Biology subjects

Christensen, A. C.

Publications and source records attributed to Christensen, A. C..

7 recordsLinked to original sources

bioRxiv2026

A specialized SUV3 RNA helicase is involved in plant mitochondrial DNA repair

Synonymous substitution rates in the coding regions of land plant mitochondrial genomes are substantially lower than those in the nucleus. In contrast, non-coding regions are difficult or impossible to align except among very closely related species, suggesting that point mutation rates in these regions are considerably higher. Rearrangement breakpoints occur frequently within non-coding DNA, generating duplications, deletions, and inversions. To reconcile these contradictory patterns of genome evolution, it has been proposed that DNA damage is converted into double-strand breaks that are repaired through a combination of template-directed mechanisms and non-homologous end joining, while purifying selection preserves the integrity of coding sequences. Here we characterized AtSUV3, a mitochondrially targeted RNA helicase encoded by Arabidopsis thaliana At4g14790, a gene previously proposed to function as part of the plant mitochondrial degradosome. Mutations in AtSUV3 confer hypersensitivity to ciprofloxacin-induced mitochondrial DNA damage, CRISPR- knockout lines display increased ectopic recombination in the mitochondrial genome, and recombinant AtSUV3 exhibits ATP-dependent RNA helicase activity with a preference for 3'-ended substrates. Together, these findings identify AtSUV3 as a factor involved in mitochondrial dsDNA break repair. Consistent with our results, Arabidopsis and other plants encode an uncharacterized gene, AT5G39840.1, with 75% amino acid similarity with AtSUV3, dubbed herein as SUV3-like. We hypothesize that the AtSUV3 paralog has undergone specialization towards DNA repair, whereas AtSUV3-like protein may play a role in the plant organellar degradosome. Collectively, these findings identify AtSUV3 as a previously unrecognized factor involved in mitochondrial dsDNA break repair and provide a framework for understanding the diversification of DNA repair proteins during plant evolution.

plant biology↗

bioRxiv2026

Reshaping Organellar Translation and tRNA Metabolism: The Consequences of Photosynthesis Loss and Massive Horizontal Gene Transfer

The transition to holoparasitism in plants precipitates the loss of photosynthesis, fundamentally altering the selective landscape acting on organellar genomes. These changes raise questions about the mechanisms by which the essential, coevolved machinery of translation responds to extreme genomic erosion and metabolic dependency. Integrating comparative genomics, tRNA sequencing, and subcellular localization assays, we elucidate the extensive rewiring of organellar translation systems and the tRNA-dependent tetrapyrrole biosynthesis pathway in the holoparasitic angiosperm family Balanophoraceae, which exhibits extreme reduction of tRNA content in plastid and mitochondrial genomes. We identified a rare evolutionary event: the putative intracellular transfer of the plastid initiator tRNA (tRNA-iMet) to the nucleus, which compensates for its loss from the plastid genome. We also demonstrate that the unusual UAG-to-Trp reassignment in the Balanophora plastid genetic code is driven by the loss of release factor pRF1 and the recruitment of a mutated nuclear tRNA-Trp. Furthermore, we reveal that the retention of organellar nuclear-encoded aminoacyl-tRNA synthetases is dictated by the presence/absence of cognate organellar tRNAs, which appear to be functional regardless of their foreign (horizontal transfer from the host plant) or native origins. Finally, we uncover a striking evolutionary asymmetry in nuclear-encoded ribosomal proteins: while plastid subunits exhibit elevated substitution rates consistent with relaxed selection and compensatory coevolution, mitochondrial subunits display high sequence conservation, likely maintaining compatibility with the extensive horizontal gene transfer observed in this lineage. Collectively, these findings represent some of the most extreme changes ever identified in the anciently conserved machinery of plant organellar translation.

evolutionary biology↗

bioRxiv2024

Running on empty: Mitochondria without mtDNA exhibit differential motility and connectivity

Plant mitochondria are in continuous motion. While providing ATP to other cellular processes, they also constantly consume ATP to move rapidly within the cell. This movement is in part related to taking up, converting and delivering metabolites and energy to and from different parts of the cell. Plant mitochondria have varying amounts of DNA even within a single cell, from none to the full mitochondrial genome. Because mitochondrial dynamics are altered in an Arabidopsis mutant with disrupted DNA maintenance, we hypothesised that exchanging DNA templates for repair is one of the functions of their movement and interactions. Here, we image mitochondrial DNA by two distinct methods while tracking mitochondrial position to investigate differences in the behaviour of mitochondria with and without DNA in Arabidopsis thaliana. In addition to staining mitochondrial DNA with SYBR Green, we have developed and implemented a fluorescent mitochondrial DNA binding protein that will also enable future understanding of mitochondrial dynamics, genome maintenance and replication. We demonstrate that mitochondria without mtDNA have altered physical behaviour and have a lower immediate connectivity to the rest of the population, further supporting a link between the physical and genetic dynamics of these complex organelles.

cell biology↗

bioRxiv2023

PHOTOSYNTHESIS DRIVES RETENTION OF BACTERIAL-LIKE TRNA METABOLISM IN PLANT ORGANELLES

Eukaryotic nuclear genomes often encode distinct sets of translation machinery for function in the cytosol vs. organelles (mitochondria and plastids). This raises questions about why multiple translation systems are maintained even though they are capable of comparable functions and whether they evolve differently depending on the compartment where they operate. These questions are particularly interesting in plants because translation machinery, including aminoacyl-tRNA synthetases (aaRS), is often dual-targeted to the plastids and mitochondria. These organelles have different functions, with much higher rates of translation in plastids to supply the abundant, rapid-turnover proteins required for photosynthesis. Previous studies have indicated that plant organellar aaRS evolve more slowly compared to mitochondrial aaRS in eukaryotes that lack plastids. Thus, we investigated the evolution of nuclear-encoded organellar and cytosolic aaRS and tRNA maturation enzymes across a broad sampling of angiosperms, including non-photosynthetic (heterotrophic) plant species with reduced plastid gene expression, to test the hypothesis that translational demands associated with photosynthesis constrain the evolution of enzymes involved in organellar tRNA metabolism. Remarkably, heterotrophic plants exhibited wholesale loss of many organelle-targeted aaRS and other enzymes, even though translation still occurs in their mitochondria and plastids. These losses were often accompanied by apparent retargeting of cytosolic enzymes and tRNAs to the organelles, sometimes preserving aaRS-tRNA charging relationships but other times creating surprising mismatches between cytosolic aaRS and mitochondrial tRNA substrates. Our findings indicate that the presence of a photosynthetic plastid drives the retention of specialized systems for organellar tRNA metabolism. SignificanceThe process by which endosymbionts are integrated into a host and become organelles results in a combination of gene loss, transfer to the nucleus, and retention in the organellar genome. It is not clear why some endosymbiont-derived genes may be retained when a functional host counterpart exists whose gene product could simply be retargeted to the organelles. This study revealed that the photosynthetic activity in plant plastids may be responsible for retention of functionally redundant tRNA processing machinery, while mitochondria are more flexible regarding substitution with cytosolic-type enzymes. Therefore, functional constraint in the plastid is likely more important than in the mitochondria for shaping the evolution and retention of functionally redundant proteins that are dual targeted to both organelles.

plant biology↗

bioRxiv2019

Perineuronal nets stabilize the grid cell network

Grid cells are part of a widespread network that supports navigation and spatial memory. Stable grid patterns appear late in development, in concert with extracellular matrix aggregates termed perineuronal nets (PNNs) that condense around inhibitory neurons. To reveal the relationship between stable spatial representations and the presence of PNNs we recorded from populations of neurons in adult rats. We show that removal of PNNs leads to lower inhibitory spiking activity, and reduces grid cells ability to create stable representations of a novel environment. Furthermore, in animals with disrupted PNNs, exposure to a novel arena corrupted the spatiotemporal relationships within grid cell modules, and the stored representations of a familiar arena. Finally, we show that PNN removal in entorhinal cortex distorted spatial representations in downstream hippocampal neurons. Together this work suggests that PNNs provide a key stabilizing element for the grid cell network.

neuroscience↗

bioRxiv2019

The alternative reality of plant mitochondrial DNA

Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held assumption that circular genome molecules are the primary form of mitochondrial DNA, despite evidence to the contrary. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sites for inter- or intramolecular recombination, leading to multiple alternative genomic arrangements (isoforms). Most mitochondrial genomes have been assembled using methods that were unable to capture the complete spectrum of isoforms within a species, leading to an incomplete inference of their structure and recombinational activity. To document and investigate underlying reasons for structural diversity in plant mitochondrial DNA, we used long-read (PacBio) and short-read (Illumina) sequencing data to assemble and compare mitochondrial genomes of domesticated (Lactuca sativa) and wild (L. saligna and L. serriola) lettuce species. This allowed us to characterize a comprehensive, complex set of isoforms within each species and to compare genome structures between species. Physical analysis of L. sativa mtDNA molecules by fluorescence microscopy revealed a variety of linear, branched linear, and circular structures. The mitochondrial genomes for L. sativa and L. serriola were identical in sequence and arrangement, and differed substantially from L. saligna, indicating that the mitochondrial genome structure did not change during domestication. From the isoforms evident in our data, we inferred that recombination occurs at repeats of all sizes at variable frequencies. The differences in genome structure between L. saligna and the two other lettuce species can be largely explained by rare recombination events that rearrange the structure. Our data demonstrate that representations of plant mitochondrial DNA as simple, genome-sized circular molecules are not accurate descriptions of their true nature and that in reality plant mitochondrial DNA is a complex, dynamic mixture of forms. Data AvailabilityBioProject: Organellar genomes of cultivated and wild lettuce (Lactuca) varieties PRJNA508811 https://www.ncbi.nlm.nih.gov/bioproject/508811 and other accessions as indicated through the text and supplemental data. FundingNSF grant MCB-1413152 to ACC and support from UC Davis to RWM.

genomics↗

bioRxiv2018

Repeats Of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution

Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have non-tandem repeats in two size groups: a few large repeats which cause isomerization of the genome by recombination, and numerous repeats longer than 50bp, often found in exactly two copies per genome. It appears that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats are not well-conserved between species, and are infrequently annotated in mitochondrial sequence assemblies. Because they are much larger than expected by chance we call them Repeats Of Unusual Size (ROUS). The repeats consist of two functional classes, those that are involved in genome isomerization through frequent crossing over, and those for which crossovers are rare unless there are mutations in DNA repair genes, or the rate of double-strand breakage is increased. We systematically described and compared these repeats, which are important clues to mechanisms of DNA maintenance in mitochondria. We developed a tool to find non-tandem repeats and analyzed the complete mitochondrial sequences from 135 plant species. We observed an interesting difference between taxa: the repeats are larger and more frequent in the vascular plants. Analysis of closely related species also shows that plant mitochondrial genomes evolve in dramatic bursts of breakage and rejoining, complete with DNA sequence gain and loss, and the repeats are included in these events. We suggest an adaptive explanation for the existence of the repeats and their evolution.

genomics↗