Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotopes

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode

TOI-561 b: A Low Density Ultra-Short Period "Rocky" Planet around a Metal-Poor Star

TOI-561 is a galactic thick disk star hosting an ultra-short period (0.45 day orbit) planet with a radius of 1.37 R$_{\oplus}$, making it one of the most metal-poor ([Fe/H] = -0.41) and oldest ($\sim$10 Gyr) sites where an Earth-sized planet has been found. We present new simultaneous radial velocity measurements (RVs) from Gemini-N/MAROON-X and Keck/HIRES, which we combined with literature RVs to derive a mass of M$_{b}$=2.24 $\pm$ 0.20 M$_{\oplus}$. We also used two new Sectors of TESS photometry to improve the radius determination, finding R$_{b}$=$1.37 \pm 0.04 R_\oplus$, and confirming that TOI-561 b is one of the lowest-density super-Earths measured to date ($\rho_b$= 4.8 $\pm$ 0.5 g/cm$^{3}$). This density is consistent with an iron-poor rocky composition reflective of the host star's iron and rock-building element abundances; however, it is also consistent with a low-density planet with a volatile envelope. The equilibrium temperature of the planet ($\sim$2300 K) suggests that this envelope would likely be composed of high mean molecular weight species, such as water vapor, carbon dioxide, or silicate vapor, and is likely not primordial. We also demonstrate that the composition determination is sensitive to the choice of stellar parameters, and that further measurements are needed to determine if TOI-561 b is a bare rocky planet, a rocky planet with an optically thin atmosphere, or a rare example of a non-primordial envelope on a planet with a radius smaller than 1.5 R$_{\oplus}$.Comment: Accepted to AJ on 11/28/202

Key steps in the structure-based optimization of the hepatitis C virus NS3/4A protease inhibitor SCH503034

Crystal structures of protease/inhibitor complexes guided optimization of the buried nonpolar surface area thereby maximizing hydrophobic binding. The resulting potent tripeptide inhibitor is in clinical trials

Crystal structure of the catalytic domain of DESC1, a new member of the type II transmembrane serine proteinase family

DESC1 was identified using gene-expression analysis between squamous cell carcinoma of the head and neck and normal tissue. It belongs to the type II transmembrane multidomain serine proteinases (TTSPs), an expanding family of serine proteinases, whose members are differentially expressed in several tissues. The biological role of these proteins is currently under investigation, although in some cases their participation in specific functions has been reported. This is the case for enteropeptidase, hepsin, matriptase and corin. Some members, including DESC1, are associated with cell differentiation and have been described as tumor markers. TTSPs belong to the type II transmembrane proteins that display, in addition to a C-terminal trypsin-like serine proteinase domain, a differing set of stem domains, a transmembrane segment and a short N-terminal cytoplasmic region. Based on sequence analysis, the TTSP family is subdivided into four subfamilies: hepsin/transmembrane proteinase, serine (TMPRSS); matriptase; corin; and the human airway trypsin (HAT)/HAT-like/DESC subfamily. Members of the hepsin and matriptase subfamilies are known structurally and here we present the crystal structure of DESC1 as a first member of the HAT/HAT-like/DESC subfamily in complex with benzamidine. The proteinase domain of DESC1 exhibits a trypsin-like serine proteinase fold with a thrombin-like S1 pocket, a urokinase-type plasminogen activator-type S2 pocket, to accept small residues, and an open hydrophobic S3/S4 cavity to accept large hydrophobic residues. The deduced substrate specificity for DESC1 differs markedly from that of other structurally known TTSPs. Based on surface analysis, we propose a rigid domain association for the N-terminal SEA domain with the back site of the proteinase domain

Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome

PremiseAn informatics approach was used for the construction of an Axiom genotyping array from heterogeneous, high-throughput sequence data to assess the complex genome of loblolly pine (Pinus taeda).MethodsHigh-throughput sequence data, sourced from exome capture and whole genome reduced-representation approaches from 2698 trees across five sequence populations, were analyzed with the improved genome assembly and annotation for the loblolly pine. A variant detection, filtering, and probe design pipeline was developed to detect true variants across and within populations. From 8.27 million variants, a total of 642,275 were evaluated and 423,695 of those were screened across a range-wide population.ResultsThe final informatics and screening approach delivered an Axiom array representing 46,439 high-confidence variants to the forest tree breeding and genetics community. Based on the annotated reference genome, 34% were located in or directly upstream or downstream of genic regions.DiscussionThe Pita50K array represents a genome-wide resource developed from sequence data for an economically important conifer, loblolly pine. It uniquely integrates independent projects that assessed trees sampled across the native range. The challenges associated with the large and repetitive genome are addressed in the development of this resource

Curiosity meets the Gediz Vallis Ridge: a remnant of a late-stage debris-flow dominated fan

International audienceRecent studies using HiRISE and CTX imagery show that fan-shaped deposits are widespread across Mars and likely formed during the Hesperian and Amazonian periods. Remote imagery and topographic analysis suggest that they may have been produced by both fluvial and debris flow processes and are generally distinct from deltaic deposits such as those in Jezero. Curiosity-based observations of the deeply eroded deposits of the Gediz Vallis Ridge (GVR), lying at the base of Mt. Sharp, now provide our first cross-sectional observation of a Martian fan, revealing episodic deposition by debris flows and reworking by fluvial processes. The fan was deposited on the Stimson formation, a pediment-mantling lithified aeolian deposit. Above the Stimson is a discontinuous fine-grained (≤ gravel size) basal unit with decimeter-scale bedding that is parallel to top of the Stimson. The unit reaches a maximum observable thickness of 15m and is unconformably onlapped by stratified gravel and boulder deposits. Discontinuous layering within these deposits ranges in thickness from 0.25 to 3 m and exhibits a mean slope of 7% oriented parallel to the ridge axis, much gentler than the slope of the basal contact. At progressively higher elevations, five depositional packages are exposed. Each package is composed two facies whose frequency and lateral extent differ: 1) a light toned typically matrix-supported coarse facies with scattered erosionally resistant dark toned gravel and boulders, and 2) a dark-toned typically clast-supported gravel and boulder facies. Grainsize analysis of Chemcam data indicates similar median grainsizes (170-190 mm) in light- and dark toned facies with isolated 1-3m boulders scattered throughout. The light-toned strata appear to be debris flow deposits. The dark toned strata are interpreted to be fluvial, probably derived from surface runoff that concentrated dark stones from the light toned unit into channels and sheetflood deposits while destroying the weaker light toned sediment during transport. The GVR is an erosional remnant of a fan that may have built 10 km downslope, likely in the late Hesperian or early Amazonian. Stratigraphic differences in the five packages suggest significant changes in the magnitude and frequency of surface runoff, but with a supply of meter scale boulders throughout fan evolution

IN SITU INVESTIGATION OF THE GEDIZ VALLIS RIDGE: A REMNANT LATE-STAGE DEBRIS FLOW DOMINATED FAN DEPOSIT IN GALE CRATER

International audienceNumerous studies using orbital HiRISE and CTX data show evidence for extensive fan formation across the Martian surface [1, 2]. Fan-shaped deposits record a combination of fluvial, debris flow, and deltaic processes, with many fans likely forming during the late Hesperian or Amazonian [1, 3]. Curiosity-based observations of the deeply eroded deposits of the Gediz Vallis ridge (GVR), near the base of Aeolis Mons (Mt. Sharp), provide our first cross-sectional observation of a Martian fan, revealing episodic deposition by debris flows and reworking by fluvial processes

IN SITU INVESTIGATION OF THE GEDIZ VALLIS RIDGE: A REMNANT LATE-STAGE DEBRIS FLOW DOMINATED FAN DEPOSIT IN GALE CRATER

International audienceNumerous studies using orbital HiRISE and CTX data show evidence for extensive fan formation across the Martian surface [1, 2]. Fan-shaped deposits record a combination of fluvial, debris flow, and deltaic processes, with many fans likely forming during the late Hesperian or Amazonian [1, 3]. Curiosity-based observations of the deeply eroded deposits of the Gediz Vallis ridge (GVR), near the base of Aeolis Mons (Mt. Sharp), provide our first cross-sectional observation of a Martian fan, revealing episodic deposition by debris flows and reworking by fluvial processes