Predicting the capsid architecture of phages from metagenomic data

Autor: Diana Y. Lee, Caitlin Bartels, Katelyn McNair, Robert A. Edwards, Manal A. Swairjo, Antoni Luque

Publikováno v: Computational and Structural Biotechnology Journal, Vol 20, Iss , Pp 721-732 (2022)

Tailed phages are viruses that infect bacteria and are the most abundant biological entities on Earth. Their ecological, evolutionary, and biogeochemical roles in the planet stem from their genomic diversity. Known tailed phage genomes range from 10

Externí odkaz: https://doaj.org/article/bb9fd56f2c484fccadd66958287af1a4

Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5'-monophosphate as the biological substrate

Autor: Shr-Hau Hung, Gregory I Elliott, Thakku R Ramkumar, Lyubomyr Burtnyak, Callum J McGrenaghan, Sana Alkuzweny, Samia Quaiyum, Dirk Iwata-Reuyl, Xiaobei Pan, Brian D Green, Vincent P Kelly, Valérie de Crécy-Lagard, Manal A Swairjo

Publikováno v: Hung, S-H, Elliott, G I, Ramkumar, T R, Burtnyak, L, McGrenaghan, C J, Alkuzweny, S, Quaiyum, S, Iwata-Reuyl, D, Pan, X, Green, B D, Kelly, V P, de Crécy-Lagard, V & Swairjo, M A 2023, ' Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5'-monophosphate as the biological substrate ', Nucleic Acids Research, vol. 51, no. 2, pp. 935–951 . https://doi.org/10.1093/nar/gkac1231

Eukaryotic life benefits from—and ofttimes critically relies upon—the de novo biosynthesis and supply of vitamins and micronutrients from bacteria. The micronutrient queuosine (Q), derived from diet and/or the gut microbiome, is used as a source

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::17c2d2b7a8865610a99c66710185cbb3
https://pubmed.ncbi.nlm.nih.gov/36610787

Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs

Autor: Sylvain Moineau, Liang Cui, Peter C. Dedon, Tue Kjærgaard Nielsen, Geoffrey Hutinet, Lars Hestbjerg Hansen, Manal A. Swairjo, Nikoline S. Olsen, Valérie de Crécy-Lagard, Alexander Byth Carstens, Witold Kot

Publikováno v: Kot, W, Olsen, N S, Nielsen, T K, Hutinet, G, de Crécy-Lagard, V, Cui, L, Dedon, P C, Carstens, A B, Moineau, S, Swairjo, M A & Hansen, L H 2020, ' Detection of preQ 0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs ', Nucleic Acids Research, vol. 48, no. 18, pp. 10383-10396 . https://doi.org/10.1093/nar/gkaa735
Kot, W, Olsen, N S, Nielsen, T K, Hutinet, G, de Crecy-Lagard, V, Cui, L, Dedon, P C, Carstens, A B, Moineau, S, Swairjo, M A & Hansen, L H 2020, ' Detection of preQ 0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs ', Nucleic Acids Symposium Series, vol. 48, no. 18, pp. 10383-10396 . https://doi.org/10.1093/nar/gkaa735
Nucleic Acids Research

In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a0a2d52f1da8c6c7688c9e9fb9d5ab94
https://pure.au.dk/portal/da/publications/detection-of-preq0-deazaguanine-modifications-in-bacteriophage-cajan-dna-using-nanopore-sequencing-reveals-same-hypermodification-at-two-distinct-dna-motifs(312622ab-1976-4b3a-a198-2fa16fa64494).html

Conformational communication mediates the reset step in t6A biosynthesis

Autor: Susan Bayooz, Manal A. Swairjo, Boguslaw Stec, William Swinehart, Jamie M. Schiffer, Naduni Paranagama, Dirk Iwata-Reuyl, Vanessa Quach, Amit Luthra, Phuc Phan

Publikováno v: Nucleic Acids Research

The universally conserved N6-threonylcarbamoyladenosine (t6A) modification of tRNA is essential for translational fidelity. In bacteria, t6A biosynthesis starts with the TsaC/TsaC2-catalyzed synthesis of the intermediate threonylcarbamoyl adenylate (

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4f5318fff0026b67d60a5fb3258533c7
https://pubmed.ncbi.nlm.nih.gov/31114923

Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold

Autor: Uttamkumar Samanta, Manal A. Swairjo, Jonathan Alvarez, Dirk Iwata-Reuyl, Adriana Bon Ramos, Xianghan Mei

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 85:103-116

The tunneling-fold (T-fold) structural superfamily has emerged as a versatile protein scaffold of diverse catalytic activities. This is especially evident in the pathways to the 7-deazaguanosine modified nucleosides of tRNA queuosine and archaeosine.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::bba9827007e3c489003a984070ffea7e
https://doi.org/10.1002/prot.25202