Identification and functional characterization of solute carrier family 6 genes in Ciona savignyi

Ren, Ping; Wei, Jiankai; Yu, Haiyan; Dong, Bo

doi:10.1016/j.gene.2019.04.056

Cited by 5 publications

(4 citation statements)

References 35 publications

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“…Osmoregulatory mechanisms of osmoconformers have been extensively assessed in mollusks, and similar to results obtained in C. savignyi here, free amino acids (FAAs) were the preferential osmolytes to regulate osmolarity ( Yancey 2005 ; Liu et al 2018 ; Sokolov and Sokolova 2019 ; Pourmozaffar et al 2020 ). The SLC6 gene family is responsible for transporting amino acids, nutrients, or other kinds of osmolytes ( Bröer and Gether 2012 ), the expansion of which was found in the genome of C. savignyi ( Ren et al 2019 ). Our results showed that SLC6 genes were significantly up-regulated under high salinity stress and down-regulated under low salinity stress, as well as the down-regulation of the amino acid biosynthetic process under low salinity stress, consistently supporting that FAA, as the main osmolytes, accumulated to increase intracellular osmolarity to cope with ambient high salinity stress but decreased under low salinity stress.…”

Section: Discussionmentioning

confidence: 99%

Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions

Huang

Shenkar

et al. 2023

RNA

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Rapid plastic response to environmental changes, which involves extremely complex underlying mechanisms, is crucial for organismal survival during many ecological and evolutionary processes such as those in global change and biological invasions. Gene expression is among the most studied molecular plasticity, while co- or post-transcriptional mechanisms are still largely unexplored. Using a model invasive ascidian Ciona savignyi, we studied multidimensional short-term plasticity in response to hyper- and hypo-salinity stresses, covering the physiological adjustment, gene expression, alternative splicing (AS), and alternative polyadenylation (APA) regulations. Our results demonstrated that rapid plastic response varied with environmental context, timescales, and molecular regulatory levels. Gene expression, AS, and APA regulations independently acted on different gene sets and corresponding biological functions, highlighting their non-redundant roles in rapid environmental adaptation. Stress-induced gene expression changes illustrated the use of a strategy of accumulating free amino acid under high salinity and losing/reducing them during low salinity to maintain the osmotic homoeostasis. Genes with more exons were inclined to use AS regulations, and isoform switches in functional genes such as SLC2a5 and Cyb5r3 resulted in enhanced transporting activities by upregulating the isoforms with more transmembrane regions. The extensive 3'-untranslated region (3'UTR) shortening through APA was induced by both salinity stresses, and APA regulation predominated transcriptomic changes at some stages of stress response. The findings here provide evidence for complex plastic mechanisms to environmental changes, and thereby highlight the importance of systemically integrating different levels of regulatory mechanisms in studying initial plasticity in evolutionary trajectories.

show abstract

Section: Discussionmentioning

confidence: 99%

Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions

Huang

Shenkar

et al. 2023

RNA

View full text Add to dashboard Cite

show abstract

“…Osmoregulatory mechanisms of osmoconformers have been extensively assessed in mollusks, and similarly to results obtained in Ciona here, free amino acids (FAAs) were the preferential osmolytes to regulate osmolarity (Liu et al 2018; Pourmozaffar et al 2020; Sokolov and Sokolova 2019; Yancey, 2005). The SLC6 gene family is responsible for transporting amino acids, nutrients, or other kinds of osmolytes (Bröer and Gether 2012), the expansion of which was found in the genome of C. savignyi (Ren et al 2019). Our results showed that SLC6 genes were significantly up-regulated under the high salinity stress and down-regulated under the low salinity stress, as well as the down-regulation of amino acid biosynthetic process under the low salinity stress, consistently supporting that FAA, as the main osmolytes, accumulated to increase intracellular osmolarity to cope with the ambient high salinity stress while decreased under the low salinity stress.…”

Section: Discussionmentioning

confidence: 99%

Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions

Huang

Shenkar

et al. 2022

Preprint

View full text Add to dashboard Cite

Rapid plastic response to environmental changes, which involves extremely complex underlying mechanisms, is crucial for organismal survival during many ecological and evolutionary processes such as those in global change and biological invasions. Gene expression is among the most studied molecular plasticity, while co- or post-transcriptional mechanisms are still largely unexplored. Using a model invasive ascidian Ciona savignyi, we studied multidimensional short-term plasticity in response to hyper- and hypo-salinity stresses, covering the physiological adjustment, gene expression, alternative splicing (AS), and alternative polyadenylation (APA) regulations. Our results demonstrated that rapid plastic response varied with environmental context, timescales, and molecular regulatory levels. Gene expression, AS, and APA regulations independently acted on different gene sets and corresponding biological functions, highlighting their non-redundant roles in rapid environmental adaptation. Stress-induced gene expression changes illustrated the use of a strategy of accumulating free amino acid under high salinity and losing/reducing them during low salinity to maintain the osmotic homoeostasis. Genes with more exons were inclined to use AS regulations, and isoform switches in functional genes such as SLC2a5 and Cyb5r3 resulted in enhanced transporting activities by upregulating the isoforms with more transmembrane regions. The extensive 3’-untranslated region (3’UTR) shortening through APA was induced by both salinity stresses, and APA regulation predominated transcriptomic changes at some stages of stress response. The findings here provide evidence for complex plastic mechanisms to environmental changes, and thereby highlight the importance of systemically integrating different levels of regulation mechanisms in studying initial plasticity in evolutionary trajectories.

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“…Figure 3 reports the results obtained for the Ciona DEG slc6a4b/scl6a2 (ENS_07757). This gene belongs to a group of Na + -dependent monoamine transporters encoded by the SLC6 gene family (Kristensen et al, 2011) that, in Ciona savignyi, is expanded into different subfamilies with a total of 40 putative genes (Ren et al, 2019). In our Ciona RNA-Seq dataset, ENS_07757 is downregulated in both OC::Rep and OC::Act conditions (Table 1), while its murine ortholog Slc6a2 is not differentially expressed in Oc1/Oc2 −/− mouse (Sapkota et al, 2014).…”

Section: Orthologous and Paralogous Oc Signaling-dependent Genes In Cmentioning

confidence: 95%

Onecut Regulates Core Components of the Molecular Machinery for Neurotransmission in Photoreceptor Differentiation

Vassalli

Colantuono

Nittoli

et al. 2021

Front. Cell Dev. Biol.

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Photoreceptor cells (PRC) are neurons highly specialized for sensing light stimuli and have considerably diversified during evolution. The genetic mechanisms that underlie photoreceptor differentiation and accompanied the progressive increase in complexity and diversification of this sensory cell type are a matter of great interest in the field. A role of the homeodomain transcription factor Onecut (Oc) in photoreceptor cell formation is proposed throughout multicellular organisms. However, knowledge of the identity of the Oc downstream-acting factors that mediate specific tasks in the differentiation of the PRC remains limited. Here, we used transgenic perturbation of the Ciona robusta Oc protein to show its requirement for ciliary PRC differentiation. Then, transcriptome profiling between the trans-activation and trans-repression Oc phenotypes identified differentially expressed genes that are enriched in exocytosis, calcium homeostasis, and neurotransmission. Finally, comparison of RNA-Seq datasets in Ciona and mouse identifies a set of Oc downstream genes conserved between tunicates and vertebrates. The transcription factor Oc emerges as a key regulator of neurotransmission in retinal cell types.

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Identification and functional characterization of solute carrier family 6 genes in Ciona savignyi

Cited by 5 publications

References 35 publications

Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions

Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions

Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions

Onecut Regulates Core Components of the Molecular Machinery for Neurotransmission in Photoreceptor Differentiation

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