Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs

Aminoacyl-tRNA synthetases (aaRS) are essential enzymes catalyzing the formation of aminoacyl-tRNAs, the immediate precursors for encoded peptides in ribosomal protein synthesis. Previous studies have suggested a link between tRNA aminoacylation and high-molecular-weight cellular complexes such as the cytoskeleton or ribosomes. However, the structural basis of these interactions and potential mechanistic implications are not well understood. To biochemically characterize these interactions we have used a system of two interacting archaeal aaRSs: an atypical methanogenic-type seryl-tRNA synthetase and an archaeal ArgRS. More specifically, we have shown by thermophoresis and surface plasmon resonance that these two aaRSs bind to the large ribosomal subunit with micromolar affinities. We have identified the L7/L12 stalk and the proteins located near the stalk base as the main sites for aaRS binding. Finally, we have performed a bioinformatics analysis of synonymous codons in the Methanothermobacter thermautotrophicus genome that supports a mechanism in which the deacylated tRNAs may be recharged by aaRSs bound to the ribosome and reused at the next occurrence of a codon encoding the same amino acid. These results suggest a mechanism of tRNA recycling in which aaRSs associate with the L7/L12 stalk region to recapture the tRNAs released from the preceding ribosome in polysome

Trends in Fisheries Science from 2000 to 2009: A Bibliometric Study

The present study applies a bibliometric approach to identify recent patterns and trends in the methods, subjects, and authorships in the literature published in fisheries science (2000-2009). The results indicate that the most frequently studied group of species were Salmonidae, although the interest for these species seems to be diminishing. The studies of the marine habitat and inland habitats, respectively, have revealed a marked increase and decrease in frequency. Genetics represents the most rapidly growing area of research. The model development was the most frequently applied method in fisheries science, although such publications have had a generally lower number of citations. The number of experimental studies was markedly low, but they were also the most frequently cited. The United States was the most productive country over the last decade with a gradually increasing output over the time, but it was surpassed by the total European Union output. An apparent difference in the research output has been recorded between the developed and developing countries. The findings of this study, however, indicate a positive tendency in this direction. A growing rate of publications based on international collaboration was recorded, and such publications also demonstrate a higher number of citations than the single-country publications

Demographic flexibility influences colonization success: profiling invasive fish species in the Danube River by the use of population models

Invasive species have the ability to modify their life-history traits in newly colonized areas, with positive shifts in specific life history traits under favourable environmental conditions. If such positive changes in their life history result in a comparably larger population growth rate, it may give them a competitive edge over native species, support faster range expansion and contribute to their invasion success. Within the present paper we hypothesized that the demographic flexibility represents an important contribution to the invasion success of exotic species, and that demographic flexibility patterns of invasive species differ from those in unsuccessful invaders. We tested this hypothesis by the use of elasticity analysis applied on simple age-structured population models of invasive fish species in the Danube River, as well as of non-native species that failed to establish or become invasive. Findings imply that the invasive fish species could have the ability to experience a more rapid population growth under favourable environmental conditions, especially those that sustain recruitment, while at the same time being more robust to changes in survival. The highest population elasticity among the assessed alien invasive species was detected in stone moroko (Pseudorasbora parva). The described approach has the potential to be used as an additional screening tool for invasive species. When combined with other invasion risk profiling methods, it can provide additional insight into characteristics of species invasions and in invasion potential of a species

Implementing population viability analysis into fisheries management

Fish populations worldwide have experienced severe decline, and some of the species are facing a serious threat of extinction. Population simulations are currently the most promising approach for the assessment of extinction risk and the evaluation of alternative management measures. The population viability analysis (PVA) represents a method that is able to cope with uncertainties present in ecological data and to support decision-making process within the field of fishery management. This chapter presents an overview of the development of the PVA within the field of fishery science, along with an evaluation of the success of its application in fishery management, and major challenges in its future implementation. Potential applications of PVA are very diverse and, beside the estimation of sustainable fishery levels, they were used to address a number of different issues, such as the efficiency of the minimum length limits, extinction risk of the target and bycatch species, impact of the climate change, effects of habitat loss and degradation, and other. Despite some unresolved limitations and problems in the PVA development and implementation, scientific knowledge and fishery management have both earned immensely from this process. PVA should be recognized as an important tool for the process of research and management planning and policy development, and as an integral evaluation and planning component within the adaptive management process. If used with necessary caution, PVA can provide invaluable help in current worldwide efforts for achieving sustainable fishery

Seasonal changes in condition, hepatosomatic index and parasitism in sterlet (Acipenser ruthenus L.)

Measurements of biomarker responses in fish from contaminated sites could provide valuable data for environmental risk assessment. Biomarkers are sensitive to both environmental pollution and confounding factors that are not related to pollution (e.g., season, nutritional status, and population density). Unfortunately, data about the latter group are scarce. Therefore, juvenile sterlet (Acipenser ruthenus L.) specimens were collected on a monthly basis from the Danube River from September 2002 through August 2003 to determine if seasonal changes exist in condition, hepatosomatic index, and parasitism. Fulton condition factor (FCF range: 0.27-0.79), hepatosomatic index (HSI range: 1.14-6.67) and Skrjabinopsolus semiarmatus parasite prevalence (range: 37.9-85.7%), intensity (range: 1-337 parasites per fish) and the mean intensity (range 9.6-89.2) in sterlet showed significant seasonal variations. This study pointed out that biomarker sampling on different locations has to be performed within the short time frame in order to avoid differences generated by confounding factors. Better understanding of the life cycle of S. semiarmatus and sensitivity of different phases to pollution is needed

Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs

Aminoacyl-tRNA synthetases (aaRS) are essential enzymes catalyzing the formation of aminoacyl-tRNAs, the immediate precursors for encoded peptides in ribosomal protein synthesis. Previous studies have suggested a link between tRNA aminoacylation and high-molecular-weight cellular complexes such as the cytoskeleton or ribosomes. However, the structural basis of these interactions and potential mechanistic implications are not well understood. To biochemically characterize these interactions we have used a system of two interacting archaeal aaRSs: an atypical methanogenic-type seryl-tRNA synthetase and an archaeal ArgRS. More specifically, we have shown by thermophoresis and surface plasmon resonance that these two aaRSs bind to the large ribosomal subunit with micromolar affinities. We have identified the L7/L12 stalk and the proteins located near the stalk base as the main sites for aaRS binding. Finally, we have performed a bioinformatics analysis of synonymous codons in the Methanothermobacter thermautotrophicus genome that supports a mechanism in which the deacylated tRNAs may be recharged by aaRSs bound to the ribosome and reused at the next occurrence of a codon encoding the same amino acid. These results suggest a mechanism of tRNA recycling in which aaRSs associate with the L7/L12 stalk region to recapture the tRNAs released from the preceding ribosome in polysomes.ISSN:1362-4962ISSN:0301-561

Water level changes affect carbon turnover and microbial community composition in lake sediments

Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. 13C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions

Water level changes affect carbon turnover and microbial community composition in lake sediments

Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. 13C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions

Identification of Amino Acids in the N-terminal Domain of Atypical Methanogenic-type Seryl-tRNA Synthetase Critical for tRNA Recognition*

Seryl-tRNA synthetase (SerRS) from methanogenic archaeon Methanosarcina barkeri, contains an idiosyncratic N-terminal domain, composed of an antiparallel β-sheet capped by a helical bundle, connected to the catalytic core by a short linker peptide. It is very different from the coiled-coil tRNA binding domain in bacterial-type SerRS. Because the crystal structure of the methanogenic-type SerRS·tRNA complex has not been obtained, a docking model was produced, which indicated that highly conserved helices H2 and H3 of the N-terminal domain may be important for recognition of the extra arm of tRNASer. Based on structural information and the docking model, we have mutated various positions within the N-terminal region and probed their involvement in tRNA binding and serylation. Total loss of activity and inability of the R76A variant to form the complex with cognate tRNA identifies Arg76 located in helix H2 as a crucial tRNA-interacting residue. Alteration of Lys79 positioned in helix H2 and Arg94 in the loop between helix H2 and β-strand A4 have a pronounced effect on SerRS·tRNASer complex formation and dissociation constants (KD) determined by surface plasmon resonance. The replacement of residues Arg38 (located in the loop between helix H1 and β-strand A2), Lys141 and Asn142 (from H3), and Arg143 (between H3 and H4) moderately affect both the serylation activity and the KD values. Furthermore, we have obtained a striking correlation between these results and in vivo effects of these mutations by quantifying the efficiency of suppression of bacterial amber mutations, after coexpression of the genes for M. barkeri suppressor tRNASer and a set of mMbSerRS variants in Escherichia coli