Alexey I. Fomenkov

A virion protein of an archaeal virus inhibits a Type V BREX defense system in Haloarcula hispanica

Julia Gordeeva, Richard Morgan, Ananya Jain, Alexey I. Fomenkov et autres

ABSTRACT Bacteriophage Exclusion (BREX) systems are a diverse family of bacterial and archaeal defense mechanisms defined by two conserved genes encoding a putative alkaline phosphatase BrxZ (PglZ) and an ATPase BrxC (PglY). Here, we characterize a Type V BREX system from the …

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Genome sequence and methylome of the extremely halophilic bacterium Salinibacter ruber strain M31 T isolated from a crystallizer pond in Mallorca, Spain

Beatriz Toledo Akiti, Gulhan Kaya, Sean Kennedy, Priya DasSarma et autres

, an extremely halophilic bacterium, was isolated from a saltern crystallizer pond in Spain. Single-molecule real-time sequencing revealed a 3.6-Mbp genome with a single 3.55-Mbp circular chromosome and a 35.5-kbp plasmid. The highly acidic proteome includes a total of 2,962 proteins, some …

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Lactococcal mobile genetic elements harbour a diverse phage defensome rich in restriction-modification systems

Brian McDonnell, Philip Kelleher, Alexey I. Fomenkov, Guillermo Ortíz Charneco et autres

The genomes of 43 distinct lactococcal strains were reconstructed by a combination of long- and short-read sequencing, resolving the plasmid complement and methylome of these strains. The genomes comprised 43 chromosomes of approximately 2.5 Mb each and 269 plasmids ranging from 2 …

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Genome sequence and methylome profile of Natrinema pallidum strain NMX15-1, a halophilic archaeon, from Permian Period halite, Carlsbad, New Mexico

Aram Khoshnaw, Beatriz Toledo Akiti, Tamas Vincze, Priya DasSarma et autres

ABSTRACT We report the 3.8-Mbp genome sequence of an extreme Haloarchaeon, Natrinema pallidum strain NMX15-1, isolated from 250-million-year-old halite samples of the Permian Period. PacBio’s long-read sequencing revealed a genome comprising a chromosome (3.5-Mbp) and three plasmids (203, 71, and 56-Kbp). The …

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Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems

Sean R. Johnson, Peter Weigele, Alexey I. Fomenkov, Andrew Ge et autres

The availability of large databases of biological sequences presents an opportunity for in-depth exploration of gene diversity and function. Bacterial defense systems are a rich source of diverse but difficult to annotate genes with biotechnological applications. In this work, we present Domainator, …

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Matching excellence: Oxford Nanopore Technologies’ rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content

Axel Soto‐Serrano, Wenwen Li, Farhad M. Panah, Hui Yan et autres

The reconstruction of complete bacterial genomes is essential for microbial research, offering insights into genetic content, ontology and regulation. While Pacific Biosciences (PacBio) provides high-quality genomes, its cost remains a limitation. Oxford Nanopore Technologies (ONT) offers long reads at a lower cost, …

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Phage defence loci of Streptococcus thermophilus—tip of the anti-phage iceberg?

Philip Kelleher, Guillermo Ortíz Charneco, Zoe Kampff, Natalia Díaz‐Garrido et autres

Bacteria possess (bacterio)phage defence systems to ensure their survival. The thermophilic lactic acid bacterium, Streptococcus thermophilus, which is used in dairy fermentations, harbours multiple CRISPR-Cas and restriction and modification (R/M) systems to protect itself against phage attack, with limited reports on other …

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Identification of an endonuclease and N6-adenine methyltransferase from Ureaplasma parvum SV3F4 strain

Heng Ning Wu, Yuya Fujisawa, Zenzaburo Tozuka, Alexey I. Fomenkov et autres

A methyltransferase) in the Ureaplasma parvum SV3F4 strain. Our previous study found that the SV3F4 strain carries 17 unique genes, which are not encoded in the two previously reported U. parvum serovar 3 strain, OMC-P162 and ATCC 700970. Of these 17 unique …

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Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems

Sean R. Johnson, Peter Weigele, Alexey I. Fomenkov, Andrew Ge et autres

The availability of large databases of biological sequences presents an opportunity for in-depth exploration of gene diversity and function. Bacterial defense systems are a rich source of diverse, but difficult to annotate genes with biotechnological applications. In this work, we present Domainator, …

us (code pays fourni par la source)

Matching Excellence: ONT’s Rise to Parity with PacBio in Genome Reconstruction of Non-Model Bacterium with High GC Content

Axel Soto‐Serrano, Wenwen Li, Farhad M. Panah, Hui Yan et autres

Abstract Reconstruction of complete bacterial genomes is a vital aspect of microbial research, as it provides complex information about genetic content, gene ontology, and regulation. It has become a domain of 3rd generation, long-read sequencing platforms, as short-read technologies can deliver mainly …

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Complete genome assembly and methylome dissection of Methanococcus aeolicus PL15/Hp

Alexey I. Fomenkov, Peter Weigele, Colleen M. McClung, Casey Madinger et autres

Although restriction-modification systems are found in both Eubacterial and Archaeal kingdoms, comparatively less is known about patterns of DNA methylation and genome defense systems in archaea. Here we report the complete closed genome sequence and methylome analysis of Methanococcus aeolicus PL15/Hp, a …

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Supplementary Figure 1 Legend from ΔNp63α Up-Regulates the Hsp70 Gene in Human Cancer

Guojun Wu, Motonobu Osada, Zhongmin Guo, Alexey I. Fomenkov et autres

Supplementary Figure 1 Legend from ΔNp63α Up-Regulates the Hsp70 Gene in Human Cancer