Structure and RNA-Binding Properties of Lsm Protein from Halobacterium salinarum

Fando, Maria; Mikhaylina, Alisa; Lekontseva, N.V.; Tishchenko, Svetlana; Nikulin, Alexei

doi:10.1134/s000629792107004x

Cited by 4 publications

(6 citation statements)

References 25 publications

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“…To characterize the role of SmAP1 (VNG_1496G) in H. salinarum NRC-1, epitope-tagged SmAP1-RNA complexes were co-immunoprecipitated from lateexponential phase cultures from standard growth conditions (Figure S1), and transcriptome-wide binding locations of SmAP1 were mapped by enrichment of sequenced transcripts (RIP-Seq; see Methods). Consistent with previous in vitro observations from diverse archaea, the RIP-Seq analysis discovered that SmAP1 preferentially binds to AU-rich transcripts (Figure S2A) (28)(29)(30)(31)51). In particular, we determined that SmAP1 binds to 15% (397/2,579) of all protein-coding transcripts in H. salinarum NRC-1, including its own coding transcript (File S1), suggesting putative autoregulation in light of the observed dynamics for mRNA and protein levels (Figure S2B).…”

Section: Evidence For Post-transcriptional Regulation By Smap1 Asrnas...supporting

confidence: 89%

“…Hfq is a member of an RNA-guided complex, a well-characterized bacterial RNA chaperone known to interfere in mRNA translation (23,24), which acts in a manner analogous to the RNA-induced silencing complex (RISC) in eukaryotes to regulate specific mRNAs (25). Notably, the Hfq homolog, Sm-like archaeal protein (SmAP1 or Lsm), has been characterized structurally across multiple archaea (26)(27)(28)(29), including Halobacterium salinarum NRC-1 (30), and shown to likely mediate post-transcriptional regulation through sRNA-binding in Haloferax volcanii (31,32) and Sulfolobus solfataricus (33). However, we do not understand the mechanism, importance, context or scale of post-transcriptional regulation mediated by SmAP1 (and other RBPs) (34,35) or, for that matter, by the large numbers of sRNAs, antisense RNAs (asRNAs), and RNases that have been discovered across archaeal genomes (36).…”

Section: Introductionmentioning

confidence: 99%

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A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon

Lorenzetti

Kusebauch

et al. 2022

Preprint

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The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation on environmental acclimation is underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating transcriptome-wide locations of transcript processing sites (TPS) and SmAP1 binding, genome-wide locations of antisense RNAs (asRNAs), and consequences of RNase_2099C knockout on differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (RNA-Seq) and protein levels (SWATH-MS) for 2,579 genes over four phases of batch culture growth in complex medium has generated additional evidence for conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation in anoxic conditions and to modulate frequency of transposition by IS elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public web resource (https://halodata.systemsbiology.net).

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Section: Evidence For Post-transcriptional Regulation By Smap1 Asrnas...supporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon

Lorenzetti

Kusebauch

et al. 2022

Preprint

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“…Bacterial Hfq proteins form stable hexamers that preferentially bind to A-U-rich sequences [ 9 ], whereas eukaryotic Lsm proteins form up to five heteroheptameric complexes. In contrast, the structures of archaeal Lsm proteins are composed of homohexameric [ 10 ] or homoheptameric complexes [ 8 , 11 , 12 , 13 , 14 ]. The hexameric or heptameric rings of the Hfq and Sm/Lsm proteins consist of Lsm subunits that assemble without RNA [ 8 , 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Lsm Protein-Mediated Regulation in the Haloarchaeon Haloferax mediterranei

Payá,

Bautista,

Pastor-Soler

et al. 2024

IJMS

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The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq found in the Eukarya, Archaea, and Bacteria domains. Archaeal Lsm proteins have been shown to bind sRNAs and are probably involved in various cellular processes, suggesting a similar function in regulating sRNAs by Hfq in bacteria. Moreover, archaeal Lsm proteins probably represent the ancestral Lsm domain from which eukaryotic Sm proteins have evolved. In this work, Haloferax mediterranei was used as a model organism because it has been widely used to investigate the nitrogen cycle and its regulation in Haloarchaea. Predicting this protein’s secondary and tertiary structures has resulted in a three-dimensional model like the solved Lsm protein structure of Archaeoglobus fulgidus. To obtain information on the oligomerization state of the protein, homologous overexpression and purification by means of molecular exclusion chromatography have been performed. The results show that this protein can form hexameric complexes, which can aggregate into 6 or 12 hexameric rings depending on the NaCl concentration and without RNA. In addition, the study of transcriptional expression via microarrays has allowed us to obtain the target genes regulated by the Lsm protein under nutritional stress conditions: nitrogen or carbon starvation. Microarray analysis has shown the first universal stress proteins (USP) in this microorganism that mediate survival in situations of nitrogen deficiency.

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“…Hfq is a member of an RNA-guided complex, a well-characterized bacterial RNA chaperone known to interfere with mRNA translation ( 24 , 25 ), which acts in a manner analogous to that of the RNA-induced silencing complex (RISC) in eukaryotes to regulate specific mRNAs ( 26 ). Notably, the Hfq homolog, Sm-like archaeal protein 1 (SmAP1) (or Lsm), has been characterized structurally across multiple archaea ( 27 – 30 ), including Halobacterium salinarum NRC-1 ( 31 ), and was shown to likely mediate post-transcriptional regulation through sRNA binding in Haloferax volcanii ( 32 , 33 ) and Sulfolobus solfataricus ( 34 ). Yet we do not fully understand the mechanism, importance, context, or scale of post-transcriptional regulation mediated by SmAP1 (and other RBPs) ( 35 , 36 ) or, for that matter, by the large numbers of sRNAs, antisense RNAs (asRNAs), and RNases that have been discovered across archaeal genomes ( 37 ).…”

Section: Introductionmentioning

confidence: 99%

A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon

Lorenzetti

Kusebauch

et al. 2023

mSystems

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While the transcriptional regulation landscape of archaea has been extensively investigated, we currently have limited knowledge about post-transcriptional regulation and its driving mechanisms in this domain of life. In this study, we collected and integrated omics data from multiple sources and technologies to infer post-transcriptionally regulated genes and the putative mechanisms modulating their expression at the protein level in Halobacterium salinarum NRC-1.

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Structure and RNA-Binding Properties of Lsm Protein from Halobacterium salinarum

Cited by 4 publications

References 25 publications

A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon

A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon

Analysis of Lsm Protein-Mediated Regulation in the Haloarchaeon Haloferax mediterranei

A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon

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