Cyclic nucleotides in archaea: Cyclic di‐AMP in the archaeon <i>Haloferax volcanii </i>and its putative role

Braun, F. N.; Thomalla, Laura; Does, Chris van der; Quax, Tessa E. F.; Allers, Thorsten; Kaever, Volkhard; Albers, Sonja‐Verena

doi:10.1002/mbo3.829

Cited by 35 publications

(35 citation statements)

References 66 publications

(109 reference statements)

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“…Quantitative PCR analysis were essentially performed as described previously ( 83 ). RNA was extracted from 4 ml logarithmically growing cells in Hv-YPC medium (OD 600nm = 0.5) using RNeasy Mini-Kit (Quiagen #74106) as recommended by the manufacturer instructions.…”

Section: Boncatmentioning

confidence: 99%

Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea

Knüppel

Trahan

Kern

et al. 2021

Nucleic Acids Research

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Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.

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Section: Boncatmentioning

confidence: 99%

Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea

Knüppel

Trahan

Kern

et al. 2021

Nucleic Acids Research

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“…We assume that SisLOG is an important enzyme in generation, sensation, and regulation of signal molecules. Supporting this is the finding that there are nucleotide molecules in archaea such as cyclic-di-and linear oligonucleotide signals, which have functions that have only just begun to be elucidated (32,33). We also do not know in what cellular process SisLOG is involved.…”

Section: Discussionmentioning

confidence: 99%

The Lonely Guy (LOG) Homologue SiRe_0427 from the Thermophilic Archaeon Sulfolobus islandicus REY15A Is a Phosphoribohydrolase Representing a Novel Group

Mayaka

Huang

Xiao

et al. 2019

Appl Environ Microbiol

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Lonely Guy (LOG) proteins are important enzymes in cellular organisms, which catalyze the final step in the production of biologically active cytokinins via dephosphoribosylation. LOG proteins are vital enzymes in plants for the activation of cytokinin precursors, which is crucial for plant growth and development. In fungi and bacteria, LOGs are implicated in pathogenic or nonpathogenic interactions with their plant hosts. However, LOGs have also been identified in the human pathogen Mycobacterium tuberculosis, and the accumulation of cytokinin-degraded products, aldehydes, within bacterial cells is lethal to the bacterium in the presence of nitric oxide, suggesting diverse roles of LOGs in various species. In this study, we conducted biochemical and genetic analysis of a LOG homologue, SiRe_0427, from the hyperthermophilic archaeon Sulfolobus islandicus REY15A. The protein possessed the LOG motif GGGxGTxxE and exhibited phosphoribohydrolase activity on adenosine-5-monophosphate (AMP), similar to LOGs from eukaryotes and bacteria. Alanine mutants at either catalytic residues or substrate binding sites lost their activity, resembling other known LOGs. SiRe_0427 is probably a homotetramer, as revealed by size exclusion chromatography and chemical cross-linking. We found that the gene encoding SiRe_0427 could be knocked out; however, the Δsire_0427 strain exhibited no apparent difference in growth compared to the wild type, nor did it show any difference in sensitivity to UV irradiation under our laboratory growth conditions. Overall, these findings indicate that archaeal LOG homologue is active as a phosphoribohydrolase. IMPORTANCE Lonely Guy (LOG) is an essential enzyme for the final biosynthesis of cytokinins, which regulate almost every aspect of growth and development in plants. LOG protein was originally discovered 12 years ago in a strain of Oryza sativa with a distinct floral phenotype of a single stamen. Recently, the presence of LOG homologues has been reported in Mycobacterium tuberculosis, an obligate human pathogen. To date, active LOG proteins have been reported in plants, pathogenic and nonpathogenic fungi, and bacteria, but there have been no experimental reports of LOG protein from archaea. In the current work, we report the identification of a LOG homologue active on AMP from Sulfolobus islandicus REY15A, a thermophilic archaeon. The protein likely forms a tetramer in solution and represents a novel evolutionary lineage. The results presented here expand our knowledge regarding proteins with phosphoribohydrolase activities and open an avenue for studying signal transduction networks of archaea and potential applications of LOG enzymes in agriculture and industry.

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“…To give researchers more options for protein purification, another plasmid pTA1392 (Fig. 1b) is available that encodes a Cterminal Streptavidin II tag (Strep II) for protein purification, alongside the established N-terminal His-tag (Braun et al 2019); both tags are compatible with high salt concentrations. For protein expression at lower levels, for example if the protein is toxic to the host cells, the pTA1926 plasmid (Fig.…”

Section: Tools For H Volcanii Applications In Biotechnologymentioning

confidence: 99%

“…For protein expression at lower levels, for example if the protein is toxic to the host cells, the pTA1926 plasmid (Fig. 1c) contains the p.tnaM3 promoter that shows 50% reduced activity compared with p.tnaA promoter present in pTA1228 and pTA1392 (Braun et al 2019). For constitutive overexpression of proteins that are not harmful to the host, the pTA1992 plasmid (Fig.…”

Section: Tools For H Volcanii Applications In Biotechnologymentioning

confidence: 99%

Haloferax volcanii for biotechnology applications: challenges, current state and perspectives

Haque

Paradisi

Allers

2019

Appl Microbiol Biotechnol

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Haloferax volcanii is an obligate halophilic archaeon with its origin in the Dead Sea. Simple laboratory culture conditions and a wide range of genetic tools have made it a model organism for studying haloarchaeal cell biology. Halophilic enzymes of potential interest to biotechnology have opened up the application of this organism in biocatalysis, bioremediation, nanobiotechnology, bioplastics and the biofuel industry. Functionally active halophilic proteins can be easily expressed in a halophilic environment, and an extensive genetic toolkit with options for regulated protein overexpression has allowed the purification of biotechnologically important enzymes from different halophiles in H. volcanii. However, corrosion mediated damage caused to stainless-steel bioreactors by high salt concentrations and a tendency to form biofilms when cultured in high volume are some of the challenges of applying H. volcanii in biotechnology. The ability to employ expressed active proteins in immobilized cells within a porous biocompatible matrix offers new avenues for exploiting H. volcanii in biotechnology. This review critically evaluates the various application potentials, challenges and toolkits available for using this extreme halophilic organism in biotechnology.

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Cyclic nucleotides in archaea: Cyclic di‐AMP in the archaeon Haloferax volcanii and its putative role

Cited by 35 publications

References 66 publications

Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea

Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea

The Lonely Guy (LOG) Homologue SiRe_0427 from the Thermophilic Archaeon Sulfolobus islandicus REY15A Is a Phosphoribohydrolase Representing a Novel Group

Haloferax volcanii for biotechnology applications: challenges, current state and perspectives

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