K. Makarova

Publications290
h-index100
Citations43,073
Highly Influential Citations2,861
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Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes
TLDR
The results demonstrate that the formation of mature guide RNAs by the CRISPR RNA endonuclease subunit of Cascade is a mechanistic requirement for antiviral defense.
Evolution and classification of the CRISPR–Cas systems
TLDR
An updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins is provided and a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of theCRISPR repeats and the architecture of the CRISpr–cas loci is proposed.
An updated evolutionary classification of CRISPR–Cas systems
TLDR
An approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes is presented.
In vivo genome editing using Staphylococcus aureus Cas9
TLDR
Six smaller Cas9 orthologues are characterized and it is shown that Cas9 from Staphylococcus aureus (SaCas9) can edit the genome with efficiencies similar to those of SpCas9, while being more than 1 kilobase shorter.
Comparative genomics of the lactic acid bacteria
TLDR
Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
Expanded microbial genome coverage and improved protein family annotation in the COG database
TLDR
An update of the Clusters of Orthologous Groups of proteins, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level are presented.
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of…
TLDR
It appears most likely that CASS is a prokaryotic system of defense against phages and plasmids that functions via the RNAi mechanism, which seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents.
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
TLDR
Functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs (eukaryotic orthologous groups or KOGs) from seven eukaryosis genomes are examined, revealing a conserved core of largely essential eukARYotic genes as well as major diversification and innovation associated with evolution of eUKaryotic genomes.
Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum
TLDR
Comparison of C. acetobutylicum to Bacillus subtilis reveals significant local conservation of gene order, which has not been seen in comparisons of other genomes with similar, or, in some cases closer, phylogenetic proximity.
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