More Like this

1. Transcribed germline-limited coding sequences in Oxytricha trifallax

   https://doi.org/10.1093/g3journal/jkab092  

   Miller, Richard V ; Neme, Rafik ; Clay, Derek M ; Pathmanathan, Jananan S ; Lu, Michael W ; Yerlici, V Talya ; Khurana, Jaspreet S ; Landweber, Laura F ( June 2021 , G3 Genes|Genomes|Genetics)

   Hughes, T (Ed.)

   Abstract The germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein-coding sequences whose gene expression is terminated by DNA elimination. 

   more » « less
2. Differential resistance and acclimation of two coral species to chronic nutrient enrichment reflect life‐history traits

   https://doi.org/10.1111/1365-2435.13780  

   Fox, Michael D. ; Nelson, Craig E. ; Oliver, Thomas A. ; Quinlan, Zachary A. ; Remple, Kristina ; Glanz, Jess ; Smith, Jennifer E. ; Putnam, Hollie M. ; Fox, ed., Charles ( March 2021 , Functional Ecology)

   The effects of nutrient pollution on coral reef ecosystems are multifaceted. Numerous experiments have sought to identify the physiological effects of nutrient enrichment on reef‐building corals, but the results have been variable and sensitive to choices of nutrient quantity, chemical composition and exposure duration.

   To test the effects of chronic, ecologically relevant nutrient enrichment on coral growth and photophysiology, we conducted a 5‐week continuous dosing experiment on two Hawaiian coral species,Porites compressaandPocillopora acuta. We acclimated coral fragments to five nutrient concentrations (0.1–7 µMand 0.06–2.24 µM) with constant stoichiometry 2.5:1 nitrate to phosphate) bracketing in situ observations from reefs throughout the Pacific.

   Nutrient enrichment linearly increased photophysiological performance of both species within 3 weeks. The effect of nutrients onP. acutaphotochemical efficiency increased through time while a consistent response inP. compressaindicated acclimation to elevated nutrients within 5 weeks. Endosymbiont densities and total chlorophyll concentrations also increased proportionally with nutrient enrichment inP. acuta, but not inP. compressa, revealing contrasting patterns of host–symbiont acclimatization.

   The two species also exhibited contrasting effects of nutrient enrichment on skeletal growth. Calcification was enhanced at low nutrient enrichment (1 µM) inP. acuta, but comparable to the control at higher concentrations, whereas calcification was reduced inP. compressa(30%–35%) above 3 µM.

   Stable isotope analysis revealed species‐specific nitrogen uptake dynamics in the coral–algal symbiosis. The endosymbionts ofP. acutaexhibited increased nitrogen uptake (decreased δ¹⁵N) and incorporation (19%–31% decrease in C:N ratios) across treatments. In contrast,P. compressaendosymbionts maintained constant δ¹⁵N values and low levels of nitrogen incorporation (9%–11% decrease in C:N ratios). The inability ofP. acutato regulate endosymbiont nutrient uptake may indicate an emerging destabilization in the coral–algal symbiosis under nutrient enrichment that could compromise resistance to additional environmental stressors.

   Our results highlight species‐specific differences in the coral–algal symbiosis, which influence responses to chronic nutrient enrichment. These findings showcase how symbioses can vary among closely related taxa and underscore the importance of considering how life‐history traits modify species response to environmental change.

   A freePlain Language Summarycan be found within the Supporting Information of this article.

    

   more » « less
3. Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis

   https://doi.org/10.1128/mSystems.00032-17  

   Darnell, Cynthia L. ; Tonner, Peter D. ; Gulli, Jordan G. ; Schmidler, Scott C. ; Schmid, Amy K. ; Shank, Elizabeth A. ( September 2017 , mSystems)

   ABSTRACT Gene regulatory networks (GRNs) are critical for dynamic transcriptional responses to environmental stress. However, the mechanisms by which GRN regulation adjusts physiology to enable stress survival remain unclear. Here we investigate the functions of transcription factors (TFs) within the global GRN of the stress-tolerant archaeal microorganism Halobacterium salinarum . We measured growth phenotypes of a panel of TF deletion mutants in high temporal resolution under heat shock, oxidative stress, and low-salinity conditions. To quantitate the noncanonical functional forms of the growth trajectories observed for these mutants, we developed a novel modeling framework based on Gaussian process regression and functional analysis of variance (FANOVA). We employ unique statistical tests to determine the significance of differential growth relative to the growth of the control strain. This analysis recapitulated known TF functions, revealed novel functions, and identified surprising secondary functions for characterized TFs. Strikingly, we observed that the majority of the TFs studied were required for growth under multiple stress conditions, pinpointing regulatory connections between the conditions tested. Correlations between quantitative phenotype trajectories of mutants are predictive of TF-TF connections within the GRN. These phenotypes are strongly concordant with predictions from statistical GRN models inferred from gene expression data alone. With genome-wide and targeted data sets, we provide detailed functional validation of novel TFs required for extreme oxidative stress and heat shock survival. Together, results presented in this study suggest that many TFs function under multiple conditions, thereby revealing high interconnectivity within the GRN and identifying the specific TFs required for communication between networks responding to disparate stressors. IMPORTANCE To ensure survival in the face of stress, microorganisms employ inducible damage repair pathways regulated by extensive and complex gene networks. Many archaea, microorganisms of the third domain of life, persist under extremes of temperature, salinity, and pH and under other conditions. In order to understand the cause-effect relationships between the dynamic function of the stress network and ultimate physiological consequences, this study characterized the physiological role of nearly one-third of all regulatory proteins known as transcription factors (TFs) in an archaeal organism. Using a unique quantitative phenotyping approach, we discovered functions for many novel TFs and revealed important secondary functions for known TFs. Surprisingly, many TFs are required for resisting multiple stressors, suggesting cross-regulation of stress responses. Through extensive validation experiments, we map the physiological roles of these novel TFs in stress response back to their position in the regulatory network wiring. This study advances understanding of the mechanisms underlying how microorganisms resist extreme stress. Given the generality of the methods employed, we expect that this study will enable future studies on how regulatory networks adjust cellular physiology in a diversity of organisms. 

   more » « less
4. CPGView : A package for visualizing detailed chloroplast genome structures

   https://doi.org/10.1111/1755-0998.13729  

   Liu, Shengyu ; Ni, Yang ; Li, Jingling ; Zhang, Xinyi ; Yang, Heyu ; Chen, Haimei ; Liu, Chang ( January 2023 , Molecular Ecology Resources)

   Chloroplast genomes have been widely used in studying plant phylogeny and evolution. Several chloroplast genome visualization tools have been developed to display the distribution of genes on the genome. However, these tools do not draw features, such as exons, introns, repetitive elements, and variable sites, disallowing in‐depth examination of the genome structures. Here, we developed and validated a software package called Chloroplast Genome Viewers (CPGView). CPGView can draw three maps showing (i) the distributions of genes, variable sites, and repetitive sequences, including microsatellites, tandem and dispersed repeats; (ii) the structure of the cis‐splicing genes after adjusting the exon‐intron boundary positions using a coordinate scaling algorithm, and (iii) the structure of the trans‐splicing generps12. To test the accuracy of CPGView, we sequenced, assembled, and annotated 31 chloroplast genomes from 31 genera of 22 families. CPGView drew maps correctly for all the 31 chloroplast genomes. Lastly, we used CPGView to examine 5998 publicly released chloroplast genomes from 2513 genera of 553 families. CPGView succeeded in plotting maps for 5882 but failed to plot maps for 116 chloroplast genomes. Further examination showed that the annotations of these 116 genomes had various errors needing manual correction. The test on newly generated data and publicly available data demonstrated the ability of CPGView to identify errors in the annotations of chloroplast genomes. CPGView will become a widely used tool to study the detailed structure of chloroplast genomes. The web version of CPGView can be accessed fromhttp://www.1kmpg.cn/cpgview.

    

   more » « less
5. The legacy of stress: Coral bleaching impacts reproduction years later

   https://doi.org/10.1111/1365-2435.13653  

   Johnston, Erika C. ; Counsell, Chelsie W. W. ; Sale, Tayler L. ; Burgess, Scott C. ; Toonen, Robert J. ; Hopkins, ed., William ( August 2020 , Functional Ecology)

   The extent to which populations persist under environmental stress depends on the reproductive output of individuals that survive the stress. In coral systems, corals bleach in response to stress from elevated water temperature. However, little is known of the extent to which thermal stress impairs the reproductive capacity of the survivors over the following years, limiting the capacity to predict how populations will persist in the Anthropocene.

   Using histology to quantify the abundance and size of oocytes and spermaries per polyp, we tested how bleaching impairs the reproductive response of the coralPocillopora meandrinaover two reproductive seasons following the 2015 mass bleaching event in the Hawaiian Islands.

   We found that smaller colonies not only had a greater probability of bleaching but also suffered greater reproductive impacts over a longer time. In contrast, larger colonies generated comparable reproductive output regardless of bleaching severity, although bleached colonies generated smaller oocytes the year after bleaching.

   These results show that reproductive impacts of bleaching are more complex and size‐specific than commonly assumed. Therefore, estimates of bleaching mortality may underestimate the true impact of thermal stress on populations, especially as populations lose larger individuals from repeated and co‐occurring stressors.

   A freePlain Language Summarycan be found within the Supporting Information of this article.

    

   more » « less