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7 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Materials Data on CaS2(ClO3)2 by Materials Project

CaS2(O3Cl)2 crystallizes in the orthorhombic Pbca space group. The structure is three-dimensional. Ca2+ is bonded to six O2- atoms to form CaO6 octahedra that share corners with six SClO3 tetrahedra. There are a spread of Ca–O bond distances ranging from 2.32–2.40 Å. There are two inequivalent S6+ sites. In the first S6+ site, S6+ is bonded to three O2- and one Cl1- atom to form distorted SClO3 tetrahedra that share corners with three equivalent CaO6 octahedra. The corner-sharing octahedra tilt angles range from 13–19°. There is two shorter (1.45 Å) and one longer (1.46 Å) S–O bond length. The S–Cl bond length is 2.05 Å. In the second S6+ site, S6+ is bonded to three O2- and one Cl1- atom to form distorted SClO3 tetrahedra that share corners with three equivalent CaO6 octahedra. The corner-sharing octahedra tilt angles range from 8–37°. All S–O bond lengths are 1.46 Å. The S–Cl bond length is 2.05 Å. There are six inequivalent O2- sites. In the first O2- site, O2- is bonded in a bent 150 degrees geometry to one Ca2+ and one S6+ atom. In the second O2- site, O2- is bonded in a distorted bent 150 degrees geometry to one Ca2+ and one S6+ atom. In the third O2- site, O2- is bonded in a distorted linear geometry to one Ca2+ and one S6+ atom. In the fourth O2- site, O2- is bonded in a distorted bent 150 degrees geometry to one Ca2+ and one S6+ atom. In the fifth O2- site, O2- is bonded in a linear geometry to one Ca2+ and one S6+ atom. In the sixth O2- site, O2- is bonded in a distorted linear geometry to one Ca2+ and one S6+ atom. There are two inequivalent Cl1- sites. In the first Cl1- site, Cl1- is bonded in a single-bond geometry to one S6+ atom. In the second Cl1- site, Cl1- is bonded in a distorted single-bond geometry to one S6+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A CRISPR-Cas9–integrase complex generates precise DNA fragments for genome integration

CRISPR-Cas9 is an RNA-guided DNA endonuclease involved in bacterial adaptive immunity and widely repurposed for genome editing in human cells, animals and plants. In bacteria, RNA molecules that guide Cas9 s activity derive from foreign DNA fragments that are captured and integrated into the host CRISPR genomic locus by the Cas1-Cas2 CRISPR integrase. How cells generate the specific lengths of DNA required for integrase capture is a central unanswered question of type II-A CRISPR-based adaptive immunity. Here, we show that an integrase supercomplex comprising guide RNA and the proteins Cas1, Cas2, Csn2 and Cas9 generates precisely trimmed 30-base pair DNA molecules required for genome integration. The HNH active site of Cas9 catalyzes exonucleolytic DNA trimming by a mechanism that is independent of the guide RNA sequence. These results show that Cas9 possesses a distinct catalytic capacity for generating immunological memory in prokaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex

CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR systems, a reverse transcriptase (RT) fusion to the Cas1 integrase and Cas6 maturase creates a single protein that enables concerted sequence integration and crRNA production. To elucidate how the RT-integrase organizes distinct enzymatic activities, we present the cryo-EM structure of a Cas6-RT-Cas1—Cas2 CRISPR integrase complex. The structure reveals a heterohexamer in which the RT directly contacts the integrase and maturase domains, suggesting functional coordination between all three active sites. Together with biochemical experiments, our data support a model of sequential enzymatic activities that enable CRISPR sequence acquisition from RNA and DNA substrates. These findings highlight an expanded capacity of some CRISPR systems to acquire diverse sequences that direct CRISPR-mediated interference.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome expansion by a CRISPR trimmer-integrase

CRISPR–Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1–Cas2 integrase is necessary but not sufficient. In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation, but many CRISPR–Cas systems lack Cas4. Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1–Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited exonucleases for faithful acquisition of new CRISPR immune sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Novel adaptive immune systems in pristine Antarctic soils

Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

C.A.D. representation of ternary and quaternary phase diagrams

This work is concerned with the utilization of C.A.D. solid-modeling software for the computer representation of three-dimensional phase diagrams. The work was undertaken in two parts. First, the C.A.D. software (I-DEAS, by Structural Dynamics Research Corp.) was integrated with a variety of auxiliary Fortran 77 and I-DEAS language programs which were written specifically for the purpose of phase diagram representation. The capabilities of the resulting suite of software for three-dimensional phase diagram representation were developed and illustrated by the construction, display and manipulation of solid-model phase diagrams for a hypothetical quaternary eutectic system. The results of this work are discussed in some detail in the attached publication ('Solid-modeling: a C.A.D. Alternative for Three-dimensional Phase Diagram Representation'). Such a technique is of general applicability, having utility in both research and education. Secondly, using the C.A.D. technique, data from the literature (gleaned from some 70 separate publications), which represent experimentally determined phase boundaries, were combined to form solid-model representations of the CMS2-M2S-S ternary space diagram and the CMS2-CAS2-M2S-S quaternary liquidus projection (where C=CaO, M=MgO, A=Al2O3, and S=SiO2). These diagrams were utilized in a concurrent study of solidification in the CMAS system.

Delao, James D.↗
DOE OSTI2020

Escherichia coli Cas1/2 Endonuclease Complex Modifies Self-Targeting CRISPR/Cascade Spacers Reducing Silencing Guide Stability

CRISPR-based interference has become common in various applications from genetic circuits to dynamic metabolic control. In E. coli, the native CRISPR Cascade system can be utilized for silencing by deletion of the cas3 nuclease along with expression of guide RNA arrays, where multiple genes can be silenced from a single transcript. We notice the loss of spacer sequences from guide arrays utilized for dynamic silencing. Here, we report that unstable guide arrays are due to expression of the Cas1/2 endonuclease complex. We propose a model wherein basal Cas1/2 endonuclease activity results in the loss of spacers from guide arrays. Subsequently, mutant guide arrays can be amplified through selection. Replacing a constitutive promoter driving Cascade complex expression with a tightly controlled inducible promoter improves guide array stability, while minimizing leaky gene silencing. Additionally, these results demonstrate the potential of Cas1/2 mediated guide deletion as a mechanism to avoid CRISPR based autoimmunity.

59 BASIC BIOLOGICAL SCIENCES↗