Jones CI et al. (2012) Wiley Interdiscip Rev RNA "The 5' 3' exoribonuclease XRN1/Pacman and its functions in cellular processes and development."

Zabolotskaya MV, Newbury SF, Jones CI

[Wiley Interdiscip Rev RNA, 2012]

XRN1 is a 5' 3' processive exoribonuclease that degrades mRNAs after they have been decapped. It is highly conserved in all eukaryotes, including homologs in Drosophila melanogaster (Pacman), Caenorhabditis elegans (XRN1), and Saccharomyces cerevisiae (Xrn1p). As well as being a key enzyme in RNA turnover, XRN1 is involved in nonsense-mediated mRNA decay and degradation of mRNAs after they have been targeted by small interfering RNAs or microRNAs. The crystal structure of XRN1 can explain its processivity and also the selectivity of the enzyme for 5' monophosphorylated RNA. In eukaryotic cells, XRN1 is often found in particles known as processing bodies (P bodies) together with other proteins involved in the 5' 3' degradation pathway, such as DCP2 and the helicase DHH1 (Me31B). Although XRN1 shows little specificity to particular 5' monophosphorylated RNAs in vitro, mutations in XRN1 in vivo have specific phenotypes suggesting that it specifically degrades a subset of RNAs. In Drosophila, mutations in the gene encoding the XRN1 homolog pacman result in defects in wound healing, epithelial closure and stem cell renewal in testes. We propose a model where specific mRNAs are targeted to XRN1 via specific binding of miRNAs and/or RNA-binding proteins to instability elements within the RNA. These guide the RNA to the 5' core degradation apparatus for controlled degradation.

Hatanaka R et al. (2024) Genetics "The impact of differential transposition activities of autonomous and non-autonomous hAT transposable elements on genome architecture and gene expression in Caenorhabditis inopinata."

Tamagawa K, Haruta N, Sugimoto A, Hatanaka R

[Genetics, 2024]

Transposable elements (TEs) are DNA sequences capable of moving within genomes and significantly influence genomic evolution. The nematode Caenorhabditis inopinata exhibits a much higher TE copy number than its sister species, C. elegans. In this study, we identified a novel autonomous TE belonging to the hAT superfamily from a spontaneous TE-insertion mutant in C. inopinata and named this transposon Ci-hAT1. Further bioinformatic analyses uncovered three additional autonomous hAT elements-Ci-hAT2, Ci-hAT3, and Ci-hAT4-along with over 1,000 copies of two non-autonomous miniature inverted-repeat transposable elements (MITEs), mCi-hAT1 and mCi-hAT4, likely derived from Ci-hAT1 and Ci-hAT4 through internal deletion. We tracked at least three sequential transpositions of Ci-hAT1 over several years. However, the transposition rates of the other three autonomous hAT elements were lower, suggesting varying activity levels. Notably, the distribution patterns of the two MITE families differed significantly: mCi-hAT1 was primarily located in the chromosome arms, a pattern observed in the TEs of other Caenorhabditis species, whereas mCi-hAT4 was more evenly distributed across chromosomes. Additionally, interspecific transcriptome analysis indicated that C. inopinata genes with upstream or intronic these MITE insertions tend to be more highly expressed than their orthologous genes in C. elegans. These findings highlight the significant role of de-silenced TEs in driving the evolution of genomes and transcriptomes, leading to species-specific genetic diversity.

Holtzman EJ et al. (1998) Am J Physiol "Cloning, characterization, and gene organization of K-Cl cotransporter from pig and human kidney and C. elegans."

Dunham PB, Logue PJ, Kumar S, Holtzman EJ, Faaland CA, Waldman J, Ricken G, Erickson SJ, Warner F

[Am J Physiol, 1998]

We isolated and characterized the cDNAs far the human, pig, and Caenorhabditis elegans K-CI cotransporters. The pig and human homologs are 94% identical and contain 1,085 and 1,086 amino acids, respectively. The deduced protein of the C. elegans K-CI cotransporter clone (CE-KCC1) contains 1,003 amino acids. The mammalian K-CI cotransporters share similar to 45% similarity with CE-KCC1. Hydropathy analyses of the three clones indicate typical KCC topology patterns with 12 transmembrane segments, large extracellular loops between transmembrane domains 5 and 6 (unique to KCC), and large COOH-terminal domains. Human KCC1 is widely expressed among various tissues. This KCC1 gene spans 23 kb and is organized in 24 exons, whereas the CE-KCC1 gene spans 3.5 kb and contains ID exons. Transiently and stably transfected human embryonic kidney cells (HEK-293) expressing the human, pig, and C. elegans K-Cl cotransporter fulfilled two (pig) or five (human and C. elegans) criteria for increased expression of the K-Cl cotransporter. The criteria employed were basal K-CI cotransport; stimulation of cotransport by swelling, N-ethylmaleimide, staurosporine, and reduced cell Mg concentration; and secondary stimulation of Na-K-CI cotransport.

Iakoubov L et al. (2013) PLoS One "A common copy number variation (CNV) polymorphism in the CNTNAP4 gene: association with aging in females."

Puzianowska-Kuznicka M, Szwed M, Iakoubov L, Duan Z, Mossakowska M, Sesti F

[PLoS One, 2013]

BACKGROUND: Aging is a biological process strongly determined by genetics. However, only a few single nucleotide polymorphisms (SNPs) have been reported to be consistently associated with aging. While investigating whether copy number variations (CNVs) could fill this gap, we focused on CNVs that have not been studied in previous SNP-based searches via tagging SNPs. METHODS: TaqMan qPCR assays were developed to quantify 20 common CNVs in 222 senior American Caucasians in order to reveal possible association with longevity. The replication study was comprised of 1283 community-dwelling senior European Caucasians. Replicated CNVs were further investigated for association with healthy aging and aging-related diseases, while association with longevity was additionally tested in Caenorhabditis elegans. RESULTS: In the discovery study of 80 vs.<80 years old seniors, a homozygous intronic CNV deletion in the CNTNAP4 gene was inversely associated with survival to the age of 80 (OR=0.51, 95%CI 0.29-0.87, p=0.015 before correction for multiple testing). After stratification by sex, association remained significant in females (OR=0.41, 95%CI 0.21-0.77, p=0.007), but not in males (OR=0.97, 95%CI 0.33-2.79, p=1). The finding was validated in a replication study (OR=0.66, 95%CI 0.48-0.90, p=0.011 for females). CNTNAP4 association with longevity was supported by a marked 25% lifespan change in C. elegans after knocking down the ortholog gene. An inverse association of the CNV del/del variant with female healthy aging was observed (OR=0.39, 95%CI 0.19-0.76, p=0.006). A corresponding positive association with aging-related diseases was revealed for cognitive impairment (OR=2.17, 95%CI 1.11-4.22, p=0.024) and, in independent studies, for Alzheimer's (OR=4.07, 95%CI 1.17-14.14, p=0.036) and Parkinson's (OR=1.59, 95%CI 1.03-2.42, p=0.041) diseases. CONCLUSION: This is the first demonstration for association of the CNTNAP4 gene and one of its intronic CNV polymorphisms with aging. Association with particular aging-related diseases awaits replication and independent validation.

Lindblade KA et al. (2007) Am J Trop Med Hyg "Elimination of Onchocercia volvulus transmission in the Santa Rosa focus of Guatemala."

Richards FO, Unnasch TR, Catu E, Lindblade KA, Zea-Flores G, Castro J, Richards J, Punkosdy GA, Porter CH, Cruz-Ortiz N, Arana B, Dominguez A, Rizzo N, Oliva O, Sauerbrey M

[Am J Trop Med Hyg, 2007]

To eliminate transmission of Onchocerca volvulus, semiannual mass treatment with ivermectin (Mectizan; donated by Merck & Co) has been underway in Guatemala since 2000. We applied the 2001 World Health Organization (WHO) elimination criteria in the Santa Rosa focus of onchocerciasis transmission in Guatemala (10,923 persons at risk). No evidence of parasite DNA was found in 2,221 Simulium ochraceum vectors (one-sided 95% confidence interval [CI], 0-0.086%), and no IgG4 antibody positives to recombinant antigen OV16 were found in a sample of 3,232 school children (95% CI, 0-0.009%). We also found no evidence of microfilariae in the anterior segment of the eye in 363 area residents (95% CI, 0-0.08%). Our interpretation of these data, together with historical information, suggest that transmission of O. volvulus is permanently interrupted in Santa Rosa and that ivermectin treatments there can be halted.

Rodriguez-Perez MA et al. (2010) Am J Trop Med Hyg "Lack of active Onchocerca volvulus transmission in the northern Chiapas focus of Mexico."

Pena-Flores GP, Prado-Velasco G, Dominguez-Vazquez A, Morales-Castro AL, Rodriguez-Perez MA, Orozco-Algarra ME, Unnasch TR, Richards F

[Am J Trop Med Hyg, 2010]

The northern Chiapas onchocerciasis focus has undergone 11 years of ivermectin mass treatment. No evidence of microfilariae in the cornea and/or anterior chamber of the eye or in skin snips was seen in residents examined in 2006 in two sentinel communities (upper limit of the 95% confidence interval [UL 95% CI] = 0.5% and 0.3%, respectively). In children 10 and under, 0 of 305 were found to harbor antibodies to Ov16, a marker of parasite exposure; 0 of 4,400 Simulium ochraceum s.l. collected in 2005 contained parasite DNA, giving an UL 95% CI for the infective rate of 0.9/2,000, and an UL 95% CI of the seasonal transmission potential of 1.2 L3/person. These data, assumed to be representative of the focus as a whole, suggest that there is no ongoing transmission of Onchocerca volvulus in the northern Chiapas focus. Community-wide treatments with ivermectin were halted in 2008, and a post-treatment surveillance phase was initiated.

Kuwabara PE (2007) Dev Cell "A complex solution to a sexual dilemma."

Kuwabara PE

[Dev Cell, 2007]

The C. elegans male sex-determining protein, FEM-1, has been identified as a substrate recognition subunit of a Cullin-2 ubiquitin ligase complex. This complex controls the level of TRA-1A, a Ci/Gli homolog and master regulator of sex determination, by ubiquitin-mediated proteolysis.

Boos, J.R. et al. (2019) International Worm Meeting "MitoNEET as a therapeutic target to treat neural circuit decline in Alzheimer's Disease."

Boos, J.R., Geldenhuys, W.J., Saralkar, P.

[International Worm Meeting, 2019]

MitoNEET (CISD1) is a dimeric iron-sulfur mitochondrial protein located on the outer mitochondrial membrane and is believed to be a key regulator in mitochondrial function. MitoNEET contains a ferredoxin cluster binding site, serving as a potential target for drugs. Previous research has suggested that mitoNEET is protective against the formation of reactive oxidative species (ROS) via the regulation of mitochondrial dysfunction and oxidative stress. In recent years, ROS-induced inflammation as a result from mitochondrial dysfunction and oxidative stress have shown to be additional contributing factors towards the progression of Alzheimer's Disease (AD) in addition to the traditional extraneuronal amyloid plaques and intraneuronal neurofibrillary tangles hypotheses. Our aims of this study are to elucidate the effects of mitoNEET as a therapeutic target throughout the progression of AD using a thiazolidinedione class compound we have synthesized (CI-987) and has shown to bind to the ferredoxin cluster binding site of mitoNEET. To examine the effects of CI-987, we used a transgenic AD strain of C. elegans that expresses the extraneuronal A?42 peptide, CL2355, and its wild-type control, CL2122. Both strains were divided into one of three treatment groups: 1) OP50 alone, 2) OP50+vehicle (DMSO), and 3) OP50+100?M CI-987. We assayed sensorimotor, chemosensory, and learning and memory neural circuit function throughout the lifespan in both strains. In this study, we found that treatment with CI-987 slowed the progression of neural circuit decline in normal aging via the CL2122 strain and also throughout the progression of AD via the CL2355 strain. We observed that treating the CL2355 strain with CI-987 showed to be effective in treating early and middle stages of AD neural circuit decline. Furthermore, CL2355 treated with CL2355 produced neural circuit behaviors similar to the CL2122 group treated with OP50. Unfortunately, during the later stages of AD, the promising effects of CI-987 were eventually not enough to combat the neurodegenerative effects as the disease progressed. While the outcomes of this study have shed light on the role of mitoNEET as a therapeutic target throughout the progression of AD and provided an initial foundation for cross-translational studies treating other animal models with CI-987, the need for developing therapeutics that target the neural circuit deficits during in the later stages of AD are still needed.

Tetsuya Sakashita et al. (2004) East Asia Worm Meeting "Effects of Ionizing Radiation on Chemotaxis of the Nematode Caenorhabditis Elegans"

Tomoo Funayama, Seiichi Wada, Yasuhiko Kobayashi, Tetsuya Sakashita

[East Asia Worm Meeting, 2004]

In the present age aiming at a manned space flight to Mars, it is important to establish better know whether nervous system is affected by exposure to space radiation (heavy ions), especially in the function of the system. The nematode Caenorhabditis Elegans (C. elegans) is an ideal model organism for functional analysis of the nervous system. Radiation-induced damages on plasticity of chemotaxis and associative learning could be evaluated by a numerical index (Chemotaxis Index: CI) using C. elegans . Our final goal is to reveal molecular mechanisms that underlie radiation induced damages on the nervous system. Here, we report effects of two kinds of ionizing radiations, i.e. gamma-rays and energetic carbon ions, on chemotaxis towards NaCl of C. elegans as a preliminary result. Caenorhabditis elegans wild-type strain var. Bristol N2, which incubated at 20 degC for 3 days and under well-fed conditions, was used for all experiments. The animals were irradiated with gamma-rays from the 60 Co source and 18.3 MeV/u carbon ions from the AVF cyclotron of TIARA (Takasaki Ion Accelerators for Advanced Radiation Application). The dose-range was 0 - 500 Gy. Collision stopping power for water, which is a parameter for understanding the differences in radiation quality , of 60 Co gamma-rays and carbon ions were 0.2 and 116 keV/(mu, Greek)m, respectively. Chemotaxis towards NaCl of irradiated and non-irradiated animals were evaluated using CI. The chemotaxis index was calculated as CI = [(number of animals within a 1.5 cm radius of the NaCl spot) - (number of animals within a 1.5 cm radius of the control spot)] / (total number of animals on the plate). The CI-value ranges from 1 (move towards the NaCl spot) to -1 (move towards the control spot). The CI-value for naive-conditioned animals was around 0.5 - 0.7. Chemotaxis towards NaCl of animals irradiated with gamma rays declined with increasing dose. The time course of recovery of CI was measured for animals irradiated with gamma rays. At present, irradiation experiments with carbon ions are in progress. The details will be reported in the meeting.

Keiper, Brett D et al. (2021) International Worm Meeting "Isoforms of eIF4G (ifg-1) are differentially expressed to modulate mRNA translation initiation mechanism in development."

Keiper, Brett D, Kim, Eun Suk, Hoffman, Jenna L

[International Worm Meeting, 2021]

Cellular identity is critically determined by new protein synthesis in cells. Oocytes, spermatocytes and early embryos use predominantly mRNA translational control to regulate in spatial and temporal gene expression rather than transcription. Repression of mRNAs by RNA binding proteins and licensing by miRNAs have been extensively studied in C. elegans germ cells. But there is far less known about the positive translation mechanisms that overcome repression. Positive regulation is mediated by the translational machinery, eIF4 factors, that recruit mRNAs to ribosomes. In recent years we have shown that recruitment, like repression, is an mRNA-selective process. Translation factor eIF4G represents the core of the mRNA recruiting complex. In all organisms there are (at least) two major forms of eIF4G that utilize different mechanisms: one brings together a complex that recognizes the m7GTP mRNA cap (cap-dependent, CD), and the other builds a complex that recruits without cap recognition (cap-independent, CI). Worms express these two isoforms [p170 (CD) and p130 (CI)] from a single ifg-1 gene. Here we show by fluorescent tagging of isoforms in vivo that the CD and CI isoforms vary greatly in abundance during late oogenesis and in early embryos. Using ifg-1 mutants and isoform RNAi we demonstrate that the CD:CI isoform balance plays a critical role in preventing germ cell apoptosis but is largely dispensable following fertilization. The exception is for P granule localization, where suppression of the CD isoform promotes ectopic P granules in early embryos. A Polysome-Seq survey identified a subset of mRNAs that preferentially translates by CI mechanism, a subset that strongly favors CD mechanism, and many that show little preference. Our findings suggest that germ cells and embryos intentionally increase and decrease the CD and CI eIF4G isoforms to regulate mRNA translation by altering initiation mechanisms.