RNA 3’-terminal phosphate cyclases and cyclase-like proteins

Filipowicz, Witold

doi:10.18388/pb.2016_32

Cited by 10 publications

(3 citation statements)

References 65 publications

(135 reference statements)

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“…The 2′,3′-cNMPs have been identified in eukaryotes, bacteria, and archaea. 2′,3′-Cyclic phosphate termini are produced during RNA cleavage by many endoribonucleases, either as intermediates or final products (Filipowicz 2016 ). In eukaryotes, they originate from trans-phosphorylation (Thompson et al 1994 ) or RNA cyclase activity (Shigematsu et al 2018 ), and in E. coli , they have been shown to originate from RNase I-dependent RNA degradation (Fontaine et al 2018 ) or RNA cyclase activity (Genschik et al 1997 ).…”

Section: Mononucleotide-based Second Messengersmentioning

confidence: 99%

Putative nucleotide-based second messengers in archaea

et al. 2023

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Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR–Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3′,5′- and 2′,3′-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3′-3′-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3′-3′-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.

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Section: Mononucleotide-based Second Messengersmentioning

confidence: 99%

Putative nucleotide-based second messengers in archaea

et al. 2023

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“…This family is specific to Sulfolobales. These proteins are encoded divergently with RNA 3 ' -terminal phosphate cyclase RCL1 (arCOG04125), which is involved in ribosomal RNA maturation and RNA repair ( 70 , 71 ). Thus, arCOG05929 could be an RNA-binding protein functioning in the same pathway.…”

Section: Resultsmentioning

confidence: 99%

Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea

Makarova,

Zhang,

Wolf

et al. 2024

mBio

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The identification of microbial genes essential for survival as those with lethal knockout phenotype (LKP) is a common strategy for functional interrogation of genomes. However, interpretation of the LKP is complicated because a substantial fraction of the genes with this phenotype remains poorly functionally characterized. Furthermore, many genes can exhibit LKP not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes (conditionally essential genes). We analyzed the sets of LKP genes for two archaea, Methanococcus maripaludis and Sulfolobus islandicus, using a variety of computational approaches aiming to differentiate between essential and conditionally essential genes and to predict at least a general function for as many of the proteins encoded by these genes as possible. This analysis allowed us to predict the functions of several LKP genes including previously uncharacterized subunit of the GINS protein complex with an essential function in genome replication and of the KEOPS complex that is responsible for an essential tRNA modification as well as GRP protease implicated in protein quality control. Additionally, several novel antitoxins (conditionally essential genes) were predicted, and this prediction was experimentally validated by showing that the deletion of these genes together with the adjacent genes apparently encoding the cognate toxins caused no growth defect. We applied principal component analysis based on sequence and comparative genomic features showing that this approach can separate essential genes from conditionally essential ones and used it to predict essential genes in other archaeal genomes. IMPORTANCE Only a relatively small fraction of the genes in any bacterium or archaeon is essential for survival as demonstrated by the lethal effect of their disruption. The identification of essential genes and their functions is crucial for understanding fundamental cell biology. However, many of the genes with a lethal knockout phenotype remain poorly functionally characterized, and furthermore, many genes can exhibit this phenotype not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes. We applied state-of-the-art computational methods to predict the functions of a number of uncharacterized genes with the lethal knockout phenotype in two archaeal species and developed a computational approach to predict genes involved in essential functions. These findings advance the current understanding of key functionalities of archaeal cells.

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“… 13 In contrast, relationships between cell function and RtcA are not well defined. 14 Bacterial RtcB and RtcA have been studied in structural and biochemical detail; however, their physiological roles are largely unknown. Potential areas of their importance include ribosome and tRNA integrity, together with cellular responses to ribotoxins, antibiotics and oxidative stress.…”

Section: Introductionmentioning

confidence: 99%