Caudy AA et al. (2003) Nature "A micrococcal nuclease homologue in RNAi effector complexes."

Caudy AA, Ketting RF, Hammond SM, Hannon GJ, Denli AM, Myers MM, Silva JM, Plasterk RHA, Bathoorn AMP, Tops BBJ

[Nature, 2003]

RNA interference (RNAi) regulates gene expression by the cleavage of messenger RNA, by mRNA degradation and by preventing protein synthesis. These effects are mediated by a ribonucleoprotein complex known as RISC (RNA-induced silencing complex)(1). We have previously identified four Drosophila components (short interfering RNAs1, Argonaute 2 (ref. 2), VIG and FXR3) of a RISC enzyme that degrades specific mRNAs in response to a double-stranded-RNA trigger. Here we show that Tudor-SN (tudor staphylococcal nuclease)-a protein containing five staphylococcal/micrococcal nuclease domains and a tudor domain-is a component of the RISC enzyme in Caenorhabditis elegans, Drosophila and mammals. Although Tudor-SN contains non-canonical active-site sequences, we show that purified Tudor-SN exhibits nuclease activity similar to that of other staphylococcal nucleases. Notably, both purified Tudor-SN and RISC are inhibited by a specific competitive inhibitor of micrococcal nuclease. Tudor-SN is the first RISC subunit to be identified that contains a recognizable nuclease domain, and could therefore contribute to the RNA

Imae R et al. (2010) Mol Biol Cell "Intracellular phospholipase A1 and acyltransferase, which are involved in Caenorhabditis elegans stem cell divisions, determine the sn-1 fatty acyl chain of phosphatidylinositol."

Inoue T, Kimura M, Kanamori T, Kage-Nakadai E, Mitani S, Imae R, Tomioka NH, Arai H

[Mol Biol Cell, 2010]

Phosphatidylinositol (PI), an important constituent of membranes, contains stearic acid as the major fatty acid at the sn-1 position. This fatty acid is thought to be incorporated into PI through fatty acid remodeling by sequential deacylation and reacylation. However, the genes responsible for the reaction are unknown, and consequently, the physiological significance of the sn-1 fatty acid remains to be elucidated. Here, we identified acl-8, -9, and -10, which are closely related to each other, and ipla-1 as strong candidates for genes involved in fatty acid remodeling at the sn-1 position of PI. In both ipla-1 mutants and acl-8 acl-9 acl-10 triple mutants of Caenorhabditis elegans, the stearic acid content of PI is reduced, and asymmetric division of stem cell-like epithelial cells is defective. The defects in asymmetric division of these mutants are suppressed by a mutation of the same genes involved in intracellular retrograde transport, suggesting that ipla-1 and acl genes act in the same pathway. IPLA-1 and ACL-10 have phospholipase A(1) and acyltransferase activity, respectively, both of which recognize the sn-1 position of PI as their substrate. We propose that the sn-1 fatty acid of PI is determined by ipla-1 and acl-8, -9, -10 and crucial for asymmetric divisions.

Mor DE et al. (2019) Mov Disord "The usual suspects, dopamine and alpha-synuclein, conspire to cause neurodegeneration."

Mor DE, Daniels MJ, Ischiropoulos H

[Mov Disord, 2019]

Parkinson's disease (PD) is primarily a movement disorder driven by the loss of dopamine-producing neurons in the substantia nigra (SN). Early identification of the oxidative properties of dopamine implicated it as a potential source of oxidative stress in PD, yet few studies have investigated dopamine neurotoxicity in vivo. The discovery of PD-causing mutations in -synuclein and the presence of aggregated -synuclein in the hallmark Lewy body pathology of PD revealed another important player. Despite extensive efforts, the precise role of -synuclein aggregation in neurodegeneration remains unclear. We recently manipulated both dopamine levels and -synuclein expression in aged mice and found that only the combination of these 2 factors caused progressive neurodegeneration of the SN and an associated motor deficit. Dopamine modified -synuclein aggregation in the SN, resulting in greater abundance of -synuclein oligomers and unique dopamine-induced oligomeric conformations. Furthermore, disruption of the dopamine--synuclein interaction rescued dopaminergic neurons from degeneration in transgenic Caenorhabditis elegans models. In this Perspective, we discuss these findings in the context of known -synuclein and dopamine biology, review the evidence for -synuclein oligomer toxicity and potential mechanisms, and discuss therapeutic implications. 2019 International Parkinson and Movement Disorder Society.

Vandecandelaere I et al. (2014) Pathog Dis "Protease production by Staphylococcus epidermidis and its effect on Staphylococcus aureus biofilms."

Coenye T, Vandecandelaere I, Depuydt P, Nelis HJ

[Pathog Dis, 2014]

Due to the resistance of Staphylococcus aureus to several antibiotics, treatment of S. aureus infections is often difficult. As an alternative to conventional antibiotics, the field of bacterial interference is investigated. Staphylococcus epidermidis produces a serine protease (Esp) which inhibits S. aureus biofilm formation and which degrades S. aureus biofilms. In this study, we investigated the protease production of 114 S. epidermidis isolates, obtained from biofilms on endotracheal tubes (ET). Most of the S. epidermidis isolates secreted a mixture of serine, cysteine and metalloproteases. We found a link between high protease production by S. epidermidis and the absence of S. aureus in ET biofilms obtained from the same patient. Treating S. aureus biofilms with the supernatant (SN) of the most active protease producing S. epidermidis isolates resulted in a significant biomass decrease compared to untreated controls, while the number of metabolically active cells was not affected. The effect on the biofilm biomass was mainly due to serine proteases. Staphylococcus aureus biofilms treated with the SN of protease producing S. epidermidis were thinner with almost no extracellular matrix. An increased survival of Caenorhabditis elegans, infected with S. aureus Mu50, was observed when the SN of protease positive S. epidermidis was added.

Gomez-Orte E et al. (2019) PLoS Genet "Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes."

Gomez-Orte E, de Toro M, Saenz-Narciso B, Cabello J, Zheleva A, Gastaca I, Lopez R, Nilsen H, Ezcurra B, Schnabel R, Sacristan MP

[PLoS Genet, 2019]

Gene expression is generally regulated by recruitment of transcription factors and RNA polymerase II (RNAP II) to specific sequences in the gene promoter region. The Integrator complex mediates processing of small nuclear RNAs (snRNAs) as well as the initiation and release of paused RNAP II at specific genes in response to growth factors. Here we show that in C. elegans, disruption of the Integrator complex leads to transcription of genes located downstream of the snRNA loci via a non-conventional transcription mechanism based on the lack of processing of the snRNAs. RNAP II read-through generates long chimeric RNAs containing snRNA, the intergenic region and the mature mRNA of the downstream gene located in sense. These chimeric sn-mRNAs remain as untranslated long non-coding RNAs, in the case of U1- and U2-derived sn-mRNAs, but can be translated to proteins in the case of SL-derived sn-mRNAs. The transcriptional effect caused by disruption of the Integrator complex is not restricted to genes located downstream of the snRNA loci but also affects key regulators of signal transduction such as kinases and phosphatases. Our findings highlight that these transcriptional alterations may be behind the correlation between mutations in the Integrator complex and tumor transformation.

Tanaka T et al. (1999) Eur J Biochem "Biosynthesis of 1,2-dieicosapentaenoyl-sn-glycero-3-phosphocholine in Caenorhabditis elegans."

Takimoto T, Yamamoto D, Matsuura F, Satouchi K, Tanaka T, Tanaka K, Izuwa S

[Eur J Biochem, 1999]

Previously, we showed that lowering the growth temperature increased the level of eicosapentaenoic acid (EPA) in the phosphatidylcholine (PtdCho) of Caenorhabditis elegans. In this study, we investigated the molecular species composition of PtdCho of C. elegans, with an emphasis on EPA-containing species. C. elegans contained a substantial amount of 1,2-dipolyunsaturated fatty acid-containing PtdCho (1,2-diPUFA-PtdCho) species, such as arachidonic acid/EPA and EPA/EPA, which are unusual phospholipids in higher animals. The EPA/EPA-PtdCho content was significantly increased in C. elegans grown at a low temperature. To examine the possibility that the acyltransferase activity involved in the remodeling of phospholipids accounts for the production of 1,2-diPUFA-PtdCho, we investigated the substrate specificity of this enzyme in C. elegans and found that it did not exhibit a preference for saturated fatty acid for acylation to the sn-1 position of PtdCho. The efficacy of the esterification of EPA to the sn-1 position was almost equal to that of stearic acid. The lack of preference for a saturated fatty acid for acylation to the sn-1 position of PtdCho is thought to result in the existence of the unusual 1,2-diEPA-PtdCho in C. elegans.

Tripathi V et al. (2015) J Biomol Struct Dyn "Universal full-length nucleosome mapping sequence probe."

Trifonov EN, Salih B, Tripathi V

[J Biomol Struct Dyn, 2015]

For the computational sequence-directed mapping of the nucleosomes, the knowledge of the nucleosome positioning motifs - 10-11 base long sequences - and respective matrices of bendability, is not sufficient, since there is no justified way to fuse these motifs in one continuous nucleosome DNA sequence. Discovery of the strong nucleosome (SN) DNA sequences, with visible sequence periodicity allows derivation of the full-length nucleosome DNA bendability pattern as matrix or consensus sequence. The SN sequences of three species (A. thaliana, C. elegans, and H. sapiens) are aligned (512 sequences for each species), and long (115 dinucleotides) matrices of bendability derived for the species. The matrices have strong common property - alternation of runs of purine-purine (RR) and pyrimidine-pyrimidine (YY) dinucleotides, with average period 10.4 bases. On this basis the universal [R,Y] consensus of the nucleosome DNA sequence is derived, with exactly defined positions of respective penta- and hexamers RRRRR, RRRRRR, YYYYY, and YYYYYY.

Mor DE et al. (2018) J Exp Neurosci "The Convergence of Dopamine and -Synuclein: Implications for Parkinson's Disease."

Mor DE, Ischiropoulos H

[J Exp Neurosci, 2018]

In Parkinson's disease (PD), the loss of dopamine-producing neurons in the substantia nigra (SN) leads to severe motor impairment, and pathological inclusions known as Lewy bodies contain aggregated -synuclein protein. The relationship of -synuclein aggregation and dopaminergic degeneration is unclear. This commentary highlights a recent study showing that the interaction of -synuclein with dopamine may be an important mechanism underlying disease. Elevating dopamine levels in mice expressing human -synuclein with the A53T familial PD mutation recapitulated key features of PD, including progressive neurodegeneration of the SN and decreased ambulation. The toxicity of dopamine was dependent on -synuclein expression; hence, raising dopamine levels in nontransgenic mice did not result in neuronal injury. This interaction is likely mediated through soluble -synuclein oligomers, which had modified conformations and were more abundant as a result of dopamine elevation in the mouse brain. Specific mutation of the dopamine interaction motif in the C-terminus of -synuclein rescued dopamine neurons from degeneration in<i>Caenorhabditis elegans</i>models. Here, these findings are discussed, particularly regarding possible mechanisms of oligomer toxicity, relevance of these models to sporadic and autosomal recessive forms of PD, and implications for current PD treatment.

Asagoshi K et al. (2012) Nucleic Acids Res "Single-nucleotide base excision repair DNA polymerase activity in C. elegans in the absence of DNA polymerase ."

Freedman JH, Braithwaite EK, Santana-Santos L, Van Houten B, Asagoshi K, Lehmann W, Prasad R, Wilson SH

[Nucleic Acids Res, 2012]

The base excision DNA repair (BER) pathway known to occur in Caenorhabditis elegans has not been well characterized. Even less is known about the DNA polymerase (pol) requirement for the gap-filling step during BER. We now report on characterization of in vitro uracil-DNA initiated BER in C. elegans. The results revealed single-nucleotide (SN) gap-filling DNA polymerase activity and complete BER. The gap-filling polymerase activity was not due to a DNA polymerase (pol ) homolog, or to another X-family polymerase, since computer-based sequence analyses of the C. elegans genome failed to show a match for a pol -like gene or other X-family polymerases. Activity gel analysis confirmed the absence of pol in the C. elegans extract. BER gap-filling polymerase activity was partially inhibited by both dideoxynucleotide and aphidicolin. The results are consistent with a combination of both replicative polymerase(s) and lesion bypass/BER polymerase pol contributing to the BER gap-filling synthesis. Involvement of pol was confirmed in experiments with extract from pol null animals. The presence of the SN BER in C. elegans is supported by these results, despite the absence of a pol -like enzyme or other X-family polymerase.

Imae R et al. (2012) J Lipid Res "LYCAT, a homologue of C. elegans acl-8, acl-9, and acl-10, determines the fatty acid composition of phosphatidylinositol in mice."

Arai H, Imae R, Kono N, Uchida Y, Ohba Y, Sasaki T, Nakanishi H, Nakasaki Y, Inoue T, Mitani S

[J Lipid Res, 2012]

Mammalian phosphatidylinositol (PI) has a unique fatty acid composition in that 1-stearoyl-2-arachidonoyl species is predominant. This fatty acid composition is formed through fatty acid remodeling by sequential deacylation and reacylation. We recently identified three Caenorhabditis elegans acyltransferases (ACL-8, ACL-9, and ACL-10) that incorporate stearic acid into the sn-1 position of PI. Mammalian LYCAT, which is the closest homolog of ACL-8, ACL-9, and ACL-10, was originally identified as a lysocardiolipin acyltransferase by an in vitro assay and was subsequently reported to possess acyltransferase activity toward various anionic lysophospholipids. However, the in vivo role of mammalian LYCAT in phospholipid fatty acid metabolism has not been well elucidated. In this study, we generated LYCAT-deficient mice and demonstrated that LYCAT determined the fatty acid composition of PI in vivo. LYCAT-deficient mice were outwardly healthy and fertile. In the mice, stearoyl-CoA acyltransferase activity toward the sn-1 position of PI was reduced, and the fatty acid composition of PI, but not those of other major phospholipids, was altered. Furthermore, expression of mouse LYCAT rescued the phenotype of C. elegans acl-8 acl-9 acl-10 triple mutants. Our data indicate that LYCAT is a determinant of PI molecular species and its function is conserved in C. elegans and mammals.