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Arnold CP, Lozano AM, Mann FG, Nowotarski SH, Haug JO, Lange JJ, Seidel CW, Alvarado AS. Hox genes regulate asexual reproductive behavior and tissue segmentation in adult animals. Nat Commun 2021; 12:6706. [PMID: 34795249 PMCID: PMC8602322 DOI: 10.1038/s41467-021-26986-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 09/21/2021] [Indexed: 12/13/2022] Open
Abstract
Hox genes are highly conserved transcription factors renowned for their roles in the segmental patterning of the embryonic anterior-posterior (A/P) axis. We report functions for Hox genes in A/P tissue segmentation and transverse fission behavior underlying asexual reproduction in adult planarian flatworms, Schmidtea mediterranea. Silencing of each of the Hox family members identifies 5 Hox genes required for asexual reproduction. Among these, silencing of hox3 genes results in supernumerary fission segments, while silencing of post2b eliminates segmentation altogether. The opposing roles of hox3 and post2b in segmentation are paralleled in their respective regulation of fission behavior. Silencing of hox3 increases the frequency of fission behavior initiation while silencing of post2b eliminates fission behavior entirely. Furthermore, we identify a network of downstream effector genes mediating Hox gene functions, providing insight into their respective mechanisms of action. In particular, we resolve roles for post2b and effector genes in the functions of the marginal adhesive organ in fission behavior regulation. Collectively, our study establishes adult stage roles for Hox genes in the regulation of tissue segmentation and behavior associated with asexual reproduction.
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Irigoitia MM, Palomba M, Braicovich PE, Lanfranchi AL, Denuncio PE, Gana JCM, Mattiucci S, Timi JT. Genetic identification of Anisakis spp. (Nematoda: Anisakidae) from cetaceans of the Southwestern Atlantic Ocean: ecological and zoogeographical implications. Parasitol Res 2021; 120:1699-1711. [PMID: 33674924 DOI: 10.1007/s00436-021-07088-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 02/15/2021] [Indexed: 02/01/2023]
Abstract
Adult Anisakis Dujardin, 1845 were found in two specimens of killer whale Orcinus orca and one specimen of franciscana Pontoporia blainvillei stranded from off the coast of Buenos Aires Province, Argentina. Genetic identification of the nematodes (N = 144) was performed by sequence analysis of the mitochondrial (mtDNA cox2) and the nuclear (nas 10 nDNA) gene loci. Anisakis pegreffii and Anisakis berlandi were detected in the two individuals of O. orca, while Anisakis typica and A. pegreffii were identified in P. blainvillei. Morphological and morphometric analysis also carried out on adult specimens of A. pegreffii and A. berlandi has allowed to underlining the usefulness of genetic/molecular markers in their recognition. This represents the first record of A. pegreffii in O. orca and P. blainvillei and of A. berlandi in O. orca. This is also the first sympatric and syntopic occurrence, as adults, of A. pegreffii and A. berlandi from the Austral Region of the Atlantic Ocean waters. These results provide insights into the knowledge of the host ranges and geographical distribution of these parasites in the basin waters of the region. Pontoporia blainvillei showed low abundance values of infection with Anisakis spp., which is the general pattern for coastal dolphins in the area, whereas O. orca harboured higher abundance of Anisakis spp. than those previously recorded among cetacean species in the Argentine Sea. Differences in the Anisakis spp. distribution and their parasitic loads, observed among the three host specimens, are discussed in relation to the oceanographic parameters, as well as to the host ecology. The usefulness of genetic/molecular markers in the recognition of adults of the sibling species A. pegreffii and A. berlandi with considerable overlapping in morphometric and morphological characters was underlined. The distribution of Anisakis species from Southwestern Atlantic waters is discussed in relation to their value as indicators for studies on the zoogeography of their hosts at a regional-scale level.
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Affiliation(s)
- M M Irigoitia
- Laboratorio de Ictioparasitología, Instituto de Investigaciones Marinas y Costeras (IIMyC), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3350, 7600, Mar del Plata, Argentina
| | - M Palomba
- Department of Public Health and Infectious Diseases, Section of Parasitology, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Sapienza-University of Rome, P.le Aldo Moro, 5, 00185, Rome, Italy
| | - P E Braicovich
- Laboratorio de Ictioparasitología, Instituto de Investigaciones Marinas y Costeras (IIMyC), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3350, 7600, Mar del Plata, Argentina.
| | - A L Lanfranchi
- Laboratorio de Ictioparasitología, Instituto de Investigaciones Marinas y Costeras (IIMyC), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3350, 7600, Mar del Plata, Argentina
| | - P E Denuncio
- Grupo de Mamíferos Marinos, Instituto de Investigaciones Marinas y Costeras (IIMyC), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3350, 7600, Mar del Plata, Argentina
| | - J C M Gana
- Grupo de Mamíferos Marinos, Instituto de Investigaciones Marinas y Costeras (IIMyC), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3350, 7600, Mar del Plata, Argentina
| | - S Mattiucci
- Department of Public Health and Infectious Diseases, Section of Parasitology, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Sapienza-University of Rome, P.le Aldo Moro, 5, 00185, Rome, Italy
| | - J T Timi
- Laboratorio de Ictioparasitología, Instituto de Investigaciones Marinas y Costeras (IIMyC), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Funes 3350, 7600, Mar del Plata, Argentina
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Chai JY, Jung BK, Chang T, Shin H, Cho J, Ryu JY, Kim HS, Park K, Jeong MH, Hoang EH, Abdullah MBM. Echinostoma miyagawai Ishii, 1932 (Echinostomatidae) from Ducks in Aceh Province, Indonesia with Special Reference to Its Synonymy with Echinostoma robustum Yamaguti, 1935. Korean J Parasitol 2021; 59:35-45. [PMID: 33684985 PMCID: PMC7939967 DOI: 10.3347/kjp.2021.59.1.35] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 11/23/2022]
Abstract
Adult echinostomes having 37 collar spines collected from the intestine of Pitalah ducks in Aceh Province, Indonesia in 2018 were morphologically and molecularly determined to be Echinostoma miyagawai Ishii, 1932 (Digenea: Echinostomatidae). Among 20 ducks examined, 7 (35.0%) were found to be infected with this echinostome, and the number of flukes collected was 48 in total with average 6.9 (1-17) worms per duck. The adult flukes were 7.2 (6.1-8.5) mm in length and 1.2 (1.0-1.4) mm in width (pre-ovarian or testicular level) and characterized by having a head collar armed with 37 collar spines (dorsal spines arranged in 2 alternating rows), including 5 end group spines, and variable morphology of the testes, irregularly or deeply lobed (3-5 lobes) at times with horizontal extension. The eggs within the worm uterus were 93 (79-105) µm long and 62 (56-70) µm wide. These morphological features were consistent with both E. miyagawai and Echinostoma robustum, for which synonymy to each other has been raised. Sequencing of 2 mitochondrial genes, cox1 and nad1, revealed high homology with E. miyagawai (98.6-100% for cox1 and 99.0-99.8% for nad1) and also with E. robustum (99.3-99.8% for nad1) deposited in GenBank. We accepted the synonymy between the 2 species and diagnosed our flukes as E. miyagawai (syn. E. robustum) with redescription of its morphology. Further studies are required to determine the biological characteristics of E. miyagawai in Aceh Province, Indonesia, including the intermediate host and larval stage information.
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Affiliation(s)
- Jong-Yil Chai
- Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul 07649, Korea
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Bong-Kwang Jung
- Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul 07649, Korea
- Corresponding author ()
| | - Taehee Chang
- Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Hyejoo Shin
- Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Jaeeun Cho
- Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Jin-Youp Ryu
- Bureau of Health Examination and Management, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Hyun-Seung Kim
- Bureau of Health Examination and Management, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Kwanghoon Park
- Bureau of Health Examination and Management, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Mun-Hyoo Jeong
- Bureau of Health Examination and Management, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Eui-Hyug Hoang
- Bureau of Health Examination and Management, Korea Association of Health Promotion, Seoul 07649, Korea
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Chai JY, Sohn WM, Cho J, Jung BK, Chang T, Lee KH, Khieu V, Huy R. Echinostoma mekongi: Discovery of Its Metacercarial Stage in Snails, Filopaludina martensi cambodjensis, in Pursat Province, Cambodia. Korean J Parasitol 2021; 59:47-53. [PMID: 33684986 PMCID: PMC7939970 DOI: 10.3347/kjp.2021.59.1.47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/16/2021] [Accepted: 01/16/2021] [Indexed: 11/23/2022]
Abstract
Echinostoma mekongi was reported as a new species in 2020 based on specimens collected from humans in Kratie and Takeo Province, Cambodia. In the present study, its metacercarial stage has been discovered in Filopaludina martensi cambodjensis snails purchased from a local market nearby the Tonle Sap Lake, Pursat Province, Cambodia. The metacercariae were fed orally to an experimental hamster, and adult flukes were recovered at day 20 post-infection. They were morphologically examined using light and scanning electron microscopes and molecularly analyzed by sequencing of their mitochondrial cox1 and nad1 genes. A total of 115 metacercariae (1-8 per snail) were detected in 60 (60.0%) out of 100 Filopaludina snails examined. The metacercariae were round, 174 µm in average diameter (163-190 µm in range), having a thin cyst wall, a head collar armed with 37 collar spines, and characteristic excretory granules. The adult flukes were elongated, ventrally curved, 7.3 (6.4-8.2)×1.4 (1.1-1.7) mm in size, and equipped with 37 collar spines on the head collar (dorsal spines in 2 alternating rows), being consistent with E. mekongi. In phylogenetic analyses, the adult flukes showed 99.0-100% homology based on cox1 sequences and 98.9-99.7% homology based on nad1 sequences with E. mekongi. The results evidenced that F. martensi cambodjensis snails act as the second intermediate host of E. mekongi, and hamsters can be used as a suitable experimental definitive host. As local people favor to eat undercooked snails, these snails seem to be an important source of human infection with E. mekongi in Cambodia.
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Affiliation(s)
- Jong-Yil Chai
- Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul 07649, Korea
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
| | - Jaeeun Cho
- Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Bong-Kwang Jung
- Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Taehee Chang
- Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Keon Hoon Lee
- Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul 07649, Korea
| | - Virak Khieu
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Rekol Huy
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
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Abstract
Glia shape the development and function of the C. elegans nervous system, especially its sense organs and central neuropil (nerve ring). Cell-type-specific promoters allow investigators to label or manipulate individual glial cell types, and therefore provide a key tool for deciphering glial function. In this technical resource, we compare the specificity, brightness, and consistency of cell-type-specific promoters for C. elegans glia. We identify a set of promoters for the study of seven glial cell types (F16F9.3, amphid and phasmid sheath glia; F11C7.2, amphid sheath glia only; grl-2, amphid and phasmid socket glia; hlh-17, cephalic (CEP) sheath glia; and grl-18, inner labial (IL) socket glia) as well as a pan-glial promoter (mir-228). We compare these promoters to promoters that are expressed more variably in combinations of glial cell types (delm-1 and itx-1). We note that the expression of some promoters depends on external conditions or the internal state of the organism, such as developmental stage, suggesting glial plasticity. Finally, we demonstrate an approach for prospectively identifying cell-type-specific glial promoters using existing single-cell sequencing data, and we use this approach to identify two novel promoters specific to IL socket glia (col-53 and col-177).
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Affiliation(s)
- Wendy Fung
- These authors contributed equally to this work
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston MA 02115
| | - Leigh Wexler
- These authors contributed equally to this work
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston MA 02115
| | - Maxwell G. Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston MA 02115
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Wei X, Liu B, Li Y, Wang K, Gao L, Yang Y. A human corneal ulcer caused by Thelazia callipaeda in Southwest China: case report. Parasitol Res 2020; 119:3531-3534. [PMID: 32827103 DOI: 10.1007/s00436-020-06850-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/09/2020] [Indexed: 11/26/2022]
Abstract
In this study, we describe a rare human case with corneal ulcer caused by thelaziosis in a 69-year-old man in Southwest China. A male nematode was discovered and removed from the patient's right eye with a long spicule and further identified by sequencing mitochondrial cox1 gene. The ophthalmologic and molecular biological evidence demonstrates the corneal ulcer caused by T. callipaeda infection, which is mainly distributed in Asian and European countries. Most T. callipaeda infections are emerged in the conjunctiva, leading to conjunctivitis. To the best knowledge of the authors, corneal ulcers caused by T. callipaeda have not been reported yet.
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Affiliation(s)
- Xiaoxing Wei
- Medical College of Qinghai University, Xining, 810016, People's Republic of China
- Department of Ophthalmology, Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
| | - Bo Liu
- Medical College of Qinghai University, Xining, 810016, People's Republic of China
- Department of Ophthalmology, Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
| | - Yijian Li
- Medical College of Qinghai University, Xining, 810016, People's Republic of China
- Department of Ophthalmology, Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
| | - Ke Wang
- Medical College of Qinghai University, Xining, 810016, People's Republic of China
- Department of Ophthalmology, Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
| | - Lixia Gao
- Medical College of Qinghai University, Xining, 810016, People's Republic of China
- Department of Ophthalmology, Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
| | - Yuli Yang
- Medical College of Qinghai University, Xining, 810016, People's Republic of China.
- Department of Ophthalmology, Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China.
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Kramer-Drauberg M, Liu JL, Desjardins D, Wang Y, Branicky R, Hekimi S. ROS regulation of RAS and vulva development in Caenorhabditis elegans. PLoS Genet 2020; 16:e1008838. [PMID: 32544191 PMCID: PMC7319342 DOI: 10.1371/journal.pgen.1008838] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 06/26/2020] [Accepted: 05/07/2020] [Indexed: 12/28/2022] Open
Abstract
Reactive oxygen species (ROS) are signalling molecules whose study in intact organisms has been hampered by their potential toxicity. This has prevented a full understanding of their role in organismal processes such as development, aging and disease. In Caenorhabditis elegans, the development of the vulva is regulated by a signalling cascade that includes LET-60ras (homologue of mammalian Ras), MPK-1 (ERK1/2) and LIN-1 (an ETS transcription factor). We show that both mitochondrial and cytoplasmic ROS act on a gain-of-function (gf) mutant of the LET-60ras protein through a redox-sensitive cysteine (C118) previously identified in mammals. We show that the prooxidant paraquat as well as isp-1, nuo-6 and sod-2 mutants, which increase mitochondrial ROS, inhibit the activity of LET-60rasgf on vulval development. In contrast, the antioxidant NAC and loss of sod-1, both of which decrease cytoplasmic H202, enhance the activity of LET-60rasgf. CRISPR replacement of C118 with a non-oxidizable serine (C118S) stimulates LET-60rasgf activity, whereas replacement of C118 with aspartate (C118D), which mimics a strongly oxidised cysteine, inhibits LET-60rasgf. These data strongly suggest that C118 is oxidized by cytoplasmic H202 generated from dismutation of mitochondrial and/or cytoplasmic superoxide, and that this oxidation inhibits LET-60ras. This contrasts with results in cultured mammalian cells where it is mostly nitric oxide, which is not found in worms, that oxidizes C118 and activates Ras. Interestingly, PQ, NAC and the C118S mutation do not act on the phosphorylation of MPK-1, suggesting that oxidation of LET-60ras acts on an as yet uncharacterized MPK-1-independent pathway. We also show that elevated cytoplasmic superoxide promotes vulva formation independently of C118 of LET-60ras and downstream of LIN-1. Finally, we uncover a role for the NADPH oxidases (BLI-3 and DUOX-2) and their redox-sensitive activator CED-10rac in stimulating vulva development. Thus, there are at least three genetically separable pathways by which ROS regulates vulval development.
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Affiliation(s)
| | - Ju-Ling Liu
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - David Desjardins
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Ying Wang
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Robyn Branicky
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Siegfried Hekimi
- Department of Biology, McGill University, Montreal, Quebec, Canada
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Abstract
Asian Taenia is a human-infecting Taenia tapeworm known as Taenia asiatica following morphological examination of adult and larval stages of the tapeworm by Eom and Rim (1993). The life cycle of T. asiatica differs from that of T. saginata in its intermediate host (pigs versus cattle) as well as in the infected organs (liver versus muscle). T. asiatica can be differentiated from T. solium and T. saginata by examination of morphological characteristics such as the scolex, mature and gravid proglottids in the adult stage, and the scolex and bladder surface in the larval stage. T. asiatica has been identified in Korea, Taiwan, the Philippines, China, Thailand, Indonesia, Vietnam, Japan, Lao PDR, Nepal and India. The molecular tools employed for T. asiatica identification have been developed to differentiate T. asiatica from other human-infecting Taenia tapeworms based on genetic information such as nucleotide sequence of mitochondrial genes, nuclear ribosomal genes and nuclear genes that lead to development of the subsequent molecular techniques, such as PCR-RFLP, PCR-RAPD, BESST-base, LAMP and qPCR. Investigation of the phylogenetic relationships among human Taenia species revealed that T. asiatica is a sister species with T. saginata, which is genetically more similar than other Taenia species in terms of the nucleotide sequences of cox1, nad1 and 28S rDNA. The mitochondrial genomes of human Taenia tapeworms comprise 13,703bp (T. asiatica), 13,670bp (T. saginata) and 13,709bp (T. solium), and contain 36 genes including 12 protein-coding genes, 2 ribosomal RNAs (rRNAs, a small and a large subunit), and 22 transfer RNAs (tRNAs). Sequence differences in the full genome of T. asiatica and T. saginata mitochondria is 4.6%, while T. solium differs by 11%. Hox gene orthology in T. asiatica was established by comparative analysis with Platyhelminthes Hox genes. T. asiatica Hox revealed six Hox orthologs including two lab/Hox1, two Hox3, one Dfd/Hox4 and one Lox/Lox4. Hybridization between T. asiatica and T. saginata was definitely observed in these species which are sympatrically endemic in the regions of Korea, Thailand, China and Lao PDR. Comparative analyses of T. asiatica, T. saginata and T. solium genomes were also reported with genome features. Taenia asiaticus nomen novum was proposed for T. asiaticaEom and Rim, 1993 which is a homonym of T. asiatica Linstow, 1901 (Davaineidae).
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Affiliation(s)
- Keeseon S Eom
- Department of Parasitology, Parasite Research Center and Parasite Resource Bank, Chungbuk National University School of Medicine, Cheongju, South Korea.
| | - Han-Jong Rim
- Department of Parasitology, Korea University College of Medicine, Seoul, South Korea
| | - Hyeong-Kyu Jeon
- Department of Parasitology, Parasite Research Center and Parasite Resource Bank, Chungbuk National University School of Medicine, Cheongju, South Korea
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Consoli E, Ruthes AC, Reinhard E, Dahlin P. First Morphological and Molecular Report of Aphelenchoides blastophthorus on Strawberry Plants in Switzerland. Plant Dis 2019; 103:2851-2856. [PMID: 31486741 DOI: 10.1094/pdis-07-18-1241-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Foliar nematodes represent a minor feeding group within the genus Aphelenchoides Fischer, 1894. The facultative plant parasitic species A. blastophthorus can cause crinkling of leaves, reduced vigor, and stunting of agricultural and ornamental plants. Here we report the first finding of A. blastophthorus in leaves, crowns, and roots of strawberry plants collected in Switzerland in 2018. Species identification was confirmed by morphological and morphometric characterization supported by molecular barcoding of 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), and cytochrome c oxidase I (COI) gene fragment analyses. Phylogenetic analysis of 18S indicated that A. blastophthorus was grouped within close distance to A. fragariae, a well-known foliar nematode affecting strawberry plants. Furthermore, the newly generated molecular barcodes of the partial 28S and COI of A. blastophthorus will support species identification in the future.
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Affiliation(s)
- Erika Consoli
- Agroscope, Research Division Plant Protection, Phytopathology and Zoology in Fruit and Vegetable Production, Wädenswil, Switzerland
| | | | - Eder Reinhard
- Agroscope, Research Division Plant Protection, Phytopathology and Zoology in Fruit and Vegetable Production, Wädenswil, Switzerland
| | - Paul Dahlin
- Agroscope, Research Division Plant Protection, Phytopathology and Zoology in Fruit and Vegetable Production, Wädenswil, Switzerland
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Gorny AM, Wang X, Hay FS, Pethybridge SJ. Development of a Species-Specific PCR for Detection and Quantification of Meloidogyne hapla in Soil Using the 16D10 Root-Knot Nematode Effector Gene. Plant Dis 2019; 103:1902-1909. [PMID: 31242131 DOI: 10.1094/pdis-09-18-1539-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Northern root-knot nematode (Meloidogyne hapla) is an important soilborne pathogen of numerous agricultural crops in temperate regions. Accurate detection and quantification is vital to supporting informed pest management decisions. However, traditional methods of manual nematode extraction and morphology-based identification are time-consuming and require highly specialized training. Molecular methods may expand the diagnostician's toolkit beyond those methods that rely on this disappearing specialized skillset. However, molecular assays targeting the internal transcribed spacer region may lead to inaccurate results because of intraspecific variability. The Meloidogyne spp. effector gene 16D10 was assessed as a target for a SYBR Green I quantitative PCR (qPCR) assay for detection and quantification of M. hapla. M. hapla-specific qPCR primers were developed and evaluated for specificity against five M. hapla isolates and 14 other plant-parasitic nematodes. A standard curve was generated by relating the quantification cycle (Cq) to the log of M. hapla population densities artificially introduced into soil. The influence of soil inhibitors on quantitative amplification was assessed by generating a dilution series from DNA extracted from pure nematode cultures and inoculated soil. Extracts from soil produced significantly higher Cq values than those produced from pure culture extracts. The utility of the qPCR was evaluated using soil samples collected from three naturally infested potato fields, resulting in a significant positive relationship between populations estimated using qPCR and populations derived from manual counting. The qPCR developed in this study provides a useful method for detecting and quantifying M. hapla in soil and demonstrates the utility of effector genes in plant-parasitic nematode diagnostics. The ability to use effector genes as targets for qPCR and other molecular detection and quantification methods may open additional avenues of novel research and support development of improved species-level diagnostics.
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Affiliation(s)
- Adrienne M Gorny
- 1Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Xiaohong Wang
- 1Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
- 2Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture Agricultural Research Service, Ithaca, NY 14850
| | - Frank S Hay
- 1Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Sarah J Pethybridge
- 1Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
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11
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Tanaka SE, Dayi M, Maeda Y, Tsai IJ, Tanaka R, Bligh M, Takeuchi-Kaneko Y, Fukuda K, Kanzaki N, Kikuchi T. Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle. Sci Rep 2019; 9:6080. [PMID: 30988401 PMCID: PMC6465311 DOI: 10.1038/s41598-019-42570-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 04/01/2019] [Indexed: 12/24/2022] Open
Abstract
The pine wood nematode Bursaphelenchus xylophilus is the causal agent of pine wilt disease, one of the most devastating forest diseases in East Asian and West European countries. The lifecycle of B. xylophilus includes four propagative larval stages and gonochoristic adults which are involved in the pathogenicity, and two stages of dispersal larvae involved in the spread of the disease. To elucidate the ecological roles of each developmental stage in the pathogenic life cycle, we performed a comprehensive transcriptome analysis using RNA-seq generated from all developmental stages of B. xylophilus and compared transcriptomes between stages. We found more than 9000 genes are differentially expressed in at least one stage of the life cycle including genes involved in general nematode biology such as reproduction and moulting but also effector genes likely to be involved in parasitism. The dispersal-stage transcriptome revealed its analogy to C. elegans dauer and the distinct roles of the two larval stages from each other regarding survival and transmission. This study provides important insights and resources to understand B. xylophilus parasitic biology.
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Affiliation(s)
- Suguru E Tanaka
- Laboratory of Forest Botany, Graduate School of Agricultural and Life Sciences, the University of Tokyo, Tokyo, 113-8657, Japan
| | - Mehmet Dayi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
- Forestry Vocational School, Duzce University, 81620, Duzce, Turkey
| | - Yasunobu Maeda
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Isheng J Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ryusei Tanaka
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Mark Bligh
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Yuko Takeuchi-Kaneko
- Laboratory of Terrestrial Microbial Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kenji Fukuda
- Laboratory of Forest Botany, Graduate School of Agricultural and Life Sciences, the University of Tokyo, Tokyo, 113-8657, Japan
| | - Natsumi Kanzaki
- Kansai Research Center, Forestry and Forest Products Research Institute, Kyoto, 612-0855, Japan
| | - Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan.
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12
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Poirier S, Dauphinais N, Van Der Heyden H, Véronneau PY, Bélair G, Gravel V, Mimee B. Host Range and Genetic Characterization of Ditylenchus dipsaci Populations from Eastern Canada. Plant Dis 2019; 103:456-460. [PMID: 30620689 DOI: 10.1094/pdis-07-18-1201-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The stem and bulb nematode, Ditylenchus dipsaci, is a plant-parasitic nematode affecting over 500 plant species worldwide. Since 2012, garlic producers from Ontario and Quebec have been particularly affected with economic losses caused by this pest. Reproduction of D. dipsaci on a particular host depends on its biological race, and races are unknown for these populations from eastern Canada. As a polyphagous pest, D. dipsaci can possibly be a threat and have negative impact on many crops grown in Quebec, such as field and vegetable crops (e.g., onion). In this study, the host range of four populations of D. dipsaci from Quebec and Ontario was determined in a greenhouse experiment using 11 crops. Garlic, onion, and green onion showed high susceptibility to the nematode, whereas reproduction on potato was poor. No reproduction was observed on corn, soybean, barley, alfalfa, mustard, carrot, and lettuce. These crops could therefore be used as rotational crops in a control program. Thirty-two populations of D. dipsaci were also genetically characterized using genotyping-by-sequencing. The comparison of allele frequencies at 481 loci showed that most of the populations had a genotype similar to a reference population from northern Ontario. However, a sample from eastern Quebec exhibited a distinct genotype and will require further phenotyping in a greenhouse to preclude the possibility of a different race.
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Affiliation(s)
- Sandra Poirier
- 1 Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, J3B 3E6, Canada
- 2 Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada; and
| | - Nathalie Dauphinais
- 1 Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, J3B 3E6, Canada
| | | | - Pierre-Yves Véronneau
- 1 Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, J3B 3E6, Canada
| | - Guy Bélair
- 1 Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, J3B 3E6, Canada
| | - Valérie Gravel
- 2 Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada; and
| | - Benjamin Mimee
- 1 Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, J3B 3E6, Canada
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13
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Scheidel N, Blacque OE. Intraflagellar Transport Complex A Genes Differentially Regulate Cilium Formation and Transition Zone Gating. Curr Biol 2018; 28:3279-3287.e2. [PMID: 30293716 DOI: 10.1016/j.cub.2018.08.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 06/08/2018] [Accepted: 08/07/2018] [Indexed: 02/03/2023]
Abstract
Cilia are found on most eukaryotic cell types, serving motility, environment sensing, and signaling (cell-cell) functions, and defects cause genetic diseases (ciliopathies), affecting the development of many tissues [1]. Cilia are built by intraflagellar transport (IFT), a bidirectional microtubule-based motility driven by kinesin-2 anterograde (toward ciliary tip) and IFT-dynein retrograde (toward ciliary base) motors together with IFT-A and IFT-B cargo adaptor complexes that control retrograde and anterograde IFT, respectively [2]. Ciliary composition is also facilitated by the transition zone (TZ) at the ciliary base and the associated Meckel-Gruber syndrome (MKS) and nephronophthisis (NPHP) modules that establish protein diffusion barriers and regulate cilium structure [3]. Although the molecular architecture of the IFT machine is emerging [2], how individual components contribute to cilium subtype formation and IFT remains relatively unexplored, especially in vivo. In addition, little is known about functional interactions between IFT and TZ modules. Here, in Caenorhabditis elegans (roundworms), we identify cell-type-specific mechanisms by which IFT-A sculpts the structures of discrete ciliary subtypes and regulates IFT. We also uncover differential roles for IFT-A subunits in controlling the TZ restriction of MKS module components and ciliary exclusion (gating) of periciliary membrane proteins, with IFT-140 controlling their ciliary entry and IFT-43/121/139 controlling their ciliary removal. Furthermore, we determine that IFT-A and MKS module components synergistically interact to determine cilium structure. Overall, this work provides insight into the functional architecture of a metazoan IFT-A complex in different cell types and uncovers new relationships between ciliopathy-associated IFT-A and TZ modules.
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Affiliation(s)
- Noémie Scheidel
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Oliver E Blacque
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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14
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Janssen T, Karssen G, Verhaeven M, Coyne D, Bert W. Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution. Sci Rep 2016; 6:22591. [PMID: 26940543 PMCID: PMC4778069 DOI: 10.1038/srep22591] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/17/2016] [Indexed: 11/17/2022] Open
Abstract
The polyphagous parthenogenetic root-knot nematodes of the genus Meloidogyne are considered to be the most significant nematode pest in sub-tropical and tropical agriculture. Despite the crucial need for correct diagnosis, identification of these pathogens remains problematic. The traditionally used diagnostic strategies, including morphometrics, host-range tests, biochemical and molecular techniques, now appear to be unreliable due to the recently-suggested hybrid origin of root-knot nematodes. In order to determine a suitable barcode region for these pathogens nine quickly-evolving mitochondrial coding genes were screened. Resulting haplotype networks revealed closely related lineages indicating a recent speciation, an anthropogenic-aided distribution through agricultural practices, and evidence for reticulate evolution within M. arenaria. Nonetheless, nucleotide polymorphisms harbor enough variation to distinguish these closely-related lineages. Furthermore, completeness of lineage sorting was verified by screening 80 populations from widespread geographical origins and variable hosts. Importantly, our results indicate that mitochondrial haplotypes are strongly linked and consistent with traditional esterase isozyme patterns, suggesting that different parthenogenetic lineages can be reliably identified using mitochondrial haplotypes. The study indicates that the barcode region Nad5 can reliably identify the major lineages of tropical root-knot nematodes.
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Affiliation(s)
- Toon Janssen
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Gerrit Karssen
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
- National Plant Protection Organization, Wageningen Nematode Collection, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Myrtle Verhaeven
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Danny Coyne
- International Institute of Tropical Agriculture (IITA), c/o icipe, Kasarani, P.O. Box 30772-00100, Nairobi, Kenya
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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15
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Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A 2015; 112:12462-7. [PMID: 26392545 PMCID: PMC4603488 DOI: 10.1073/pnas.1516718112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50=222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.
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Affiliation(s)
- Kaja Wasik
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - James Gurtowski
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Xin Zhou
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Molecular and Cellular Biology Graduate Program, Stony Brook University, NY 11794
| | - Olivia Mendivil Ramos
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - M Joaquina Delás
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Giorgia Battistoni
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Osama El Demerdash
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Dita B Vizoso
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Andrew D Smith
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Peter Ladurner
- Department of Evolutionary Biology, Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Lukas Schärer
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - W Richard McCombie
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;
| | - Michael Schatz
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
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16
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Spiró Z, Gönczy P. Polarity-dependent asymmetric distribution and MEX-5/6-mediated translational activation of the Era-1 mRNA in C. elegans embryos. PLoS One 2015; 10:e0120984. [PMID: 25821955 PMCID: PMC4378847 DOI: 10.1371/journal.pone.0120984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/09/2015] [Indexed: 11/18/2022] Open
Abstract
The early C. elegans embryo is an attractive model system to investigate fundamental developmental processes. With the exception of mex-3 mRNA, maternally contributed mRNAs are thought to be distributed uniformly in the one-cell embryo. Here, we report and characterize the striking distribution of the mRNA encoding the novel protein ERA-1. We found that era-1 mRNA is enriched in the anterior of the one-cell embryo and present solely in anterior blastomeres thereafter. Although era-1 is not an essential gene, we uncovered that era-1 null mutant embryos are sensitive to slight impairment of embryonic polarity. We found that the asymmetric distribution of era-1 mRNA depends on anterior-posterior polarity cues and on the era-1 3’UTR. Similarly to the era-1 mRNA, the YFP-ERA-1 protein is enriched in anterior blastomeres. Interestingly, we found that the RNA-binding protein MEX-5 is required for era-1 mRNA asymmetry. Furthermore, we show that MEX-5, together with its partially redundant partner MEX-6, are needed to activate era-1 mRNA translation in anterior blastomeres. These findings lead us to propose that MEX-5/6–mediated regulation of era-1 mRNA contributes to robust embryonic development.
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Affiliation(s)
- Zoltán Spiró
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL) Lausanne, Lausanne, Switzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL) Lausanne, Lausanne, Switzerland
- * E-mail:
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17
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Eom HJ, Kim H, Kim BM, Chon TS, Choi J. Integrative assessment of benzene exposure to Caenorhabditis elegans using computational behavior and toxicogenomic analyses. Environ Sci Technol 2014; 48:8143-8151. [PMID: 24846693 DOI: 10.1021/es500608e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this study, we investigated the toxic effects of benzene to the nematode Caenorhabditis elegans in an integrative manner, using computational behavior and toxicogenomics analyses, along with survival and reproduction. Benzene exposure led to changes in locomotive behavior and reproduction decline in C. elegans. Microarray followed by pathway analysis revealed that 228 genes were differentially expressed by benzene exposure, and cyp-35a2, pmk-1, and cep-1 were selected for further reproduction and multiparametric behavior analysis. Mutant analysis showed that benzene induced reproduction decline was rescued in cyp-35a2(gk317) mutant, whereas it was significantly exacerbated in pmk-1(km25) mutant, compared with the wildtype. The multiparametric behavior analysis on the mutants of selected genes revealed that each strain exhibits different response patterns, particularly, enhanced linear movement in the cyp-35a2(gk317) mutant, whereas the changes in partial body movement were observed in the pmk-1(km25) mutant by benzene exposure. A self-organizing map revealed that the pmk-1(km25) mutant group was the most densely clustered and located on the opposite side of the map of the cyp-35a2(gk317) mutant, each crossing that of the wildtype. Overall results suggest distinct roles of cyp-35a2 and pmk-1 genes in benzene-induced alterations in behavior and reproduction in C. elegans. This study also suggests computational behavior analysis is a suitable tool for addressing the integrative impact of chemical stress alongside with toxicogenomic approach.
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Affiliation(s)
- Hyun-Jeong Eom
- School of Environmental Engineering, Graduate School of Energy and Environmental System Engineering, University of Seoul , 163 Siripdaero, Dongdaemun-gu, Seoul 130-743, Korea
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18
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Cunningham KA, Bouagnon AD, Barros AG, Lin L, Malard L, Romano-Silva MA, Ashrafi K. Loss of a neural AMP-activated kinase mimics the effects of elevated serotonin on fat, movement, and hormonal secretions. PLoS Genet 2014; 10:e1004394. [PMID: 24921650 PMCID: PMC4055570 DOI: 10.1371/journal.pgen.1004394] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 04/07/2014] [Indexed: 12/30/2022] Open
Abstract
AMP-activated protein kinase (AMPK) is an evolutionarily conserved master regulator of metabolism and a therapeutic target in type 2 diabetes. As an energy sensor, AMPK activity is responsive to both metabolic inputs, for instance the ratio of AMP to ATP, and numerous hormonal cues. As in mammals, each of two genes, aak-1 and aak-2, encode for the catalytic subunit of AMPK in C. elegans. Here we show that in C. elegans loss of aak-2 mimics the effects of elevated serotonin signaling on fat reduction, slowed movement, and promoting exit from dauer arrest. Reconstitution of aak-2 in only the nervous system restored wild type fat levels and movement rate to aak-2 mutants and reconstitution in only the ASI neurons was sufficient to significantly restore dauer maintenance to the mutant animals. As in elevated serotonin signaling, inactivation of AAK-2 in the ASI neurons caused enhanced secretion of dense core vesicles from these neurons. The ASI neurons are the site of production of the DAF-7 TGF-β ligand and the DAF-28 insulin, both of which are secreted by dense core vesicles and play critical roles in whether animals stay in dauer or undergo reproductive development. These findings show that elevated levels of serotonin promote enhanced secretions of systemic regulators of pro-growth and differentiation pathways through inactivation of AAK-2. As such, AMPK is not only a recipient of hormonal signals but can also be an upstream regulator. Our data suggest that some of the physiological phenotypes previously attributed to peripheral AAK-2 activity on metabolic targets may instead be due to the role of this kinase in neural serotonin signaling.
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Affiliation(s)
- Katherine A. Cunningham
- Department of Physiology, University of California, San Francisco, San Francisco, California, United States of America
| | - Aude D. Bouagnon
- Department of Physiology, University of California, San Francisco, San Francisco, California, United States of America
| | - Alexandre G. Barros
- Instituto Nacional de Ciência e Tecnologia de Medicina Molecular, Faculdade de Medicina da Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lin Lin
- Department of Physiology, University of California, San Francisco, San Francisco, California, United States of America
| | - Leandro Malard
- Departamento de Física, Instituto de Ciências Exatas da Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marco Aurélio Romano-Silva
- Instituto Nacional de Ciência e Tecnologia de Medicina Molecular, Faculdade de Medicina da Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Kaveh Ashrafi
- Department of Physiology, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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Huang HC, Yao LL, Song ZM, Li XP, Hua QQ, Li Q, Pan CW, Xia CM. Development-specific differences in the proteomics of Angiostrongylus cantonensis. PLoS One 2013; 8:e76982. [PMID: 24204717 PMCID: PMC3808366 DOI: 10.1371/journal.pone.0076982] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/27/2013] [Indexed: 11/18/2022] Open
Abstract
Angiostrongyliasis is an emerging communicable disease. Several different hosts are required to complete the life cycle of Angiostrongylus cantonensis. However, we lack a complete understanding of variability of proteins across different developmental stages and their contribution to parasite survival and progression. In this study, we extracted soluble proteins from various stages of the A. cantonensis life cycle [female adults, male adults, the fifth-stage female larvae (FL5), the fifth-stage male larvae (ML5) and third-stage larvae (L3)], separated those proteins using two-dimensional difference gel electrophoresis (2D-DIGE) at pH 4-7, and analyzed the gel images using DeCyder 7.0 software. This proteomic analysis produced a total of 183 different dominant protein spots. Thirty-seven protein spots were found to have high confidence scores (>95%) by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Comparative proteomic analyses revealed that 29 spots represented cytoskeleton-associated proteins and functional proteins. Eight spots were unnamed proteins. Twelve protein spots that were matched to the EST of different-stage larvae of A. cantonensis were identified. Two genes and the internal control 18s were chosen for quantitative real-time PCR (qPCR) and the qPCR results were consistent with those of the DIGE studies. These findings will provide a new basis for understanding the characteristics of growth and development of A. cantonensis and the host-parasite relationship. They may also assist searches for candidate proteins suitable for use in diagnostic assays and as drug targets for the control of eosinophilic meningitis caused by A. cantonensis.
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Affiliation(s)
- Hui-Cong Huang
- Department of Parasitology, Medical College of Soochow University, Suzhou, Jiangsu, P. R. China
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Li-Li Yao
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Zeng-Mei Song
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Xing-Pan Li
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Qian-Qian Hua
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Qiang Li
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Wenzhou Medical University, Ruian, Zhejiang, P. R. China
| | - Chang-Wang Pan
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Chao-Ming Xia
- Department of Parasitology, Medical College of Soochow University, Suzhou, Jiangsu, P. R. China
- * E-mail:
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20
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Haegeman A, Bauters L, Kyndt T, Rahman MM, Gheysen G. Identification of candidate effector genes in the transcriptome of the rice root knot nematode Meloidogyne graminicola. Mol Plant Pathol 2013; 14:379-90. [PMID: 23279209 PMCID: PMC6638898 DOI: 10.1111/mpp.12014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plant-parasitic nematodes secrete so-called effectors into their host plant which are able to suppress the plant's defence responses, alter plant signalling pathways and, in the case of root knot nematodes, induce the formation of giant cells. Putative effectors have been successfully identified by genomics, transcriptomics and proteomics approaches. In this study, we investigated the transcriptome of the rice root knot nematode Meloidogyne graminicola by 454 sequencing of second-stage juveniles as well as mRNA-seq of rice infected tissue. Over 350 000 reads derived from M. graminicola preparasitic juveniles were assembled, annotated and checked for homologues in different databases. From infected rice tissue, 1.4% of all reads generated were identified as being derived from the nematode. Using multiple strategies, several putative effector genes were identified, both pioneer genes and genes corresponding to already known effectors. To check whether these genes could be involved in the interaction with the plant, in situ hybridization was performed on a selection of genes to localize their expression in the nematode. Most were expressed in the gland cells or amphids of the nematode, confirming possible secretion of the proteins and hence a role in infection. Other putative effectors showed a different expression pattern, potentially linked with the excretory/secretory system. This transcriptome study is a good starting point to functionally investigate novel effectors derived from M. graminicola. This will lead to better insights into the interaction between these nematodes and the model plant rice. Moreover, the transcriptome can be used to identify possible target genes for RNA interference (RNAi)-based control strategies. Four genes proved to be interesting targets by showing up to 40% higher mortality relative to the control treatment when soaked in gene-specific small interfering RNAs (siRNAs).
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Affiliation(s)
- Annelies Haegeman
- Department of Molecular Biotechnology, Ghent University, B-9000, Ghent, Belgium
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21
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Haegeman A, Bauters L, Kyndt T, Rahman MM, Gheysen G. Identification of candidate effector genes in the transcriptome of the rice root knot nematode Meloidogyne graminicola. Mol Plant Pathol 2013; 14:379-390. [PMID: 23279209 DOI: 10.1111/mpp.12014 [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Plant-parasitic nematodes secrete so-called effectors into their host plant which are able to suppress the plant's defence responses, alter plant signalling pathways and, in the case of root knot nematodes, induce the formation of giant cells. Putative effectors have been successfully identified by genomics, transcriptomics and proteomics approaches. In this study, we investigated the transcriptome of the rice root knot nematode Meloidogyne graminicola by 454 sequencing of second-stage juveniles as well as mRNA-seq of rice infected tissue. Over 350 000 reads derived from M. graminicola preparasitic juveniles were assembled, annotated and checked for homologues in different databases. From infected rice tissue, 1.4% of all reads generated were identified as being derived from the nematode. Using multiple strategies, several putative effector genes were identified, both pioneer genes and genes corresponding to already known effectors. To check whether these genes could be involved in the interaction with the plant, in situ hybridization was performed on a selection of genes to localize their expression in the nematode. Most were expressed in the gland cells or amphids of the nematode, confirming possible secretion of the proteins and hence a role in infection. Other putative effectors showed a different expression pattern, potentially linked with the excretory/secretory system. This transcriptome study is a good starting point to functionally investigate novel effectors derived from M. graminicola. This will lead to better insights into the interaction between these nematodes and the model plant rice. Moreover, the transcriptome can be used to identify possible target genes for RNA interference (RNAi)-based control strategies. Four genes proved to be interesting targets by showing up to 40% higher mortality relative to the control treatment when soaked in gene-specific small interfering RNAs (siRNAs).
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Affiliation(s)
- Annelies Haegeman
- Department of Molecular Biotechnology, Ghent University, B-9000, Ghent, Belgium
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Liau WS, Nasri U, Elmatari D, Rothman J, LaMunyon CW. Premature sperm activation and defective spermatogenesis caused by loss of spe-46 function in Caenorhabditis elegans. PLoS One 2013; 8:e57266. [PMID: 23483899 PMCID: PMC3590197 DOI: 10.1371/journal.pone.0057266] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/21/2013] [Indexed: 12/05/2022] Open
Abstract
Given limited resources for motility, sperm cell activation must be precisely timed to ensure the greatest likelihood of fertilization. Like those of most species, the sperm of C. elegans become active only after encountering an external signaling molecule. Activation coincides with spermiogenesis, the final step in spermatogenesis, when the spherical spermatid undergoes wholesale reorganization to produce a pseudopod. Here, we describe a gene involved in sperm activation, spe-46. This gene was identified in a suppressor screen of spe-27(it132ts), a sperm-expressed gene whose product functions in the transduction of the spermatid activation signal. While spe-27(it132ts) worms are sterile at 25°C, the spe-46(hc197)I; spe-27(it132ts)IV double mutants regain partial fertility. Single nucleotide polymorphism mapping, whole genome sequencing, and transformation rescue were employed to identify the spe-46 coding sequence. It encodes a protein with seven predicted transmembrane domains but with no other predicted functional domains or homology outside of nematodes. Expression is limited to spermatogenic tissue, and a transcriptional GFP fusion shows expression corresponds with the onset of the pachytene stage of meiosis. The spe-46(hc197) mutation bypasses the need for the activation signal; mutant sperm activate prematurely without an activation signal in males, and mutant males are sterile. In an otherwise wild-type genome, the spe-46(hc197) mutation induces a sperm defective phenotype. In addition to premature activation, spe-46(hc197) sperm exhibit numerous defects including aneuploidy, vacuolization, protruding spikes, and precocious fusion of membranous organelles. Hemizygous worms [spe-46(hc197)/mnDf111] are effectively sterile. Thus, spe-46 appears to be involved in the regulation of spermatid activation during spermiogenesis, with the null phenotype being an absence of functional sperm and hypomorphic phenotypes being premature spermatid activation and numerous sperm cell defects.
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Affiliation(s)
- Wei-Siang Liau
- Department of Biological Science, California State Polytechnic University, Pomona, California, United States of America
| | - Ubaydah Nasri
- Department of Biological Science, California State Polytechnic University, Pomona, California, United States of America
| | - Daniel Elmatari
- Department of Biological Science, California State Polytechnic University, Pomona, California, United States of America
| | - Jason Rothman
- Department of Biological Science, California State Polytechnic University, Pomona, California, United States of America
| | - Craig W. LaMunyon
- Department of Biological Science, California State Polytechnic University, Pomona, California, United States of America
- * E-mail:
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23
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Abstract
The principle of commonly used methods to create mutations in the nematode Caenorhabditis elegans (C. elegans) is straightforward. In general, worms are exposed to a dose of mutagen resulting in DNA damages and mutations. Screening the progeny of the mutagenized animals for a certain phenotype is the regular forward genetic approach in C. elegans. A mutant selected from such a population is stabilized to recover a pure homozygous strain. In this chapter, we categorize the protocol into mutagenesis, phenotype screen, and outcross and provide time-tested procedures for their implementation to create long-lived worm mutants.
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Affiliation(s)
- Dayong Wang
- Key Laboratory of Developmental Genes and Human Diseases in Ministry of Education, Medical School of Southeast University, Nanjing, People's Republic of China
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24
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Palomares-Rius JE, Hedley PE, Cock PJA, Morris JA, Jones JT, Vovlas N, Blok V. Comparison of transcript profiles in different life stages of the nematode Globodera pallida under different host potato genotypes. Mol Plant Pathol 2012; 13:1120-34. [PMID: 22863280 PMCID: PMC6638826 DOI: 10.1111/j.1364-3703.2012.00821.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The potato cyst nematodes (PCNs) Globodera pallida and Globodera rostochiensis are important parasites of potato. PCNs undergo complex biotrophic interactions with their hosts that involve gene expression changes in both the nematode and the host plant. The aim of this study was to determine key genes that are differentially expressed in Globodera pallida life cycle stages and during the initiation of the feeding site in susceptible and partially resistant potato genotypes. For this purpose, two microarray experiments were designed: (i) a comparison of eggs, infective second-stage juveniles (J2s) and sedentary parasitic-stage J2s (SJ2); (ii) a comparison of SJ2s at 8 days after inoculation (DAI) in the susceptible cultivar (Desirée) and two partially resistant lines. The results showed differential expression of G. pallida genes during the stages studied, including previously characterized effectors. In addition, a large number of genes changed their expression between SJ2s in the susceptible cultivar and those infecting partially resistant lines; the number of genes with modified expression was lower when the two partially resistant lines were compared. Moreover, a histopathological study was performed at several time points (7, 14 and 30 DAI) and showed the similarities between both partially resistant lines with a delay and degeneration in the formation of the syncytia in comparison with the susceptible cultivar. Females at 30 DAI in partially resistant lines showed a delay in their development in comparison with those in the susceptible cultivar.
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Affiliation(s)
- Juan E Palomares-Rius
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
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25
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Abstract
Dietary restriction (DR) extends lifespan in man species and modulates evolutionary conserved signalling and metabolic pathways. Most of these studies were done in adult animals. Here we investigated fat phenotypes of C. elegans larvae and adults which were exposed to DR during development. This approach was named "developmental-DR" (dDR). Moderate as well as stringent dDR increased the triglyceride to protein ratio in L4 larvae and adult worms. This alteration was accompanied by a marked expansion of intestinal and hypodermal lipid droplets. In comparison to ad libitum condition, the relative proportion of fat stored in large lipid droplets (>50 µm(3)) was increased by a factor of about 5 to 6 in larvae exposed to dDR. Microarray-based expression profiling identified several dDR-regulated genes of lipolysis and lipogenesis which may contribute to the observed fat phenotypes. In conclusion, dDR increases the triglyceride to protein ratio, enlarges lipid droplets and alters the expression of genes functioning in lipid metabolism in C. elegans. These changes might be an effective adaptation to conserve fat stores in animals subjected to limiting food supply during development.
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Affiliation(s)
| | | | - Frank Döring
- Department of Molecular Prevention, Institute of Human Nutrition and Food Science, Christian-Albrechts-University of Kiel, Kiel, Germany
- * E-mail:
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26
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Tacutu R, Shore DE, Budovsky A, de Magalhães JP, Ruvkun G, Fraifeld VE, Curran SP. Prediction of C. elegans longevity genes by human and worm longevity networks. PLoS One 2012; 7:e48282. [PMID: 23144747 PMCID: PMC3483217 DOI: 10.1371/journal.pone.0048282] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 09/21/2012] [Indexed: 11/18/2022] Open
Abstract
Intricate and interconnected pathways modulate longevity, but screens to identify the components of these pathways have not been saturating. Because biological processes are often executed by protein complexes and fine-tuned by regulatory factors, the first-order protein-protein interactors of known longevity genes are likely to participate in the regulation of longevity. Data-rich maps of protein interactions have been established for many cardinal organisms such as yeast, worms, and humans. We propose that these interaction maps could be mined for the identification of new putative regulators of longevity. For this purpose, we have constructed longevity networks in both humans and worms. We reasoned that the essential first-order interactors of known longevity-associated genes in these networks are more likely to have longevity phenotypes than randomly chosen genes. We have used C. elegans to determine whether post-developmental inactivation of these essential genes modulates lifespan. Our results suggest that the worm and human longevity networks are functionally relevant and possess a high predictive power for identifying new longevity regulators.
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Affiliation(s)
- Robi Tacutu
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - David E. Shore
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Arie Budovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vadim E. Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail: (VEF); (SPC)
| | - Sean P. Curran
- Division of Biogerontology, Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Department of Molecular and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (VEF); (SPC)
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27
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Chalmers IW, Hoffmann KF. Platyhelminth Venom Allergen-Like (VAL) proteins: revealing structural diversity, class-specific features and biological associations across the phylum. Parasitology 2012; 139:1231-45. [PMID: 22717097 PMCID: PMC3435950 DOI: 10.1017/s0031182012000704] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/23/2012] [Accepted: 03/23/2012] [Indexed: 12/31/2022]
Abstract
During platyhelminth infection, a cocktail of proteins is released by the parasite to aid invasion, initiate feeding, facilitate adaptation and mediate modulation of the host immune response. Included amongst these proteins is the Venom Allergen-Like (VAL) family, part of the larger sperm coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) superfamily. To explore the significance of this protein family during Platyhelminthes development and host interactions, we systematically summarize all published proteomic, genomic and immunological investigations of the VAL protein family to date. By conducting new genomic and transcriptomic interrogations to identify over 200 VAL proteins (228) from species in all 4 traditional taxonomic classes (Trematoda, Cestoda, Monogenea and Turbellaria), we further expand our knowledge related to platyhelminth VAL diversity across the phylum. Subsequent phylogenetic and tertiary structural analyses reveal several class-specific VAL features, which likely indicate a range of roles mediated by this protein family. Our comprehensive analysis of platyhelminth VALs represents a unifying synopsis for understanding diversity within this protein family and a firm context in which to initiate future functional characterization of these enigmatic members.
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Affiliation(s)
- Iain W Chalmers
- Institute of Biological, Environmental and Rural Sciences, Edward Llwyd Building, Penglais Campus, Aberystwyth University, Aberystwyth SY23 3DA, UK.
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28
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Fu Y, Lan J, Zhang Z, Hou R, Wu X, Yang D, Zhang R, Zheng W, Nie H, Xie Y, Yan N, Yang Z, Wang C, Luo L, Liu L, Gu X, Wang S, Peng X, Yang G. Novel insights into the transcriptome of Dirofilaria immitis. PLoS One 2012; 7:e41639. [PMID: 22911833 PMCID: PMC3402454 DOI: 10.1371/journal.pone.0041639] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 06/22/2012] [Indexed: 01/17/2023] Open
Abstract
Background The heartworm Dirofilaria immitis is the causal agent of cardiopulmonary dirofilariosis in dogs and cats, and also infects a wide range of wild mammals as well as humans. One bottleneck for the design of fundamentally new intervention and management strategies against D. immitis may be the currently limited knowledge of fundamental molecular aspects of D. immitis. Methodology/Principal Findings A next-generation sequencing platform combining computational approaches was employed to assess a global view of the heartworm transcriptome. A total of 20,810 unigenes (mean length = 1,270 bp) were assembled from 22.3 million clean reads. From these, 15,698 coding sequences (CDS) were inferred, and about 85% of the unigenes had orthologs/homologs in public databases. Comparative transcriptomic study uncovered 4,157 filarial-specific genes as well as 3,795 genes potentially involved in filarial-Wolbachia symbiosis. In addition, the potential intestine transcriptome of D. immitis (1,101 genes) was mined for the first time, which might help to discover ‘hidden antigens’. Conclusions/Significance This study provides novel insights into the transcriptome of D. immitis and sheds light on its molecular processes and survival mechanisms. Furthermore, it provides a platform to discover new vaccine candidates and potential targets for new drugs against dirofilariosis.
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Affiliation(s)
- Yan Fu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Jingchao Lan
- The Sichuan Key Laboratory for Conservation Biology on Endangered Wildlife – Developing toward a State Key Laboratory for China, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Zhihe Zhang
- The Sichuan Key Laboratory for Conservation Biology on Endangered Wildlife – Developing toward a State Key Laboratory for China, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology on Endangered Wildlife – Developing toward a State Key Laboratory for China, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Xuhang Wu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Deying Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Runhui Zhang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Wanpeng Zheng
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Huaming Nie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Ning Yan
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Zhi Yang
- The Sichuan Key Laboratory for Conservation Biology on Endangered Wildlife – Developing toward a State Key Laboratory for China, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Chengdong Wang
- The Sichuan Key Laboratory for Conservation Biology on Endangered Wildlife – Developing toward a State Key Laboratory for China, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Li Luo
- The Sichuan Key Laboratory for Conservation Biology on Endangered Wildlife – Developing toward a State Key Laboratory for China, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Li Liu
- The Sichuan Key Laboratory for Conservation Biology on Endangered Wildlife – Developing toward a State Key Laboratory for China, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Shuxian Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Ya’an, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, China
- * E-mail:
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29
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Abstract
Caenorhabditis elegans enter an alternate developmental stage called dauer in unfavorable conditions such as starvation, overcrowding, or high temperature. Several evolutionarily conserved signaling pathways control dauer formation. DAF-7/TGFβ and serotonin, important ligands in these signaling pathways, affect not only dauer formation, but also the expression of one another. The heterotrimeric G proteins GOA-1 (Gαo) and EGL-30 (Gαq) mediate serotonin signaling as well as serotonin biosynthesis in C. elegans. It is not known whether GOA-1 or EGL-30 also affect dauer formation and/or daf-7 expression, which are both modulated in part by serotonin. The purpose of this study is to better understand the relationship between proteins important for neuronal signaling and developmental plasticity in both C. elegans and humans. Using promoter-GFP transgenic worms, it was determined that both goa-1 and egl-30 regulate daf-7 expression during larval development. In addition, the normal daf-7 response to high temperature or starvation was altered in goa-1 and egl-30 mutants. Despite the effect of goa-1 and egl-30 mutations on daf-7 expression in various environmental conditions, there was no effect of the mutations on dauer formation. This paper provides evidence that while goa-1 and egl-30 are important for normal daf-7 expression, mutations in these genes are not sufficient to disrupt dauer formation.
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Affiliation(s)
- Edith M Myers
- Department of Biological and Allied Health Sciences, Fairleigh Dickinson University, College at Florham, Madison, New Jersey, United States of America.
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30
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Mullen GP, Grundahl KM, Gu M, Watanabe S, Hobson RJ, Crowell JA, McManus JR, Mathews EA, Jorgensen EM, Rand JB. UNC-41/stonin functions with AP2 to recycle synaptic vesicles in Caenorhabditis elegans. PLoS One 2012; 7:e40095. [PMID: 22808098 PMCID: PMC3393740 DOI: 10.1371/journal.pone.0040095] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 05/31/2012] [Indexed: 11/20/2022] Open
Abstract
The recycling of synaptic vesicles requires the recovery of vesicle proteins and membrane. Members of the stonin protein family (Drosophila Stoned B, mammalian stonin 2) have been shown to link the synaptic vesicle protein synaptotagmin to the endocytic machinery. Here we characterize the unc-41 gene, which encodes the stonin ortholog in the nematode Caenorhabditis elegans. Transgenic expression of Drosophila stonedB rescues unc-41 mutant phenotypes, demonstrating that UNC-41 is a bona fide member of the stonin family. In unc-41 mutants, synaptotagmin is present in axons, but is mislocalized and diffuse. In contrast, UNC-41 is localized normally in synaptotagmin mutants, demonstrating a unidirectional relationship for localization. The phenotype of snt-1 unc-41 double mutants is stronger than snt-1 mutants, suggesting that UNC-41 may have additional, synaptotagmin-independent functions. We also show that unc-41 mutants have defects in synaptic vesicle membrane endocytosis, including a ∼50% reduction of vesicles in both acetylcholine and GABA motor neurons. These endocytic defects are similar to those observed in apm-2 mutants, which lack the µ2 subunit of the AP2 adaptor complex. However, no further reduction in synaptic vesicles was observed in unc-41 apm-2 double mutants, suggesting that UNC-41 acts in the same endocytic pathway as µ2 adaptin.
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Affiliation(s)
- Gregory P. Mullen
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Kiely M. Grundahl
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Mingyu Gu
- Howard Hughes Medical Institute and Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Shigeki Watanabe
- Howard Hughes Medical Institute and Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Robert J. Hobson
- Howard Hughes Medical Institute and Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - John A. Crowell
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - John R. McManus
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Eleanor A. Mathews
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Erik M. Jorgensen
- Howard Hughes Medical Institute and Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - James B. Rand
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- * E-mail:
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31
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Mbanefo EC, Chuanxin Y, Kikuchi M, Shuaibu MN, Boamah D, Kirinoki M, Hayashi N, Chigusa Y, Osada Y, Hamano S, Hirayama K. Origin of a novel protein-coding gene family with similar signal sequence in Schistosoma japonicum. BMC Genomics 2012; 13:260. [PMID: 22716200 PMCID: PMC3434034 DOI: 10.1186/1471-2164-13-260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 06/11/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Evolution of novel protein-coding genes is the bedrock of adaptive evolution. Recently, we identified six protein-coding genes with similar signal sequence from Schistosoma japonicum egg stage mRNA using signal sequence trap (SST). To find the mechanism underlying the origination of these genes with similar core promoter regions and signal sequence, we adopted an integrated approach utilizing whole genome, transcriptome and proteome database BLAST queries, other bioinformatics tools, and molecular analyses. RESULTS Our data, in combination with database analyses showed evidences of expression of these genes both at the mRNA and protein levels exclusively in all developmental stages of S. japonicum. The signal sequence motif was identified in 27 distinct S. japonicum UniGene entries with multiple mRNA transcripts, and in 34 genome contigs distributed within 18 scaffolds with evidence of genome-wide dispersion. No homolog of these genes or similar domain was found in deposited data from any other organism. We observed preponderance of flanking repetitive elements (REs), albeit partial copies, especially of the RTE-like and Perere class at either side of the duplication source locus. The role of REs as major mediators of DNA-level recombination leading to dispersive duplication is discussed with evidence from our analyses. We also identified a stepwise pathway towards functional selection in evolving genes by alternative splicing. Equally, the possible transcription models of some protein-coding representatives of the duplicons are presented with evidence of expression in vitro. CONCLUSION Our findings contribute to the accumulating evidence of the role of REs in the generation of evolutionary novelties in organisms' genomes.
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Affiliation(s)
- Evaristus Chibunna Mbanefo
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University, 1-12-4 Sakamoto, 852-8523, Nagasaki, Japan
- Department of Parasitology and Entomology, Faculty of Bioscience, Nnamdi Azikiwe University, P.M.B. 5025, Awka, Nigeria
| | - Yu Chuanxin
- Laboratory on Technology for Parasitic Disease Prevention and Control, Jiangsu Institute of Parasitic Diseases, 117 Yangxiang, Meiyuan, Wuxi, 214064, People's Republic of China
| | - Mihoko Kikuchi
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University, 1-12-4 Sakamoto, 852-8523, Nagasaki, Japan
| | - Mohammed Nasir Shuaibu
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University, 1-12-4 Sakamoto, 852-8523, Nagasaki, Japan
| | - Daniel Boamah
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University, 1-12-4 Sakamoto, 852-8523, Nagasaki, Japan
| | - Masashi Kirinoki
- Laboratory of Tropical Medicine and Parasitology, Dokkyo Medical University, Tochigi, Japan
| | - Naoko Hayashi
- Laboratory of Tropical Medicine and Parasitology, Dokkyo Medical University, Tochigi, Japan
| | - Yuichi Chigusa
- Laboratory of Tropical Medicine and Parasitology, Dokkyo Medical University, Tochigi, Japan
| | - Yoshio Osada
- Department of Immunology and Parasitology, The University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Shinjiro Hamano
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University, 1-12-4 Sakamoto, 852-8523, Nagasaki, Japan
| | - Kenji Hirayama
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), and Global COE Program, Nagasaki University, 1-12-4 Sakamoto, 852-8523, Nagasaki, Japan
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32
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Abstract
Early endosomal membrane compartments are required for the formation and recycling of synaptic vesicles, but how these compartments are regulated is incompletely understood. We performed a forward genetic screen in C. elegans for mutations that affect RAB-5 labeled early endosomal compartments in GABAergic motoneurons. Here we report the isolation and characterization of one mutation, rabx-5. The rabx-5 mutation leads to decreased intensity of YFP::RAB-5 in the cell soma but increased intensity in the synaptic and intersynaptic regions of the axon. This effect is due to the bias of the cycling state of RAB-5, and results from a change in the organization of the early endosomal compartment as well as the membrane binding state of RAB-5. Synaptic vesicle accumulation is altered in rabx-5 mutants, and synaptic transmission from cholinergic neurons is decreased. Early endosomal membrane compartments show disorganization with ageing and rabx-5 mutant animals age faster. These results suggest that rabx-5 regulation of RAB-5 compartments is important for maintaining proper synaptic function throughout the lifetime.
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Affiliation(s)
- Sharon B. Sann
- Neurobiology Section, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (SS); (YJ)
| | - Matthew M. Crane
- Interdisciplinary Program in Bioengineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Hang Lu
- Interdisciplinary Program in Bioengineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Yishi Jin
- Neurobiology Section, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- Howard Hughes Medical Institute University of California San Diego, La Jolla, California, United States of America
- * E-mail: (SS); (YJ)
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Tsyusko OV, Unrine JM, Spurgeon D, Blalock E, Starnes D, Tseng M, Joice G, Bertsch PM. Toxicogenomic responses of the model organism Caenorhabditis elegans to gold nanoparticles. Environ Sci Technol 2012; 46:4115-24. [PMID: 22372763 DOI: 10.1021/es2033108] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We used Au nanoparticles (Au-NPs) as a model for studying particle-specific effects of manufactured nanomaterials (MNMs) by examining the toxicogenomic responses in a model soil organism, Caenorhabditis elegans . Global genome expression for nematodes exposed to 4-nm citrate-coated Au-NPs at the LC(10) level (5.9 mg·L(-1)) revealed significant differential expression of 797 genes. The levels of expression for five genes (apl-1, dyn-1, act-5, abu-11, and hsp-4) were confirmed independently with qRT-PCR. Seven common biological pathways associated with 38 of these genes were identified. Up-regulation of 26 pqn/abu genes from noncanonical unfolded protein response (UPR) pathway and molecular chaperones (hsp-16.1, hsp-70, hsp-3, and hsp-4) were observed and are likely indicative of endoplasmic reticulum stress. Significant increase in sensitivity to Au-NPs in a mutant from noncanonical UPR (pqn-5) suggests possible involvement of the genes from this pathway in a protective mechanism against Au-NPs. Significant responses to Au-NPs in endocytosis mutants (chc-1 and rme-2) provide evidence for endocytosis pathway being induced by Au-NPs. These results demonstrate that Au-NPs are bioavailable and cause adverse effects to C. elegans by activating both general and specific biological pathways. The experiments with mutants further support involvement of several of these pathways in Au-NP toxicity and/or detoxification.
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Affiliation(s)
- Olga V Tsyusko
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, United States.
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Cox-Paulson EA, Grana TM, Harris MA, Batzli JM. Studying human disease genes in Caenorhabditis elegans: a molecular genetics laboratory project. CBE Life Sci Educ 2012; 11:165-79. [PMID: 22665589 PMCID: PMC3366902 DOI: 10.1187/cbe-11-06-0045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Scientists routinely integrate information from various channels to explore topics under study. We designed a 4-wk undergraduate laboratory module that used a multifaceted approach to study a question in molecular genetics. Specifically, students investigated whether Caenorhabditis elegans can be a useful model system for studying genes associated with human disease. In a large-enrollment, sophomore-level laboratory course, groups of three to four students were assigned a gene associated with either breast cancer (brc-1), Wilson disease (cua-1), ovarian dysgenesis (fshr-1), or colon cancer (mlh-1). Students compared observable phenotypes of wild-type C. elegans and C. elegans with a homozygous deletion in the assigned gene. They confirmed the genetic deletion with nested polymerase chain reaction and performed a bioinformatics analysis to predict how the deletion would affect the encoded mRNA and protein. Students also performed RNA interference (RNAi) against their assigned gene and evaluated whether RNAi caused a phenotype similar to that of the genetic deletion. As a capstone activity, students prepared scientific posters in which they presented their data, evaluated whether C. elegans was a useful model system for studying their assigned genes, and proposed future directions. Assessment showed gains in understanding genotype versus phenotype, RNAi, common bioinformatics tools, and the utility of model organisms.
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Sancar F, Touroutine D, Gao S, Oh HJ, Gendrel M, Bessereau JL, Kim H, Zhen M, Richmond JE. The dystrophin-associated protein complex maintains muscle excitability by regulating Ca(2+)-dependent K(+) (BK) channel localization. J Biol Chem 2011; 286:33501-10. [PMID: 21795674 PMCID: PMC3190934 DOI: 10.1074/jbc.m111.227678] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 07/07/2011] [Indexed: 11/06/2022] Open
Abstract
The dystrophin-associated protein complex (DAPC) consists of several transmembrane and intracellular scaffolding elements that have been implicated in maintaining the structure and morphology of the vertebrate neuromuscular junction (NMJ). Genetic linkage analysis has identified loss-of-function mutations in DAPC genes that give rise to degenerative muscular dystrophies. Although much is known about the involvement of the DAPC in maintaining muscle integrity, less is known about the precise contribution of the DAPC in cell signaling events. To better characterize the functional role of the DAPC at the NMJ, we used electrophysiology, immunohistochemistry, and fluorescent labeling to directly assess cholinergic synaptic transmission, ion channel localization, and muscle excitability in loss-of-function (lf) mutants of Caenorhabditis elegans DAPC homologues. We found that all DAPC mutants consistently display mislocalization of the Ca(2+)-gated K(+) channel, SLO-1, in muscle cells, while ionotropic acetylcholine receptor (AChR) expression and localization at the NMJ remained unaltered. Synaptic cholinergic signaling was also not significantly impacted across DAPC(lf) mutants. Consistent with these findings and the postsynaptic mislocalization of SLO-1, we observed an increase in muscle excitability downstream of cholinergic signaling. Based on our results, we conclude that the DAPC is not involved in regulating AChR architecture at the NMJ, but rather functions to control muscle excitability, in an activity-dependent manner, through the proper localization of SLO-1 channels.
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Affiliation(s)
- Feyza Sancar
- From the Department of Biological Sciences, University of Illinois-Chicago, Chicago, Illinois 60607
| | - Denis Touroutine
- the Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Shangbang Gao
- the Samuel Lunenfeld Research Institute, University of Toronto, Toronto, Ontario M5G 1X5, Canada
| | - Hyun J. Oh
- the Department of Cell Biology and Anatomy, Rosalind Franklin University of Science and Medicine, North Chicago, Illinois 60064
| | - Marie Gendrel
- the Biology Department, Institut de Biologie de l'Ecole Normale Superieure, F-75005 Paris, France
| | - Jean-Louis Bessereau
- the Biology Department, Institut de Biologie de l'Ecole Normale Superieure, F-75005 Paris, France
- the Inserm, Unite 1024, F-75005 Paris, France, and
- the Centre National de la Recherche Scientifique, Unit e Mixte de Recherche 8197, F-75005 Paris, France
| | - Hongkyun Kim
- the Department of Cell Biology and Anatomy, Rosalind Franklin University of Science and Medicine, North Chicago, Illinois 60064
| | - Mei Zhen
- the Samuel Lunenfeld Research Institute, University of Toronto, Toronto, Ontario M5G 1X5, Canada
| | - Janet E. Richmond
- From the Department of Biological Sciences, University of Illinois-Chicago, Chicago, Illinois 60607
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Maule AG, McVeigh P, Dalzell JJ, Atkinson L, Mousley A, Marks NJ. An eye on RNAi in nematode parasites. Trends Parasitol 2011; 27:505-13. [PMID: 21885343 DOI: 10.1016/j.pt.2011.07.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/27/2011] [Accepted: 07/29/2011] [Indexed: 11/19/2022]
Abstract
RNA interference (RNAi) has revolutionised approaches to gene function determination. From a parasitology perspective, gene function studies have the added dimension of providing validation data, increasingly deemed essential to the initial phases of drug target selection, pre-screen development. Notionally advantageous to those working on nematode parasites is the fact that Caenorhabditis elegans research spawned RNAi discovery and continues to seed our understanding of its fundamentals. Unfortunately, RNAi data for nematode parasites illustrate variable and inconsistent susceptibilities which undermine confidence and exploitation. Now well-ensconced in an era of nematode parasite genomics, we can begin to unscramble this variation.
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Affiliation(s)
- Aaron G Maule
- Molecular Bioscience-Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK.
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Laing R, Hunt M, Protasio AV, Saunders G, Mungall K, Laing S, Jackson F, Quail M, Beech R, Berriman M, Gilleard JS. Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans. PLoS One 2011; 6:e23216. [PMID: 21858033 PMCID: PMC3156134 DOI: 10.1371/journal.pone.0023216] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/12/2011] [Indexed: 11/30/2022] Open
Abstract
The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes.
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Affiliation(s)
- Roz Laing
- Welcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Faculty of Veterinary Medicine, University of Glasgow, Glasgow, Strathclyde, United Kingdom
| | - Martin Hunt
- Welcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Anna V. Protasio
- Welcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gary Saunders
- Faculty of Veterinary Medicine, University of Glasgow, Glasgow, Strathclyde, United Kingdom
| | - Karen Mungall
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven Laing
- Faculty of Veterinary Medicine, University of Glasgow, Glasgow, Strathclyde, United Kingdom
| | - Frank Jackson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, United Kingdom
| | - Michael Quail
- Welcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Robin Beech
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
| | - Matthew Berriman
- Welcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - John S. Gilleard
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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Abstract
With the growing number of microRNAs (miRNAs) being identified each year, more innovative molecular tools are required to efficiently characterize these small RNAs in living animal systems. Caenorhabditis elegans is a powerful model to study how miRNAs regulate gene expression and control diverse biological processes during development and in the adult. Genetic strategies such as large-scale miRNA deletion studies in nematodes have been used with limited success since the majority of miRNA genes do not exhibit phenotypes when individually mutated. Recent work has indicated that miRNAs function in complex regulatory networks with other small RNAs and protein-coding genes, and therefore the challenge will be to uncover these functional redundancies. The use of miRNA inhibitors such as synthetic antisense 2'-O-methyl oligoribonucleotides is emerging as a promising in vivo approach to dissect out the intricacies of miRNA regulation.
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Affiliation(s)
- Jeanyoung Jo
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23507, USA
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Piao X, Cai P, Liu S, Hou N, Hao L, Yang F, Wang H, Wang J, Jin Q, Chen Q. Global expression analysis revealed novel gender-specific gene expression features in the blood fluke parasite Schistosoma japonicum. PLoS One 2011; 6:e18267. [PMID: 21494327 PMCID: PMC3071802 DOI: 10.1371/journal.pone.0018267] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 02/24/2011] [Indexed: 01/17/2023] Open
Abstract
Background Schistosoma japonicum is one of the remarkable
Platyhelminths that are endemic in China and Southeast Asian countries. The
parasite is dioecious and can reside inside the host for many years. Rapid
reproduction by producing large number of eggs and count-react host
anti-parasite responses are the strategies that benefit long term survival
of the parasite. Praziquantel is currently the only drug that is effective
against the worms. Development of novel antiparasite reagents and
immune-prevention measures rely on the deciphering of parasite biology. The
decoding of the genomic sequence of the parasite has made it possible to
dissect the functions of genes that govern the development of the parasite.
In this study, the polyadenylated transcripts from male and female
S. japonicum were isolated for deep sequencing and the
sequences were systematically analysed. Results First, the number of genes actively expressed in the two sexes of S.
japonicum was similar, but around 50% of genes were
biased to either male or female in expression. Secondly, it was, at the
first time, found that more than 50% of the coding region of the
genome was transcribed from both strands. Among them, 65% of the
genes had sense and their cognate antisense transcripts co-expressed,
whereas 35% had inverse relationship between sense and antisense
transcript abundance. Further, based on gene ontological analysis, more than
2,000 genes were functionally categorized and biological pathways that are
differentially functional in male or female parasites were elucidated. Conclusions Male and female schistosomal parasites differ in gene expression patterns,
many metabolic and biological pathways have been identified in this study
and genes differentially expressed in gender specific manner were presented.
Importantly, more than 50% of the coding regions of the S.
japonicum genome transcribed from both strands, antisense
RNA-mediated gene regulation might play a critical role in the parasite
biology.
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Affiliation(s)
- Xianyu Piao
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Pengfei Cai
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuai Liu
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Hou
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lili Hao
- College of Life Science and Technology,
Southwest University of Nationalities, Chengdu, Sichuan, China
| | - Fan Yang
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Heng Wang
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Jin
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qijun Chen
- Laboratory of Parasitology, Institute of
Pathogen Biology/Institute of Basic Medical Sciences, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory for Molecular Virology
and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of
Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Zoonosis, Ministry of
Education, Institute of Zoonosis, Jilin University, Changchun, China
- * E-mail:
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Marsh EK, van den Berg MCW, May RC. A two-gene balance regulates Salmonella typhimurium tolerance in the nematode Caenorhabditis elegans. PLoS One 2011; 6:e16839. [PMID: 21399680 PMCID: PMC3047536 DOI: 10.1371/journal.pone.0016839] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 01/03/2011] [Indexed: 12/21/2022] Open
Abstract
Lysozymes are antimicrobial enzymes that perform a critical role in resisting infection in a wide-range of eukaryotes. However, using the nematode Caenorhabditis elegans as a model host we now demonstrate that deletion of the protist type lysozyme LYS-7 renders animals susceptible to killing by the fatal fungal human pathogen Cryptococcus neoformans, but, remarkably, enhances tolerance to the enteric bacteria Salmonella Typhimurium. This trade-off in immunological susceptibility in C. elegans is further mediated by the reciprocal activity of lys-7 and the tyrosine kinase abl-1. Together this implies a greater complexity in C. elegans innate immune function than previously thought.
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Affiliation(s)
- Elizabeth K. Marsh
- School of Biosciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
| | | | - Robin C. May
- School of Biosciences, University of Birmingham, Birmingham, West Midlands, United Kingdom
- * E-mail:
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O'Rourke SM, Carter C, Carter L, Christensen SN, Jones MP, Nash B, Price MH, Turnbull DW, Garner AR, Hamill DR, Osterberg VR, Lyczak R, Madison EE, Nguyen MH, Sandberg NA, Sedghi N, Willis JH, Yochem J, Johnson EA, Bowerman B. A survey of new temperature-sensitive, embryonic-lethal mutations in C. elegans: 24 alleles of thirteen genes. PLoS One 2011; 6:e16644. [PMID: 21390299 PMCID: PMC3046959 DOI: 10.1371/journal.pone.0016644] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/04/2011] [Indexed: 11/18/2022] Open
Abstract
To study essential maternal gene requirements in the early C. elegans embryo, we have screened for temperature-sensitive, embryonic lethal mutations in an effort to bypass essential zygotic requirements for such genes during larval and adult germline development. With conditional alleles, multiple essential requirements can be examined by shifting at different times from the permissive temperature of 15°C to the restrictive temperature of 26°C. Here we describe 24 conditional mutations that affect 13 different loci and report the identity of the gene mutations responsible for the conditional lethality in 22 of the mutants. All but four are mis-sense mutations, with two mutations affecting splice sites, another creating an in-frame deletion, and one creating a premature stop codon. Almost all of the mis-sense mutations affect residues conserved in orthologs, and thus may be useful for engineering conditional mutations in other organisms. We find that 62% of the mutants display additional phenotypes when shifted to the restrictive temperature as L1 larvae, in addition to causing embryonic lethality after L4 upshifts. Remarkably, we also found that 13 out of the 24 mutations appear to be fast-acting, making them particularly useful for careful dissection of multiple essential requirements. Our findings highlight the value of C. elegans for identifying useful temperature-sensitive mutations in essential genes, and provide new insights into the requirements for some of the affected loci.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bruce Bowerman
- The Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
- * E-mail:
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Wang G, Peng D, Sun J, Huang W, Peng H, Long H. [Cloning and sequence analysis of a new cathepsin L-like cysteine proteinase gene from Ditylenchus destructor]. Sheng Wu Gong Cheng Xue Bao 2011; 27:60-68. [PMID: 21553491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Cathepsin L-like cysteine proteinase genes (cpls) are multifunction genes related to the parasitic abilities of plant parasitic nematodes. A new cathepsin L-like cysteine proteinase gene (Dd-cpl-1) (GenBank Accession GQ 180107) was cloned from Ditylenchus destructor by RT-PCR and RACE. The cDNA sequence consisted of a 1 131 bp open reading frame (ORF) encoding 376 amino acid residues that were franked by a 29 bp 5'-untranslated region (UTR) and a 159 bp 3'-UTR. Genomic sequence analysis showed that Dd-cpl-1 contained 7 introns, obeyed the GT/AG rule in the splice-site junctions. Homology analysis showed that the identity was 77% between Dd-cpl-1 deduced protein Dd-CPL-1 and cathepsin L-like cysteine proteinase of Bursaphelenchus xylophilus. Multi-sequence alignment indicated that there were the catalytic triad (Cys183, His322 and Asn343) and two motifs ERFNIN motif and GNFD motif in deduced protein Dd-CPL-1. Cysteine proteinases phylogenetic analysis showed that Dd-cpl-1 belonged to the sub-clade of cathepsin L-like cysteine proteinases.
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Affiliation(s)
- Gaofeng Wang
- College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
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Fujiwara M, Teramoto T, Ishihara T, Ohshima Y, McIntire SL. A novel zf-MYND protein, CHB-3, mediates guanylyl cyclase localization to sensory cilia and controls body size of Caenorhabditis elegans. PLoS Genet 2010; 6:e1001211. [PMID: 21124861 PMCID: PMC2991246 DOI: 10.1371/journal.pgen.1001211] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 10/19/2010] [Indexed: 12/01/2022] Open
Abstract
Cilia are important sensory organelles, which are thought to be essential regulators of numerous signaling pathways. In Caenorhabditis elegans, defects in sensory cilium formation result in a small-body phenotype, suggesting the role of sensory cilia in body size determination. Previous analyses suggest that lack of normal cilia causes the small-body phenotype through the activation of a signaling pathway which consists of the EGL-4 cGMP-dependent protein kinase and the GCY-12 receptor-type guanylyl cyclase. By genetic suppressor screening of the small-body phenotype of a cilium defective mutant, we identified a chb-3 gene. Genetic analyses placed chb-3 in the same pathway as egl-4 and gcy-12 and upstream of egl-4. chb-3 encodes a novel protein, with a zf-MYND motif and ankyrin repeats, that is highly conserved from worm to human. In chb-3 mutants, GCY-12 guanylyl cyclase visualized by tagged GFP (GCY-12::GFP) fails to localize to sensory cilia properly and accumulates in cell bodies. Our analyses suggest that decreased GCY-12 levels in the cilia of chb-3 mutants may cause the suppression of the small-body phenotype of a cilium defective mutant. By observing the transport of GCY-12::GFP particles along the dendrites to the cilia in sensory neurons, we found that the velocities and the frequencies of the particle movement are decreased in chb-3 mutant animals. How membrane proteins are trafficked to cilia has been the focus of extensive studies in vertebrates and invertebrates, although only a few of the relevant proteins have been identified. Our study defines a new regulator, CHB-3, in the trafficking process and also shows the importance of ciliary targeting of the signaling molecule, GCY-12, in sensory-dependent body size regulation in C. elegans. Given that CHB-3 is highly conserved in mammal, a similar system may be used in the trafficking of signaling proteins to the cilia of other species. Caenorhabditis elegans is a 1–2 mm long nematode. Its body size is controlled by sensory inputs; some mutants with defects in sensory perception grow into small size (20%–30% decrease in body volume), although the animals seem to feed normally. The EGL-4 cGMP-dependent protein kinase and the GCY-12 guanylyl cyclase act in sensory neurons to control body size downstream of sensory inputs. GCY-12 is localized to cilia, antenna-like cellular structures of sensory neurons. In the cilia, a number of signaling molecules are localized. Dysfunction of cilia is known to cause several human disorders such as Bardet-Biedl syndrome, illustrating the importance of these organelles. In this study, we identified a novel protein, CHB-3, involved in sensory-dependent body size regulation. Our analyses suggest that CHB-3 protein regulates the trafficking of GCY-12 from the cell bodies to the cilia. Without CHB-3 protein, GCY-12 fails to localize to cilia and body size is not controlled properly. Thus, the cilia are a special place for sensory information processing in body size regulation. Our analyses identified CHB-3 as a novel trafficking regulator of ciliary protein(s).
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Affiliation(s)
- Manabi Fujiwara
- Department of Biology, Kyushu University, Hakozaki, Higashi-ku, Fukuoka, Japan.
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Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS One 2010; 5:e13922. [PMID: 21085631 PMCID: PMC2978686 DOI: 10.1371/journal.pone.0013922] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 10/14/2010] [Indexed: 11/18/2022] Open
Abstract
Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication.
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Affiliation(s)
- Katherine P. Weber
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Subhajyoti De
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | | | - M. Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Mario de Bono
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- * E-mail:
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Du J, Zhang W, Wang YN, Wang J, Wang SJ, Zhang Y, Gao P, Li JY, Zhao W. [Cloning, expression and immunologic identification of Eg10 gene of Echinococcus granulosus]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi 2010; 28:339-342. [PMID: 21351544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
OBJECTIVE To clone and express Eg10 gene of Echinococcus granulosus, and investigate the immunological characteristic of the recombinant. METHODS Eg10 gene was subcloned into pET28a vector. The recombinant plasmid was transformed into E. coli BL21 and induced with IPTG. The recombinant protein was purified with His-bind purification kit. Forty-eight mice were randomly divided into 4 groups. Mice in groups A and B were injected with PBS and PBS+Freund's adjuvant (100 microl) as control. Mice in groups C and D were immunized with 10 mg and 50 microg purified Eg10 antigen formulated in Freund's adjuvant, respectively. All the mice received three immunizations at 2-week intervals with the same dose of antigen. Serum samples were collected at pre-immunization and certain time after immunization. The immunological characteristics of recombinant Eg10 was analyzed by Western blotting and ELISA. RESULTS The recombinant Eg10 protein (Mr 31 000) was expressed in E. coli BL21. The recombinant Eg10 and expression product of PET28a/Eg10 were recognized by sera from mice immunized with recombinant Eg10. ELISA showed that the titer of IgG reached a peak at the 8th week in groups C and D, the level of IgG in sera of groups C or D was higher than that of groups A or B (P < 0.05) at the 2nd, 4th, 6th, 8th, and 10th week. There was no significant difference in the level of IgG between group C and group D (P > 0.05). CONCLUSION The Eg10 gene has been expressed with immunogenicity.
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Affiliation(s)
- Juan Du
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China
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Thyagarajan B, Blaszczak AG, Chandler KJ, Watts JL, Johnson WE, Graves BJ. ETS-4 is a transcriptional regulator of life span in Caenorhabditis elegans. PLoS Genet 2010; 6:e1001125. [PMID: 20862312 PMCID: PMC2940738 DOI: 10.1371/journal.pgen.1001125] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 08/13/2010] [Indexed: 01/05/2023] Open
Abstract
Aging is a complex phenotype responsive to a plethora of environmental inputs; yet only a limited number of transcriptional regulators are known to influence life span. How the downstream expression programs mediated by these factors (or others) are coordinated into common or distinct set of aging effectors is an addressable question in model organisms, such as C. elegans. Here, we establish the transcription factor ETS-4, an ortholog of vertebrate SPDEF, as a longevity determinant. Adult worms with ets-4 mutations had a significant extension of mean life span. Restoring ETS-4 activity in the intestine, but not neurons, of ets-4 mutant worms rescued life span to wild-type levels. Using RNAi, we demonstrated that ets-4 is required post-developmentally to regulate adult life span; thus uncoupling the role of ETS-4 in aging from potential functions in worm intestinal development. Seventy ETS-4-regulated genes, identified by gene expression profiling of two distinct ets-4 alleles and analyzed by bioinformatics, were enriched for known longevity effectors that function in lipid transport, lipid metabolism, and innate immunity. Putative target genes were enriched for ones that change expression during normal aging, the majority of which are controlled by the GATA factors. Also, some ETS-4-regulated genes function downstream of the FOXO factor, DAF-16 and the insulin/IGF-1 signaling pathway. However, epistasis and phenotypic analyses indicate that ets-4 functioned in parallel to the insulin/IGF-1 receptor, daf-2 and akt-1/2 kinases. Furthermore, ets-4 required daf-16 to modulate aging, suggesting overlap in function at the level of common targets that affect life span. In conclusion, ETS-4 is a new transcriptional regulator of aging, which shares transcriptional targets with GATA and FOXO factors, suggesting that overlapping pathways direct common sets of lifespan-related genes. Animal life span is regulated in response to developmental and environmental inputs through coordinate changes in gene expression. Thus, longevity determinants include DNA-binding proteins that regulate gene expression by controlling transcription. Here, we explored the physiological role of the transcriptional regulator, ETS-4, in the roundworm Caenorhabditis elegans. Our data showed that worms that lack ETS-4 lived significantly longer, revealing ETS-4′s role in the transcription network that regulates life span. We identified 70 genes whose expression was modulated by ETS-4 that function in lipid transport, lipid metabolism and innate immunity. Some of the ETS-4-regulated genes were also controlled by two other regulators of aging, the FOXO and GATA factors. We concluded that a common set of transcriptional targets orchestrate the network of physiological factors that affect aging. ETS-4 is closely related to the human ETS protein SPDEF that exhibits aberrant expression in breast and prostate tumors. Because the genetic pathways that regulate aging are well conserved in other organisms, including humans, our findings could lead to a better understanding of SPDEF function and longevity regulation in mammals.
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Affiliation(s)
- Bargavi Thyagarajan
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Adam G. Blaszczak
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Katherine J. Chandler
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Jennifer L. Watts
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - W. Evan Johnson
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- Department of Statistics, Brigham Young University, Provo, Utah, United States of America
| | - Barbara J. Graves
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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Rechtsteiner A, Ercan S, Takasaki T, Phippen TM, Egelhofer TA, Wang W, Kimura H, Lieb JD, Strome S. The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny. PLoS Genet 2010; 6:e1001091. [PMID: 20824077 PMCID: PMC2932692 DOI: 10.1371/journal.pgen.1001091] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 07/26/2010] [Indexed: 11/25/2022] Open
Abstract
Methylation of histone H3K36 in higher eukaryotes is mediated by multiple methyltransferases. Set2-related H3K36 methyltransferases are targeted to genes by association with RNA Polymerase II and are involved in preventing aberrant transcription initiation within the body of genes. The targeting and roles of the NSD family of mammalian H3K36 methyltransferases, known to be involved in human developmental disorders and oncogenesis, are not known. We used genome-wide chromatin immunoprecipitation (ChIP) to investigate the targeting and roles of the Caenorhabditis elegans NSD homolog MES-4, which is maternally provided to progeny and is required for the survival of nascent germ cells. ChIP analysis in early C. elegans embryos revealed that, consistent with immunostaining results, MES-4 binding sites are concentrated on the autosomes and the leftmost ∼2% (300 kb) of the X chromosome. MES-4 overlies the coding regions of approximately 5,000 genes, with a modest elevation in the 5′ regions of gene bodies. Although MES-4 is generally found over Pol II-bound genes, analysis of gene sets with different temporal-spatial patterns of expression revealed that Pol II association with genes is neither necessary nor sufficient to recruit MES-4. In early embryos, MES-4 associates with genes that were previously expressed in the maternal germ line, an interaction that does not require continued association of Pol II with those loci. Conversely, Pol II association with genes newly expressed in embryos does not lead to recruitment of MES-4 to those genes. These and other findings suggest that MES-4, and perhaps the related mammalian NSD proteins, provide an epigenetic function for H3K36 methylation that is novel and likely to be unrelated to ongoing transcription. We propose that MES-4 transmits the memory of gene expression in the parental germ line to offspring and that this memory role is critical for the PGCs to execute a proper germline program. Germ cells transmit the genome from one generation to the next. The identity and immortality of germ cells are crucial for the perpetuation of species, yet the mechanisms that regulate these properties remain elusive. In C.elegans, a histone methyltransferase MES-4 is required for survival of the primordial germ cells. MES-4 methylates histone H3 at lysine 36 (H3K36), a modification previously linked to transcription elongation and involved in preventing aberrant transcription initiation within the body of genes. Surprisingly, our genome-wide analysis of MES-4 binding sites in C. elegans embryos revealed that MES-4 is capable of associating with genes that were expressed in the germ line of the parent worms but are no longer being actively transcribed in embryos. To our knowledge, this is the first example of transcription-uncoupled H3K36 methylation. We suggest that MES-4-generated H3K36 methylation serves an “epigenetic role,” by marking germline-expressed genes and by carrying the memory of gene expression from one generation of germ cells to the next.
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Affiliation(s)
- Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Sevinc Ercan
- Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Teruaki Takasaki
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Taryn M. Phippen
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Thea A. Egelhofer
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Wenchao Wang
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Hiroshi Kimura
- Graduate School for Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Jason D. Lieb
- Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (SS); (JDL)
| | - Susan Strome
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (SS); (JDL)
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Spanier B, Rubio-Aliaga I, Hu H, Daniel H. Altered signalling from germline to intestine pushes daf-2;pept-1 Caenorhabditis elegans into extreme longevity. Aging Cell 2010; 9:636-46. [PMID: 20550516 DOI: 10.1111/j.1474-9726.2010.00591.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The insulin-like signalling pathway is a central regulator of development, metabolism, stress resistance and lifespan in eukaryotes. Caenorhabditis elegans daf-2(e1370) animals with a loss-of-function mutation in the insulin-like receptor live twice as long as wild-type animals, and the additional knockout of the intestinal di- and tripeptide transporter pept-1 further increases lifespan by 60%. In assessing the underlying molecular mechanisms for this phenomenon, microarray-based transcriptome data sets of daf-2(e1370) and daf-2(e1370);pept-1(lg601) animals were compared with a focus on genes that showed significantly higher changes in expression levels in daf-2;pept-1 than in daf-2. We identified 187 genes with at least fourfold decreased transcript levels and 170 with more than a fourfold increase. A large fraction of the down-regulated genes encode proteins involved in germline proliferation and reproduction. The DAF-9/DAF-12 signalling cascade was identified as a prime pathway that mediates the longevity of daf-2;pept-1 with a strict dependance on DAF-16. Loss of DAF-9/DAF-12 or KRI-1 reduces the lifespan of daf-2;pept-1 to that of the daf-2 mutant. Amongst the DAF-16 target genes, numerous enzymes involved in the defence of reactive oxygen species were with increased expression level in daf-2;pept-1. On a functional level, it was demonstrated that amongst those, a high de novo synthesis rate of glutathione is most important for the longevity phenotype of this strain. Taken together, a close interdependence of endocrine hormone signalling from germline to intestine was identified as an essential element in the control of the extreme longevity of C. elegans lacking a proper function of the insulin receptor and lacking the intestinal peptide transporter.
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Affiliation(s)
- Britta Spanier
- ZIEL Research Center of Nutrition and Food Sciences, Technische Universität München, Freising, Germany.
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Iwasa H, Yu S, Xue J, Driscoll M. Novel EGF pathway regulators modulate C. elegans healthspan and lifespan via EGF receptor, PLC-gamma, and IP3R activation. Aging Cell 2010; 9:490-505. [PMID: 20497132 DOI: 10.1111/j.1474-9726.2010.00575.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Improving health of the rapidly growing aging population is a critical medical, social, and economic goal. Identification of genes that modulate healthspan, the period of mid-life vigor that precedes significant functional decline, will be an essential part of the effort to design anti-aging therapies. Because locomotory decline in humans is a major contributor to frailty and loss of independence and because slowing of movement is a conserved feature of aging across phyla, we screened for genetic interventions that extend locomotory healthspan of Caenorhabditis elegans. From a group of 54 genes previously noted to encode secreted proteins similar in sequence to extracellular domains of insulin receptor, we identified two genes for which RNAi knockdown delayed age-associated locomotory decline, conferring a high performance in advanced age phenotype (Hpa). Unexpectedly, we found that hpa-1 and hpa-2 act through the EGF pathway, rather than the insulin signaling pathway, to control systemic healthspan benefits without detectable developmental consequences. Further analysis revealed a potent role of EGF signaling, acting via downstream phospholipase C-gammaplc-3 and inositol-3-phosphate receptor itr-1, to promote healthy aging associated with low lipofuscin levels, enhanced physical performance, and extended lifespan. This study identifies HPA-1 and HPA-2 as novel negative regulators of EGF signaling and constitutes the first report of EGF signaling as a major pathway for healthy aging. Our data raise the possibility that EGF family members should be investigated for similar activities in higher organisms.
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Affiliation(s)
- Hiroaki Iwasa
- Department of Medical Biochemistry, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
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Lee AY, Perreault R, Harel S, Boulier EL, Suderman M, Hallett M, Jenna S. Searching for signaling balance through the identification of genetic interactors of the Rab guanine-nucleotide dissociation inhibitor gdi-1. PLoS One 2010; 5:e10624. [PMID: 20498707 PMCID: PMC2869356 DOI: 10.1371/journal.pone.0010624] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 03/22/2010] [Indexed: 12/27/2022] Open
Abstract
Background The symptoms of numerous diseases result from genetic mutations that disrupt the homeostasis maintained by the appropriate integration of signaling gene activities. The relationships between signaling genes suggest avenues through which homeostasis can be restored and disease symptoms subsequently reduced. Specifically, disease symptoms caused by loss-of-function mutations in a particular gene may be reduced by concomitant perturbations in genes with antagonistic activities. Methodology/Principal Findings Here we use network-neighborhood analyses to predict genetic interactions in Caenorhabditis elegans towards mapping antagonisms and synergisms between genes in an animal model. Most of the predicted interactions are novel, and the experimental validation establishes that our approach provides a gain in accuracy compared to previous efforts. In particular, we identified genetic interactors of gdi-1, the orthologue of GDI1, a gene associated with mental retardation in human. Interestingly, some gdi-1 interactors have human orthologues with known neurological functions, and upon validation of the interactions in mammalian systems, these orthologues would be potential therapeutic targets for GDI1-associated neurological disorders. We also observed the conservation of a gdi-1 interaction between different cellular systems in C. elegans, suggesting the involvement of GDI1 in human muscle degeneration. Conclusions/Significance We developed a novel predictor of genetic interactions that may have the ability to significantly streamline the identification of therapeutic targets for monogenic disorders involving genes conserved between human and C. elegans.
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Affiliation(s)
- Anna Y. Lee
- McGill Centre for Bioinformatics, McGill University, Montréal, Québec, Canada
- School of Computer Science, McGill University, Montréal, Québec, Canada
| | - Richard Perreault
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Sharon Harel
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Elodie L. Boulier
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Matthew Suderman
- McGill Centre for Bioinformatics, McGill University, Montréal, Québec, Canada
| | - Michael Hallett
- McGill Centre for Bioinformatics, McGill University, Montréal, Québec, Canada
- School of Computer Science, McGill University, Montréal, Québec, Canada
- Rosalind and Morris Goodman Cancer Centre, McGill University, Montréal, Québec, Canada
| | - Sarah Jenna
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec, Canada
- Pharmaqam, Université du Québec à Montréal, Montréal, Québec, Canada
- Biomed, Université du Québec à Montréal, Montréal, Québec, Canada
- * E-mail:
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