Physical mapping of ribosomal DNA sites in Festuca arundinacea and related species by in situ hybridization.

The positions of the 18S-5.8S-26S and 5S rRNA genes have been physically mapped on the chromosomes of diploid, tetraploid, and hexaploid Festuca species by in situ hybridization. The number and position of the rDNA sites in the species were compared. The results confirm some of the earlier phylogenetic studies of these species but suggest that some structural rearrangements have occurred and that sites have been lost during polyploidization. Keywords: Festuca, in situ hybridization, phylogeny, physical mapping, rDNA.     

Identification of phosphorylation sites in native lamina-associated polypeptide 2 beta.

Lamina-associated polypeptide 2 beta (LAP 2 beta), an integral protein of the inner nuclear membrane, appears to be involved in the spatial organization of the interface between nucleoplasma, lamina, and nuclear envelope. Its ability to interact with other proteins and the structural integrity of the nuclear envelope is probably regulated by phosphorylation. Here, we report nonmitotic LAP 2 beta phosphorylation sites that are phosphorylated in the native protein when purified from nuclear envelopes of mouse neuroblastoma Neuro2a cells. Five phosphorylation sites were detected by nano-electrospray mass spectrometric analysis of tryptic LAP 2 beta peptides using parent ion scans specific for phosphopeptides. By mass spectrometric sequencing of these peptides, we identified as phosphorylated residues Thr 74, Thr 159, Ser 176, and Ser 179. Two of the phosphorylation sites, Thr 74 (within a region known to bind chromatin) and Thr 159, are part of consensus sequences of proline-directed kinases. Ser 179 is part of a consensus site for protein kinase C which is able to highly phosphorylate LAP 2 beta in vitro. Three phosphorylation sites, Thr 159, Ser 176, and Ser 179, are located within a stretch of 20 amino acids, thereby forming a highly phosphorylated protein domain which may integrate signaling by multiple protein kinases. Additionally, we identified for the first time at the protein level the LAP 2 splice variant LAP 2 epsilon in nuclear envelopes.     

Preliminary karyotype and chromosomal localization of ribosomal DNA sites in white spruce using fluorescence in situ hybridization.

We have localized the major ribosomal DNA (rDNA) loci on metaphase chromosomes and in interphase nuclei of white spruce (2n = 24) by fluorescence in situ hybridization. Hybridization sites of the biotin-labelled rDNA probe were detected using antibody-fluorochrome conjugates and a confocal laser scanning microscope. White spruce has at least 12, and possibly as many as 14, rDNA sites, 1 site present on each of seven separate chromosome pairs. This is one of the highest numbers of rDNA loci yet reported among plant species. The position of the rDNA loci together with secondary constriction patterns permit, for the first time, all homologous pairs of white spruce chromosomes to be distinguished. We discuss the application of molecular cytogenetics in studies relating to the organization and evolution of DNA sequences within conifer genomes.     

Identification and characterization of E.coli ribosomal binding sites by free energy computation.

Sequences upstream from translational initiation sites of different E.coli genes show various degrees of complementarity to the Shine-Dalgarno (SD) sequence at the 3' end of the 16S rRNA. We propose a quantitative measure for the SD region on the mRNA, that reflects its degree of complementarity to the rRNA. This measure is based on the stability of the rRNA-mRNA duplex as established by free energy computations. The free energy calculations are based on the same principles that are used for folding a single RNA molecule, and are executed by similar algorithms. Bulges and internal loops in the rRNA and mRNA are allowed. The mRNA string with maximum free energy gain upon binding to the rRNA is selected as the most favorable SD sequence of a gene. The free energy value that represents the SD region provides a quantitative measure that can be used for comparing SD sequences of different genes. The distribution of this measure in more than 1000 E.coli genes is presented and discussed.     

Anchored simple-sequence repeats as primers to generate species-specific DNA markers in Lolium and Festuca grasses

Simple-sequence repeats (SSRs) comprising three tetranucleotide repeat sequences with two-base ’anchors’, namely 5′-(AGAC)₄GC, 5′-AC(GACA)₄ and 5′-(GACA)₄GT, were used in PCR reactions as primers to develop inter-SSR DNA fingerprints of the outbreeding grass species Lolium multiflorum, L. perenne, Festuca pratensis and F. arundinacea. Each species was represented by DNA samples from 3 to 6 varieties. In all four species distinctive species-specific DNA profiles were produced that were common across a number of varieties despite their diverse origin. While the fingerprints of the two ryegrasses, L. multiflorum and L. perenne, were the most similar, a number of inter-SSR DNA markers were generated that enabled them to be distinguished from each other. Some slight variations were found between varieties, which provided putative variety-specific markers for cultivar identification. In addition, variations in the DNA profiles of the genotypes of L. multiflorum and F. pratensis were examined, and the results showed that variety-specific fingerprints are integrated patterns made up from the profiles of individual genotypes. Amongst the primers used, AC(GACA)₄ generated the best distinction between Lolium and Festuca individuals and provides an effective new tool for genome identification. A number of species-discriminating sequences, ranging in size between 550 bp and 1,600 bp, were cloned: three clones for F. pratensis, one clone for L. multiflorum and one clone for F. arundinacea. A F. pratensis fragment pFp 78H582 was sequenced. Southern hybridization confirmed the presence of this fragment in F. arundinacea (which contains one genome of F. pratensis), but no homology was found with L. multiflorum. However, a F. arundinacea clone amplified with (GACA)₄GT, pFa 104H1350, was found to be unique to the F. arundinacea genome. Received: 23 June 1999 / Accepted: 27 August 1999     

Identification of phosphorylation sites in mammalian mitochondrial ribosomal protein DAP3

Mammalian mitochondrial ribosomes synthesize 13 proteins that are essential for oxidative phosphorylation. In addition to their role in protein synthesis, some of the mitochondrial ribosomal proteins have acquired functions in other cellular processes such as apoptosis. Death-associated protein 3 (DAP3), also referred to as mitochondrial ribosomal protein S29 (MRP-S29), is a GTP-binding pro-apoptotic protein located in the small subunit of the ribosome. Previous studies have shown that phosphorylation is one of the most likely regulatory mechanisms for DAP3 function in apoptosis and may be in protein synthesis; however, no phosphorylation sites were identified. In this study, we have investigated the phosphorylation status of ribosomal DAP3 and mapped the phosphorylation sites by tandem mass spectrometry. Mitochondrial ribosomal DAP3 is phosphorylated at Ser215 or Thr216, Ser220, Ser251 or Ser252, and Ser280. In addition, phosphorylation of recombinant DAP3 by Protein kinase A and Protein kinase Cdelta at residues that are endogenously phosphorylated in ribosomal DAP3 suggests both of these kinases as potential candidates responsible for the in vivo phosphorylation of DAP3 in mammalian mitochondria. Interestingly, the majority of the phosphorylation sites detected in our study are clustered around the highly conserved GTP-binding motifs, speculating on the significance of these residues on protein conformation and activity. Site-directed mutagenesis studies on selected phosphorylation sites were performed to determine the effect of phosphorylation on cell proliferation and PARP cleavage as indication of caspase activation. Overall, our findings suggest DAP3, a mitochondrial ribosomal small subunit protein, is a novel phosphorylated target.     

Dominance of native grasses leads to community convergence in wetland restoration

Wetland restoration is a pressing conservation priority, but there are few replicated field studies that provide a scientific foundation for these activities. We conducted a 3-year, replicated field experiment to examine the effectiveness of initial site preparation techniques (combinations of solarization, herbicide, tilling, and thermal weed control) in restoring native plant biodiversity to an agricultural field in a former wetland prairie in Oregon, USA. Post-treatment, plots were sown with a typical restoration mix of native graminoids and forbs. Treatments were compared to three high-quality managed reference wetlands and the adjacent agricultural field. Site preparation treatments varied in their effectiveness in suppressing extant vegetation and eliminating the residual seed bank. After 1 year, the solarization and fall herbicide application treatments were the most effective at reducing exotic cover. However, after 3 years, plant community composition converged in all treatments due to a loss of annual species and increasing dominance of native perennial bunchgrasses. Plant community composition became more similar to the reference wetlands each year, but diversity and richness diverged, apparently due to a trade-off between the cover of the dominant native bunchgrasses and diversity. Successional theory offers insights into how priority effects and competitive inhibition may influence community trajectories, and offers a useful model for restoring plant communities with high native diversity and dominance. Finding ways to mitigate the tradeoff between native plant cover and diversity by actively managing successional trajectories is an important challenge in wetland restoration that deserves further investigation.     

Dynamics of root growth and decay in two grasses native to semi-arid Argentina

The pattern of root growth and decay in Stipa tenuis Phil, and Piptochaetium napostaense (Speg.) Hack, was examined under field conditions in root observation chambers. The roots of both species grew uninterruptedly throughout the whole year. Root elongation during spring, summer, and early autumn can be six and five times as high as that in the late autumn to winter period for S. tenuis and P. napostaense, respectively. Root decay was a continuous process in both species throughout the year, with maximum decay rates occurring from late spring through to the middle of autumn. Comparison of minimum and maximum values registered during the year showed a root decay ratio of about 4:1 for S. tenuis and one of 5:1 for P. napostaense. During the period of maximum root growth, both species showed a pulse-like pattern of root elongation in response to rapid changes in water availability. In a semi-arid region in which the soil is notably shallow, root growth behaviour of this kind should allow these species to respond opportunistically to water.     

Movement of Anastrepha fraterculus from native breeding sites into apple orchards in Southern Brazil

We report movements exhibited by adults of Anastrepha fraterculus (Wiedemann) (Diptera: Tephritidae) from patches of native forests into apple orchards in Southern Brazil. Two mark-release-recapture experiments were conducted using wild flies. Released flies behaved as wild unmarked flies, and periods of peak captures of marked adults coincided with those of unmarked ones. In the first experiment (December 94), out of 2154 released adults, 7.1% were recaptured from day 2 through day 20 after release. Captures peaked from day 7–9 after release. Most marked flies (94.7%) were trapped within 200 m of the release point but eight adults (seven females and one male) were captured in traps placed in an apple orchard, 400–800 m from the release point. The vegetation found between forest and orchard consisted of pastures and annual crops. In the second experiment (January 95), a total of 3284 flies was released in an area where native host plants were abundant and located at ca. 900 m from an apple orchard. In all, 37.1% of marked flies were captured, 99.0% of them at a distance of less than 200 m from the release point. Four adults were captured in an apple orchard, 7 to 24 days after release. They may have reached the orchard through a large and continuous area of native forest. Our results unequivocally demonstrate that A. fraterculus adults are able to disperse from native forests where they originate and invade apple orchards, probably foraging for food and oviposition sites.     

Response of the invasive Centaurea maculosa and two native grasses to N-pulses

Nitrogen is often a limiting resource on semi-arid grasslands. During the growing season, N is often only available during short-term pulses associated with wetting events. The Eurasian forb Centaurea maculosa Lam. has invaded millions of hectares of semi-arid grasslands in western North America. C. maculosa's success could be attributed to greater use of N-pulses, or more efficient use of N supplied in those pulses compared with native grasses. In a glasshouse, C. maculosa and two native grasses, the caespitose Pseudoroegneria spicata [Scribn. and Smith] A. Love and the rhizomatous Pascopyrum smithii [Rybd.] A. Love, were established in mixed- and monoculture combinations, and then conditioned to weekly N-pulses of 8, 24, or 72 h for 8 weeks. These pulse durations are typical on semi-arid grasslands. At the end of the 8 weeks, plants were exposed to ¹⁵N-labeled nitrate (¹⁵NO₃ ^–) for 8 h and harvested 16 h later to compare short-term root uptake of ¹⁵NO₃ ^–. C. maculosa did not have greater enrichment (atom % ¹⁵N), rate of ¹⁵N-uptake (mol g^–1 h^–1), or ¹⁵N acquired (relative to ¹⁵N applied) than the grasses. C. maculosa's ¹⁵N-uptake per unit mass was relatively consistent across pulse durations, whereas ¹⁵N-uptake was lower at the longer pulse durations for the grasses. In general, C. maculosa acquired more of the applied ¹⁵N than P. spicata but less than P. smithii. ¹⁵N acquired was often influenced by the neighbour's identity. Regarding growth responses, C. maculosa produced more total biomass than the grasses, except for P. smithii plants growing with C. maculosa conditioned to 72 h pulses of N. Root mass ratios varied depending on the neighbor. Overall, C. maculosa used nitrogen less efficiently than the grasses. C. maculosa's success as an invasive species cannot be explained wholly by a greater response to N-pulses or more efficient use of N-pulses compared with native grasses with which it competes.     

Germination responses of native and invasive Cerrado grasses to simulated fire temperatures

Background: Fire is an important ecological factor in the Cerrado (Brazilian savanna). However, comparative studies on the effect of high temperatures experienced during fires on seed germination of native and invasive grass species are few.

Aims: To assess germination responses to simulated fire temperatures by seeds of invasive and native Cerrado grasses.

Methods: Heat-shock treatments (50 °C, 70 °C, 90 °C, 110 °C, 130 °C or 150 °C) were applied to seeds of 10 species of native and invasive grasses. For each temperature, the seeds were heated in a dry-air flow for 2 or 5 min. This combination of temperatures and exposure times simulated the soil conditions during typical Cerrado fires.

Results: Temperature treatment was significantly related to germination, and the effect varied according to species. Heat shock did not increase germination in either the native or the invasive species. Exposure time was important for only two species, and four species showed a significant increase in mean germination time.

Conclusions: Species showed different tolerances to high temperatures. It was not possible to differentiate the native and invasive grasses only by their tolerance to high temperatures, suggesting that fire alone may not be an efficient management tool to control the invasive species studied here.     

Response of native grasses and Cicer arietinum to soil polluted with mining wastes: Implications for the management of land adjacent to mine sites

Mine tailings are an environmental problem in Southern Spain because wind and water erosion of bare surfaces results in the dispersal of toxic metals over nearby urban or agricultural areas. Revegetation with tolerant native species may reduce this risk. We grew two grasses, Lygeum spartum and Piptatherum miliaceum, and the crop species Cicer arietinum (chickpea) under controlled conditions in pots containing a mine tailings mixed into non-polluted soil to give treatments of 0%, 25%, 50%, 75% and 100% mine tailings. We tested a neutral (pH 7.4) mine tailings which contained high concentrations of Cd, Cu, Pb and Zn. Water-extractable metal concentrations increased in proportion to the amount of tailings added. The biomass of the two grasses decreased in proportion to the rate of neutral mine-tailing addition, while the biomass of C. arietinum only decreased in relation to the control treatment. Neutron radiography revealed that root development of C. arietinum was perturbed in soil amended with the neutral tailings compared to those of the control treatment, despite a lack of toxicity symptoms in the shoots. In all treatments and for all metals, the plants accumulated higher concentrations in the roots than in shoots. The highest concentrations occurred in the roots of P. miliaceum (2500 mg kg^?1 Pb, 146 mg kg^?1 Cd, 185 mg kg^?1 Cu, 2700 mg kg^?1 Zn). C. arietinum seeds had normal concentrations of Zn (70–90 mg kg^?1) and Cu (6–9 mg kg^?1). However, the Cd concentration in this species was ～1 mg kg^?1 in the seeds and 14.5 mg kg^?1 in shoots. Consumption of these plant species by cattle and wild fauna may present a risk of toxic metals entering the food chain.     

Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis.

New techniques for mapping mammalian DNA replication origins are needed. We have modified the existing nascent-strand size analysis technique (L. Vassilev and E.M. Johnson, Nucleic Acids Res. 17:7693-7705, 1989) to provide an independent means of studying replication initiation sites. We call the new method nascent-strand abundance analysis. We confirmed the validity of this method with replicating simian virus 40 DNA as a model. We then applied nascent-strand abundance and nascent-strand size analyses to mapping of initiation sites in human (HeLa) ribosomal DNA (rDNA), a region previously examined exclusively by two-dimensional gel electrophoresis methods (R.D. Little, T.H.K. Platt, and C.L. Schildkraut, Mol. Cell. Biol. 13:6600-6613, 1993). Our results partly confirm those obtained by two-dimensional gel electrophoresis techniques. Both studies suggest that replication initiates at relatively high frequency a few kilobase pairs upstream of the transcribed region and that many additional low-frequency initiation sites are distributed through most of the remainder of the ribosomal DNA repeat unit.     

Identification of insulin-induced sites of ribosomal protein S6 phosphorylation in Drosophila melanogaster

Insulin treatment of Drosophila melanogaster Kc 167 cells induces the multiple phosphorylation of a Drosophila ribosomal protein, as judged by its decreased electrophoretic mobility on two-dimensional polyacrylamide gels. The extent to which insulin induces this response is potentiated by cycloheximide and blocked by pretreatment with rapamycin. Isolation and mass spectrometric analysis revealed that the multiply phosphorylated protein was the larger of two Drosophila melanogaster orthologues of mammalian 40S ribosomal protein S6, termed here DS6A. Proteolytic cleavage of DS6A derived from stimulated Kc 167 cells with the endoproteinase Lys-C released a number of peptides, one of which contained all the putative phosphorylation sites. Conversion of phosphoserines to dehydroalanines with Ba(OH)(2) showed that the sites of phosphorylation reside at the carboxy terminus of DS6A. The sites of phosphorylation were identified by Edman degradation after conversion of the phosphoserine residues to S-ethylcysteine as Ser(233), Ser(235), Ser(239), Ser(242), and Ser(245). Finally, phosphopeptide mapping of individual phosphoderivatives, isolated from two-dimensional polyacrylamide gels, indicated that DS6A phosphorylation, in analogy to mammalian S6 phosphorylation, appears to proceed in an ordered fashion. The importance of these observations in cell growth and development is discussed.     

Statistical analysis and prediction of bacterial sites for ribosomal binding]

An algorithm for recognition of prokaryotic ribosomal binding sites is suggested. The parameter library contains weight matrices for mapping of gene starts in various bacterial genomes. Comparison of the ribosome binding starts in different taxonomic groups demonstrates that the signals in Gram-positive bacteria are stronger than in Gram-negative bacteria, and in particular, Enterobacteria. The recognition matrices are available by e-mail misha@imb.imb.ac.ru.     

Spatial and temporal variability in propagule limitation of California native grasses

Community composition and diversity arise from limitations in propagule supply (i.e. propagule or seed limitation) and propagule establishment after arriving at a site (i.e. establishment or microsite limitation). Recent meta‐analyses suggest that the degree of propagule limitation depends on local abiotic and biotic conditions, which in turn are likely to vary spatially and temporally. Nevertheless, seed addition studies testing propagule limitation are rarely replicated in multiple locations and years and often lack experimental manipulations of critical determinants of propagule limitation, such as the density and species richness of the propagule pool and disturbance and resource supply of recipient site. The invasion of California (USA) grasslands by exotic annual species from the Mediterranean region is unique in its scope (over 9 million ha) and persistence (more than 150 years). This invasion provides an exciting context in which to test the role of spatial and temporal variability in mediating propagule limitation and ultimately the potential for restoration. Here I present the results of native‐grass, seed‐addition trials conducted along a 500 km gradient in California in three consecutive years spanning a wide range of environmental conditions and initial conditions (e.g. rainfall, seeding density and disturbance). While native grasses were able to establish at many locations, per capita seed survival was low suggesting that the fate of these species is governed by interplay between propagule and establishment limitation. Establishment primarily varied spatially, with the most successful establishment occurring at fertile locations with low resident species richness. While recruitment was highly variable among years initially, there was no difference among seedling trials after three years.     

An electrophoretic karyotype and assignment of ribosomal genes to resolved chromosomes of Pneumocystis carinii

Pulsed-field gel electrophoresis was used to generate a molecular karyotype of chromosomes from the opportunistic AIDS pathogen, Pneumocystis carinii. P. carinii cysts and trophozoites were isolated from immunosuppressed rats, lysed in situ in agarose blocks, and subjected to orthogonal-field gel electrophoresis (OFAGE) and contour-clamped homogeneous-field gel electrophoresis (CHEF). OFAGE and CHEF gels resolved, respectively, 16 or 20 chromosome bands ranging in size from 0.32-1.5 megabase pairs. Summation of the estimated sizes of these chromosomes suggested a total genome complexity for P. carinii of 8-16 megabase pairs. Homologous probes for the genes encoding the 18S, 5.8S, and 5S ribosomal RNAs were hybridized to filter blots of the pulsed-field gels to map these genes to specific P. carinii chromosomes.     

Mitogen-activated 70K S6 kinase. Identification of in vitro 40 S ribosomal S6 phosphorylation sites

Recently we purified and cloned the mitogen/oncogene-activated Mr 70,000 (70K) S6 kinase from the livers of rats treated with cycloheximide (Kozma, S. C., Lane, H. A., Ferrari, S., Luther, H., Siegmann, M., and Thomas, G. (1989) EMBO J. 8, 4125-4132; Kozma, S. C., Ferrari, S., Bassand, P., Siegmann, M., Totty, N., and Thomas, G. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 7365-7369). Prior to determining the ability of this kinase to phosphorylate the same sites observed in S6 in vivo, we established the effects of different cations and autophosphorylation on kinase activity. The results show that the 70K S6 kinase is dependent on Mg2+ for activity and that this requirement cannot be substituted for by Mn2+. Furthermore, 50-fold lower concentrations of Mn2+ block the effect of Mg2+ on the kinase. This effect is not limited to Mn2+ but can be substituted for by a number of cations, with Zn2+ being the most potent inhibitor, IC50 approximately 2 microM. In the presence of optimum Mg2+ concentrations the enzyme incorporates an average of 1.2 mol of phosphate/mol of kinase and an average of 3.7 mol of phosphate/mol of S6. The autophosphorylation reaction appears to be intramolecular and leads to a 25% reduction in kinase activity toward S6. In the case of S6 all of the sites of phosphorylation are found to reside in a 19-amino acid peptide at the carboxyl end of the protein. Four of these sites have been identified as Ser235, Ser236, Ser240, and Ser244, equivalent to four of the five sites previously observed in vivo (Krieg, J., Hofsteenge, J., and Thomas, G. (1988) J. Biol. Chem. 263, 11473-11477). A fifth mole of phosphate is incorporated at low stoichiometry into the peptide, but the amino acid which is phosphorylated cannot be unequivocally assigned. The low level of phosphorylation of the fifth site in vitro is discussed with regard to known results and to a potential three-dimensional model for the carboxyl terminus of S6.     

Identification of Escherichia coli and Bacillus stearothermophilus ribosomal protein binding sites on Escherichia coli 5S RNA.

Summary E. coli [³²P]-labelled 5S RNA was complexed with E. coli and B. stearothermophilus 50S ribosomal proteins. Limited T₁ RNase digestion of each complex yielded three major fragments which were analysed for their sequences and rebinding of proteins. The primary binding sites for the E. coli binding proteins were determined to be sequences 18 to 57 for E-L5, 58 to 100 for E-L18 and 101 to 116 for E-L25. Rebinding experiments of purified E. coli proteins to the 5S RNA fragments led to the conclusion that E-L5 and E-L25 have secondary binding sites in the section 58 to 100, the primary binding site for E-L18. Since B. stearothermophilus proteins B-L5 and BL22 were found to interact with sequences 18 to 57 and 58 to 100 it was established that the thermophile proteins recognize and interact with RNA sequences similar to those of E. coli. Comparison of the E. coli 5S RNA sequence with those of other prokaryotic 5S RNAs reveals that the ribosomal proteins interact with the most conserved sections of the RNA.Paper number 12 on structure and function of 5S RNA.Preceding paper: Wrede, P. and Erdmann, V.A. Proc. Natl. Acad. Sci. USA 74, 2706–2709 (1977)