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Abstract Marine SAR116 bacterioplankton are ubiquitous in surface waters across global oceans and form their own order, Puniceispirillales, within the Alphaproteobacteria. To date no comparative physiology among diverse SAR116 isolates has been performed to capture the functional diversity within the clade, and further, diversity through the lens of metabolic potential and environmental preferences via clade-wide pangenomics continues to evolve with the addition of new genomes. Using high-throughput dilution-to-extinction cultivation, we isolated and genome sequenced five new and diverse SAR116 isolates from the northern Gulf of Mexico. Here we present a comparative physiological analysis of these SAR116 isolates, along with a pangenomic investigation of the SAR116 clade using a combination of metagenome-assembled genomes (MAGs, n = 258), single-amplified genomes (SAGs, n = 84), previously existing (n = 2), and new isolate genomes (n = 5), totaling 349 SAR116 genomes. Phylogenomic investigation supported the division of SAR116 into three distinct subclades, each with additional structure totaling 15 monophyletic groups. Our SAR116 isolates belonged to three groups within subclade I representing distinct genera with different morphologies and varied phenotypic responses to salinity and temperature. Overall, SAR116 genomes encoded differences in vitamin and amino acid synthesis, trace metal transport, and osmolyte synthesis and transport. They also had genetic potential for diverse sulfur oxidation metabolisms, placing SAR116 at the confluence of the organic and inorganic sulfur pools. SAR116 subclades showed distinct patterns in habitat preferences across open ocean, coastal, and estuarine environments, and three of our isolates represented the most abundant coastal and estuarine subclade. This investigation provides the most comprehensive exploration of SAR116 to date anchored by new culture genomes and physiology. 

RNAs are critical regulators of gene expression, and their functions are often mediated by complex secondary and tertiary structures. Structured regions in RNA can selectively interact with small molecules—via well-defined ligand-binding pockets—to modulate the regulatory repertoire of an RNA. The broad potential to modulate biological function intentionally via RNA–ligand interactions remains unrealized, however, due to challenges in identifying compact RNA motifs with the ability to bind ligands with good physicochemical properties (often termed drug-like). Here, we devisefpocketR, a computational strategy that accurately detects pockets capable of binding drug-like ligands in RNA structures. Remarkably few, roughly 50, of such pockets have ever been visualized. We experimentally confirmed the ligandability of novel pockets detected withfpocketRusing a fragment-based approach introduced here, Frag-MaP, that detects ligand-binding sites in cells. Analysis of pockets detected byfpocketRand validated by Frag-MaP reveals dozens of sites able to bind drug-like ligands, supports a model for RNA secondary structural motifs able to bind quality ligands, and creates a broad framework for understanding the RNA ligand-ome. 

Abstract Rieske dioxygenases have a long history of being utilized as green chemical tools in the organic synthesis of high‐value compounds, due to their capacity to perform thecis‐dihydroxylation of a wide variety of aromatic substrates. The practical utility of these enzymes has been hampered however by steric and electronic constraints on their substrate scopes, resulting in limited reactivity with certain substrate classes. Herein, we report the engineering of a widely used member of the Rieske dioxygenase class of enzymes, toluene dioxygenase (TDO), to produce improved variants with greatly increased activity for thecis‐dihydroxylation of benzoates. Through rational mutagenesis and screening, TDO variants with substantially improved activity over the wild‐type enzyme were identified. Homology modeling, docking studies, molecular dynamics simulations, and substrate tunnel analysis were applied in an effort to elucidate how the identified mutations resulted in improved activity for this polar substrate class. These analyses revealed modification of the substrate tunnel as the likely cause of the improved activity observed with the best‐performing enzyme variants. 

Abstract The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all Roseobacters in surface oceans and has predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best-known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name Candidatus Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007T (= ATCC TSD-433T = NCMA B160T). 

Cretaceous eolian deposits provide evidence of variations in the tropical-subtropical atmospheric circulation under greenhouse conditions. However, the misinterpretation of many such deposits as fluvial or deltaic originally hindered precise paleoclimatic reconstructions. Here we report a newly identified Early Cretaceous desert in the Hami Basin, China, which helps understand spatial-temporal variations in aridity and atmospheric circulations within central East Asia during the Early Cretaceous. The Liushuquan Formation is composed of >300-m-thick eolian deposits interpreted as an intermontane erg environment. Paleocurrent indicators within the straight-crested dunes of the Liushuquan Formation yield a mean trend of 101.3° (± 10.1°, 1 standard deviation) throughout the formation, consistent with near-surface westerly winds. Paleo-atmospheric circulation superimposed on topographic effects led to widespread eolianite accumulation during the Early Cretaceous. Combined with the spatiotemporal changes in desert distributions and prevailing surface wind patterns in East Asia, these observations are consistent with the migration of the subtropical high-pressure belt during the Early Cretaceous. We propose the following paleo-atmospheric model: (1) During the late Berriasian−Valanginian, the subtropical high belt drifted southward and northward over shorter time scales within the spatial domain of the paleo-Ordos Basin, then shifted southward at least past the Ordos Basin; (2) until the late Hauterivian−Barremian, the subtropical high-pressure zone was primarily located between the northwestern Tarim Basin and the Ordos Basin; and (3) a significant southward shift of the subtropical high-pressure zone occurred during the Aptian−Albian.