OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

Waterhouse, Robert M.; Tegenfeldt, Fredrik; Li, Jia; Zdobnov, Evgeny M.; Kriventseva, Evgenia V.

doi:10.1093/nar/gks1116

Cited by 359 publications

(336 citation statements)

References 59 publications

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“…To identify highly conserved ("core") processes involved in the response to territory intrusion, we analyzed orthologous and paralogous genes (Materials and Methods and SI Materials and Methods). Where possible, we assigned genes to a metazoan evolutionarily orthologous group (EOG) (21) and then filtered each species gene list to contain only EOGs shared across all three species. For each shared EOG, we identified a "homologous triplet" with one gene per species, calculated a combined significance score for the triplet, and ranked triplets on this basis (Dataset S4).…”

Section: Cross-species Core Processes In the Response To Territory Inmentioning

confidence: 99%

Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee

Rittschof

Bukhari

Sloofman

et al. 2014

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

142

196

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Certain complex phenotypes appear repeatedly across diverse species due to processes of evolutionary conservation and convergence. In some contexts like developmental body patterning, there is increased appreciation that common molecular mechanisms underlie common phenotypes; these molecular mechanisms include highly conserved genes and networks that may be modified by lineage-specific mutations. However, the existence of deeply conserved mechanisms for social behaviors has not yet been demonstrated. We used a comparative genomics approach to determine whether shared neuromolecular mechanisms could underlie behavioral response to territory intrusion across species spanning a broad phylogenetic range: house mouse (Mus musculus), stickleback fish (Gasterosteus aculeatus), and honey bee (Apis mellifera). Territory intrusion modulated similar brain functional processes in each species, including those associated with hormone-mediated signal transduction and neurodevelopment. Changes in chromosome organization and energy metabolism appear to be core, conserved processes involved in the response to territory intrusion. We also found that several homologous transcription factors that are typically associated with neural development were modulated across all three species, suggesting that shared neuronal effects may involve transcriptional cascades of evolutionarily conserved genes. Furthermore, immunohistochemical analyses of a subset of these transcription factors in mouse again implicated modulation of energy metabolism in the behavioral response. These results provide support for conserved genetic "toolkits" that are used in independent evolutions of the response to social challenge in diverse taxa.genetic hotspot | NF-κB signaling | brain metabolism | aggression S imilar phenotypes can have a shared molecular basis, even among distantly related species (1-3). This phenomenon has been observed for an array of traits, including morphological adaptations like coat color or wing patterning, rapid adaptations like drug resistance, and artificially selected phenological traits like flowering time (reviewed in ref. 2). Shared molecular mechanisms can arise convergently as a result of de novo mutations at genetic hotspots (2) or as a result of conservation. Both of these processes result in "genetic toolkits" or genes that are repeatedly used over evolutionary time to give rise to similar phenotypes (3). The phenomenon of genetic toolkits challenges fundamental notions about evolutionary convergence, conservation, and the origins of biodiversity.The role of genetic toolkits in shaping behavioral phenotypes is unclear (4, 5). Behaviors are typically polygenic (6) and they show great nuance and plasticity within a species, raising the possibility that cross-species similarities in behavior are superficial. Social behaviors in particular present a challenge to the genetic toolkit concept: these behaviors are critical to survival and reproductive success, but across species there is significant variation in the contexts for an...

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Section: Cross-species Core Processes In the Response To Territory Inmentioning

confidence: 99%

Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee

Rittschof

Bukhari

Sloofman

et al. 2014

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

142

196

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“…To assess the possibility of incorrect topologies stemming from inadvertent inclusion of paralogues, we identified in Matrices 1 -4 all tick (Ixodes scapularis) orthologues that were found to occur in single-copy across Arthropoda, as identified in the BUSCO-Ar database of OrthoDB [43]. The intersection of BUSCO-Ar orthologues and Matrices 1 -4 constituted the basis for Matrices 11 -14, respectively (figure 2a).…”

Section: (C) Phylogenomic Analyses Of Supermatricesmentioning

confidence: 99%

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

Sharma

Fernández

Esposito³

et al. 2015

Proc. R. Soc. B.

113

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Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships with up to 5025 genes. Analyses of supermatrices as well as species tree approaches converged upon a robust basal topology of scorpions that is entirely at odds with traditional systematics and controverts previous understanding of scorpion evolutionary history. All analyses unanimously support a single origin of katoikogenic development, a form of parental investment wherein embryos are nurtured by direct connections to the parent's digestive system. Based on the phylogeny obtained herein, we propose the following systematic emendations: Caraboctonidae is transferred to Chactoidea new superfamilial assignment; superfamily Bothriuroidea revalidated is resurrected and Bothriuridae transferred therein; and Chaerilida and Pseudochactida are synonymized with Buthida new parvordinal synonymies."All scorpions look generally alike." Gary Allan Polis (1990)

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“…1). As well as being ubiquitous in plants, and frequently manifesting in a staggering number of isoforms (more than 66 for Arabidopsis thaliana) (8,10), PMEs are found in phytopathogenic bacteria and fungi (17)(18)(19)(20)(21)(22)(23)(24)(25)(26) and in Archaea (especially Halobacteriaceae (27)), and they have also been observed in the genomes of several phytophagous insects (28 -30) and in human gut microflora (31). Recently, plant pollen PMEs have been identified as a key human allergen (32,33).…”

mentioning

confidence: 99%

Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control

Kent

Loo

Melton

et al. 2016

Journal of Biological Chemistry

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Many pectin methylesterases (PMEs) are expressed in plants to modify plant cell-wall pectins for various physiological roles. These pectins are also attacked by PMEs from phytopathogens and phytophagous insects. The de-methylesterification by PMEs of the O6-methyl ester groups of the homogalacturonan component of pectin, exposing galacturonic acids, can occur processively or non-processively, respectively, describing sequential versus single de-methylesterification events occurring before enzyme-substrate dissociation. The high resolution x-ray structures of a PME from Aspergillus niger in deglycosylated and Asn-linked N-acetylglucosamine-stub forms reveal a 10 2 ⁄ 3-turn parallel ␤-helix (similar to but with less extensive loops than bacterial, plant, and insect PMEs). Capillary electrophoresis shows that this PME is non-processive, halophilic, and acidophilic. Molecular dynamics simulations and electrostatic potential calculations reveal very different behavior and properties compared with processive PMEs. Specifically, uncorrelated rotations are observed about the glycosidic bonds of a partially de-methyl-esterified decasaccharide model substrate, in sharp contrast to the correlated rotations of processive PMEs, and the substrate-binding groove is negatively not positively charged.The heterogeneous polysaccharide pectin (1-4) is a key component of the plant cell wall (5). A host of enzymes, including pectin methylesterase (PME) 3 as well as endo-and exopolygalacturonases, modifies pectin fine-structure locally in space and time for purposes of plant-cell differentiation, cell adhesion/separation, growth, and development from roots to meristem, morphogenesis, seed and fruit development, and defense against pathogens (6 -16). PMEs hydrolyze the O6-methyl ester groups of the homogalacturonan (HG) chains that form the backbone of pectin (Fig. 1). As well as being ubiquitous in plants, and frequently manifesting in a staggering number of isoforms (more than 66 for Arabidopsis thaliana) (8, 10), PMEs are found in phytopathogenic bacteria and fungi (17-26) and in Archaea (especially Halobacteriaceae (27)), and they have also been observed in the genomes of several phytophagous insects (28 -30) and in human gut microflora (31). Recently, plant pollen PMEs have been identified as a key human allergen (32, 33). Bacterial and plant PMEs that have been functionally characterized are generally observed to be processive (34 -55), i.e. the enzyme binds to the HG substrate and then successively hydrolyzes a block of methyl ester groups before dissociating. In all cases characterized to date, the direction of processivity is from the non-reducing end of the HG chain toward the reducing end, as shown in Fig. 1. The degree of processivity (also called the action pattern) has been reported to be dependent on ionic strength and pH (56), and various classifications of PMEs exist (48,49,(57)(58)(59)(60). In general, processive PMEs have their isoelectric points, pI, and pH for optimum activity at near-neutral to basic pH, although ...

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OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

Cited by 359 publications

References 59 publications

Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee

Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control

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