of these steps. The early reactions in the production of an ssDNA transfer intermediate (T-strand), mediated by the VirD1/D2 proteins, are chemically similar to formation of a relaxosome in bacterial conjugation. The T-strand is coated by the ssDNA binding protein VirE2; however, whether this binding occurs in the bacterium or in planta is disputed. VirB proteins, related to proteins for the conjugal transfer of DNA between bacteria, most likely form the transfer apparatus. VirD2, which remains covalently bound to the 5′ end of the T-strand, and VirE2 both localize to the nucleus of plant cells. VirE2 also mediates the nuclear accumulation of ssDNA but only when the protein is bound to the ssDNA. Genetically, VirD2 is required for faithful integration of the 5′ end and VirE2 for the 3′ end of the T-strand. The steps of the process currently under active investigation are the assembly of the export apparatus and the enzymology of integration.     

PHOTOSYNTHETIC RESPONSES TO LIGHT AND TEMPERATURE OF THE HETEROMORPHIC MARINE ALGA MASTOCARPUS PAPILLATUS (RHODOPHYTA)1

Physiological differentiation of the heteromorphic life-history phases of the red alga Mastocarpus papillatus (C. Agardh) Kützing was assessed. Photosynthetic responses to light and temperature of the erect, foliose gametophyte were compared to those of the crustose tetrasporophyte. Plants of both phases were collected from four locations on the Pacific coast of Baja California, Mexico, and California, USA, between 32–4l° N latitude. Within each location, the chlorophyll-specific, light-saturated photosynthetic rates of gametophytes were generally five times greater than those of tetrasporophytes. Initial slopes of photosynthesis: irradiance curves were greater for gametophytes than for tetrasporophytes. The crust and the blade from each location were similar with respect to dark respiration rates. For tetrasporophytes from all locations, the photosynthetic temperature optima were between 12–15° C. The photosynthetic temperature optima for gametophytes ranged from 15–17° C for plants from Trinidad Head (41° N) to 22–25° C for plants from Punta Descanso (32° N). Both gametophytes and tetrasporophytes from the northernmost location had significantly higher photosynthetic rates than the same phase from the other three locations. The photosynthetic responses to light support models for the life history in which life history phases have different ecological roles. The gametophyte, thought to be specialized for rapid growth and competition, may allocate more resources to photosynthetic machinery, hence the higher maximum photosynthetic rates. The tetrasporophyte, thought to be specialized for resistance to herbivores, may allocate more resources to structural or chemical defenses in preference to photosynthetic machinery. Consequently, the tetrasporophyte has lower photosynthetic capacity.     

Cellulolytic activity of four Fusarium spp.

Fusarium lini, F. lycopersici, F. pallidoroseum and F. semitectum grown in shake flasks produced, respectively, 0.19, 0.33, 0.13 and 0.09 units filter-paper cellulase/ml. Trichoderma reesei, in comparison, produced 0.8 U/ml.The authors are with Defence Food Research Laboratory, Mysore-570 011, India.     

Age-Related and Heteroplasmy-Related Variation in Human mtDNA Copy Number

The mitochondrial (mt) genome is present in many copies in human cells, and intra-individual variation in mtDNA sequences is known as heteroplasmy. Recent studies found that heteroplasmies are highly tissue-specific, site-specific, and allele-specific, however the functional implications have not been explored. This study investigates variation in mtDNA copy numbers (mtCN) in 12 different tissues obtained at autopsy from 152 individuals (ranging in age from 3 days to 96 years). Three different methods to estimate mtCN were compared: shotgun sequencing (in 4 tissues), capture-enriched sequencing (in 12 tissues) and droplet digital PCR (ddPCR, in 2 tissues). The highest precision in mtCN estimation was achieved using shotgun sequencing data. However, capture-enrichment data provide reliable estimates of relative (albeit not absolute) mtCNs. Comparisons of mtCN from different tissues of the same individual revealed that mtCNs in different tissues are, with few exceptions, uncorrelated. Hence, each tissue of an individual seems to regulate mtCN in a tissue-related rather than an individual-dependent manner. Skeletal muscle (SM) samples showed an age-related decrease in mtCN that was especially pronounced in males, while there was an age-related increase in mtCN for liver (LIV) samples. MtCN in SM samples was significantly negatively correlated with both the total number of heteroplasmic sites and with minor allele frequency (MAF) at two heteroplasmic sites, 408 and 16327. Heteroplasmies at both sites are highly specific for SM, accumulate with aging and are part of functional elements that regulate mtDNA replication. These data support the hypothesis that selection acting on these heteroplasmic sites is reducing mtCN in SM of older individuals.     

Host–Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes

Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins. We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen''s genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system.