Insertional Editing of Mitochondrial tRNAs of Physarum polycephalum and Didymium nigripes

tRNAs encoded on the mitochondrial DNA of Physarum polycephalum and Didymium nigripes require insertional editing for their maturation. Editing consists of the specific insertion of a single cytidine or uridine relative to the mitochondrial DNA sequence encoding the tRNA. Editing sites are at 14 different locations in nine tRNAs. Cytidine insertion sites can be located in any of the four stems of the tRNA cloverleaf and usually create a G·C base pair. Uridine insertions have been identified in the T loop of tRNA^Lys from Didymium and tRNA^Glu from Physarum. In both tRNAs, the insertion creates the GUUC sequence, which is converted to GTΨC (Ψ = pseudouridine) in most tRNAs. This type of tRNA editing is different from other, previously described types of tRNA editing and resembles the mRNA and rRNA editing in Physarum and Didymium. Analogous tRNAs in Physarum and Didymium have editing sites at different locations, indicating that editing sites have been lost, gained, or both since the divergence of Physarum and Didymium. Although cDNAs derived from single tRNAs are generally fully edited, cDNAs derived from unprocessed polycistronic tRNA precursors often lack some of the editing site insertions. This enrichment of partially edited sequences in unprocessed tRNAs may indicate that editing is required for tRNA processing or at least that RNA editing occurs as an early event in tRNA synthesis.     

Bioprospecting microalgae as potential sources of "green energy"--challenges and perspectives (review)

Microalgae and cyanobacteria are potential foods, feeds, sources of high-value bioactive molecules and biofuels, and find tremendous applications in bioremediation and agriculture. Although few efforts have been undertaken to index the microalgal germplasm available in terms of lipid content, information on suitability of strains for mass multiplication and advances in development of methods for extraction and generating biofuel are scarce. Our review summarizes the potential of microalgae, latest developments in the field and analyzes the "pitfalls" in oversimplification of their promise in the years to come. Microalgae represent "green gold mines" for generating energy; however, the path to success is long and winding and needs tremendous and concerted efforts from science and industry, besides political will and social acceptance for overcoming the limitations. The major advantages of second generation biofuels based on microalgal systems, include their higher photon conversion efficiency, growth all around the year, even in wastewaters, and production of environment friendly biodegradable biofuels.     

Algal diversity in flowing waters at an acidic mine drainage “barrens” in central Pennsylvania,USA

Microscopic investigations were undertaken to decipher the diversity in the lotic algal communities from acidic waters (pH 2.4–3.2) flowing overland in sheets and channels at an acid mine drainage (AMD) barrens near Kylertown, PA, USA. Microscopic observations, supplemented with taxonomic keys, aided in identification of the dominant algae, and measurement of carbon from adjacent soils was undertaken. The unicellular protist Euglena sp. was most abundant in slower flowing waters (i.e., pool near point of emergence and surficial flow sheets), while Ulothrix sp. was most abundant in faster flowing water from the central stream channel. A diverse range of unicellular microalgae such as Chlorella, Cylindrocystis, Botryococcus, and Navicula and several filamentous forms identified as Microspora, Cladophora, and Binuclearia were also recorded. The observed high algal diversity may be related to the long duration of AMD flow at this site which has led to the development of adapted algal communities. The comparatively higher carbon content in soil materials adjacent to slower flowing water sampling locations provides evidence for the important role of algae as primary producers in this extreme environment.     

Induction of ureogenesis in perfused liver of a freshwater teleost, Heteropneustes fossilis, infused with different concentrations of ammonium chloride

The induction pattern of urea cycle enzymes and the rate of urea-N excretion were studied with relation to ammonia load in the perfused liver of a freshwater ammoniotelic teleost, Heteropneustes fossilis, when infused with different concentrations of ammonium chloride for 60 min. Both urea-N excretion and uptake of ammonia by the perfused liver were found to be a saturable process. The V_max of urea-N excretion (0.45 μmol/g liver/min) was obtained at ammonium chloride addition of 1.18 μmol/g liver/min. The maximum induction of carbamyl phosphate synthetase (ammonia dependent), 200%, and of ornithine transcarbamylase, 120%, was seen by the addition of 0.58 μmol/g liver/min, and for argininosuccinate synthetase and argininosuccinate lyase of 150% and 115%, respectively, by the addition of 2.8 μmol/g liver/min of ammonium chloride. However, arginase activity did not alter in any of the concentrations of ammonium chloride added. An increase of ammonia load of 3–5 μmol/g wet wt from the physiological level in the perfused liver was sufficient to initiate and to cause maximum induction of most of the urea cycle enzymes activitty. These results further confirm the capacity of transition from ammoniotelism to ureotelism in this unique freshwater air-breathing teleost to tolerate a very high ambient ammonia.     

Biophysical Characterization of Essential Phosphorylation at the Flexible C-Terminal Region of C-Raf with 14-3-3ζ Protein

Phosphorylation at the C-terminal flexible region of the C-Raf protein plays an important role in regulating its biological activity. Auto-phosphorylation at serine 621 (S621) in this region maintains C-Raf stability and activity. This phosphorylation mediates the interaction between C-Raf and scaffold protein 14-3-3ζ to activate the downstream MEK kinase pathway. In this study, we have defined the interaction of C-terminal peptide sequence of C-Raf with 14-3-3ζ protein and determined the possible structural adaptation of this region. Biophysical elucidation of the interaction was carried out using phosphopeptide (residue number 615–630) in the presence of 14-3-3ζ protein. Using isothermal titration calorimetry (ITC), a high binding affinity with micro-molar range was found to exist between the peptide and 14-3-3ζ protein, whereas the non-phosphorylated peptide did not show any appreciable binding affinity. Further interaction details were investigated using several biophysical techniques such as circular dichroism (CD), fluorescence, and nuclear magnetic resonance (NMR) spectroscopy, in addition to molecular modeling. This study provides the molecular basis for C-Raf C-terminal-derived phosphopeptide interaction with 14-3-3ζ protein as well as structural insights responsible for phosphorylated S621-mediated 14-3-3ζ binding at an atomic resolution.     

Does fish represent an intermediate stage in the evolution of ureotelic cytosolic arginase I?

Arginase catalyses the last step of the urea cycle. At least two isoenzymes of arginase are known; cytosolic ARG I and mitochondrial ARG II. ARG I is predominantly expressed in liver cytosol, as a part of urea cycle in ureotelic animals. The second isoform ARG II is primarily responsible for non-ureogenic functions, expressed in mitochondria of both hepatic and non-hepatic tissues in most vertebrates. Most micro-organisms and invertebrates are known to have only one type of arginase, whose function is unrelated to ornithine-urea cycle (OUC). However, in ureo-osmotic marine elasmobranchs arginase is localized in liver mitochondria as a part of OUC to synthesize urea for osmoregulation. An evolutionary transition occurred in arginase enzyme in terrestrial ureotelic vertebrates, with the evolution of ARG I from a pre-existing ancestral mitochondrial ARG II. This cytosolic ARG I activity is supposed to have first appeared in lung fishes, but the 40% and 60% distribution of arginase I and II activity in liver and kidney tissue of Heteropneustes fossilis indicates reconsideration of the above fact.     

Ureogenesis in a freshwater teleost: an unusual sub-cellular localization of ornithine-urea cycle enzymes in the freshwater air-breathing teleost Heteropneustes fossilis.

Sub-cellular localization of different ornithine-urea cycle enzymes was studied in the liver and kidney of a freshwater air-breathing teleost. Carbamyl phosphate synthetase, ornithine transcarbamylase, and arginase were found to be localized inside the mitochondria, and argininosuccinate synthetase and argininosuccinate lyase were found in the soluble fraction. Mitochondrial localization of arginase, a feature known in marine elasmobranchs and toadfishes, indicates the evolutionary position of H. fossilis to be different from that of present day freshwater teleosts.