Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase

Hajj, Mirna; Langendijk-Genevaux, Petra S.; Batista, Manon; Quentin, Yves; Laurent, Sébastien; Razzak, Ziad Abdel; Flament, Didier; Chamieh, Hala; Fichant, Gwennaële; Clouet‐d’Orval, Béatrice; Bouvier, Marlène

doi:10.20944/preprints202103.0477.v1

Cited by 3 publications

(2 citation statements)

References 41 publications

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“…CC-BY 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprint this version posted July 23, 2021. ; https://doi.org/10.1101/2021.07.23.453527 doi: bioRxiv preprint hypothetical protein that it might be involved in iron ion binding, DNA and RNA metabolisms and numerous repair mechanisms that maintain cellular integrity [29,74].…”

Section: Three-dimensional (3d) Predictionmentioning

confidence: 99%

“…Protein-protein interaction network analysis showed that the query protein (TDB29877.1, shown as LBA0468 in Fig 4) highly interacted with proteins LBA0469, LBA0470 and LBA0471 within the network; they are also neighborhood in the genome. These interactions give an indication about the selected hypothetical protein that it might be involved in iron ion binding, DNA and RNA metabolisms and numerous repair mechanisms that maintain cellular integrity [29,74].…”

Section: Three-dimensional (3d) Predictionmentioning

confidence: 99%

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Molecular characterization and functional annotation of a hypothetical protein (TDB29877.1) from probiotic bacteria Lactobacillus acidophilus: an in-silico approach

Rabbani

2021

Preprint

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Lactobacillus acidophilus bacteria are widely used as probiotic and to produce various healthy fermented food products. The PNW3 strain of the bacteria has numerous proteins in its genome and some are considered as hypothetical proteins. The aim of the present study was to predict the structures and biological functions of the hypothetical protein (accession number: TDB29877.1) from L. acidophilus through an in-silico approach applying various bioinformatics tools. The sequence similarity was searched on the available biological databases using BLASTp program to find out the homologues proteins. Besides, determination of various properties like physicochemical characteristics, subcellular localization, phylogenetic analysis, functional annotation, protein-protein interaction, determination of secondary and tertiary structures, active site detection and further quality assessment analysis were done using appropriate computational methods of bioinformatics. In-silico analysis revealed that the hypothetical protein has contained TerB-N and TerB-C domains with the presence of YjbR-like superfamily. The Protein-protein interaction network analysis revealed that the protein highly interacted with various known and unknown proteins responsible for iron ion binding, DNA and RNA metabolisms and numerous repair mechanisms that maintain cellular integrity. It was also found that the protein has predominantly alpha-helices in its secondary structure and the three dimensional model has been found to be novel as it possessed expected quality while gone through various quality assessment tools. Thus, the present result indicated that the selected hypothetical protein which is cytoplasmic in nature with Belta-grasp fold, plays important role in responding during stress condition or phage defense mechanism.

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Section: Three-dimensional (3d) Predictionmentioning

confidence: 99%

Section: Three-dimensional (3d) Predictionmentioning

confidence: 99%

Molecular characterization and functional annotation of a hypothetical protein (TDB29877.1) from probiotic bacteria Lactobacillus acidophilus: an in-silico approach

Rabbani

2021

Preprint

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Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius

et al. 2021

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Homologous recombination (HR) refers to the process of information exchange between homologous DNA duplexes and is composed of four main steps: end resection, strand invasion and formation of a Holliday junction (HJ), branch migration, and resolution of the HJ. Within each step of HR in Archaea, the helicase-promoting branch migration is not fully understood. Previous biochemical studies identified three candidates for archaeal helicase promoting branch migration in vitro: Hjm/Hel308, PINA, and archaeal long helicase related (aLhr) 2. However, there is no direct evidence of their involvement in HR in vivo. Here, we identified a novel helicase encoded by Saci_0814, isolated from the thermophilic crenarchaeon Sulfolobus acidocaldarius; the helicase dissociated a synthetic HJ. Notably, HR frequency in the Saci_0814-deleted strain was lower than that of the parent strain (5-fold decrease), indicating that Saci_0814 may be involved in HR in vivo. Saci_0814 is classified as an aLhr1 under superfamily 2 helicases; its homologs are conserved among Archaea. Purified protein produced in Escherichia coli showed branch migration activity in vitro. Based on both genetic and biochemical evidence, we suggest that aLhr1 is involved in HR and may function as a branch migration helicase in S. acidocaldarius.

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The Impact of Single-Stranded DNA-Binding Protein SSB and Putative SSB-Interacting Proteins on Genome Integrity in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius

Suzuki

Kurosawa

2023

IJMS

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The study of DNA repair in hyperthermophiles has the potential to elucidate the mechanisms of genome integrity maintenance systems under extreme conditions. Previous biochemical studies have suggested that the single-stranded DNA-binding protein (SSB) from the hyperthermophilic crenarchaeon Sulfolobus is involved in the maintenance of genome integrity, namely, in mutation avoidance, homologous recombination (HR), and the repair of helix-distorting DNA lesions. However, no genetic study has been reported that elucidates whether SSB actually maintains genome integrity in Sulfolobus in vivo. Here, we characterized mutant phenotypes of the ssb-deleted strain Δssb in the thermophilic crenarchaeon S. acidocaldarius. Notably, an increase (29-fold) in mutation rate and a defect in HR frequency was observed in Δssb, indicating that SSB was involved in mutation avoidance and HR in vivo. We characterized the sensitivities of Δssb, in parallel with putative SSB-interacting protein-encoding gene-deleted strains, to DNA-damaging agents. The results showed that not only Δssb but also Δalhr1 and ΔSaci_0790 were markedly sensitive to a wide variety of helix-distorting DNA-damaging agents, indicating that SSB, a novel helicase SacaLhr1, and a hypothetical protein Saci_0790, were involved in the repair of helix-distorting DNA lesions. This study expands our knowledge of the impact of SSB on genome integrity and identifies novel and key proteins for genome integrity in hyperthermophilic archaea in vivo.

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Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase

Cited by 3 publications

References 41 publications

Molecular characterization and functional annotation of a hypothetical protein (TDB29877.1) from probiotic bacteria Lactobacillus acidophilus: an in-silico approach

Molecular characterization and functional annotation of a hypothetical protein (TDB29877.1) from probiotic bacteria Lactobacillus acidophilus: an in-silico approach

Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius

The Impact of Single-Stranded DNA-Binding Protein SSB and Putative SSB-Interacting Proteins on Genome Integrity in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius

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