OrthoList: A Compendium of C. elegans Genes with Human Orthologs

Shaye, Daniel D.; Greenwald, Iva

doi:10.1371/journal.pone.0020085

Cited by 417 publications

(363 citation statements)

References 57 publications

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“…Orthologous gene pairs. Orthologous gene pairs were obtained from a previous publication (18) or annotation in WormBase (www.wormbase.org) or TreeFam (www.treefam.org). A 1:N ortholog relationship is allowed.…”

Section: Methodsmentioning

confidence: 99%

Conserved gene regulatory module specifies lateral neural borders across bilaterians

Zhao

Horie

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The lateral neural plate border (NPB), the neural part of the vertebrate neural border, is composed of central nervous system (CNS) progenitors and peripheral nervous system (PNS) progenitors. In invertebrates, PNS progenitors are also juxtaposed to the lateral boundary of the CNS. Whether there are conserved molecular mechanisms determining vertebrate and invertebrate lateral neural borders remains unclear. Using single-cell-resolution gene-expression profiling and genetic analysis, we present evidence that orthologs of the NPB specification module specify the invertebrate lateral neural border, which is composed of CNS and PNS progenitors. First, like in vertebrates, the conserved neuroectoderm lateral border specifier Msx/vab-15 specifies lateral neuroblasts in Caenorhabditis elegans. Second, orthologs of the vertebrate NPB specification module (Msx/vab-15, Pax3/7/pax-3, and Zic/ref-2) are significantly enriched in worm lateral neuroblasts. In addition, like in other bilaterians, the expression domain of Msx/vab-15 is more lateral than those of Pax3/7/pax-3 and Zic/ref-2 in C. elegans. Third, we show that Msx/vab-15 regulates the development of mechanosensory neurons derived from lateral neural progenitors in multiple invertebrate species, including C. elegans, Drosophila melanogaster, and Ciona intestinalis. We also identify a novel lateral neural border specifier, ZNF703/tlp-1, which functions synergistically with Msx/vab-15 in both C. elegans and Xenopus laevis. These data suggest a common origin of the molecular mechanism specifying lateral neural borders across bilaterians.C. elegans | neural plate border | neural border | Msx/vab-15 | ZNF703/tlp-1 T he vertebrate neural border is a transient embryonic domain located between the neural plate and nonneurogenic ectoderm from late gastrulation to early neurulation. The neural border is composed of the lateral neural plate border (NPB) and preplacode ectoderm (PPE) subdomains (1, 2). The NPB and PPE give rise to the neural crest and placode, respectively, both of which undergo epithelial-to-mesenchymal transition/delamination, migrate in prototypical paths, and give rise to the peripheral nervous system (PNS) and many other cell types (3, 4). However, the NPB and PPE also have many different features (5). For example, the PPE is confined to the anterior half of embryos and does not contribute to the central nervous system (CNS), whereas the NPB is the lateral border of the whole neural plate and consists not only of progenitors for the PNS but also those for the CNS in the dorsal neural tube. The juxtaposed localization of the CNS neuroectoderm and PNS progenitors also occurs in the trunk of invertebrate embryos such as nematodes, arthropods, annelids, and urochordates (6-9), reminiscent of vertebrate NPB. In Caenorhabditis elegans, lateral neuroblasts (P, Q, and V5 cells) are located between the embryonic CNS and skin from the birth of these cells (10). In addition, worm lateral neuroblasts possess several key cellular and developmental features of vertebra...

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Section: Methodsmentioning

confidence: 99%

Conserved gene regulatory module specifies lateral neural borders across bilaterians

Zhao

Horie

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…guanylate cyclase-activating proteins (GCAPs) and 74% identical to human frequenin (Shaye and Greenwald, 2011), to membrane current in AFD. As found for pde-2 mutants, loss of NCS-1 prolongs ThRCs and elevates their threshold.…”

mentioning

confidence: 99%

GCY-8, PDE-2, and NCS-1 are critical elements of the cGMP-dependent thermotransduction cascade in the AFD neurons responsible for C. elegans thermotaxis

Wang¹,

O'Halloran²,

Goodman³

2013

J Cell Biol

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“…Specifically, within group 1, 12 predicted proteins with close homology to Na-ASP-2 and Hc24 (Yatsuda et al, 2003;Asojo et al, 2005a) grouped separately (pp = 0.59-1.00) to the exclusion of CAP proteins with homology to C. elegans LON-1 protein (Hc-CAP-15 and -16) and GLIPR-1 (Hc-CAP-17) (cf. Shaye and Greenwald, 2011). Within group 2, three predicted proteins (Hc-CAP-22, -23 and -24) that shared homology to Ac-ASP-7 (Datu et al, 2008;Osman et al, 2012) formed a separate clade to the exclusion of Hc-CAP-25.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

“…1). Table 1), which is a secreted protein similar to the venom allergen-like (VAL) proteins found in a number of invertebrates, including parasitic nematodes, and a human homolog of cysteine-rich secretory protein 3 isoform 2 precursor (Shaye and Greenwald, 2011). The genes Hc-cap-36 and Hc-cap-37 usually exhibited higher transcription in the free-living stages of H. contortus (particularly L1 and L2) compared with parasitic (haematophagous) stages in which females displayed higher transcription than males.…”

Section: Single-domain Proteinsmentioning

confidence: 99%

“…Although Ce-vap-1 and Ce-vap-2 do not directly interact with each other, all of the 17 Ce-scl paralogs are predicted to interact with Ce-vap-2 (Lee et al, 2008), which itself interacts specifically with egl-9 (Gort et al, 2008). Ce-scl-20 encodes an ortholog of human cysteine-rich secretory protein (HGNC:GLIPR1) (Shaye and Greenwald, 2011), which is a p53 target gene with pro-apoptotic activity mediated by an increased production of reactive oxygen species (ROS) (Pinkston-Gosse and Kenyon, 2007;Li et al, 2008). Ce-scl-18 and -19 encode orthologs of human cysteine-rich secretory protein LCCL domain containing 1 (HGNC:CRISPLD1), whose function is presently unknown, but which might be involved in the parasite-host interplay and sustaining parasitism.…”

Section: Double-domain Proteinsmentioning

confidence: 99%

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The barber's pole worm CAP protein superfamily — A basis for fundamental discovery and biotechnology advances

Mohandas

Young

Jabbar

et al. 2015

Biotechnology Advances

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Parasitic worm proteins that belong to the cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 (CAP) superfamily are proposed to play key roles in the infection process and the modulation of immune responses in host animals. However, there is limited information on these proteins for most socio-economically important worms. Here, we review the CAP protein superfamily of Haemonchus contortus (barber's pole worm), a highly significant parasitic roundworm (order Strongylida) of small ruminants. To do this, we mined genome and transcriptomic datasets, predicted and curated full-length amino acid sequences (n = 45), undertook systematic phylogenetic analyses of these data and investigated transcription throughout the life cycle of H. contortus. We inferred functions for selected C. elegans orthologs (including vap-1, vap-2, scl-5 and lon-1) based on genetic networking and by integrating data and published information, and were able to infer that a subset of orthologs and their interaction partners play pivotal roles in growth and development via the insulin-like and/or the TGF-beta signaling pathways. The identification of the important and conserved growth regulator LON-1 led us to appraise the threedimensional structure of this CAP protein by comparative modelling. This model revealed the presence of different topological moieties on the canonical fold of the CAP domain, which coincide with an overall charge separation as indicated by the electrostatic surface potential map. These observations suggest the existence of separate sites for effector binding and receptor interactions, and thus support the proposal that these worm molecules act in similar ways as venoms act as ligands for chemokine receptors or G protein-coupled receptor effectors. In conclusion, this review should guide future molecular studies of these molecules, and could support the development of novel interventions against haemonchosis.

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OrthoList: A Compendium of C. elegans Genes with Human Orthologs

Cited by 417 publications

References 57 publications

Conserved gene regulatory module specifies lateral neural borders across bilaterians

Conserved gene regulatory module specifies lateral neural borders across bilaterians

GCY-8, PDE-2, and NCS-1 are critical elements of the cGMP-dependent thermotransduction cascade in the AFD neurons responsible for C. elegans thermotaxis

The barber's pole worm CAP protein superfamily — A basis for fundamental discovery and biotechnology advances

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