A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms.

Algae and plants carry 2 organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages and organelle changes likely accompanied the adaptation to new ecological niches such as the terrestrial habitat. Based on organelle proteome data and the genomes of 168 phototrophic (Archaeplastida) versus a broad range of 518 non-phototrophic eukaryotes, we screened for changes in plastid and mitochondrial biology across 1 billion years of evolution. Taking into account 331,571 protein families (or orthogroups), we identify 31,625 protein families that are unique to primary plastid-bearing eukaryotes. The 1,906 and 825 protein families are predicted to operate in plastids and mitochondria, respectively. Tracing the evolutionary history of these protein families through evolutionary time uncovers the significant remodeling the organelles experienced from algae to land plants. The analyses of gained orthogroups identifies molecular changes of organelle biology that connect to the diversification of major lineages and facilitated major transitions from chlorophytes en route to the global greening and origin of angiosperms.

One-Year Water-Stable and Porous Bi(III) Halide Semiconductor with Broad-Spectrum Antibacterial Performance.

Hybrid metal halide semiconductors are a unique family of materials with immense potential for numerous applications. For this to materialize, environmental stability and toxicity deficiencies must be simultaneously addressed. We report here a porous, visible light semiconductor, namely, (DHS)Bi2I8 (DHS = [2.2.2] cryptand), which consists of nontoxic, earth-abundant elements, and is water-stable for more than a year. Gas- and vapor-sorption studies revealed that it can selectively and reversibly adsorb H2O and D2O at room temperature (RT) while remaining impervious to N2 and CO2. Solid-state NMR measurements and density functional theory (DFT) calculations verified the incorporation of H2O and D2O in the molecular cages, validating the porous nature. In addition to porosity, the material exhibits broad band-edge light emission centered at 600 nm with a full width at half-maximum (fwhm) of 99 nm, which is maintained after 6 months of immersion in H2O. Moreover, (DHS)Bi2I8 exhibits bacteriocidal action against three Gram-positive and three Gram-negative bacteria, including antibiotic-resistant strains. This performance, coupled with the recorded water stability and porous nature, renders it suitable for a plethora of applications, from solid-state batteries to water purification and disinfection.

Mitochondrial evolution: Gene shuffling, endosymbiosis, and signaling.

Genes for cardiolipin and ceramide synthesis occur in some alphaproteobacterial genomes. They shed light on mitochondrial origin and signaling in the first eukaryotic cells.

Chemical Behavior and Local Structure of the Ruddlesden-Popper and Dion-Jacobson Alloyed Pb/Sn Bromide 2D Perovskites.

The alloyed lead/tin (Pb/Sn) halide perovskites have gained significant attention in the development of tandem solar cells and other optoelectronic devices due to their widely tunable absorption edge. To gain a better understanding of the intriguing properties of Pb/Sn perovskites, such as their anomalous bandgap's dependence on stoichiometry, it is important to deepen the understanding of their chemical behavior and local structure. Herein, we investigate a series of two-dimensional Ruddlesden-Popper (RP) and Dion-Jacobson (DJ) phase alloyed Pb/Sn bromide perovskites using butylammonium (BA) and 3-(aminomethyl)pyridinium (3AMPY) as the spacer cations: (BA)2(MA)n-1PbxSnn-xBr3n+1 (n = 1-3) and (3AMPY)(MA)n-1PbxSnn-xBr3n+1 (n = 1-3) through a solution-based approach. Our results show that the ratio and site preference of Pb/Sn atoms are influenced by the layer thickness (n) and spacer cations (A'), as determined by single-crystal X-ray diffraction. Solid-state 1H, 119Sn, and 207Pb NMR spectroscopy analysis shows that the Pb atoms prefer the outer layers in n = 3 members: (BA)2(MA)PbxSnn-xBr10 and (3AMPY)(MA)PbxSnn-xBr10. Layered 2D DJ alloyed Pb/Sn bromide perovskites (3AMPY)(MA)n-1PbxSnn-xBr3n+1 (n = 1-3) demonstrate much narrower optical band gaps, lower energy PL emission peaks, and longer carrier lifetimes compared to those of RP analogs. Density functional theory calculations suggest that Pb-rich alloys (Pb:Sn ∼4:1) for n = 1 compounds are thermodynamically favored over 50:50 (Pb:Sn ∼1:1) compositions. From grazing-incidence wide-angle X-ray scattering (GIWAXS), we see that films in the RP phase orient parallel to the substrate, whereas for DJ cases, random orientations are observed relative to the substrate.

Boron Adsorption Kinetics of Microcrystalline Cellulose and Polymer Resin.

Tailoring boron-polysaccharide interactions is an important strategy for developing functional soft materials such as hydrogels, fire retardants, and sorbents for environmental remediation, for example, using lignocellulosic biomass. For such applications to be realized, it is paramount to understand the adsorption kinetics of borate anions on cellulose and their local structures. Here, the kinetic aspects of boron adsorption by microcrystalline cellulose, lignin, and polymeric resin are investigated and compared. Borate anions interact with the vicinal diols in the glucopyranoside moieties of cellulose to yield chemisorbed boron chelate complexes. In contrast to cellulose, technical lignin contains fewer cis-vicinal diols, and it does not have a tendency to form such chelate complexes upon treatment with the aqueous boric acid solution. The formation kinetics and stability of these chelate complexes strongly depend on nanoscale structures, as well as reaction conditions such as pH and concentration of the sorbate and sorbent. Specifically, insights into the distinct boron adsorption sites were obtained by solid-state one-dimensional (1D) 11B magic-angle spinning NMR and the local structures and intermolecular interactions in the vicinities of boron chelate complexes are elucidated by analyzing two-dimensional (2D) 1H-13C and 11B-1H heteronuclear correlation NMR spectra. The total boron adsorption capacity of cellulose is estimated to be in the 1.3-3.0 mg range per gram of sorbent, which is lower than the boron adsorption capacity of a polystyrene-based resin, ∼17.2 mg of boron per gram of Amberlite IRA 743. Our study demonstrates that the local backbone and side chain flexibility as well as the structures of polyol groups play a significant role in determining the kinetic and thermodynamic stability of chelate complexes, yielding to different boron adsorption capabilities of lignocellulosic polymers.

The layered costs and benefits of translational redundancy.

The rate and accuracy of translation hinges upon multiple components - including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules - many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on growth rate. However, we lack empirical measurements of the fitness costs and benefits of redundancy, and we have poor a understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of Escherichia coli by deleting 28 tRNA genes, 3 tRNA modifying systems, and 4 rRNA operons in various combinations. We find that redundancy in tRNA pools is beneficial when nutrients are plentiful and costly under nutrient limitation. This nutrient-dependent cost of redundant tRNA genes stems from upper limits to translation capacity and growth rate, and therefore varies as a function of the maximum growth rate attainable in a given nutrient niche. The loss of redundancy in rRNA genes and tRNA modifying enzymes had similar nutrient-dependent fitness consequences. Importantly, these effects are also contingent upon interactions across translation components, indicating a layered hierarchy from copy number of tRNA and rRNA genes to their expression and downstream processing. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species' evolutionary history with feasts and famines.

Translation is the process by which cellular machines called ribosomes use the information encoded in genes to make proteins . Every organism requires two types of RNA molecules to make new proteins: ribosomal RNAs (rRNAs, which form part of the ribosome) and transfer RNAs (tRNAs, which transport the amino acid molecules that form proteins to the ribosomes). These RNA molecules are coded in the genome, but different organisms have different 'copy numbers': some genomes contain just a few copies of each of these genes, while others have thousands. This apparent redundancy ­ the presence of several copies of the same gene ­ is puzzling because it is costly to make and maintain DNA and RNA. This leads to an important question: how does redundancy in these important genes (coding for tRNAs and rRNAs) evolve? The answer is key to understanding how one of the most fundamental cellular processes, the making of proteins from DNA, has evolved. A possible reason for organisms to have many copies of the genes required to make proteins is to allow rapid translation, which allows cells to divide faster, and populations of cells to grow more quickly. However, this would likely mean that, when nutrients are scarce, carrying and translating many copies of the same gene would become a burden on the cell. Raval et al. set out to test this idea by measuring the costs and benefits of seemingly redundant translation components. To do this, Raval et al. deleted some of the redundant gene copies in the bacterium Escherichia coli and asked if that changed bacterial growth. The experiments showed that when nutrients were plentiful, cells with more copies of the genes (high redundancy) were better able to use the nutrients and divide rapidly. However, when nutrients were limited, bacteria with extra gene copies divided more slowly, showing that the extra genes are indeed a big burden on the cell. Raval et al. propose that nutrients available in the environment ultimately determine whether redundancy of the translation machinery is a blessing or a curse. This suggests that the redundancy and underlying growth strategies of different organisms are forged by their experiences of feast and famine during their evolutionary past. Importantly, by testing the joint effect of many different molecules involved in translation, Raval et al. uncovered several strategies that may maximize bacterial growth and protein production. Their results could thus be useful for optimizing the synthesis of important products that use growing cells as factories ­ from beer to insulin ­ where the rate of growth is critical.

Porous and Water Stable 2D Hybrid Metal Halide with Broad Light Emission and Selective H2 O Vapor Sorption.

In this work we report a strategy for generating porosity in hybrid metal halide materials using molecular cages that serve as both structure-directing agents and counter-cations. Reaction of the [2.2.2] cryptand (DHS) linker with PbII in acidic media gave rise to the first porous and water-stable 2D metal halide semiconductor (DHS)2 Pb5 Br14 . The corresponding material is stable in water for a year, while gas and vapor-sorption studies revealed that it can selectively and reversibly adsorb H2 O and D2 O at room temperature (RT). Solid-state NMR measurements and DFT calculations verified the incorporation of H2 O and D2 O in the organic linker cavities and shed light on their molecular configuration. In addition to porosity, the material exhibits broad light emission centered at 617 nm with a full width at half-maximum (FWHM) of 284 nm (0.96 eV). The recorded water stability is unparalleled for hybrid metal halide and perovskite materials, while the generation of porosity opens new pathways towards unexplored applications (e.g. solid-state batteries) for this class of hybrid semiconductors.

Endosymbiotic selective pressure at the origin of eukaryotic cell biology.

The dichotomy that separates prokaryotic from eukaryotic cells runs deep. The transition from pro- to eukaryote evolution is poorly understood due to a lack of reliable intermediate forms and definitions regarding the nature of the first host that could no longer be considered a prokaryote, the first eukaryotic common ancestor, FECA. The last eukaryotic common ancestor, LECA, was a complex cell that united all traits characterising eukaryotic biology including a mitochondrion. The role of the endosymbiotic organelle in this radical transition towards complex life forms is, however, sometimes questioned. In particular the discovery of the asgard archaea has stimulated discussions regarding the pre-endosymbiotic complexity of FECA. Here we review differences and similarities among models that view eukaryotic traits as isolated coincidental events in asgard archaeal evolution or, on the contrary, as a result of and in response to endosymbiosis. Inspecting eukaryotic traits from the perspective of the endosymbiont uncovers that eukaryotic cell biology can be explained as having evolved as a solution to housing a semi-autonomous organelle and why the addition of another endosymbiont, the plastid, added no extra compartments. Mitochondria provided the selective pressures for the origin (and continued maintenance) of eukaryotic cell complexity. Moreover, they also provided the energetic benefit throughout eukaryogenesis for evolving thousands of gene families unique to eukaryotes. Hence, a synthesis of the current data lets us conclude that traits such as the Golgi apparatus, the nucleus, autophagosomes, and meiosis and sex evolved as a response to the selective pressures an endosymbiont imposes.

Chemical exchange of labile protons by deuterium enables selective detection of pharmaceuticals in solid formulations.

Chemically assisted swapping of labile protons by deuterons is presented for amino acids, polysaccharides, pharmaceutical compounds, and their solid formulations. Solid-state packing interactions in these compounds are elucidated by 1H-2H isotope correlation NMR spectroscopy (iCOSY). A minuscule concentration of dopamine, 5 wt% or ∼100 µg, in a solid formulation can be detected by 2H NMR at 28.2 T (1H, 1200 MHz) in under a minute.

Combining heteronuclear correlation NMR with spin-diffusion to detect relayed Cl-H-H and N-H-H proximities in molecular solids.

Analysis of short-to-intermediate range intermolecular interactions offers a great way of characterizing the solid-state organization of small molecules and materials. This can be achieved by two-dimensional (2D) homo- and heteronuclear correlation NMR spectroscopy, for example, by carrying out experiments at high magnetic fields in conjunction with fast magic-angle spinning (MAS) techniques. But, detecting 2D peaks for heteronuclear dipolar coupled spin pairs separated by greater than 3 Å is not always straightforward, particularly when low-gamma quadrupolar nuclei are involved. Here, we present a 2D correlation NMR experiment that combines the advantages of heteronuclear-multiple quantum coherence (HMQC) and proton-based spin-diffusion (SD) pulse sequences using radio-frequency-driven-recouping (RFDR) to probe inter and intramolecular 1H-X (X = 14N, 35Cl) interactions. This experiment can be used to acquire 2D 1H{X}-HMQC filtered 1H-1H correlation as well as 2D 1H-X HMQC spectra. Powder forms of dopamine·HCl and l-histidine·HCl·H2O are characterized at high fields (21.1 T and 18.8 T) with fast MAS (60 kHz) using the 2D HMQC-SD-RFDR approach. Solid-state NMR results are complemented with NMR crystallography analyses using the gauge-including projector augmented wave (GIPAW) approach. For histidine·HCl·H2O, 2D peaks associated with 14N-1H-1H and 35Cl-1H-1H distances of up to 4.4 and 3.9 Å have been detected. This is further corroborated by the observation of 2D peaks corresponding to 14N-1H-1H and 35Cl-1H-1H distances of up to 4.2 and 3.7 Å in dopamine·HCl, indicating the suitability of the HMQC-SD-RFDR experiments for detecting medium-range proximities in molecular solids.