Search for: All records

Plant mitochondrial genomes (mitogenomes) experience remarkable levels of horizontal gene transfer, including the recent discovery that orchids anciently acquired DNA from fungal mitogenomes. Thus far, however, there is no evidence that any of the genes from this interkingdom horizontal gene transfer are functional in orchid mitogenomes. Here, we applied a specialized sequencing approach to the orchid Corallorhiza maculata and found that some fungal-derived tRNA genes in the transferred region are transcribed, post-transcriptionally modified, and aminoacylated. In contrast, all the transferred protein-coding sequences appear to be pseudogenes. These findings show that fungal horizontal gene transfer has altered the composition of the orchid mitochondrial tRNA pool and suggest that these foreign tRNAs function in translation. The exceptional capacity of tRNAs for horizontal gene transfer and functional replacement is further illustrated by the diversity of tRNA genes in the C. maculata mitogenome, which also include genes of plastid and bacterial origin in addition to their native mitochondrial counterparts. 

Abstract Stress‐driven melt segregation may have important geochemical and geophysical effects but remains a poorly understood process. Few constraints exist on the permeability and distribution of melt in deformed partially molten rocks. Here, we characterize the 3D melt network and resulting permeability of an experimentally deformed partially molten rock containing several melt‐rich bands based on an X‐ray microtomography data set. Melt fractions range from 0.08 to 0.28 in the ∼20‐μm‐thick melt‐rich bands, and from 0.02 to 0.07 in the intervening ∼30‐μm‐thick regions. We simulated melt flow through subvolumes extracted from the reconstructed rock at five length scales ranging from the grain scale (3 μm) to the minimum length required to fully encompass two melt‐rich bands (64 μm). At grain scale, few subvolumes contain interconnected melt, and permeability is isotropic. As the length scale increases, more subvolumes contain melt that is interconnected parallel to the melt bands, but connectivity diminishes in the direction perpendicular to them. Even if melt is connected in all directions, permeability is lower perpendicular to the bands, in agreement with the elongation of melt pockets. Permeability parallel to the bands is proportional to melt fraction to the power of an exponent that increases from ∼2 to 5 with increasing length scale. The permeability in directions parallel to the bands is comparable to that for an isotropic partially molten rock. However, no flow is possible perpendicular to the bands over distances similar to the band spacing. Melt connectivity limits sample scale melt flow to the plane of the melt‐rich bands. 

The strength of lithospheric plates is a central component of plate tectonics, governed by brittle processes in the shallow portion of the plate and ductile behavior in the deeper portion. We review experimental constraints on ductile deformation of olivine, the main mineral in the upper mantle and thus the lithosphere. Olivine deforms by four major mechanisms: low-temperature plasticity, dislocation creep, dislocation-accommodated grain-boundary sliding (GBS), and diffusion-accommodated grain-boundary sliding (diffusion creep). Deformation in most of the lithosphere is dominated by GBS, except in shear zones—in which diffusion creep dominates—and in the brittle-ductile transition—in which low-temperature plasticity may dominate. We find that observations from naturally deformed rocks are consistent with extrapolation of the experimentally constrained olivine flow laws to geological conditions but that geophysical observations predict a weaker lithosphere. The causes of this discrepancy are unresolved but likely reside in the uncertainty surrounding processes in the brittle-ductile transition, at which the lithosphere is strongest. ▪ Ductile deformation of the lithospheric mantle is constrained by experimental data for olivine. ▪ Olivine deforms by four major mechanisms: low-temperature plasticity, dislocation creep, dislocation-accommodated grain-boundary sliding, and diffusion creep. ▪ Observations of naturally deformed rocks are consistent with extrapolation of olivine flow laws from experimental conditions. ▪ Experiments predict stronger lithosphere than geophysical observations, likely due to gaps in constraints on deformation in the brittle-ductile transition. 

Abstract Trace element concentrations in abyssal peridotite olivine provide insights into the formation and evolution of the oceanic lithosphere. We present olivine trace element compositions (Al, Ca, Ti, V, Cr, Mn, Co, Ni, Zn, Y, Yb) from abyssal peridotites to investigate partial melting, melt–rock interaction, and subsolidus cooling at mid-ocean ridges and intra-oceanic forearcs. We targeted 44 peridotites from fast (Hess Deep, East Pacific Rise) and ultraslow (Gakkel and Southwest Indian Ridges) spreading ridges and the Tonga trench, including 5 peridotites that contain melt veins. We found that the abundances of Ti, Mn, Co, and Zn increase, while Ni decreases in melt-veined samples relative to unveined samples, suggesting that these elements are useful tracers of melt infiltration. The abundances of Al, Ca, Cr, and V in olivine are temperature sensitive. Thermometers utilizing Al and Ca in olivine indicate temperatures of 650–1000 °C, with variations corresponding to the contrasting cooling rates the peridotites experienced in different tectonic environments. Finally, we demonstrate with a two-stage model that olivine Y and Yb abundances reflect both partial melting and subsolidus re-equilibration. Samples that record lower Al- and Ca-in-olivine temperatures experienced higher extents of diffusive Y and Yb loss during cooling. Altogether, we demonstrate that olivine trace elements document both high-temperature melting and melt–rock interaction events, as well as subsolidus cooling related to their exhumation and emplacement onto the seafloor. This makes them useful tools to study processes associated with seafloor spreading and mid-ocean ridge tectonics. 

Abstract Eukaryotes maintain separate protein translation systems for nuclear and organellar genes, including distinct sets of tRNAs and aminoacyl-tRNA synthetases (aaRSs). In animals, mitochondrial-targeted aaRSs are expressed at lower levels and are less conserved in sequence than cytosolic aaRSs involved in translation of nuclear mRNAs, likely reflecting lower translational demands in mitochondria. In plants, translation is further complicated by the presence of plastids, which share most aaRSs with mitochondria. In addition, plant mitochondrial tRNA pools have a dynamic history of gene loss and functional replacement by tRNAs from other compartments. To investigate the consequences of these distinctive features of translation in plants, we analyzed sequence evolution in angiosperm aaRSs. In contrast to previously studied eukaryotic systems, we found that plant organellar and cytosolic aaRSs exhibit only a small difference in expression levels, and organellar aaRSs are slightly more conserved than cytosolic aaRSs. We hypothesize that these patterns result from high translational demands associated with photosynthesis in mature chloroplasts. We also investigated aaRS evolution in Sileneae, an angiosperm lineage with extensive mitochondrial tRNA replacement and aaRS retargeting. We predicted positive selection for changes in aaRS sequence resulting from these recent changes in subcellular localization and tRNA substrates but found little evidence for accelerated sequence divergence. Overall, the complex tripartite translation system in plant cells appears to have imposed more constraints on the long-term evolutionary rates of organellar aaRSs compared with other eukaryotic lineages, and plant aaRS protein sequences appear largely robust to more recent perturbations in subcellular localization and tRNA interactions. 

Abstract The number of tRNAs encoded in plant mitochondrial genomes varies considerably. Ongoing loss of bacterial-like mitochondrial tRNA genes in many lineages necessitates the import of nuclear-encoded counterparts that share little sequence similarity. Because tRNAs are involved in highly specific molecular interactions, this replacement process raises questions about the identity and trafficking of enzymes necessary for the maturation and function of newly imported tRNAs. In particular, the aminoacyl-tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar (mitochondrial and plastid) or nuclear-encoded (cytosolic) tRNAs. Here, we investigate the evolution of aaRS subcellular localization in a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion and confirmed these results with colocalization microscopy assays. However, we also found cases where aaRS localization does not appear to change despite functional tRNA replacement, suggesting evolution of novel interactions and charging relationships. Therefore, the history of repeated tRNA replacement in Sileneae mitochondria reveals that differing constraints on tRNA/aaRS interactions may determine which of these alternative coevolutionary paths is used to maintain organellar translation in plant cells. 

Scientists organized a trio of expeditions to document the buildup of stress leading to a large earthquake on a seafloor fault, developing innovations for successful seagoing research in the process. 

Abstract There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes—even single-nucleotide substitutions—create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities. In this review, we explore whether there are general principles that can explain why certain genes are prone to incompatibilities while others maintain interchangeability. We summarize evidence pointing to four genetic features that may contribute to greater resistance to functional replacement: (1) function in multisubunit enzyme complexes and protein–protein interactions, (2) sensitivity to changes in gene dosage, (3) rapid rate of sequence evolution, and (4) overall importance to cell viability, which creates sensitivity to small perturbations in molecular function. We discuss the relative levels of support for these different hypotheses and lay out future directions that may help explain the striking contrasts in patterns of incompatibility and interchangeability throughout the history of molecular evolution.