CRISPR/Cas12a-Mediated Gene Editing in Geodia barretti Sponge Cell Culture

Hesp, Kylie; Alvarez, John L. Flores; Alexandru, Ana Maria; Linden, Jip van der; Martens, Dirk E.; Wijffels, René H.; Pomponi, Shirley A.

doi:10.3389/fmars.2020.599825

Cited by 4 publications

(3 citation statements)

References 69 publications

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“…2023 ), with 3 of them published after submission of this study; the G. barretti genome is the first deep-sea genome of a demosponge. This genome will firmly establish the North Atlantic G. barretti as a prominent deep-sea sponge species for future studies, allowing the generation of new hypotheses about multicellularity, immunity, chemistry, and symbiont/cell recognition and interaction, which could be tested in vitro, thanks to the successful G. barretti cell line and CRISPR/Cas12a gene-editing system ( Hesp et al . 2020 , 2023 ).…”

Section: Resultsmentioning

confidence: 99%

Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae)

Steffen,

Proux-Wéra,

Soler

et al. 2023

G3: Genes, Genomes, Genetics

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Sponges are among the earliest branching extant animals. As such, genetic data from this group is valuable for understanding the evolution of various traits and processes in other animals. However, like many marine organisms, they are notoriously difficult to sequence and hence genomic data is scarce. Here, we present the draft genome assembly for the North Atlantic deep-sea high-microbial abundance species Geodia barretti Bowerbank, 1858, from a single individual collected on the West coast of Sweden. The nuclear genome assembly has 4,535 scaffolds, an N50 of 48,447 bp and a total length of 144 Mbp; the mitochondrial genome is 17,996 bp long. BUSCO completeness was 71.5%. The genome was annotated using a combination of ab initio and evidence-based methods finding 31,884 protein coding genes.

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Section: Resultsmentioning

confidence: 99%

Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae)

Steffen,

Proux-Wéra,

Soler

et al. 2023

G3: Genes, Genomes, Genetics

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“…4 B) could indicate active host gene silencing by symbionts, to prevent becoming target material for degradation. Functional studies are imperative to validate the processes in which the detected DEGs are involved, yet this remains a challenge in sponges as models for genetic manipulation are currently limited to explants or cells of two sponge species [ 86 , 87 ].…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic responses of Mediterranean sponges upon encounter with symbiont microbial consortia

Marulanda-Gomez,

Ribes,

Franzenburg

et al. 2024

BMC Genomics

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Background Sponges (phylum Porifera) constantly interact with microbes. They graze on microbes from the water column by filter-feeding and they harbor symbiotic partners within their bodies. In experimental setups, sponges take up symbionts at lower rates compared with seawater microbes. This suggests that sponges have the capacity to differentiate between microbes and preferentially graze in non-symbiotic microbes, although the underlying mechanisms of discrimination are still poorly understood. Genomic studies showed that, compared to other animal groups, sponges present an extended repertoire of immune receptors, in particular NLRs, SRCRs, and GPCRs, and a handful of experiments showed that sponges regulate the expression of these receptors upon encounter with microbial elicitors. We hypothesize that sponges may rely on differential expression of their diverse repertoire of poriferan immune receptors to sense different microbial consortia while filter-feeding. To test this, we characterized the transcriptomic response of two sponge species, Aplysina aerophoba and Dysidea avara, upon incubation with microbial consortia extracted from A. aerophoba in comparison with incubation with seawater microbes. The sponges were sampled after 1 h, 3 h, and 5 h for RNA-Seq differential gene expression analysis. Results D. avara incubated with A. aerophoba-symbionts regulated the expression of genes related to immunity, ubiquitination, and signaling. Within the set of differentially-expressed immune genes we identified different families of Nucleotide Oligomerization Domain (NOD)-Like Receptors (NLRs). These results represent the first experimental evidence that different types of NLRs are involved in microbial discrimination in a sponge. In contrast, the transcriptomic response of A. aerophoba to its own symbionts involved comparatively fewer genes and lacked genes encoding for immune receptors. Conclusion Our work suggests that: (i) the transcriptomic response of sponges upon microbial exposure may imply “fine-tuning” of baseline gene expression as a result of their interaction with microbes, (ii) the differential response of sponges to microbial encounters varied between the species, probably due to species-specific characteristics or related to host’s traits, and (iii) immune receptors belonging to different families of NLR-like genes played a role in the differential response to microbes, whether symbionts or food bacteria. The regulation of these receptors in sponges provides further evidence of the potential role of NLRs in invertebrate host-microbe interactions. The study of sponge responses to microbes exemplifies how investigating different animal groups broadens our knowledge of the evolution of immune specificity and symbiosis.

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“…3B) could indicate active host gene silencing by symbionts, to prevent becoming target material for degradation. Functional studies are imperative to validate the processes in which the detected DEGs are involved, yet this remains a challenge in sponges as models for genetic manipulation are currently limited to explants or cells of two sponge species (Hesp et al, 2020;Revilla-I-Domingo et al, 2018). S7) of the differentially expressed NLRs in D. avara against the freshwater sponge Ephydatia muelleri, for which a chromosome-level genome is available (Kenny et al, 2020).…”

Section: Avara and A Aerophoba Employ Different Sets Of Genesmentioning

confidence: 99%

Transcriptomic responses of Mediterranean sponges upon encounter with seawater or symbiont microbial consortia

Marulanda-Gomez,

Ribes,

Franzenburg

et al. 2023

Preprint

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Sponges (phylum Porifera) constantly interact with microbes from the water column while filter-feeding and with the symbiotic partners they harbor within their mesohyl. Despite early observations on differential uptake between symbiont and seawater bacteria, it is still poorly understood how sponges discriminate between different microbial consortia. Initial evidence of the diverse repertoire of sponge immune receptors suggests their involvement in specific microbial recognition, yet experimental data is still scarce. We characterized the transcriptomic response of two sponge species,Aplysina aerophobaandDysidea avara, upon incubation with two different microbial consortia, which were either enriched from ambient seawater or extracted fromA. aerophoba.The sponges were sampled after 1 h, 3 h, and 5 h for RNA-Seq differential gene expression analysis.D. avarashowed higher expression levels of genes related to immunity, ubiquitination, and signaling when incubated withA. aerophobasymbionts, than in incubations with seawater microbial consortia. Interestingly, the different bacteria consortia triggered changes in Nucleotide Oligomerization Domain (NOD)-Like Receptors (NLRs) gene expression inD. avara. We here provide the first experimental evidence for NLRs playing a role in distinguishing between different microbes in a sponge. In contrast, the response ofA. aerophobainvolved comparatively few genes and lacked genes encoding for immune receptors. This indicates thatA. aerophobais less responsive to microbial encounters thanD. avara. Our study further reveals different transcriptomic responses between the two sponge species to microbes. The study of sponge responses to microbes aids in understanding the evolution of immune specificity and animal-microbe interactions.Significant statementAnimals rely on components of the immune system to recognize specific microbes, whether they are pathogens, food, or beneficial symbionts. However, in marine invertebrates, the mechanisms of microbial discrimination and specificity are not well understood. Our work suggests that:(i) the transcriptomic response by the sponge can be scaled according to the type of exposure, (ii) the response to microbial encounters is species-specific and (iii) NLRs seem to have a prominent role in the differential response to microorganisms, whether symbionts or food bacteria.

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CRISPR/Cas12a-Mediated Gene Editing in Geodia barretti Sponge Cell Culture

Cited by 4 publications

References 69 publications

Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae)

Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae)

Transcriptomic responses of Mediterranean sponges upon encounter with symbiont microbial consortia

Transcriptomic responses of Mediterranean sponges upon encounter with seawater or symbiont microbial consortia

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