Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance DOI Creative Commons
Masaru Usui, Yutaka Yoshii, Stanislas Thiriet-Rupert

et al.

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: March 16, 2023

Abstract Bacterial antibiotic resistance is a global health concern of increasing importance and intensive study. Although biofilms are common source infections in clinical settings, little known about the development within biofilms. Here, we use experimental evolution to compare selection mutations planktonic biofilm Escherichia coli populations exposed clinically relevant cycles lethal treatment with aminoglycoside amikacin. Consistently, sbmA , encoding an inner membrane peptide transporter, fusA essential elongation factor G, rapidly selected biofilms, but not cells. This due combination enhanced mutation rate, increased adhesion capacity protective biofilm-associated tolerance. These results show that environment favors rapid provide new insights into dynamic

Language: Английский

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization DOI Creative Commons
Kazutaka Katoh,

John Rozewicki,

Kazunori Yamada

et al.

Briefings in Bioinformatics, Journal Year: 2017, Volume and Issue: 20(4), P. 1160 - 1166

Published: Aug. 7, 2017

This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances sequencing technologies, huge numbers biological sequences are available and need MSAs with large is increasing. To extract biologically relevant information from such data, sophistication algorithms necessary but not sufficient. Intuitive interactive tools experimental biologists to semiautomatically handle data becoming important. We working on development toward these two directions. Here, we explain (i) Web interface recently developed options (ii) usage refine sets MSAs.

Language: Английский

Citations

6889
Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice DOI Creative Commons
Gil Sharon,

Nikki Jamie Cruz,

Dae‐Wook Kang

et al.

Cell, Journal Year: 2019, Volume and Issue: 177(6), P. 1600 - 1618.e17

Published: May 1, 2019

Language: Английский

Citations

915
Parallelization of MAFFT for large-scale multiple sequence alignments DOI Creative Commons
Tsukasa Nakamura, Kazunori Yamada, Kentaro Tomii

et al.

Bioinformatics, Journal Year: 2018, Volume and Issue: 34(14), P. 2490 - 2492

Published: Feb. 28, 2018

Abstract Summary We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers sequences. The G-INS-1 option was recently reported have higher accuracy than other methods data, but this method has been impractical most large-scale analyses, due requirement computational resources. introduce a scalable variant, G-large-INS-1, which equivalent and is applicable 50 000 or more Availability implementation This feature available in versions 7.355 later at https://mafft.cbrc.jp/alignment/software/mpi.html. Supplementary information data are Bioinformatics online.

Language: Английский

Citations

869
MAFFT-DASH: integrated protein sequence and structural alignment DOI Creative Commons

John Rozewicki,

Songling Li,

Karlou Mar Amada

et al.

Nucleic Acids Research, Journal Year: 2019, Volume and Issue: unknown

Published: April 25, 2019

Here, we describe a web server that integrates structural alignments with the MAFFT multiple sequence alignment (MSA) tool. For this purpose, have prepared web-based Database of Aligned Structural Homologs (DASH), which provides at domain and chain levels for all proteins in Protein Data Bank (PDB), can be queried interactively or by simple REST-like API. MAFFT-DASH integration invoked single flag on either (https://mafft.cbrc.jp/alignment/server/) command-line versions MAFFT. In our benchmarks using 878 cases from BAliBase, HomFam, OXFam, Mattbench SISYPHUS datasets, showed 10–20% improvement over standard MSA problems weak similarity, terms Sum-of-Pairs (SP), measure how well program succeeds aligning input sequences comparison to reference alignment. When were supplemented homologous sequences, further was observed. Potential applications DASH beyond enrichment include functional annotation through detection remote homology assembly template libraries modeling.

Language: Английский

Citations

671
The genetic and epigenetic landscape of the Arabidopsis centromeres DOI
Matthew Naish, Michael Alonge, Piotr Włodzimierz

et al.

Science, Journal Year: 2021, Volume and Issue: 374(6569)

Published: Nov. 11, 2021

A closer look at centromeres Centromeres are key for anchoring chromosomes to the mitotic spindle, but they have been difficult sequence because can contain many repeating DNA elements. These repeats, however, carry regularly spaced, distinctive markers of heterogeneity between mostly, not completely, identical repeats. Such differences aid assembly. Naish et al . used ultra-long-read sequencing establish a reference assembly that resolves all five in small mustard plant Arabidopsis Their view into subtly homogenized world reveals retrotransposons interrupt centromere organization and repressive methylation excludes from meiotic crossover repair. Thus, evolve under opposing forces homogenization retrotransposon disruption. —PJH

Language: Английский

Citations

295
Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life DOI Creative Commons
Rosa Fernández, Robert J. Kallal, Dimitar Dimitrov

et al.

Current Biology, Journal Year: 2018, Volume and Issue: 28(9), P. 1489 - 1497.e5

Published: April 26, 2018

Language: Английский

Citations

240
A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16) DOI Creative Commons

Alexander Holm Viborg,

Nicolas Terrapon, Vincent Lombard

et al.

Journal of Biological Chemistry, Journal Year: 2019, Volume and Issue: 294(44), P. 15973 - 15986

Published: Sept. 9, 2019

Glycoside hydrolase family (GH) 16 comprises a large and taxonomically diverse of glycosidases transglycosidases that adopt common β-jelly-roll fold are active on range terrestrial marine polysaccharides. Presently, broadly insightful sequence–function correlations in GH16 hindered by lack systematic subfamily structure. To fill this gap, we have used highly scalable protein sequence similarity network analysis to delineate nearly 23,000 sequences into 23 robust subfamilies, which strongly supported hidden Markov model maximum likelihood molecular phylogenetic analyses. Subsequent evaluation over 40 experimental three-dimensional structures has highlighted key tertiary structural differences, predominantly manifested active-site loops, dictate substrate specificity across the evolutionary landscape. As for other GH families (i.e. GH5, GH13, GH43), new classification provides roadmap functional glycogenomics will guide future bioinformatics structure–function The is publicly available CAZy database. workflow here, SSNpipe, freely from GitHub.

Language: Английский

Citations

154
A complete telomere-to-telomere assembly of the maize genome DOI Creative Commons
Jian Chen,

Zijian Wang,

Kaiwen Tan

et al.

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(7), P. 1221 - 1231

Published: June 15, 2023

Abstract A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a assembly maize with each chromosome entirely traversed in single contig. The 2,178.6 Mb T2T Mo17 base accuracy over 99.99% unveiled structural features all repetitive regions genome. There were several super-long simple-sequence-repeat arrays having consecutive thymine–adenine–guanine (TAG) tri-nucleotide repeats up to 235 kb. entire nucleolar organizer region 26.8 array 2,974 45S rDNA copies revealed enormously complex patterns duplications transposon insertions. Additionally, assemblies ten centromeres enabled us precisely dissect repeat compositions both CentC-rich CentC-poor centromeres. represents major step forward understanding complexity highly recalcitrant higher plant genomes.

Language: Английский

Citations

151
The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling DOI Creative Commons
Song‐Can Chen, Guo‐Xin Sun, Yu Yan

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2020, Volume and Issue: 117(19), P. 10414 - 10421

Published: April 29, 2020

The rise of oxygen on the early Earth about 2.4 billion years ago reorganized redox cycle harmful metal(loids), including that arsenic, which doubtlessly imposed substantial barriers to physiology and diversification life. Evaluating adaptive biological responses these environmental challenges is inherently difficult because paucity fossil records. Here we applied molecular clock analyses 13 gene families participating in principal pathways arsenic resistance cycling, explore nature biogeocycles decipher feedbacks associated with planetary oxygenation. Our results reveal advent nascent systems under anoxic environment predating Great Oxidation Event (GOE), primary function detoxifying reduced compounds were abundant Archean environments. To cope increased toxicity oxidized species occurred as built up Earth's atmosphere, found parts preexisting detoxification for trivalent arsenicals merged newly emerged originated via convergent evolution. Further expansion was made feasible by incorporation oxygen-dependent enzymatic into network. These genetic innovations, together other redox-sensitive metals, provided organisms novel mechanisms adaption changes global a consequence GOE.

Language: Английский

Citations

147
A catalog of the diversity and ubiquity of bacterial microcompartments DOI Creative Commons
Markus Sutter, Matthew R. Melnicki, Frederik Schulz

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: June 21, 2021

Bacterial microcompartments (BMCs) are organelles that segregate segments of metabolic pathways which incompatible with surrounding metabolism. BMCs consist a selectively permeable shell, composed three types structurally conserved proteins, together sequestered enzymes vary among functionally distinct BMCs. Genes encoding shell proteins typically clustered those for the encapsulated enzymes. Here, we report number identifiable BMC loci has increased twenty-fold since last comprehensive census 2014, and doubled. The new expand range compartmentalized catalysis suggest there is more biochemistry yet to be discovered. Our catalog provides framework their identification, correlation bacterial niche adaptation, experimental characterization, development BMC-based nanoarchitectures biomedical bioengineering applications.

Language: Английский

Citations

106