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

Lorenzetti, Alan Péricles Rodrigues; Kusebauch, Ulrike; Wu, Wei-Ju; Almeida, João Fernando Lourenço de; Turkarslan, Serdar; Lomana, Adrián López García de; Gomes-Filho, José Vicente; Vêncio, Ricardo Z. N.; Moritz, Robert L.; Koide, Tie; Baliga, Nitin S.

doi:10.1128/msystems.00816-22

Cited by 5 publications

(7 citation statements)

References 115 publications

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“…We propose, there is also potential to use RNA-seq to understand how some halophilic species evolved and survived in so-called hostile environments (Figure 1). Our hypothesis is bolstered by these reports on using RNA-seq in halophiles research as described below: Chromohalobacter salexigens (Salvador et al, 2018), Cenococcum geophilum (Li J. et al, 2022), Halobacterium salinarum NRC-1 (Pastor et al, 2022;Lorenzetti et al, 2023;Ten-Caten et al (2018), Haloferax mediterranei ATCC33500 (Artieri et al, 2017;Payá et al, 2020;Pastor et al, 2022), Haloarcula hispainca DF60 (Pastor et al, 2022), Halolamina sp. YKT1 (Kurt-Kızıldoğan et al, 2017), Halomonas bluephagenesis TD01 (Xu et al, 2022), Halomonas socia NY-011 (Peng et al, 2020), Haloferax volcanii (Ammar et al, 2012;Babski et al, 2016;Artieri et al, 2017;Gebetsberger et al, 2017;Laass et al, 2019;Gelsinger and DiRuggiero, 2022;Pastor et al, 2022;Pastor et al, 2023), Haloferax alexandrinus DSM 27206 (Buda et al, 2023), Dunaliella bardawil (Liang et al, 2020), Tetraselmis sp.…”

Section: Utilization Of Rna-seq To Determine Gene Expressions In Plan...mentioning

confidence: 71%

The use of RNA-seq for the study of physiological adaptations of halophiles in extreme environments for astrobiological data interpretation

Basu,

Perl

2024

Front. Astron. Space Sci.

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Section: Utilization Of Rna-seq To Determine Gene Expressions In Plan...mentioning

confidence: 71%

The use of RNA-seq for the study of physiological adaptations of halophiles in extreme environments for astrobiological data interpretation

Basu,

Perl

2024

Front. Astron. Space Sci.

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“…The lower correlation in TP3 and TP4 is likely a result of post-transcriptional [57][58][59] and post-translational regulation mechanisms 60 . We aimed to explore this in more detail in a recent study by integrating 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 H. salinarum NRC-1 61 . Moreover, we successfully used the assay library to measure protein level changes in assembled ribosomal proteins investigating the interplay of transcriptional and translational regulation in H. salinarum NRC-1 47 .…”

Section: Measuring Global Protein Abundance Changes By Dia/swath-msmentioning

confidence: 99%

A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS

Kusebauch,

Lorenzetti,

Campbell

et al. 2023

Sci Data

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Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon. Data and spectral assay libraries are available via ProteomeXchange (PXD042770, PXD042774) and SWATHAtlas (SAL00312-SAL00319).

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“…Therefore, more work is needed to elucidate if Lsm proteins, e.g., act as chaperones that facilitate the folding of sRNAs as in bacteria and/or act as structural scaffolds for the assembly of RNPs as in eukaryotes [ 21 ]. Recently, it has been reported that SmAP1 or Lsm binding to RNA is one of the mechanisms of post-transcriptional regulation in Halobacterium salinarum [ 35 ].…”

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

Cited by 5 publications

References 115 publications

The use of RNA-seq for the study of physiological adaptations of halophiles in extreme environments for astrobiological data interpretation

The use of RNA-seq for the study of physiological adaptations of halophiles in extreme environments for astrobiological data interpretation

A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS

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

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