A Vibrio cholerae anti-phage system depletes nicotinamide adenine dinucleotide to restrict virulent bacteriophages DOI Creative Commons

Yishak A. Woldetsadik,

David W. Lazinski,

Andrew Camilli

и другие.

mBio, Год журнала: 2024, Номер 15(11)

Опубликована: Окт. 8, 2024

ABSTRACT Bacteria and their predatory viruses (bacteriophages or phages) are in a perpetual molecular arms race. This has led to the evolution of numerous phage defensive systems bacteria that still being discovered, as well ways interference circumvention on part phages. Here, we identify unique battle between classical biotype Vibrio cholerae virulent phages ICP1, ICP2, ICP3. We show strains resist almost all isolates these due 25-kb genomic island harboring several putative anti-phage systems. observed one systems, Nezha, encoding SIR2 - like helicase proteins, inhibited replication three Bacterial SIR2-like enzymes degrade essential metabolic coenzyme nicotinamide adenine dinucleotide (NAD + ), thereby preventing invading phage. In support this mechanism, identified isolate, ICP1_2001, which circumvents Nezha by two NAD regeneration enzymes. By restoring pool, hypothesize system antagonizes without directly interacting with its proteins should be able antagonize other deplete . IMPORTANCE race, evolving an extensive arsenal mechanisms overcome study identifies previously uncharacterized facet race -depleting called potent against Remarkably, encodes regenerate counter effects Nezha. Without genes detrimental Our provides new insight into co-evolutionary dynamics informs microbial ecology therapy fields.

Язык: Английский

Renewed insights into Ackermannviridae phage biology and applications DOI Creative Commons
Anders Nørgaard Sørensen, Lone Brøndsted

npj Viruses, Год журнала: 2024, Номер 2(1)

Опубликована: Авг. 21, 2024

Abstract The Ackermannviridae family was established in 2017, containing phages previously classified within the Myoviridae under Viunalikevirus genus. have been increasingly studied due to their broad range of hosts among Enterobacteriaceae , and currently, 174 complete genomes are available on NCBI. Instrumental for wide host infectivity, display a branched complex multiple Tail Spike Proteins (TSPs). These TSPs recognize diverse surface polysaccharide receptors, allowing target strains with distinct lipopolysaccharides or capsular polysaccharides. This review gives an updated overview taxonomy expanding significant emphasis recent advances structural computational biology elucidating TSP diversity, domains, assembly complex. Furthermore, we explore potential engineering discuss challenges using transducing wildtype biocontrol. Finally, this identifies bottlenecks hindering further understanding phage applications.

Язык: Английский

Процитировано

1
Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts DOI Creative Commons
Jackie Chen,

Erick D. Nilsen,

Chutikarn Chitboonthavisuk

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 11, 2024

Understanding core and conditional gene essentiality is crucial for decoding genotype-phenotype relationships in organisms. We present PhageMaP, a high-throughput method to create genome-scale phage knockout libraries systematically assessing bacteriophages. Using we generate maps across hundreds of genes the model T7 non-model Bas63, on diverse hosts. These provide fundamental insights into genome organization, function, host-specific essentiality. By applying PhageMaP collection anti-phage defense systems, uncover that either inhibit or activate eight defenses offer novel mechanistic hypotheses. Furthermore, engineer synthetic phages with enhanced infectivity by modular transfer PhageMaP-discovered inhibitor from Bas63 T7. generalizable, as it leverages homologous recombination, universal cellular process, locus-specific barcoding. This versatile tool advances bacteriophage functional genomics accelerates rational design therapy.

Язык: Английский

Процитировано

1
Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses DOI Open Access
Jillian F. Banfield, Luis E. Valentin-Alvarado, Ling-Dong Shi

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 6, 2024

ABSTRACT Borgs are huge extrachromosomal elements of anaerobic methane-oxidizing archaea. They exist in exceedingly complex microbiomes, lack cultivated hosts and have few protein functional annotations, precluding their classification as plasmids, viruses or other. Here, we used silico structure prediction methods to investigate potential roles for ∼10,000 Borg proteins. Prioritizing analysis multicopy genes that could signal importance lifestyles, uncovered highly represented de-ubiquitination-like Zn-metalloproteases may counter host targeting proteins proteolysis. Also prevalent clusters production diverse glycoconjugates contribute decoration the cell surface, putative capsid predict multimerize into hexagonal arrays. Features including megabase-scale linear genomes with inverted terminal repeats, genomic repertoires energy metabolism, central carbon compound transformations translation, pervasive direct repeat regions shared giant eukaryotes, although analyses suggest these parallels arose via convergent evolution. If archaeal they would fill gap tri(um)virate all three domains life. One Sentence Summary Protein analyses, informed by prediction, revealed share numerous features eukaryotic viruses, suggesting a viral-like lifestyle evolutionary convergence large across Domains Life.

Язык: Английский

Процитировано

1
T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome of Escherichia coli during infection through a phage-encoded decapping enzyme DOI Creative Commons
Maik Wolfram-Schauerte, Anastassiya Moskalchuk, Nadiia Pozhydaieva

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 4, 2024

ABSTRACT Nicotinamide adenine dinucleotide (NAD) serves as a cap-like structure on cellular RNAs (NAD-RNAs) in all domains of life including the bacterium Escherichia coli . NAD also acts key molecule phage-host interactions, where bacterial immune systems deplete to abort phage infection. Nevertheless, NAD-RNAs have not yet been identified during infections bacteria and mechanisms their synthesis degradation are unknown this context. The T4 that specifically infects E. presents an important model study infections, but systematic analysis presence dynamics infection is lacking. Here, we investigate dual manner. By applying time-resolved captureSeq, identify NAD-capped host transcripts dynamic regulation We provide evidence – reported earlier generated by RNA polymerase initiating transcription with at canonical start sites. In addition, characterize NudE.1 phage-encoded Nudix hydrolase first NAD-RNA decapping enzyme. phages carrying inactive display delayed lysis phenotype. This investigates for time epitranscriptome its host, thereby introducing epitranscriptomics field research.

Язык: Английский

Процитировано

0
A Vibrio cholerae Anti-Phage System Depletes Nicotinamide Adenine Dinucleotide to Restrict Virulent Bacteriophages DOI Creative Commons

Yishak A. Woldetsadik,

David W. Lazinski,

Andrew Camilli

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 17, 2024

Bacteria and their predatory viruses (bacteriophages or phages) are in a perpetual molecular arms race. This has led to the evolution of numerous phage defensive systems bacteria that still being discovered, as well ways interference circumvention on part phages. Here, we identify unique battle between classical biotype

Язык: Английский

Процитировано

0
A Vibrio cholerae anti-phage system depletes nicotinamide adenine dinucleotide to restrict virulent bacteriophages DOI Creative Commons

Yishak A. Woldetsadik,

David W. Lazinski,

Andrew Camilli

и другие.

mBio, Год журнала: 2024, Номер 15(11)

Опубликована: Окт. 8, 2024

ABSTRACT Bacteria and their predatory viruses (bacteriophages or phages) are in a perpetual molecular arms race. This has led to the evolution of numerous phage defensive systems bacteria that still being discovered, as well ways interference circumvention on part phages. Here, we identify unique battle between classical biotype Vibrio cholerae virulent phages ICP1, ICP2, ICP3. We show strains resist almost all isolates these due 25-kb genomic island harboring several putative anti-phage systems. observed one systems, Nezha, encoding SIR2 - like helicase proteins, inhibited replication three Bacterial SIR2-like enzymes degrade essential metabolic coenzyme nicotinamide adenine dinucleotide (NAD + ), thereby preventing invading phage. In support this mechanism, identified isolate, ICP1_2001, which circumvents Nezha by two NAD regeneration enzymes. By restoring pool, hypothesize system antagonizes without directly interacting with its proteins should be able antagonize other deplete . IMPORTANCE race, evolving an extensive arsenal mechanisms overcome study identifies previously uncharacterized facet race -depleting called potent against Remarkably, encodes regenerate counter effects Nezha. Without genes detrimental Our provides new insight into co-evolutionary dynamics informs microbial ecology therapy fields.

Язык: Английский

Процитировано

0