Why UV vision and red vision are important for damselfish (Pomacentridae): structural and expression variation in opsin genes

AbstractWe isolated five classes of retinal opsin genes rh1Cl, rh2Cl, sws1Cl, sws2Cl, and lwsCl from the pigeon; these encode RH1Cl, RH2Cl, SWS1Cl, SWS2Cl, and LWSCl opsins, respectively. Upon binding to 11-cis-retinal, these opsins regenerate the corresponding photosensitive molecules, visual pigments. The absorbance spectra of visual pigments have a broad bell shape with the peak, being called λmax. Previously, the SWS1Cl opsin cDNA was isolated from the pigeon retinal RNA, expressed in cultured COS1 cells, reconstituted with 11-cis-retinal, and the λmax of the resulting SWS1Cl pigment was shown to be 393 nm. In this article, using the same methods, the λmax values of RH1Cl, RH2Cl, SWS2Cl, and LWSCl pigments were determined to be 502, 503, 448, and 559 nm, respectively. The pigeon is also known for its UV vision, detecting light at 320–380 nm. Being the only pigments that absorb light below 400 nm, the SWS1Cl pigments must mediate its UV vision. We also determined that a nonretinal PCl pigment in the pineal gland of the pigeon has a λmax value at 481 nm.

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Faculty Opinions recommendation of Analysis of the opsin repertoire in the tardigrade Hypsibius dujardini provides insights into the evolution of opsin genes in panarthropoda.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718634983.793499815 ◽

2014 ◽

Author(s):

Todd Oakley

Keyword(s):

Opsin Genes ◽

Hypsibius Dujardini

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Faculty Opinions recommendation of Abundant contribution of short tandem repeats to gene expression variation in humans.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725994101.793513449 ◽

2016 ◽

Author(s):

Melanie Bahlo

Keyword(s):

Gene Expression ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Gene Expression Variation ◽

Expression Variation ◽

Short Tandem

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Evolution of regulatory networks associated with traits under selection in cichlids

Genome Biology ◽

10.1186/s13059-020-02208-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Tarang K. Mehta ◽

Christopher Koch ◽

Will Nash ◽

Sara A. Knaack ◽

Padhmanand Sudhakar ◽

...

Keyword(s):

Visual System ◽

Regulatory Sequence ◽

Potential Candidate ◽

East African ◽

Regulatory Regions ◽

A Genome ◽

Opsin Genes ◽

East African Cichlids ◽

Gene Regulatory ◽

African Cichlids

Abstract Background Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. Results To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait—the visual system—for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. Conclusions Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits.

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Massively parallel gene expression variation measurement of a synonymous codon library

BMC Genomics ◽

10.1186/s12864-021-07462-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Alexander Schmitz ◽

Fuzhong Zhang

Keyword(s):

Gene Expression ◽

Codon Usage ◽

Single Cells ◽

Massively Parallel ◽

Protein Abundance ◽

Translation Efficiency ◽

Gene Expression Variation ◽

Expression Variation ◽

Change In Mean ◽

Adaptation Index

Abstract Background Cell-to-cell variation in gene expression strongly affects population behavior and is key to multiple biological processes. While codon usage is known to affect ensemble gene expression, how codon usage influences variation in gene expression between single cells is not well understood. Results Here, we used a Sort-seq based massively parallel strategy to quantify gene expression variation from a green fluorescent protein (GFP) library containing synonymous codons in Escherichia coli. We found that sequences containing codons with higher tRNA Adaptation Index (TAI) scores, and higher codon adaptation index (CAI) scores, have higher GFP variance. This trend is not observed for codons with high Normalized Translation Efficiency Index (nTE) scores nor from the free energy of folding of the mRNA secondary structure. GFP noise, or squared coefficient of variance (CV2), scales with mean protein abundance for low-abundant proteins but does not change at high mean protein abundance. Conclusions Our results suggest that the main source of noise for high-abundance proteins is likely not originating at translation elongation. Additionally, the drastic change in mean protein abundance with small changes in protein noise seen from our library implies that codon optimization can be performed without concerning gene expression noise for biotechnology applications.

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