Biology subjects

Palos, K.

Publications and source records attributed to Palos, K..

5 recordsLinked to original sources

bioRxiv2025

Cryptochrome 2 is necessary for promoting a blue light-independent chloroplast signal to control cellular degradation

To thrive in dynamic environments, plants can use their photosynthetic plastid (chloroplast) organelles to sense environmental changes and relay this information to the cell. This signaling can be initiated within chloroplasts by the accumulation of reactive oxygen species (ROS) such as singlet oxygen (1O2), which can accumulate under stress and initiate retrograde (chloroplast-to-nucleus) signaling, chloroplast degradation, and programmed cell death (PCD). However, the mechanisms driving these signals, and the relationship between gene expression and cellular degradation, are unknown. To understand this physiology, here we use the Arabidopsis thaliana plastid ferrochelatase 2 (fc2) mutant, which conditionally produces chloroplast 1O2 and initiates signaling. We show that the blue light photoreceptor cryptochrome 2 (CRY2) is necessary to promote 1O2-induced chloroplast degradation and PCD in the fc2 mutant and that cry2 blocks cellular degradation without affecting bulk 1O2 levels, suggesting that signaling, rather than photo-oxidative stress, has been blocked. Furthermore, a global RNA transcript analysis demonstrated that the impact of the cry2 mutation on retrograde signaling is limited and that the effect of 1O2 on nuclear gene expression and cellular degradation can be uncoupled. Under permissive conditions, fc2 cry2 mutants exhibited constitutive expression of photo-oxidative stress genes, suggesting that cry2 may lead to transcriptional priming to photo-oxidative stress. Finally, we demonstrate that this function of CRY2 is independent of blue light-signaling and that CRY2 isoforms lacking canonical blue light signaling capabilities restore 1O2-induced PCD to fc2 cry2. Together, these results reveal a blue light-independent role for CRY2 in chloroplast signaling and stress acclimation pathways.

plant biology↗

bioRxiv2025

A field-focused systems approach reveals mRNA covalent modifications linked to sorghum growth and development under drought stress

RNA Covalent Modifications (RCMs) are post-transcriptional chemical alterations that influence RNA stability and translation efficiency, thus play critical roles in eukaryotic growth and development. However, their role in regulating plant performance under abiotic stress remain largely unexplored. Here, we integrated multi-omics data in six Sorghum bicolor accessions under water-limiting conditions in the field to explore the relationship between RCMs and drought response. Within a stress and photosynthesis-associated gene co-expression module, we identified SbDUS2, a member of family of enzymes, conserved across eukaryotes, which catalyzes the reduction of uracil to dihydrouridine (DHU) on RNA molecules. DHU-modified transcripts in this module were enriched for photosynthetic functions and showed strong correlation with photosynthetic traits. To elucidate the function of this RCM, we characterized loss of function dus2 mutants in the genetic model, Arabidopsis thaliana. Under control conditions, these DHU-deficient mutants exhibited impaired germination and delayed development. Furthermore, when exposed to heat or water-limiting conditions, these mutants showed significantly reduced net CO2 assimilation and survival. Using multiple transcriptome-wide RNA stability assays, we demonstrated that transcripts associated with lower DHU level in a dus2 background generally exhibited increased stability compared to Col-0 controls. Particularly, lack of DUS2 led to the hyperstability of photosynthesis-related transcripts, impeding their turnover and likely preventing proper photosynthetic acclimation during stress. We propose a model based on these data where DHU acts as a critical post-transcriptional regulator marking mRNAs for rapid turnover under stress, highlighting an overlooked regulatory layer contributing to plant resilience.

plant biology↗

bioRxiv2020

Cytidine triphosphate synthase two provides nucleotides for chloroplast development and stress responses

O_LIReactive oxygen species (ROS) produced in chloroplasts cause oxidative damage, but also signal to initiate chloroplast quality control pathways, cell death, and gene expression. The mechanisms behind these signals are largely unknown. C_LIO_LIThe Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant produces the ROS singlet oxygen in chloroplasts that activates such signaling pathways. Here we mapped one fc2 suppressor mutation to CYTIDINE TRIPHOSPHATE SYNTHASE TWO (CTPS2), which encodes one of five enzymes in Arabidopsis necessary for de novo cytoplasmic CTP (and dCTP) synthesis. C_LIO_LIThe ctps2 mutation reduces chloroplast transcripts and DNA content without similarly affecting mitochondria. Chloroplast nucleic acid content and singlet oxygen signaling are restored by exogenous feeding of the dCTP precursor deoxycytidine, suggesting ctps2 blocks signaling by limiting nucleotides for chloroplast genome maintenance. C_LIO_LIAn investigation of CTPS orthologs in Brassicaceae showed CTPS2 is a member of an ancient lineage distinct from CTPS3. Complementation studies confirmed this analysis; CTPS3 was unable to compensate for CTPS2 function in providing nucleotides for chloroplast DNA and signaling. C_LIO_LIOur studies link cytoplasmic nucleotide metabolism with chloroplast quality control pathways. Such a connection is achieved by a conserved clade of CTPS enzymes that may have evolved specialized functions in providing nucleotides to specific subcellular compartments. C_LI

plant biology↗

bioRxiv2019

Evolutionary and biochemical analyses reveal conservation of the Brassicaceae telomerase ribonucleoprotein complex

The telomerase ribonucleoprotein complex (RNP) is essential for genome stability and performs this role through the addition of repetitive DNA to the ends of chromosomes. The telomerase enzyme is composed of a reverse transcriptase (TERT), which utilizes a template domain in an RNA subunit (TER) to reiteratively add telomeric DNA at the ends of chromosomes. Multiple TERs have been identified in the model plant Arabidopsis thaliana. Here we combine a phylogenetic and biochemical approach to understand how the telomerase RNP has evolved in Brassicaceae, the family that includes A. thaliana. Because of the complex phylogenetic pattern of template domain loss and alteration at the previously characterized A. thaliana TER loci, TER1 and TER2, across the plant family Brassicaceae, we bred double mutants from plants with a template deletion at AtTER1 and T-DNA insertion at AtTER2. These double mutants exhibited no telomere length deficiency, a definitive indication that neither of these loci encode a functional telomerase RNA. Moreover, we determined that the telomerase components TERT, Dyskerin, and the KU heterodimer are under strong purifying selection, consistent with the idea that the TER with which they interact is also conserved. To test this hypothesis further, we analyzed the substrate specificity of telomerase from species across Brassicaceae and determined that telomerase from close relatives bind and extend substrates in a similar manner, supporting the idea that TERs in different species are highly similar to one another and are likely encoded from an orthologous locus. Lastly, TERT proteins from across Brassicaceae were able to complement loss of function tert mutants in vivo, indicating TERTs from other species have the ability to recognize the native TER of A. thaliana. Finally, we immunoprecipitated the telomerase complex and identified associated RNAs via RNA-seq. Using our evolutionary data we constrained our analyses to conserved RNAs within Brassicaceae that contained a template domain. These analyses revealed a highly expressed locus whose disruption by a T-DNA resulted in a telomeric phenotype similar to the loss of other telomerase core proteins, indicating that the RNA has an important function in telomere maintenance.

genetics↗

bioRxiv2017

Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifyingsequence conserved lincRNAs for functional analysis.

Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering ~90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on lincRNA emergence and persistence. Here we present Evolinc, a two-module pipeline designed to facilitate lincRNA discovery and characterize aspects of lincRNA evolution. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analyses workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species. Evolinc-II builds families of homologous lincRNA loci, aligns constituent sequences, infers gene trees, and then uses gene tree / species tree reconciliation to reconstruct evolutionary processes such as gain, loss, or duplication of the locus. Here we demonstrate that Evolinc-I is agnostic to target organism by validating against previously annotated Arabidopsis and human lincRNA data. Using Evolinc-II, we examine ways in which conservation can rapidly be used to winnow down large lincRNA datasets to a small set of candidates for functional analysis. Finally, we show how Evolinc-II can be used to recover the evolutionary history of a known lincRNA, the human telomerase RNA (TERC). The analyses revealed unexpected duplication events as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice and rats. The Evolinc pipeline is currently integrated in CyVerses Discovery Environment and is free to use by researchers.

bioinformatics↗