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Phylogenomics of Cas4 family nucleases

Overview of attention for article published in BMC Evolutionary Biology, November 2017
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  • Average Attention Score compared to outputs of the same age and source

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1 Wikipedia page

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Title
Phylogenomics of Cas4 family nucleases
Published in
BMC Evolutionary Biology, November 2017
DOI 10.1186/s12862-017-1081-1
Pubmed ID
Authors

Sanjarbek Hudaiberdiev, Sergey Shmakov, Yuri I. Wolf, Michael P. Terns, Kira S. Makarova, Eugene V. Koonin

Abstract

The Cas4 family endonuclease is a component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. Unlike most of the other Cas proteins, Cas4 is often encoded outside CRISPR-cas loci (solo-Cas4) and is also found in mobile genetic elements (MGE-Cas4). As part of our ongoing investigation of CRISPR-Cas evolution, we explored the phylogenomics of the Cas4 family. About 90% of the archaeal genomes encode Cas4 compared to only about 20% of the bacterial genomes. Many archaea encode both the CRISPR-associated form (CAS-Cas4) and solo-Cas4, whereas in bacteria, this combination is extremely rare. The solo-cas4 genes are over-represented in environmental bacteria and archaea with small genomes that typically lack CRISPR-Cas, suggesting that Cas4 could perform uncharacterized defense or repair functions in these microbes. Phylogenomic analysis indicates that both the CRISPR-associated cas4 genes are often transferred horizontally but almost exclusively, as part of the adaptation module. The evolutionary integrity of the adaptation module sharply contrasts the rampant shuffling of CRISPR-cas modules whereby a given variant of the adaptation module can combine with virtually any effector module. The solo-cas4 genes evolve primarily via vertical inheritance and are subject only to occasional horizontal transfer. The selection pressure on cas4 genes does not substantially differ between CAS-Cas4 and solo-cas4, and is close to the genomic median. Thus, cas4 genes, similarly to cas1 and cas2, evolve similarly to 'regular' microbial genes involved in various cellular functions, showing no evidence of direct involvement in virus-host arms races. A notable feature of the Cas4 family evolution is the frequent recruitment of cas4 genes by various mobile genetic elements (MGE), particularly, archaeal viruses. The functions of Cas4 in these elements are unknown and potentially might involve anti-defense roles. Unlike most of the other Cas proteins, Cas4 family members are as often encoded by stand-alone genes as they are incorporated in CRISPR-Cas systems. In addition, cas4 genes were repeatedly recruited by MGE, perhaps, for anti-defense functions. Experimental characterization of the solo and MGE-encoded Cas4 nucleases is expected to reveal currently uncharacterized defense and anti-defense systems and their interactions with CRISPR-Cas systems.

Twitter Demographics

The data shown below were collected from the profiles of 6 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 87 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 87 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 18 21%
Student > Ph. D. Student 15 17%
Student > Bachelor 10 11%
Researcher 8 9%
Other 4 5%
Other 12 14%
Unknown 20 23%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 41 47%
Agricultural and Biological Sciences 13 15%
Immunology and Microbiology 7 8%
Environmental Science 2 2%
Computer Science 2 2%
Other 4 5%
Unknown 18 21%

Attention Score in Context

This research output has an Altmetric Attention Score of 5. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 07 January 2020.
All research outputs
#4,880,197
of 18,382,898 outputs
Outputs from BMC Evolutionary Biology
#1,159
of 2,830 outputs
Outputs of similar age
#122,253
of 424,307 outputs
Outputs of similar age from BMC Evolutionary Biology
#132
of 241 outputs
Altmetric has tracked 18,382,898 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 2,830 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 10.8. This one has gotten more attention than average, scoring higher than 58% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 424,307 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 71% of its contemporaries.
We're also able to compare this research output to 241 others from the same source and published within six weeks on either side of this one. This one is in the 45th percentile – i.e., 45% of its contemporaries scored the same or lower than it.