Structural and functional characterization of Cas2 of CRISPR-Cas subtype I-C lacking the CRISPR component

Anand, Vineet; Prabhakaran, Harshini Sheeja; Gogoi, Prerana; Kanaujia, Shankar Prasad; Kumar, Manish

doi:10.3389/fmolb.2022.988569

Cited by 5 publications

(2 citation statements)

References 60 publications

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“…This suggests that BPSL1038 is unique as most Cas2 proteins have been classified as metallonucleases 11 – 13 , 15 , 32 . The divalent-ion-independent catalytic mechanism towards cleavage of RNA was previous reported for VapD 16 and Lin_Cas2 15 , however, divalent ion-independent DNAse activity has not been described for Cas2 proteins.…”

Section: Discussionmentioning

confidence: 99%

Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family

Shaibullah,

Shuhaimi,

Ker

et al. 2023

Commun Biol

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Burkholderia pseudomallei is a highly versatile pathogen with ~25% of its genome annotated to encode hypothetical proteins. One such hypothetical protein, BPSL1038, is conserved across seven bacterial genera and 654 Burkholderia spp. Here, we present a 1.55 Å resolution crystal structure of BPSL1038. The overall structure folded into a modified βαββαβα ferredoxin fold similar to known Cas2 nucleases. The Cas2 equivalent catalytic aspartate (D11) pairs are conserved in BPSL1038 although B. pseudomallei has no known CRISPR associated system. Functional analysis revealed that BPSL1038 is a nuclease with endonuclease activity towards double-stranded DNA. The DNase activity is divalent ion independent and optimum at pH 6. The concentration of monovalent ions (Na+ and K+) is crucial for nuclease activity. An active site with a unique D11(X20)SST motif was identified and proposed for BPSL1038 and its orthologs. Structure modelling indicates the catalytic role of the D11(X20)SST motif and that the arginine residues R10 and R30 may interact with the nucleic acid backbone. The structural similarity of BPSL1038 to Cas2 proteins suggests that BPSL1038 may represent a sub-family of nucleases that share a common ancestor with Cas2.

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Section: Discussionmentioning

confidence: 99%

Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family

Shaibullah,

Shuhaimi,

Ker

et al. 2023

Commun Biol

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“…The alignment was colored using http://www.bioinformatics.org/sms2/color_align_cons.html tool with default parameters for amino acid grouping and consensus 80%. The alignment with two previously studied Cas2 (104, 105) is based on HHpred results. The positions corresponding to catalytic residues of Cas2 are highlighted in red.…”

Section: Supplementary Materialsmentioning

confidence: 99%

Diversity, Origin and Evolution of the ESCRT Systems

Makarova,

Tobiasson,

Wolf

et al. 2024

Preprint

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Endosomal Sorting Complexes Required for Transport (ESCRT) play key roles in protein sorting between membrane-bounded compartments of eukaryotic cells. Homologs of many ESCRT components are identifiable in various groups of archaea, especially in Asgardarchaeota, the archaeal phylum that is currently considered to include the closest relatives of eukaryotes, but not in bacteria. We performed a comprehensive search for ESCRT protein homologs in archaea and reconstructed ESCRT evolution using the phylogenetic tree of Vps4 ATPase (ESCRT IV) as a scaffold, using sensitive protein sequence analysis and comparison of structural models to identify previously unknown ESCRT proteins. Several distinct groups of ESCRT systems in archaea outside of Asgard were identified, including proteins structurally similar to ESCRT-I and ESCRT-II, and several other domains involved in protein sorting in eukaryotes, suggesting an early origin of these components. Additionally, distant homologs of CdvA proteins were identified in Thermoproteales which are likely components of the uncharacterized cell division system in these archaea. We propose an evolutionary scenario for the origin of eukaryotic and Asgard ESCRT complexes from ancestral building blocks, namely, the Vps4 ATPase, ESCRT-III components, wH (winged helix-turn-helix fold) and possibly also coiled-coil, and Vps28-like domains. The Last Archaeal Common Ancestor likely encompassed a complex ESCRT system that was involved in protein sorting. Subsequent evolution involved either simplification, as in the TACK superphylum, where ESCRT was co-opted for cell division, or complexification as in Asgardarchaeota. In Asgardarchaeota, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was already established.ImportanceAll eukaryotic cells possess complex intracellular membrane organization. ESCRT (Endosomal Sorting Complexes Required for Transport) plays a central role in membrane remodeling which is essential for cellular functionality in eukaryotes. Recently, it has been shown that Asgard archaea, the archaeal phylum that includes the closest known relatives of eukaryotes, encode homologs of many components of the ESCRT systems. We employed protein sequence and structure comparisons to reconstruct the evolution of ESCRT systems in archaea and identified several previously unknown homologs of ESCRT subunits, some of which can be predicted to participate in cell division. The results of this reconstruction indicate that the Last Archaeal Common ancestor already encoded a complex ESCRT system that was involved in protein sorting. In Asgard archaea, ESCRT systems evolved towards greater complexity, and in particular, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was established.

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A Review: CRISPR Cas System and the Mechanism With an Inhibition of Binding of CRISPR Cas‐9

Hosen,

Nishat,

Soaib

et al. 2024

Nano Select

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CRISPR Cas system is a revolutionary and precise genome editing system that induces bacterial and archaeal adaptive immunity and already has shown several promising applications in the treatment of genetic diseases and detection of nucleic acid targets. It is a complex tool, comprising diverse effector proteins and guide RNA that can be applied to dissociate and modify genes in living organisms along with the in vitro process. The review concentrates on the advances accomplished from some recent years to 2023 for the emergence of predicting actions of Cas protein with the guide RNA (gRNA), playing a key role in genome editing. This review emphasizes the effect of DNA structure and chromosomal protein on Cas 9 binding with a distinct classification of Cas types. The relevance of this review is highlighted by the significance of the rapid development of wide study methods and their potential impacts on the efficiency of the CRISPR Cas system. We have analyzed recent kinds of literature in this work to integrate a deep learning way that contributes over the next time with some important discussion about viral resistance in eukaryotes along with some cancer treatment strategies, and crop improvement by the CRISPR Cas system.

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Structural and functional characterization of Cas2 of CRISPR-Cas subtype I-C lacking the CRISPR component

Cited by 5 publications

References 60 publications

Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family

Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family

Diversity, Origin and Evolution of the ESCRT Systems

A Review: CRISPR Cas System and the Mechanism With an Inhibition of Binding of CRISPR Cas‐9

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