Comparative genomic analysis of innate immunity reveals novel and conserved components in crustacean food crop species

Lai, Alvina G.; Aboobaker, A. Aziz

doi:10.1186/s12864-017-3769-4

Cited by 41 publications

(54 citation statements)

References 251 publications

(227 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This assumption, which was already suggested by Christiaens et al (2015) and Taning et al (2016a) is also supported by reports of Loquacious being functional as cofactor to Dicer-2 in the siRNA pathway in D. melanogaster (Czech et al, 2008;Marques et al, 2010;Okamura et al, 2008). In Crustacea, another protein has been identified as a cofactor for Dicer-2, namely an orthologue of the transactivating response (TAR) RNA binding protein (TRBP) (Lai and Aboobaker, 2017).…”

Section: Rnai Machinery Genes Repertoiresupporting

confidence: 55%

Literature review of baseline information on RNAi to support the environmental risk assessment of RNAi‐based GM plants

Christiaens

Dzhambazova

Kostov

et al. 2018

EFS3

View full text Add to dashboard Cite

This report is the outcome of an EFSA procurement (OC/EFSA/GMO/2015/02) which aims at reviewing relevant scientific information on RNA interference (RNAi) that could serve as baseline information for the environmental risk assessment of RNAi‐based genetically modified (GM) plants. The report is based on a systematic literature search on the use of RNAi molecules in arthropods, nematodes, annelids and molluscs with dsRNA, siRNA and miRNA applied primarily through feeding and soaking (oral ingestion). The numbers of retrieved publications covering these areas are reported, along with the species name, life stages tested, the target gene and its function, details of the test substances and their concentrations used, methods of delivery and effects. Separate sections discuss the available information on: (1) the uptake and systematic spread of RNAi activity, including a description of the various components involved in this process; (2) the mechanisms of dsRNA‐, siRNA‐ and miRNA‐elicited gene silencing and the different factors involved in RNAi efficiency; (3) routes of exposure of the biotic and abiotic environment to dsRNA, siRNA and miRNA from GM plants; (4) the environmental fate of dsRNA, siRNA and miRNA; and (5) the various factors that may limit non‐target effects including exposure, factors influencing the silencing efficiency of dsRNA, siRNA and miRNA, possible unintended and off‐target effects, and their mechanisms. Finally, an overview of the species of arthropods, nematodes, annelids and molluscs for which genomic data are available is also presented. The report identifies some of the challenges involved in developing plants with RNAi systems which affect invertebrate gene expression. The report also concludes that, currently, knowledge on issues such as exposure, specificity, offtarget effects, sequence similarities and bioinformatics is very limited, as only a few RNAi expressing plants which specifically target invertebrate species have been developed and comprehensively studied.

show abstract

Section: Rnai Machinery Genes Repertoiresupporting

confidence: 55%

Literature review of baseline information on RNAi to support the environmental risk assessment of RNAi‐based GM plants

Christiaens

Dzhambazova

Kostov

et al. 2018

EFS3

View full text Add to dashboard Cite

show abstract

“…Sequence analysis of terrestrial isopod ALFs indicated that they have two conserved cysteine residues suggestive of disulfite bridge formation [27] (Supplementary File S1), as previously described for other malacostracan ALFs [27]. The region located between these cysteine residues is considered as a LPS-binding domain formed with positively charged amino acids [27]. As this domain is also present in other malacostracan ALFs [27], it suggests LPS-binding conservation across the whole gene family.…”

Section: Description Of the Alf And Crustin Repertoire Of Terrestrialsupporting

confidence: 53%

“…The highest number of ALFs (15 transcripts) was identified in Trachelipus rathkei (Figure 1 and Supplementary Table S2). Sequence analysis of terrestrial isopod ALFs indicated that they have two conserved cysteine residues suggestive of disulfite bridge formation [27] (Supplementary File S1), as previously described for other malacostracan ALFs [27]. The region located between these cysteine residues is considered as a LPS-binding domain formed with positively charged amino acids [27].…”

Section: Description Of the Alf And Crustin Repertoire Of Terrestrialmentioning

confidence: 70%

“…The region located between these cysteine residues is considered as a LPS-binding domain formed with positively charged amino acids [27]. As this domain is also present in other malacostracan ALFs [27], it suggests LPS-binding conservation across the whole gene family. To investigate ALF evolutionary history in terrestrial isopods, we performed a phylogenetic analysis using the amino acid sequences of the 78 ALF transcripts ≥ 100 amino acids in length.…”

Section: Description Of the Alf And Crustin Repertoire Of Terrestrialmentioning

confidence: 99%

“…The highest number of crustins in terrestrial isopods (five transcripts) was identified in Armadillidium tunisiense, Eluma purpurascens and Porcellio laevis (Figure 3 and Supplementary Table S2). The crustin WAP domains from terrestrial isopods contained 12 conserved cysteines residues, as previously described for other malacostracans [27]. To investigate crustin evolutionary history in terrestrial isopods, we performed a phylogenetic analysis using the amino acid sequences of the 63 crustin transcripts ≥ 90 amino acids in length.…”

Section: Description Of the Alf And Crustin Repertoire Of Terrestrialmentioning

confidence: 99%

See 2 more Smart Citations

Shedding Light on the Antimicrobial Peptide Arsenal of Terrestrial Isopods: Focus on Armadillidins, a New Crustacean AMP Family

Becking

Delaunay

Cordaux

et al. 2020

Genes

View full text Add to dashboard Cite

In crustaceans, antimicrobial peptides (AMPs) are clustered into four major groups according to their amino acid composition and structure: (1) single-domain peptides containing cysteine residues such as anti-lipopolysaccharide-factor (ALF), (2) multi-domain or chimeric AMPs such as crustins, (3) non-conventional AMPs, and (4) linear single-domain AMPs. The majority of AMPs has been described in commercially exploited crustaceans, particularly decapods living in aquatic environments (crab, shrimp, lobster, and crayfish). Here, we aimed at establishing the AMPs repertoire of terrestrial isopods (Oniscidea), an original suborder of crustaceans adapted to life outside of the aquatic environment. Using transcriptomic data from 21 species, we identified 110 ALF and 73 crustin sequences. We also characterized the full-length sequence of armadillidins from 17 species, similar to the AMP previously described in the terrestrial isopod Armadillidium vulgare. Furthermore, we tested the antimicrobial activity of three armadillidin peptides characterized from three distantly related species. This analysis revealed similar activity spectra against pathogens, despite extensive structural variation among the tested peptides. In addition to conventional crustacean AMPs, our work highlights armadillidins as a new and independent family of AMPs specific to the Oniscidea, thus opening new perspectives concerning the study of the immune system of terrestrial isopods.

show abstract

Transcriptomic and Histological Analysis of the Greentail Prawn (Metapenaeus bennettae) Following Light Crude Oil Exposure

Armstrong

Mondon

Miller

et al. 2022

Enviro Toxic and Chemistry

View full text Add to dashboard Cite

Oil spills pose a significant threat to marine biodiversity. Crude oil can partition into sediments where it may be persistent, placing benthic species such as decapods at particular risk of exposure. Transcriptomic and histological tools are often used to investigate the effects of hydrocarbon exposure on marine organisms following oil spill events, allowing for the identification of metabolic pathways impacted by oil exposure. However, there is limited information available for decapod crustaceans, many of which carry significant economic value. In the present study, we assess the sublethal impacts of crude oil exposure in the commercially important Australian greentail prawn (Metapenaeus bennettae) using transcriptomic and histological analyses. Prawns exposed to light, unweathered crude oil "spiked" sediments for 90 h were transferred to clean sediments for a further 72 h to assess recovery. Chemical analyses indicated that polycyclic aromatic hydrocarbons increased by approximately 65% and 91% in prawn muscle following 24 and 90 h of exposure, respectively, and significantly decreased during 24-and 72-h recovery periods. Transcriptomic responses followed an exposure and recovery pattern with innate immunity and nutrient metabolism transcripts significantly lowered in abundance after 24 h of exposure and were higher in abundance after 72 h of recovery. In addition, transcription/translation, cellular responses, and DNA repair pathways were significantly impacted after 24 h of exposure and recovered after 72 h of recovery. However, histological alterations such as tubule atrophy indicated an increase in severity after 24 and 72 h of recovery. The present study provides new insights into the sublethal impacts of crude oil exposure in greentail prawns and identifies molecular pathways altered by exposure. We expect these findings to inform future management associated with oil extraction activity and spills.

show abstract

Comparative genomic analysis of innate immunity reveals novel and conserved components in crustacean food crop species

Cited by 41 publications

References 251 publications

Literature review of baseline information on RNAi to support the environmental risk assessment of RNAi‐based GM plants

Literature review of baseline information on RNAi to support the environmental risk assessment of RNAi‐based GM plants

Shedding Light on the Antimicrobial Peptide Arsenal of Terrestrial Isopods: Focus on Armadillidins, a New Crustacean AMP Family

Transcriptomic and Histological Analysis of the Greentail Prawn (Metapenaeus bennettae) Following Light Crude Oil Exposure

Contact Info

Product

Resources

About