Nature Search

Petabase-scale sequence alignment catalyses viral discovery

Serratus, an open-source cloud-computing infrastructure, can be used to screen millions of nucleic acid sequencing libraries at the petabase scale, and has enabled many new RNA viruses to be identified efficiently.

Robert C. Edgar
Brie Taylor
Artem Babaian
Research26 Jan 2022
Nature

Volume: 602, P: 142-147
Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Borgs are huge extrachromosomal elements associated with anaerobic methane-consuming archaea. Here, the authors use nanopore sequencing to identify new Borgs from peatland soil and their hosts, uncover their DNA modifications and activities, and elucidate the evolutionary relationships of Borgs.

Marie C. Schoelmerich
Lynn Ly
Jillian F. Banfield
ResearchOpen Access26 Jun 2024
Nature Communications

Volume: 15, P: 1-17
Clades of huge phages from across Earth’s ecosystems

Genomic analyses of major clades of huge phages sampled from across Earth’s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR–Cas systems and translation-relevant genes.

Basem Al-Shayeb
Rohan Sachdeva
Jillian F. Banfield
ResearchOpen Access12 Feb 2020
Nature

Volume: 578, P: 425-431
Genome expansion by a CRISPR trimmer-integrase

CRISPR systems lacking Cas4 can use fused or recruited exonucleases for faithful acquisition of new CRISPR immune sequences.

Joy Y. Wang
Owen T. Tuck
Jennifer A. Doudna
ResearchOpen Access14 Jun 2023
Nature

Volume: 618, P: 855-861
Borgs are giant genetic elements with potential to expand metabolic capacity

Borgs are remarkably large, divergent archaeal extrachromosomal elements with metabolic genes linked to the methane cycle.

Basem Al-Shayeb
Marie C. Schoelmerich
Jillian F. Banfield
ResearchOpen Access19 Oct 2022
Nature

Volume: 610, P: 731-736
Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex

In some systems, a single protein comprising reverse transcriptase (RT), integrase and maturase enables concerted sequence integration and crRNA production. Here, analyses including the structure of a Cas6-RT-Cas1—Cas2 complex suggest coordination between all three active sites and capacity to acquire CRISPR sequences from RNA and DNA substrates.

Joy Y. Wang
Christopher M. Hoel
Jennifer A. Doudna
ResearchOpen Access06 May 2021
Nature Communications

Volume: 12, P: 1-14
Author Correction: CasX enzymes comprise a distinct family of RNA-guided genome editors

Jun-Jie Liu
Natalia Orlova
Jennifer A. Doudna
Amendments and Corrections03 Apr 2019
Nature

Volume: 568, P: E8-E10
CasX enzymes comprise a distinct family of RNA-guided genome editors

CRISPR–CasX represents a distinct RNA-guided platform that is functionally separate from Cas9 and Cas12a and is active for bacterial and human genome modification.

Jun-Jie Liu
Natalia Orlova
Jennifer A. Doudna
Research04 Feb 2019
Nature

Volume: 566, P: 218-223
DNA interference states of the hypercompact CRISPR–CasΦ effector

Cryo-EM structures of CRISPR–CasΦ, a small RNA-guided enzyme unique to bacteriophages, reveal how CasΦ binds to and cleaves DNA, paving the way for engineering of improved CasΦ variants for diagnostics and genome-editing applications.

Patrick Pausch
Katarzyna M. Soczek
Jennifer A. Doudna
Research11 Aug 2021
Nature Structural & Molecular Biology

Volume: 28, P: 652-661
Broad-spectrum enzymatic inhibition of CRISPR-Cas12a

Doudna and colleagues determine the mechanisms used by type V anti-CRISPR proteins. AcrVA1 is a multiple-turnover inhibitor that triggers cleavage of the Cas12a-bound guide RNA, while AcrVA4 and AcrVA5 inhibit recognition of dsDNA.

Gavin J. Knott
Brittney W. Thornton
Jennifer A. Doudna
Research01 Apr 2019
Nature Structural & Molecular Biology

Volume: 26, P: 315-321
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

Computational analyses reveal widespread recoding in gut phages, which is hypothesized to control timing of lysis.

Adair L. Borges
Yue Clare Lou
Jillian F. Banfield
Research26 May 2022
Nature Microbiology

Volume: 7, P: 918-927
A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters

Alexander Crits-Christoph
Spencer Diamond
Jillian F. Banfield
ResearchOpen Access13 Aug 2022
ISME Communications

Volume: 2, P: 1-8

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