An official website of the United States government
The loss of previously adaptive traits is typically linked to relaxation in selection, yet the molecular steps leading to such repeated losses are rarely known. Molecular studies of loss have tended to focus on gene sequences alone, but overlooking other aspects of protein expression might underestimate phenotypic diversity. Insights based almost solely on opsin gene evolution, for instance, have made mammalian color vision a textbook example of phenotypic loss. We address this gap by investigating retention and loss of opsin genes, transcripts, and proteins across ecologically diverse noctilionoid bats. We find multiple, independent losses of short-wave-sensitive opsins. Mismatches between putatively functional DNA sequences, mRNA transcripts, and proteins implicate transcriptional and post-transcriptional processes in the ongoing loss of S-opsins in some noctilionoid bats. Our results provide a snapshot of evolution in progress during phenotypic trait loss, and suggest vertebrate visual phenotypes cannot always be predicted from genotypes alone.
more »
« less
Differences in both expression and protein activity contribute to the distinct functions of AINTEGUMENTA compared with AINTEGUMENTA-LIKE 5 and AINTEGUMENTA-LIKE 7
Abstract Three members of the Arabidopsis AINTEGUMENTA-LIKE/PLETHORA (AIL/PLT) transcription factor family, AIL5/PLT5, AIL6/PLT3, and AIL7/PLT7, exhibit partially overlapping roles with AINTEGUMENTA (ANT) during flower development. Loss ofANTfunction alone results in smaller floral organs and female sterility indicating that some ANT functions cannot be provided by these related transcription factors. Previously, we showed that expression ofAIL6at the same levels and spatial pattern asANTcould largely rescue the defects ofantmutants. This suggested that the functional differences betweenANTandAIL6were primarily a consequence of expression differences. Here, we investigated the functional differences betweenANTand bothAIL5andAIL7by expressing these twoAILs under the control of theANTpromoter. We found that onlyANT:gAIL5lines with much higher amounts ofAIL5mRNA as compared withANTcould compensate for loss ofANTfunction.ANT:gAIL7lines withAIL7mRNA levels similar to those ofANTwere able to rescue some but not all aspects of theantmutant phenotype. Thus, expression differences alone cannot explain the functional differences between ANT and these two related proteins. Studies in yeast show that AIL5 and AIL7 have lower transcriptional activation activities as compared with ANT and AIL6 when bound to the consensus ANT DNA binding site. Our results suggest that differences in both expression and protein activity contribute to the functional specificity of ANT compared with AIL5 and AIL7.
more »
« less
- Award ID(s):
- 2211715
- PAR ID:
- 10444459
- Publisher / Repository:
- Springer Science + Business Media
- Date Published:
- Journal Name:
- Plant Molecular Biology
- Volume:
- 113
- Issue:
- 1-3
- ISSN:
- 0167-4412
- Format(s):
- Medium: X Size: p. 75-88
- Size(s):
- p. 75-88
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
ABSTRACT SMAX1-LIKE (SMXL) proteins are transcriptional co-repressors that regulate many aspects of plant growth and development. Proteins from the SMAX1- and SMXL78-clades of this family are targeted for degradation after karrikin or strigolactone perception, triggering downstream responses. We investigated how SMXL proteins control development.SMXL7can partially replicateSMAX1function in seeds and seedlings, butSMAX1cannot replaceSMXL7in shoot branching control. Therefore, the distinct roles of these genes arise from differences in protein activity more than expression. Analysis of chimeras and domain deletions of SMAX1 and SMXL7 proteins revealed that an N-terminal domain is necessary and sufficient to specify developmental functions. We screened 158 transcription factors for interactions with SMAX1. The N-terminal domain is necessary and/or sufficient for the majority of candidate interactions. These discoveries enable cross-wiring of karrikin and strigolactone control of plant development and lay a foundation for understanding how SMXL proteins evolved functional differences.more » « less
-
SUMMARY The DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs) are crucial for RNA‐directed DNA methylation (RdDM) in plant species.Setaria viridisis a model monocot species with a relatively compact genome that has limited transposable element (TE) content. CRISPR‐based genome editing approaches were used to create loss‐of‐function alleles for the two putative functional DRM genes inS. viridisto probe the role of RdDM. Double mutant (drm1ab)plants exhibit some morphological abnormalities but are fully viable. Whole‐genome methylation profiling provided evidence for the widespread loss of methylation in CHH sequence contexts, particularly in regions with high CHH methylation in wild‐type plants. Evidence was also found for the locus‐specific loss of CG and CHG methylation, even in some regions that lack CHH methylation. Transcriptome profiling identified genes with altered expression in thedrm1abmutants. However, the majority of genes with high levels of CHH methylation directly surrounding the transcription start site or in nearby promoter regions in wild‐type plants do not have altered expression in thedrm1abmutant, even when this methylation is lost, suggesting limited regulation of gene expression by RdDM. Detailed analysis of the expression of TEs identified several transposons that are transcriptionally activated indrm1abmutants. These transposons are likely to require active RdDM for the maintenance of transcriptional repression.more » « less
-
Summary The ability of plant somatic cells to dedifferentiate, form somatic embryos and regenerate whole plantsin vitrohas been harnessed for both clonal propagation and as a key component of plant genetic engineering systems. Embryogenic culture response is significantly limited, however, by plant genotype in most species. This impedes advancements in both plant transformation‐based functional genomics research and crop improvement efforts. We utilized natural variation among maize inbred lines to genetically map somatic embryo generation potential in tissue culture and identify candidate genes underlying totipotency. Using a series of maize lines derived from crosses involving the culturable parent A188 and the non‐responsive parent B73, we identified a region on chromosome 3 associated with embryogenic culture response and focused on three candidate genes within the region based on genetic position and expression pattern. Two candidate genes showed no effect when ectopically expressed in B73, but the geneWox2awas found to induce somatic embryogenesis and embryogenic callus proliferation. Transgenic B73 cells with strong constitutive expression of the B73 and A188 coding sequences ofWox2awere found to produce somatic embryos at similar frequencies, demonstrating that sufficient expression of either allele could rescue the embryogenic culture phenotype. Transgenic B73 plants were regenerated from the somatic embryos without chemical selection and no pleiotropic effects were observed in theWox2aoverexpression lines in the regenerated T0 plants or in the two independent events which produced T1 progeny. In addition to linking natural variation in tissue culture response toWox2a, our data support the utility ofWox2ain enabling transformation of recalcitrant genotypes.more » « less
-
Macdonald, Stuart (Ed.)Abstract Gene regulatory networks specify the gene expression patterns needed for traits to develop. Differences in these networks can result in phenotypic differences between organisms. Although loss-of-function genetic screens can identify genes necessary for trait formation, gain-of-function screens can overcome genetic redundancy and identify loci whose expression is sufficient to alter trait formation. Here, we leveraged transgenic lines from the Transgenic RNAi Project at Harvard Medical school to perform both gain- and loss-of-function CRISPR/Cas9 screens for abdominal pigmentation phenotypes. We identified measurable effects on pigmentation patterns in the Drosophila melanogaster abdomen for 21 of 55 transcription factors in gain-of-function experiments and 7 of 16 tested by loss-of-function experiments. These included well-characterized pigmentation genes, such as bab1 and dsx, and transcription factors that had no known role in pigmentation, such as slp2. Finally, this screen was partially conducted by undergraduate students in a Genetics Laboratory course during the Spring semesters of 2021 and 2022. We found this screen to be a successful model for student engagement in research in an undergraduate laboratory course, that can be readily adapted to evaluate the effect of hundreds of genes on many different Drosophila traits, with minimal resources.more » « less
