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1.
Genes Dev ; 38(1-2): 31-45, 2024 Feb 13.
Artículo en Inglés | MEDLINE | ID: mdl-38242633

RESUMEN

Bacterial spores can remain dormant for decades yet rapidly germinate and resume growth in response to nutrients. GerA family receptors that sense and respond to these signals have recently been shown to oligomerize into nutrient-gated ion channels. Ion release initiates exit from dormancy. Here, we report that a distinct ion channel, composed of SpoVAF (5AF) and its newly discovered partner protein, YqhR (FigP), amplifies the response. At high germinant concentrations, 5AF/FigP accelerate germination; at low concentrations, this complex becomes critical for exit from dormancy. 5AF is homologous to the channel-forming subunit of GerA family receptors and is predicted to oligomerize around a central pore. 5AF mutations predicted to widen the channel cause constitutive germination during spore formation and membrane depolarization in vegetative cells. Narrow-channel mutants are impaired in germination. A screen for suppressors of a constitutively germinating 5AF mutant identified FigP as an essential cofactor of 5AF activity. We demonstrate that 5AF and FigP interact and colocalize with GerA family receptors in spores. Finally, we show that 5AF/FigP accelerate germination in B. subtilis spores that have nutrient receptors from another species. Our data support a model in which nutrient-triggered ion release by GerA family receptors activates 5AF/FigP ion release, amplifying the response to germinant signals.


Asunto(s)
Bacillus subtilis , Proteínas de la Membrana , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Proteínas de la Membrana/genética , Esporas Bacterianas/genética , Esporas Bacterianas/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Canales Iónicos/genética , Canales Iónicos/metabolismo
2.
Nucleic Acids Res ; 52(D1): D590-D596, 2024 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-37889041

RESUMEN

CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.


Asunto(s)
Proteínas Asociadas a CRISPR , Sistemas CRISPR-Cas , Bases de Datos Genéticas , Endodesoxirribonucleasas , Sistemas CRISPR-Cas/genética , Filogenia , Proteínas Asociadas a CRISPR/química , Proteínas Asociadas a CRISPR/clasificación , Proteínas Asociadas a CRISPR/genética , Endodesoxirribonucleasas/química , Endodesoxirribonucleasas/clasificación , Endodesoxirribonucleasas/genética , Enciclopedias como Asunto
3.
Science ; 380(6643): 387-391, 2023 04 28.
Artículo en Inglés | MEDLINE | ID: mdl-37104613

RESUMEN

Bacterial spores resist antibiotics and sterilization and can remain metabolically inactive for decades, but they can rapidly germinate and resume growth in response to nutrients. Broadly conserved receptors embedded in the spore membrane detect nutrients, but how spores transduce these signals remains unclear. Here, we found that these receptors form oligomeric membrane channels. Mutations predicted to widen the channel initiated germination in the absence of nutrients, whereas those that narrow it prevented ion release and germination in response to nutrients. Expressing receptors with widened channels during vegetative growth caused loss of membrane potential and cell death, whereas the addition of germinants to cells expressing wild-type receptors triggered membrane depolarization. Therefore, germinant receptors act as nutrient-gated ion channels such that ion release initiates exit from dormancy.


Asunto(s)
Bacillus megaterium , Bacillus subtilis , Proteínas Bacterianas , Canales Iónicos , Esporas Bacterianas , Proteínas Bacterianas/genética , Canales Iónicos/genética , Canales Iónicos/metabolismo , Mutación , Esporas Bacterianas/genética , Esporas Bacterianas/metabolismo , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Bacillus megaterium/genética , Bacillus megaterium/metabolismo
4.
PLoS One ; 17(4): e0263547, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35436289

RESUMEN

Short segments of RNA displace one strand of a DNA duplex during diverse processes including transcription and CRISPR-mediated immunity and genome editing. These strand exchange events involve the intersection of two geometrically distinct helix types-an RNA:DNA hybrid (A-form) and a DNA:DNA homoduplex (B-form). Although previous evidence suggests that these two helices can stack on each other, it is unknown what local geometric adjustments could enable A-on-B stacking. Here we report the X-ray crystal structure of an RNA-5'/DNA-3' strand exchange junction at an anisotropic resolution of 1.6 to 2.2 Å. The structure reveals that the A-to-B helical transition involves a combination of helical axis misalignment, helical axis tilting and compression of the DNA strand within the RNA:DNA helix, where nucleotides exhibit a mixture of A- and B-form geometry. These structural principles explain previous observations of conformational stability in RNA/DNA exchange junctions, enabling a nucleic acid architecture that is repeatedly populated during biological strand exchange events.


Asunto(s)
Ácidos Nucleicos , ARN , ADN/química , Conformación de Ácido Nucleico , Nucleótidos , ARN/química
5.
Nat Struct Mol Biol ; 29(4): 395-402, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35422516

RESUMEN

In bacterial defense and genome editing applications, the CRISPR-associated protein Cas9 searches millions of DNA base pairs to locate a 20-nucleotide, guide RNA-complementary target sequence that abuts a protospacer-adjacent motif (PAM). Target capture requires Cas9 to unwind DNA at candidate sequences using an unknown ATP-independent mechanism. Here we show that Cas9 sharply bends and undertwists DNA on PAM binding, thereby flipping DNA nucleotides out of the duplex and toward the guide RNA for sequence interrogation. Cryogenic-electron microscopy (cryo-EM) structures of Cas9-RNA-DNA complexes trapped at different states of the interrogation pathway, together with solution conformational probing, reveal that global protein rearrangement accompanies formation of an unstacked DNA hinge. Bend-induced base flipping explains how Cas9 'reads' snippets of DNA to locate target sites within a vast excess of nontarget DNA, a process crucial to both bacterial antiviral immunity and genome editing. This mechanism establishes a physical solution to the problem of complementarity-guided DNA search and shows how interrogation speed and local DNA geometry may influence genome editing efficiency.


Asunto(s)
Sistemas CRISPR-Cas , ARN Guía de Kinetoplastida , Sistemas CRISPR-Cas/genética , ADN/metabolismo , Endonucleasas/metabolismo , Edición Génica , ARN Guía de Kinetoplastida/metabolismo
6.
Elife ; 92020 06 10.
Artículo en Inglés | MEDLINE | ID: mdl-32519675

RESUMEN

Type V CRISPR-Cas interference proteins use a single RuvC active site to make RNA-guided breaks in double-stranded DNA substrates, an activity essential for both bacterial immunity and genome editing. The best-studied of these enzymes, Cas12a, initiates DNA cutting by forming a 20-nucleotide R-loop in which the guide RNA displaces one strand of a double-helical DNA substrate, positioning the DNase active site for first-strand cleavage. However, crystal structures and biochemical data have not explained how the second strand is cut to complete the double-strand break. Here, we detect intrinsic instability in DNA flanking the RNA-3' side of R-loops, which Cas12a can exploit to expose second-strand DNA for cutting. Interestingly, DNA flanking the RNA-5' side of R-loops is not intrinsically unstable. This asymmetry in R-loop structure may explain the uniformity of guide RNA architecture and the single-active-site cleavage mechanism that are fundamental features of all type V CRISPR-Cas systems.


Asunto(s)
Proteínas Bacterianas , Proteínas Asociadas a CRISPR , Sistemas CRISPR-Cas/genética , Roturas del ADN de Doble Cadena , Endodesoxirribonucleasas , Edición Génica/métodos , Estructuras R-Loop/genética , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas Asociadas a CRISPR/genética , Proteínas Asociadas a CRISPR/metabolismo , ADN/genética , ADN/metabolismo , Endodesoxirribonucleasas/genética , Endodesoxirribonucleasas/metabolismo , Escherichia coli/genética , ARN Guía de Kinetoplastida/genética , ARN Guía de Kinetoplastida/metabolismo
7.
Proc Natl Acad Sci U S A ; 117(11): 5853-5860, 2020 03 17.
Artículo en Inglés | MEDLINE | ID: mdl-32123105

RESUMEN

The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.


Asunto(s)
Proteínas Asociadas a CRISPR/química , Sistemas CRISPR-Cas , ADN/química , Emparejamiento Base , Proteínas Asociadas a CRISPR/metabolismo , División del ADN , Endonucleasas/metabolismo , Edición Génica , Genoma , Estructuras R-Loop , ARN/química , ARN Guía de Kinetoplastida/metabolismo
8.
Bio Protoc ; 10(20): e3787, 2020 Oct 20.
Artículo en Inglés | MEDLINE | ID: mdl-33659442

RESUMEN

Biochemical investigations into DNA-binding and DNA-cutting proteins often benefit from the specific attachment of a radioactive label to one of the two DNA termini. In many cases, it is essential to perform two versions of the same experiment: one with the 5' DNA end labeled and one with the 3' DNA end labeled. While homogeneous 5'-radiolabeling can be accomplished using a single kinase-catalyzed phosphorylation step, existing procedures for 3'-radiolabeling often result in probe heterogeneity, prohibiting precise DNA fragment identification in downstream experiments. We present here a new protocol to efficiently attach a 32P-phosphate to the 3' end of a DNA oligonucleotide of arbitrary sequence, relying on inexpensive DNA oligonucleotide modifications (2'-O-methylribonucleotide and ribonucleotide sugar substitutions), two enzymes (T4 polynucleotide kinase and T4 RNA ligase 2), and the differential susceptibility of DNA and RNA to hydroxide treatment. Radioactive probe molecules produced by this protocol are homogeneous and oxidant-compatible, and they can be used for precise cleavage-site mapping in the context of both DNase enzyme characterization and DNA footprinting assays. Graphic abstract.

9.
Science ; 362(6416): 839-842, 2018 11 16.
Artículo en Inglés | MEDLINE | ID: mdl-30337455

RESUMEN

CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids and are widely employed as genome editing tools. These tools use RNA-guided Cas proteins whose large size (950 to 1400 amino acids) has been considered essential to their specific DNA- or RNA-targeting activities. Here we present a set of CRISPR-Cas systems from uncultivated archaea that contain Cas14, a family of exceptionally compact RNA-guided nucleases (400 to 700 amino acids). Despite their small size, Cas14 proteins are capable of targeted single-stranded DNA (ssDNA) cleavage without restrictive sequence requirements. Moreover, target recognition by Cas14 triggers nonspecific cutting of ssDNA molecules, an activity that enables high-fidelity single-nucleotide polymorphism genotyping (Cas14-DETECTR). Metagenomic data show that multiple CRISPR-Cas14 systems evolved independently and suggest a potential evolutionary origin of single-effector CRISPR-based adaptive immunity.


Asunto(s)
Proteínas Arqueales/química , Proteínas Arqueales/clasificación , Proteínas Asociadas a CRISPR/química , Proteínas Asociadas a CRISPR/clasificación , División del ADN , ADN de Cadena Simple/química , Endodesoxirribonucleasas/química , Endodesoxirribonucleasas/clasificación , Proteínas Arqueales/genética , Proteínas Asociadas a CRISPR/genética , Conjuntos de Datos como Asunto , Endodesoxirribonucleasas/genética , Evolución Molecular , Metagenómica , Filogenia
10.
Nat Struct Mol Biol ; 24(10): 825-833, 2017 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-28892041

RESUMEN

CRISPR adaptive immune systems protect bacteria from infections by deploying CRISPR RNA (crRNA)-guided enzymes to recognize and cut foreign nucleic acids. Type VI-A CRISPR-Cas systems include the Cas13a enzyme, an RNA-activated RNase capable of crRNA processing and single-stranded RNA degradation upon target-transcript binding. Here we present the 2.0-Å resolution crystal structure of a crRNA-bound Lachnospiraceae bacterium Cas13a (LbaCas13a), representing a recently discovered Cas13a enzyme subtype. This structure and accompanying biochemical experiments define the Cas13a catalytic residues that are directly responsible for crRNA maturation. In addition, the orientation of the foreign-derived target-RNA-specifying sequence in the protein interior explains the conformational gating of Cas13a nuclease activation. These results describe how Cas13a enzymes generate functional crRNAs and how catalytic activity is blocked before target-RNA recognition, with implications for both bacterial immunity and diagnostic applications.


Asunto(s)
Sistemas CRISPR-Cas , Clostridiales/enzimología , Endonucleasas/química , Endonucleasas/metabolismo , ARN Guía de Kinetoplastida/química , ARN Guía de Kinetoplastida/metabolismo , Cristalografía por Rayos X , Conformación Proteica
11.
Cell ; 170(6): 1224-1233.e15, 2017 Sep 07.
Artículo en Inglés | MEDLINE | ID: mdl-28844692

RESUMEN

CRISPR-Cas9 proteins function within bacterial immune systems to target and destroy invasive DNA and have been harnessed as a robust technology for genome editing. Small bacteriophage-encoded anti-CRISPR proteins (Acrs) can inactivate Cas9, providing an efficient off switch for Cas9-based applications. Here, we show that two Acrs, AcrIIC1 and AcrIIC3, inhibit Cas9 by distinct strategies. AcrIIC1 is a broad-spectrum Cas9 inhibitor that prevents DNA cutting by multiple divergent Cas9 orthologs through direct binding to the conserved HNH catalytic domain of Cas9. A crystal structure of an AcrIIC1-Cas9 HNH domain complex shows how AcrIIC1 traps Cas9 in a DNA-bound but catalytically inactive state. By contrast, AcrIIC3 blocks activity of a single Cas9 ortholog and induces Cas9 dimerization while preventing binding to the target DNA. These two orthogonal mechanisms allow for separate control of Cas9 target binding and cleavage and suggest applications to allow DNA binding while preventing DNA cutting by Cas9.


Asunto(s)
Sistemas CRISPR-Cas , Endonucleasas/antagonistas & inhibidores , Proteínas Virales/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/antagonistas & inhibidores , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Bacteriófagos/genética , Bacteriófagos/metabolismo , Endonucleasas/química , Endonucleasas/genética , Endonucleasas/metabolismo , Evolución Molecular , Células HEK293 , Humanos , Dominios Proteicos , Alineación de Secuencia
12.
Elife ; 62017 07 07.
Artículo en Inglés | MEDLINE | ID: mdl-28686159

RESUMEN

Ras proteins are highly conserved signaling molecules that exhibit regulated, nucleotide-dependent switching between active and inactive states. The high conservation of Ras requires mechanistic explanation, especially given the general mutational tolerance of proteins. Here, we use deep mutational scanning, biochemical analysis and molecular simulations to understand constraints on Ras sequence. Ras exhibits global sensitivity to mutation when regulated by a GTPase activating protein and a nucleotide exchange factor. Removing the regulators shifts the distribution of mutational effects to be largely neutral, and reveals hotspots of activating mutations in residues that restrain Ras dynamics and promote the inactive state. Evolutionary analysis, combined with structural and mutational data, argue that Ras has co-evolved with its regulators in the vertebrate lineage. Overall, our results show that sequence conservation in Ras depends strongly on the biochemical network in which it operates, providing a framework for understanding the origin of global selection pressures on proteins.


Asunto(s)
Proteínas ras/genética , Proteínas ras/metabolismo , Secuencia Conservada , Análisis Mutacional de ADN , Evolución Molecular , Humanos , Mutagénesis , Mapas de Interacción de Proteínas
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