Stadler M et al. (2011) RNA "Wobble base-pairing slows in vivo translation elongation in metazoans."

Fire A, Stadler M

[RNA, 2011]

In the universal genetic code, most amino acids can be encoded by multiple trinucleotide codons, and the choice among available codons can influence position-specific translation elongation rates. By using sequence-based ribosome profiling, we obtained transcriptome-wide profiles of in vivo ribosome occupancy as a function of codon identity in Caenorhabditis elegans and human cells. Particularly striking in these profiles was a universal trend of higher ribosome occupancy for codons translated via G:U wobble base-pairing compared with synonymous codons that pair with the same tRNA family using G:C base-pairing. These data support a model in which ribosomal translocation is slowed at wobble codon positions.

Stadler M et al. (2013) PLoS Genet "Conserved translatome remodeling in nematode species executing a shared developmental transition."

Stadler M, Fire A

[PLoS Genet, 2013]

Nematodes of the genus Caenorhabditis enter a developmental diapause state after hatching in the absence of food. To better understand the relative contributions of distinct regulatory modalities to gene expression changes associated with this developmental transition, we characterized genome-wide changes in mRNA abundance and translational efficiency associated with L1 diapause exit in four species using ribosome profiling and mRNA-seq. We found a strong tendency for translational regulation and mRNA abundance processes to act synergistically, together effecting a dramatic remodeling of the gene expression program. While gene-specific differences were observed between species, overall translational dynamics were broadly and functionally conserved. A striking, conserved feature of the response was strong translational suppression of ribosomal protein production during L1 diapause, followed by activation upon resumed development. On a global scale, ribosome footprint abundance changes showed greater similarity between species than changes in mRNA abundance, illustrating a substantial and genome-wide contribution of translational regulation to evolutionary maintenance of stable gene expression.

Stadler M et al. (1994) Planta Med "Nematicidal activities of two phytoalexins from Taverniera abyssinica."

Anke H, Dagne E, Stadler M

[Planta Med, 1994]

The traditional analgesic and antipyretic Ethiopian drug ''Dingetegna'' is made of dried root material of Taverniera abyssinica A. Rich (Leguminosae). In a screening for nematicidal natural products, ''Dingetegna'' extracts showed strong nematicidal activities towards C. elegans. In the following, medicarpin and 4-hydroxymedicarpin were isolated as nematicidal constituents from the extracts. In a microwell plate assay for nematicidal activity, both compounds exhibited an LDS, of 25 mu g/ml towards C. elegans. Beside these nematicidal effects, weak cytotoxic and antimicrobial activities were observed. In addition, both compounds inhibited oxygen consumption of axenically grown C. elegans, L 1210 cells, and filamentous fungi. Respiration in sensitive bacteria was not affected. In L1210 cells, the incorporation of precursors into macromolecules was affected in the presence of glucose, indicating that inhibition of respiration is not the only target site of the compounds.

Stadler M et al. (2006) Mycol Res "Changes in secondary metabolism during stromatal ontogeny of Hypoxylon fragiforme."

Quang DN, Asakawa Y, Tomita A, Stadler M, Hashimoto T

[Mycol Res, 2006]

Stromata of Hypoxylon fragiforme were studied during the vegetation period by hplc profiling, revealing changes in the composition during stromatal development. Cytochalasin H and two new cytochalasins named fragiformins A-B were identified as major constituents of the young, maturing stromata, whereas mature, ascogenous material yielded large amounts of mitorubrin-type azaphilones. The above compounds, further cytochalasins from Xylariaceae and other fungi, and additional azaphilones of the mitorubrin type were assayed for their nematicidal effects against Caenorhabditis elegans and their antimicrobial activities against Bacillus subtilis, Yarrowia lipolytica, and various filamentous fungi. The results confirmed data in the literature on broad-spectrum non-selective activities of azaphilones and cytochalasins in biological systems. Most interestingly, laboratory cultures of the above Hypoxylon spp. mainly produced dihydroisocoumarin derivatives and were found devoid of mitorubrins and cytochalasins. These rather drastic changes in the secondary metabolism of H. fragiforme and the above biological activities are discussed in relation to the possible biological functions of secondary metabolites (extrolites) in the Hypoxyloideae.

Stadler M et al. (1994) Planta Med "Fatty acids and other compounds with nematicidal activity from cultures of Basidiomycetes."

Sterner O, Mayer A, Anke H, Stadler M

[Planta Med, 1994]

In a screening for nematicidal activities in cultures of Basidiomycetes, cultures of Pleurotus pulmonarius and Hericium coralloides exhibited toxic effects towards the saprophytic nematode Caenorhabditis elegans. Subsequently S-coriolic acid (1), linoleic acid (2), p-anisaldehyde (3), p-anisyl alcohol (4), 1-(4-methoxyphenyl)-1,2-propanediol (5), and 2-hydroxy-(4'-methoxy)-propiophenone (6) were isolated from submerged cultures of P. pulmonarius. All compounds showed nematicidal activities towards C. elegans. The most active compounds were 1 and 2 with LD50 values between 5 and 10 ppm. Compounds 1, 4, and 5 have not been previously isolated from higher fungi, 6 is a new natural product. From cultures of H. coralloides, which exhibited both repellant and nematicidal effects, a nematicidal fatty acid mixture was obtained, containing linoleic acid, oleic acid, and palmitic acid as its main components.

Stadler M et al. (2012) Genome Res "Contributions of mRNA abundance, ribosome loading, and post- or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets."

Artiles K, Fire A, Pak J, Stadler M

[Genome Res, 2012]

miRNAs are post-transcriptional regulators of gene activity that reduce protein accumulation from target mRNAs. Elucidating precise molecular effects that animal miRNAs have on target transcripts has proven complex, with varied evidence indicating that miRNA regulation may produce different molecular outcomes in different species, systems, and/or physiological conditions. Here we use high-throughput ribosome profiling to analyze detailed translational parameters for five well-studied targets of miRNAs that regulate C. elegans developmental timing. For two targets of the miRNA lin-4 (lin-14 and lin-28), functional down-regulation was associated with decreases in both overall mRNA abundance and ribosome loading; however, these changes were of substantially smaller magnitude than corresponding changes observed in protein abundance. For three functional targets of the let-7 miRNA family for which down-regulation is critical in temporal progression of the animal (daf-12, hbl-1, and lin-41), we observed only modest changes in mRNA abundance and ribosome loading. lin-41 provides a striking example in that populations of ribosome-protected fragments from this gene remained essentially unchanged during the L3-L4 time interval when lin-41 activity is substantially down-regulated by let-7. Spectra of ribosomal positions were also examined for the five lin-4 and let-7 target mRNAs as a function of developmental time, with no indication of miRNA-induced ribosomal drop-off or significant pauses in translation. These data are consistent with models in which physiological regulation by this set of C. elegans miRNAs derives from combinatorial effects including suppressed recruitment/activation of translational machinery, compromised stability of target messages, and post- or peri-translational effects on lifetimes of polypeptide products.

Wypijewska A et al. (2012) Biochemistry "7-methylguanosine diphosphate (m(7)GDP) is not hydrolyzed but strongly bound by decapping scavenger (DcpS) enzymes and potently inhibits their activity."

Wypijewska A, Darzynkiewicz E, Davis RE, Jemielity J, Bojarska E, Lukaszewicz M, Stepinski J

[Biochemistry, 2012]

Decapping scavenger (DcpS) enzymes catalyze the cleavage of a residual cap structure following 3' 5' mRNA decay. Some previous studies suggested that both m(7)GpppG and m(7)GDP were substrates for DcpS hydrolysis. Herein, we show that mononucleoside diphosphates, m(7)GDP (7-methylguanosine diphosphate) and m(3)(2,2,7)GDP (2,2,7-trimethylguanosine diphosphate), resulting from mRNA decapping by the Dcp1/2 complex in the 5' 3' mRNA decay, are not degraded by recombinant DcpS proteins (human, nematode, and yeast). Furthermore, whereas mononucleoside diphosphates (m(7)GDP and m(3)(2,2,7)GDP) are not hydrolyzed by DcpS, mononucleoside triphosphates (m(7)GTP and m(3)(2,2,7)GTP) are, demonstrating the importance of a triphosphate chain for DcpS hydrolytic activity. m(7)GTP and m(3)(2,2,7)GTP are cleaved at a slower rate than their corresponding dinucleotides (m(7)GpppG and m(3)(2,2,7)GpppG, respectively), indicating an involvement of the second nucleoside for efficient DcpS-mediated digestion. Although DcpS enzymes cannot hydrolyze m(7)GDP, they have a high binding affinity for m(7)GDP and m(7)GDP potently inhibits DcpS hydrolysis of m(7)GpppG, suggesting that m(7)GDP may function as an efficient DcpS inhibitor. Our data have important implications for the regulatory role of m(7)GDP in mRNA metabolic pathways due to its possible interactions with different cap-binding proteins, such as DcpS or eIF4E.

O'Connell EM et al. (2015) J Infect Dis "Targeting Filarial Abl-like Kinases: Orally Available, Food and Drug Administration-Approved Tyrosine Kinase Inhibitors Are Microfilaricidal and Macrofilaricidal."

Nutman TB, O'Connell EM, Bennuru S, Steel C, Dolan MA

[J Infect Dis, 2015]

BACKGROUND: Elimination of onchocerciasis and lymphatic filariasis is targeted for 2020. Given the coincident Loa loa infections in Central Africa and the potential for drug resistance development, the need for new microfilaricides and macrofilaricides has never been greater. With the genomes of L. loa, Onchocerca volvulus, Wuchereria bancrofti, and Brugia malayi available, new drug targets have been identified. METHODS: The effects of the tyrosine kinase inhibitors imatinib, nilotinib, and dasatinib on B. malayi adult males, adult females, L3 larvae, and microfilariae were assessed using a wide dose range (0-100 M) in vitro. RESULTS: For microfilariae, median inhibitory concentrations (IC50 values) on day 6 were 6.06 M for imatinib, 3.72 M for dasatinib, and 81.35 M for nilotinib; for L3 larvae, 11.27 M, 13.64 M, and 70.98 M, respectively; for adult males, 41.6 M, 3.87 M, and 68.22 M, respectively; and for adult females, 42.89 M, 9.8 M, and >100 M, respectively. Three-dimensional modeling suggests how these tyrosine kinase inhibitors bind and inhibit filarial protein activity. CONCLUSIONS: Given the safety of imatinib in humans, plans are underway for pilot clinical trials to assess its efficacy in patients with filarial infections.

Anke H et al. (1995) Canadian Journal of Botany "Secondary metabolites with nematicidal and antimicrobial activity from nematophagous fungi and Ascomycetes."

Stadler M, Mayer A, Anke H, Sterner O

[Canadian Journal of Botany, 1995]

Screening of nematode-trapping fungi for antimicrobial and nematicidal activities gave three new antimicrobial metabolites from cultures of five Arthrobotrys strains. The compounds exhibited no nematicidal activities towards Caenorhabditis elegans and Meloidogyne incognita. From trap-forming submerged cultures of Arthrobotrys conoides, linoleic acid was isolated as a nematicidal principle. Its production increased with the number of traps formed in both Arthrobotrys oligospora and Arthrobotrys conoides. Nematoctonus robustus and Nematoctonus concurrens produced pleurotin, dihydropleurotinic acid, and leucopleurotin, metabolites previously isolated from cultures of Hohenbuehelia species, suggesting that the same biosynthetic pathways function in both the teleomorph and anamorph. Several strains of Ascomycetes had nematicidal activities; linoleic acid was responsible for the activity in cultures of a Chlorosplenium species, 14-epicochlioquinone B in cultures of Neobulgaria pura, and two naphthalenes derived from the melanin biosynthetic pathway in Daldinia concentrica. 5-Pentyl-2-furaldehyde, previously known as a metabolite from a Basidiomycete, was produced by an unidentified Australian Ascomycete. More than 30 mostly new metabolites have been isolated from cultures of Lachnum papyraceum, many being chlorinated. Under different conditions the fungus incorporated bromine instead of chlorine.

Wood WB (1976) Worm Breeder's Gazette "maternal effects among ts zygote-defective (zyg) mutants."

Wood WB

[Worm Breeder's Gazette, 1976]

We have studied maternal effects in 23 zyg ts mutants to estimate the times of expression of genes whose products are required in embryogenesis. We have used the following three tests, called arbitrarily A, B, and C. A test: Heterozygous (m/+) L4's are shifted to 25 C and allowed to self-fertilize. If 100% of their eggs yield larvae (25% of which express the mutant phenotype as adults), then the mutant is scored as maternal (M). If 25% of the F1 eggs fail to hatch, then the mutant is scored as non-maternal (N). An M result indicates that expression of the + allele in the parent allows m/m zygotes to hatch and grow to adulthood. A result of N indicates the opposite: that the + allele must be expressed in the zygote for hatching to occur. Out of 23 zyg mutants tested, 3 were scored N and 20 were scored M in the A test. Therefore, for most of the genes defined by these mutants, expression in the parent is sufficient for zygote survival, even if the gene is not expressed in the zygote. B test: Homozygous (m/m) hermaphrodites reared at 25 C are mated with N2 (+/+) males. If eggs fail to hatch at 25 C, but mated hermaphrodites shifted to 16 C produce cross progeny to give proof of mating, then the mutant is scored M. If cross progeny appear in the 25 C mating, then the mutant is scored N. An M result indicates that expression of the + allele in the zygote is not sufficient to allow m/+ progeny of an m/m hermaphrodite to survive. Conversely an N result indicates either that zygotic expression of the + allele is sufficient for survival, or that a sperm function or factor needed for early embryogenesis can be supplied paternally (see C test below). Out of the 23 zyg mutants tested, 11 were scored M and 12 were scored N. The combined results of A and B tests and their simplest interpretation are as follows. Ten mutants are M,M; the genes defined by these mutants must be expressed in the hermaphrodite parent for the zygote to survive. Ten mutants are M,N; these genes can be expressed either in the parent or in the zygote. Two mutants are N,N; these genes must be expressed in the zygote. One mutant is N,M; this gene must be expressed both in the maternal parent and in the zygote. C test: Homozygous (m/m) hermaphrodites reared at 25 C are mated with heterozygous (m/+) males. If rescue by a +/+ male in the B test depends on the + allele, then only half the cross progeny zygotes of a C test mating (m/+ male x m/m hermaphrodite) should survive. However, if rescue depends on a function or cytoplasmic component from the male sperm, then all the cross progeny zygotes in a C test should survive. Of the 10 M,N mutants, 6 have been C tested; one exhibited paternal rescue independent of the + allele. The A and B tests also were carried out on 16 mutants that arrest before the L3 molt (acc mutants). In the A test on 2 of these mutants, all m/m progeny of m/+ parents grew to adulthood at 25 C. Therefore, parental contributions are sufficient to overcome a progeny mutational block as late as the L2 stage. All 16 acc mutants scored N in the B test.