Flossing DNA in a Dual Nanopore Device.

Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single-molecule data. Here, an active control technique termed "flossing" that uses a dual nanopore device is presented to trap a proteintagged DNA molecule and up to 100's of back-and-forth electrical scans of the molecule are performed in a few seconds. The protein motifs bound to 48.5 kb λ-DNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multiscan data to produce averaged intertag distance estimates that are comparable to their known values. Since nanopore feature-mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans-pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual-pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.

Controlling DNA Tug-of-War in a Dual Nanopore Device.

Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. A method is created for reducing and controlling the speed of DNA that uses two independently controllable nanopores operated with an active control logic. The pores are positioned sufficiently close to permit cocapture of a single DNA by both pores. Once cocapture occurs, control logic turns on constant competing voltages at the pores leading to a "tug-of-war" whereby opposing forces are applied to regions of the molecules threading through the pores. These forces exert both conformational and speed control over the cocaptured molecule, removing folds and reducing the translocation rate. When the voltages are tuned so that the electrophoretic force applied to both pores comes into balance, the life time of the tug-of-war state is limited purely by diffusive sliding of the DNA between the pores. A tug-of-war state is produced on 76.8% of molecules that are captured with a maximum two-order of magnitude increase in average pore translocation time relative to the average time for single-pore translocation. Moreover, the translocation slow-down is quantified as a function of voltage tuning and it is shown that the slow-down is well described by a first passage analysis for a 1D subdiffusive process. The ionic current of each nanopore provides an independent sensor that synchronously measures a different region of the same molecule, enabling sequential detection of physical labels, such as monostreptavidin tags. With advances in devices and control logic, future dual-pore applications include genome mapping and enzyme-free sequencing.

Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing.

Alternative splicing of pre-messenger RNAs diversifies gene products in eukaryotes and is guided by factors that enable spliceosomes to recognize particular splice sites. Here we report that alternative splicing of Saccharomyces cerevisiae SRC1 pre-mRNA is promoted by the conserved ubiquitin-like protein Hub1. Structural and biochemical data show that Hub1 binds non-covalently to a conserved element termed HIND, which is present in the spliceosomal protein Snu66 in yeast and mammals, and Prp38 in plants. Hub1 binding mildly alters spliceosomal protein interactions and barely affects general splicing in S. cerevisiae. However, spliceosomes that lack Hub1, or are defective in Hub1-HIND interaction, cannot use certain non-canonical 5' splice sites and are defective in alternative SRC1 splicing. Hub1 confers alternative splicing not only when bound to HIND, but also when experimentally fused to Snu66, Prp38, or even the core splicing factor Prp8. Our study indicates a novel mechanism for splice site utilization that is guided by non-covalent modification of the spliceosome by an unconventional ubiquitin-like modifier.

Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation.

Alternative splicing contributes to muscle development, but a complete set of muscle-splicing factors and their combinatorial interactions are unknown. Previous work identified ACUAA ("STAR" motif) as an enriched intron sequence near muscle-specific alternative exons such as Capzb exon 9. Mass spectrometry of myoblast proteins selected by the Capzb exon 9 intron via RNA affinity chromatography identifies Quaking (QK), a protein known to regulate mRNA function through ACUAA motifs in 3' UTRs. We find that QK promotes inclusion of Capzb exon 9 in opposition to repression by polypyrimidine tract-binding protein (PTB). QK depletion alters inclusion of 406 cassette exons whose adjacent intron sequences are also enriched in ACUAA motifs. During differentiation of myoblasts to myotubes, QK levels increase two- to threefold, suggesting a mechanism for QK-responsive exon regulation. Combined analysis of the PTB- and QK-splicing regulatory networks during myogenesis suggests that 39% of regulated exons are under the control of one or both of these splicing factors. This work provides the first evidence that QK is a global regulator of splicing during muscle development in vertebrates and shows how overlapping splicing regulatory networks contribute to gene expression programs during differentiation.

Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control.

We present an electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA. Previously developed "DNA flossing" control logic generates multiple scans of each captured DNA. We extended this logic in two ways: first, to automate "zooming out" on each molecule to progressively increase the number of tags scanned during flossing, and second, to automate recapture of a molecule that exited flossing to enable interrogation of the same and/or different regions of the molecule. Custom analysis methods were developed to produce consensus alignments from each multiscan event. The combined multiscanning and multicapture method was applied to the challenge of mapping from a heterogeneous mixture of single-molecule fragments that make up the Escherichia coli (E. coli) chromosome. Coverage of 3.1× across 2355 resolvable sites of the E. coli genome was achieved after 5.6 h of recording time. The recapture method showed a 38% increase in the merged-event alignment length compared to single-scan alignments. The observed intertag resolution was 150 bp in engineered DNA molecules and 166 bp natively within fragments of E. coli DNA, with detection of 133 intersite intervals shorter than 200 bp in the E. coli reference map. We present results on estimating distances in repetitive regions of the E. coli genome. With an appropriately designed array, higher throughput implementations could enable human-sized genome and epigenome mapping applications.

Exploring functional relationships between components of the gene expression machinery.

Eukaryotic gene expression requires the coordinated activity of many macromolecular machines including transcription factors and RNA polymerase, the spliceosome, mRNA export factors, the nuclear pore, the ribosome and decay machineries. Yeast carrying mutations in genes encoding components of these machineries were examined using microarrays to measure changes in both pre-mRNA and mRNA levels. We used these measurements as a quantitative phenotype to ask how steps in the gene expression pathway are functionally connected. A multiclass support vector machine was trained to recognize the gene expression phenotypes caused by these mutations. In several cases, unexpected phenotype assignments by the computer revealed functional roles for specific factors at multiple steps in the gene expression pathway. The ability to resolve gene expression pathway phenotypes provides insight into how the major machineries of gene expression communicate with each other.

Prp43p is a DEAH-box spliceosome disassembly factor essential for ribosome biogenesis.

The known function of the DEXH/D-box protein Prp43p is the removal of the U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex. We demonstrate that affinity-purified Prp43p-associated material includes the expected spliceosomal components; however, we also identify several preribosomal complexes that are specifically purified with Prp43p. Conditional prp43 mutant alleles confer a 35S pre-rRNA processing defect, with subsequent depletion of 27S and 20S precursors. Upon a shift to a nonpermissive temperature, both large and small-ribosomal-subunit proteins accumulate in the nucleolus of prp43 mutants. Pulse-chase analysis demonstrates delayed kinetics of 35S, 27S, and 20S pre-rRNA processing with turnover of these intermediates. Microarray analysis of pre-mRNA splicing defects in prp43 mutants shows a very mild effect, similar to that of nonessential pre-mRNA splicing factors. Prp43p is the first DEXH/D-box protein shown to function in both RNA polymerase I and polymerase II transcript metabolism. Its essential function is in its newly characterized role in ribosome biogenesis of both ribosomal subunits, positioning Prp43p to regulate both pre-mRNA splicing and ribosome biogenesis.

Differential gene expression as a toxicant-sensitive endpoint in zebrafish embryos and larvae.

The zebrafish (Danio rerio) embryo toxicity test (DarT) is under consideration as an alternative to the acute fish toxicity test. Microscopically visible developmental disorders or death are the endpoints used to report on toxicity in DarT. These endpoints are easily observed. They, however, rarely reveal mechanisms leading to a toxic effect and are relatively insensitive compared to chronic toxic effects. We hypothesized that, by using gene expression profiles as an additional endpoint, it may be possible to increase the sensitivity and predictive value of DarT. Therefore, as a proof of principle, we exposed zebrafish embryos to the reference compound 3,4-dichloroaniline (3,4-DCA) and analyzed gene expression patterns with a 14k oligonucleotide array. Important stress response genes not included in the microarray were additionally quantified by reverse transcriptase polymerase chain reaction. Six genes involved in biotransformation (cyp1a, ahr2), stress response (nfe212, maft, hmox1) and cell cycle control (fzr1) were significantly regulated. With the exception of fzr1, these genes proved to be differentially expressed in post hatch life stages as well. The identified genes point toward an aryl hydrocarbon receptor-mediated response. Differential gene expression in embryos exposed for 48 h was observed at 3,4-DCA concentrations as low as 0.78 microM, which is more than 10-fold below the concentrations that elicited visible toxic effects. Upon exposure for 5 days, differential expression was detected at concentrations as low as 0.22 microM of 3,4-DCA, which was close to the lowest observed effect concentration (0.11 microM) in the 30-day early life stage test. This study therefore indicates that gene expression analysis in DarT is able to reveal mechanistic information and may also be exploited for the development of replacement methods for chronic fish tests.

Establishment of a functional genomics platform for Leifsonia xyli subsp. xyli.

Leifsonia xyli subsp. xyli, the causal agent of ratoon stunting disease in sugarcane, is a xylem-limited, nutritionally fastidious, slow growing, gram-positive coryneform bacterium. Because of the difficulties in growing this bacterium in pure culture, little is known about the molecular mechanisms of pathogenesis. Currently, the genome sequence of L. xyli subsp. xyli is being completed by the Agronomical and Environmental Genomes group from the Organization for Nucleotide Sequencing and Analysis in Brazil. To complement this work, we produced 712 Lxx::Tn4431 transposon mutants and sequenced flanking regions from 383 of these, using a rapid polymerase chain reaction-based approach. Tn4431 insertions appeared to be widespread throughout the L. xyli subsp. xyli genome; however, there were regions that had significantly higher concentrations of insertions. The Tn4431 mutant library was screened for individuals unable to colonize sugarcane, and one noncolonizing mutant was found. The mutant contained a transposon insertion disrupting two open reading frames (ORF), one of which had homology to an integral membrane protein from Mycobacterium leprae. Sequencing of the surrounding regions revealed two operons, pro and cyd, both of which are believed to play roles in disease. Complementation studies were carried out using the noncolonizing Lxx::Tn4431 mutant. The noncolonizing mutant was transformed with a cosmid containing 40 kbp of wild-type sequence, which included the two ORF disrupted in the mutant, and several transformants were subsequently able to colonize sugarcane. However, analysis of each of these transformants, before and after colonization, suggests that they have all undergone various recombinant events, obscuring the roles of these ORF in L. xyli subsp. xyli pathogenesis.

On the relevance of genotoxicity for fish populations I: effects of a model genotoxicant on zebrafish (Danio rerio) in a complete life-cycle test.

Genotoxicity may be detected in surface waters by means of various genotoxicity assays. In order to enable an ecotoxicological assessment of the consequences of such genotoxic potential for fish populations, a complete life-cycle test with zebrafish (Danio rerio) and the model genotoxicant 4-nitroquinoline-1-oxide (NQO) was conducted. Zebrafish (f1) were continuously exposed to NQO (i.e. 0.1, 0.3, 1.1, 2.9, and 14.6 microg/l, respectively) from fertilised eggs until sexual maturity. In addition to reproduction studies in the f1-generation, f2-fish were exposed to NQO during the first 6 weeks of development. Up to 2.9 microg/l NQO, fish did not display differences in survival and growth (P < 0.05). A NQO concentration of 14.6 microg/l, however, was lethal. Female fish exposed to all NQO concentrations up to 2.9 microg/l displayed a significant reduction in egg production (P < 0.05). A mathematical simulation revealed that exposure to weak concentrations of NQO is leading to an elevated extinction risk.

On the relevance of genotoxicity for fish populations II: genotoxic effects in zebrafish (Danio rerio) exposed to 4-nitroquinoline-1-oxide in a complete life-cycle test.

In order to characterize the impact of genotoxic potentials on populations of aquatic organisms in surface waters, zebrafish (Danio rerio) were exposed to the model genotoxicant 4-nitroquinoline-1-oxide (NQO) in a complete life-cycle test. Fish exposed to mean NQO concentrations of 0, 0.1, 0.3, 1.1, and 2.9 microg/l were examined by several genotoxicity assays with different endpoints. Assays included the unscheduled DNA synthesis (UDS) test, the comet assay, the alkaline filter elution, and the micronucleus test. The genotoxicity assays revealed an increasing genotoxicity, ranging from induction of DNA repair (even at the lowest concentration tested) to primary and secondary DNA alterations at higher concentrations of 1.1 and 2.9 microg/l NQO. Whether the lowered reproductivity observed in the life-cycle test is caused by genotoxic pathways of NQO, remains unclear. However, the results indicate a contradiction to an earlier assumption that genotoxicants as found in the environment are likely to not impact natural populations.

Ecotoxicological characterisation and classification of existing chemicals. Examples from the ICCA HPV initiative and comparison with other existing chemicals.

GOAL, SCOPE AND BACKGROUND: In 1998, the International Council of Chemical Associations (ICCA) launched a global initiative to investigate more than 1,000 HPV chemicals (High Production Volume, > or = 1,000 t/a) within the refocused OECD HPV Chemicals Programme. Up to the OECD SIDS Initial Assessment Meeting in April 2004 (SIAM 18) 147 ICCA dossiers (ca. 230 CAS-No) have been assessed based on a harmonised data set. The environmental profile and an ecotoxicological characterisation of these chemicals are presented here. Data for acute aquatic toxicity were correlated among each other, as well as data for fish (LC50, LD50) and rodents (LD50). The data for acute aquatic toxicity are compared with other existing chemicals. METHODS: Data of the ICCA HPV chemicals from the OECD SIAM 11-18 are presented for: log Kow (as an indicator for bioaccumulation potential), biodegradation, acute aquatic toxicity and availability of long-term toxicity data. Correlation analysis was performed with log transformed data and a linear regression model was fitted to the data, if a significant correlation was found. Acute toxicity for fish and acute oral toxicity for rodents were correlated on a molar basis. Acute aquatic toxicity of the chemicals is compared with data from BUA reports 1-234 and a random EINECS sample (Knacker et al. 1995). RESULTS AND DISCUSSION: According to the dossier information, 71 of the 147 ICCA chemicals are not 'readily biodegradable', 21 have a log Kow > or = 3, and 44 are 'toxic' (LC/EC50 < or = 10 mg/L) or 'very toxic' (LC/EC50 < or = 1 mg/L) to aquatic organisms. For 77, only the base set (acute fish, Daphnia and algae) is available, for the rest at least one long-term test (fish or Daphnia) is available and three tests for a mere 14 others. Based on the data presented, the SIAM gives recommendations for Environment and Human Health. 22 chemicals have been identified as a 'candidate for further work' for Environment and 16 for Human Health. The highest correlation coefficient was obtained correlating fish and Daphnia (r2 = 0.79). LC50 (fish) is significantly correlated with LD50 (rodent), but data are widely scattered. The correlation is not improved after transforming LC50 (fish) to LD50 (fish), using BCF QSAR. Based on acute aquatic toxicity, 25.1% of the chemicals from the BUA reports 1-234 are classified as 'very toxic' (LC/EC50 < or = 1 mg/L). This proportion is 2.5-fold higher than the ICCA HPV chemicals and 1.4-fold higher than the random EINECS sample. CONCLUSIONS: Correlation coefficients for aquatic toxicity data are rather uniform (0.57-0.79) compared with literature data, but also the best correlation was observed between fish and Daphnia. Because the scatter around the regression lines is still considerable, simple predictions of ecotoxicity between species are not possible. Correlation of LC50 (fish) and LD50 (rodent) indicates that toxicity is different. Surprisingly, the correlation of fish and rodent toxicity is not improved by transforming LC50 values to internal LD50s. The selection of ICCA chemicals by market significance (production volume) leads to a classification of toxicity, which is more comparable to a random sample of EINECS chemicals than to German BUA chemicals. The latter were chosen for concern (for Environment or Human Health). RECOMMENDATIONS AND OUTLOOK: Of 147 dossiers assessed between SIAM 11-18, ca. 75% were sponsored by the three following countries: Germany (42), USA (37) and Japan (33). The current output is about 50 dossiers per year (70-100 CAS-No), but a trend for an increase of output is noticeable. Industry, national authorities, and OECD work on a further development to speed up the output. The number of chemicals with 'low priority for further work' and the work recommended for the 'candidates' (mainly exposure assessment) indicate that the data presented were adequate for an initial hazard assessment according to OECD requirements. From the ICCA HPV list (n = 880, state of 1999) 44% of the chemicals have data available to cover all SIDS endpoints for Environment and only 33% for Human Health (Allanou et al. 1999). This indicates the importance of the Initiative to provide information on existing chemicals. The authors agree with the expectation "...that the scientific information provided by this global initiative will be considered as an internationally accepted and harmonised basis for further steps of chemicals management." (ICCA 2002 b).

Development of a new screening assay to identify proteratogenic substances using zebrafish danio rerio embryo combined with an exogenous mammalian metabolic activation system (mDarT).

The assessment of teratogenic effects of chemicals is generally performed using in vivo teratogenicity assays, for example, in rats or rabbits. We have developed an in vitro teratogenicity assay using the zebrafish Danio rerio embryo combined with an exogenous mammalian metabolic activation system (MAS), able to biotransform proteratogenic compounds. Cyclophosphamide (CPA) and ethanol were used as proteratogens to test the efficiency of this assay. Briefly, the zebrafish embryos were cocultured at 2 hpf (hours postfertilization) with the test material at varying concentrations, induced male rat liver microsomes and nicotinamide adenine dinucleotide phosphate (reduced) for 60 min at 32 degrees C under moderate agitation in Tris-buffer. The negative control (test material alone) and the MAS control (MAS alone) were incubated in parallel. For each test group, 20 eggs were used for statistical robustness. Afterward fish embryos were transferred individually into 24-well plates filled with fish medium for 48 h at 26 degrees C with a 12-h light cycle. Teratogenicity was scored after 24 and 48 hpf using morphological endpoints. No teratogenic effects were observed in fish embryos exposed to the proteratogens alone, that is, without metabolic activation. In contrast, CPA and ethanol induced abnormalities in fish embryos when coincubated with microsomes. The severity of malformations increased with increasing concentrations of the proteratogens. We conclude that the application of microsomes will improve and refine the D. rerio teratogenicity assay as a predictive and valuable alternative method to screen teratogenic substances.

Sex steroid receptor evolution and signalling in aquatic invertebrates.

In vertebrate reproductive endocrinology sex steroids play a pivotal role via binding to receptors. However, information on the origin and relevance of sex steroids in invertebrates is limited. This review highlights current literature on steroid receptors in aquatic invertebrates and reports on some new findings. It has been shown that invertebrates of the deuterostome clade, such as Acrania and Echinodermata, respond to estrogens and androgens and, at least in Branchiostoma, an estrogen receptor has been cloned. Within the protostomes, most findings are related to aquatic molluscs. Sex steroid receptor-like proteins are abundant in gastropods, bivalves and cephalopods and also sex hormone signalling shows partial similarity to the deuterostomes. In ecdysozoans, however, the impact of sex steroids is still a matter of debate even though there is evidence on the presence of estrogen receptor-like proteins in Crustacea and on physiological effects of estrogens in both Nematoda and Crustacea. Recent findings suggest the presence of an estrogen receptor alpha-like protein of unclear physiological role in Gammarus fossarum (Crustacea). Binding studies revealed the crustacean Hyalella azteca to possess specific binding sites only for androgens but not for estrogens suggesting a possible limitation to functional androgen receptors in this species. Further studies have to be conducted to shed more light into the discussion about the controversy about sex steroid receptors in invertebrates.

Bisphenol A in artificial indoor streams: II. Stress response and gonad histology in Gammarus fossarum (Amphipoda).

The effects of the world wide-distributed chemical bisphenol A (BPA) on the endocrine system of vertebrates have been demonstrated in several studies. Here, we report on the impact of BPA (0, 5, 50 and 500 microg/l nominally, deduced effective concentrations 0, 0.24, 2.4, and 24.1 microg/l, respectively, all at 15 degrees C) on the 70 kD stress protein family (hsp70), the 90 kD stress protein family (hsp90), and gonad histology of the crustacean Gammarus fossarum exposed in artificial indoor streams. The animals were exposed for a maximum of 103 days and samples were taken at the beginning and at days 34, 69 and 103 of the experiment. Exposure to BPA resulted in accelerated maturation of oocytes in females and in a decline in the number and size of early vitellogenic oocytes. The level of hsp90, which plays a pivotal role in vertebrate sex steroid signal transduction, was significantly reduced by BPA. In all five streams, measured parameters did not indicate any captivity stress for a period of 69 days. Beyond this time, the mortality rate and proteotoxic effects, the latter measured by hsp70 expression, were found to be elevated.

DarT: The embryo test with the Zebrafish Danio rerio--a general model in ecotoxicology and toxicology.

The acute fish test is an animal test whose ecotoxicological relevance is worthy of discussion. The primary aim of protection in ecotoxicology is the population and not the individual. Furthermore the concentration of pollutants in the environment is normally not in the lethal range. Therefore the acute fish test covers solely the situation after chemical spills. Nevertheless, acute fish toxicity data still belong to the base set used for the assessment of chemicals. The embryo test with the zebrafish Danio rerio (DarT) is recommended as a substitute for the acute fish test. For validation an international laboratory comparison test was carried out. A summary of the results is presented in this paper. Based on the promising results of testing chemicals and waste water the test design was validated by the DIN-working group "7.6 Fischei-Test". A normed test guideline for testing waste water with fish is available. The test duration is short (48 h) and within the test different toxicological endpoints can be examined. Endpoints from the embryo test are suitable for QSAR-studies. Besides the use in ecotoxicology the introduction as a toxicological model was investigated. Disturbance of pigmentation and effects on the frequency of heart-beat were examined. A further important application is testing of teratogenic chemicals. Based on the results DarT could be a screening test within preclinical studies.

Long-term effects of fenoxycarb on two mayfly species in artificial indoor streams.

The effects of the juvenile hormone analog fenoxycarb (CAS No. 72490-01-8) were investigated in artificial indoor streams. The results from aufwuchs and two mayfly species (Rhithrogena semicolorata and Ephemerella ignita) are presented. Four concentrations ranging from 0.05 to 50 microg/L (with a spacing factor of 10) were tested. Fenoxycarb disappeared rapidly from the water phase (DT(50) approximately 5 days in the highest concentration, less in the other concentrations). Physico-chemical parameters and aufwuchs were not affected by fenoxycarb. The mayfly R. semicolorata, introduced at the start of the experiment, was affected by treatments of 5 and 50 microg/L. For the larvae in the streams a LC(50) of 3.3 microg/L and for the larvae in the enclosures a LC(50) of 2.5 microg/L were calculated. The second species (E. ignita) was introduced 72 days after the application, at which time no fenoxycarb was detectable in the water of the streams (limit of detection of 0.5 ng/L). The emergence of E. ignita was affected in the highest treatment (50 microg/L). Ninety percent of the emerged imagoes showed morphological abnormalities at the abdomen.

Bisphenol-A in artificial indoor streams: I. Fate and effects on aufwuchs.

The disappearance (DT50) from water-phase and effects on aufwuchs of three nominal concentrations (5, 50 and 500 microg/l) of bisphenol-A (BPA) were investigated in artificial indoor streams over a period of 103 days. HPLC was used for analyses of BPA in water. Because of the disappearance of BPA from the water-phase, a pulse dosed exposure in weekly intervals was established. At the beginning of the exposure, a lag-phase of approximately 3-8 days was noted. Afterwards DT50 values (time, when 50% of initial BPA disappeared) were about 1 day with no clear trend to lower values during the experiment. The dynamics of aufwuchs was investigated on artificial substrates (unglazed ceramic tiles) in 14-day intervals and quantified by ash free dry weight (AFDW). As an ecotoxicological endpoint the area under the biomass/time curve (AUC) was calculated for: (a) the absolute AFDW-values and (b) values as percentage of start biomass (value of day-2 set as 100%). The reduction of AUC by 10% (EC10) and 50% (EC50) for absolute values was 11 microg/l (nominal: 38) and 46 microg/l (450), respectively; for values as percentage of start biomass: EC10 20 microg/l (239) and EC50 73 microg/l (806). These values are 20-70-fold lower compared to results from standard algae tests (EbC, 96 h).

A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III.

Rnt1 endoribonuclease, the yeast homolog of RNAse III, plays an important role in the maturation of a diverse set of RNAs. The enzymatic activity requires a conserved catalytic domain, while RNA binding requires the double-stranded RNA-binding domain (dsRBD) at the C-terminus of the protein. While bacterial RNAse III enzymes cleave double-stranded RNA, Rnt1p specifically cleaves RNAs that possess short irregular stem-loops containing 12-14 base pairs interrupted by internal loops and bulges and capped by conserved AGNN tetraloops. Consistent with this substrate specificity, the isolated Rnt1p dsRBD and the 30-40 amino acids that follow bind to AGNN-containing stem-loops preferentially in vitro. In order to understand how Rnt1p recognizes its cognate processing sites, we have defined its minimal RNA-binding domain and determined its structure by solution NMR spectroscopy and X-ray crystallography. We observe a new carboxy-terminal helix following a canonical dsRBD structure. Removal of this helix reduces binding to Rnt1p substrates. The results suggest that this helix allows the Rnt1p dsRBD to bind to short RNA stem-loops by modulating the conformation of helix alpha1, a key RNA-recognition element of the dsRBD.