Functions of Archaeal Nucleoid Proteins: Archaeal Silencers are Still Missing

Maruyama, Hugo; Kent, Nicholas A.; Nishida, Hiromi; Oshima, Taku

doi:10.1007/978-981-13-3411-5_2

Cited by 4 publications

(3 citation statements)

References 96 publications

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“…TF-like proteins are found in both Euryarchaeota and Crenarchaeota. Possible functions of such TF-like proteins might include architectural roles as well as the suppression of horizontally transferred genetic elements (Maruyama et al, 2019). Further, the interplay between the chromosomal proteins, as well as differential expression and post-translational modifications, might contribute to higher-order folding and regulation of the archaeal chromosomes (Figure 7A).…”

Section: Discussionmentioning

confidence: 99%

“…The functions of TrmBL2 resemble those of bacterial H-NS, a NAP that suppresses the transcription of horizontally acquired genetic elements by forming a nucleoprotein filament on genomic DNA (Navarre et al, 2006;Oshima et al, 2006;Higashi et al, 2016). Considering the functional similarity between H-NS and TrmBL2 and the fact that HGT occurs between bacteria and Archaea (López-García et al, 2015;Wagner et al, 2017), TrmBL2 might also function in suppressing the expression of genes acquired by horizontal transfer in Archaea (Maruyama et al, 2019). Proteins homologous to TrmBL2 have been found in Archaea other than members of the Thermococcales, as well as in bacteria (Maruyama et al, 2011).…”

Section: Role Of Transcription Factor-like Proteins In P Calidifontis and T Kodakarensismentioning

confidence: 99%

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Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis

et al. 2020

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Archaeal species encode a variety of distinct lineage-specific chromosomal proteins. We have previously shown that in Thermococcus kodakarensis, histone, Alba, and TrmBL2 play distinct roles in chromosome organization. Although our understanding of individual archaeal chromosomal proteins has been advancing, how archaeal chromosomes are folded into higher-order structures and how they are regulated are largely unknown. Here, we investigated the primary and higher-order structures of archaeal chromosomes from different archaeal lineages. Atomic force microscopy of chromosome spreads out of Thermoplasma acidophilum and Pyrobaculum calidifontis cells revealed 10-nm fibers and 30-40-nm globular structures, suggesting the occurrence of higher-order chromosomal folding. Our results also indicated that chromosome compaction occurs toward the stationary phase. Micrococcal nuclease digestion indicated that fundamental structural units of the chromosome exist in T. acidophilum and T. kodakarensis but not in P. calidifontis or Sulfolobus solfataricus. In vitro reconstitution showed that, in T. acidophilum, the bacterial HU protein homolog HTa formed a 6-nm fiber by wrapping DNA, and that Alba was responsible for the formation of the 10-nm fiber by binding along the DNA without wrapping. Remarkably, Alba could form different higher-order complexes with histone or HTa on DNA in vitro. Mass spectrometry detected HTa and Rad50 in the T. acidophilum chromosome but not in other species. A putative transcriptional regulator of the AsnC/Lrp family (Pcal_1183) was detected on the P. calidifontis chromosome, but not on that of other species studied. Putative membrane-associated proteins were detected in the chromosomes of the three archaeal species studied, including T. acidophilum, P. calidifontis, and T. kodakarensis. Collectively, our data show that Archaea use different combinations of proteins to achieve chromosomal architecture and functional regulation.

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Section: Discussionmentioning

confidence: 99%

Section: Role Of Transcription Factor-like Proteins In P Calidifontis and T Kodakarensismentioning

confidence: 99%

Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis

et al. 2020

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“…Recently, a model was proposed that the archaeal chromosomal protein TrmBL2 plays a role similar to that of H-NS in suppressing horizontally transferred genes [76]. TrmBL2 is a transcription factor-like protein with a helix-turn-helix DNA-binding motif, which was initially identified as an abundant chromosomal protein that forms a thick (~14 nm) nucleoprotein filament on DNA without shortening (wrapping) DNA.…”

Section: Suppression Of Horizontally Transferred Genes By Global Regulatory Proteinsmentioning

confidence: 99%

Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life

Maruyama

Nambu

Mashimo

et al. 2021

IJMS

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Comparative structural/molecular biology by single-molecule analyses combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution have been powerful tools for elucidating the mechanisms underlying genome DNA folding. All genomes in the three domains of life undergo stepwise folding from DNA to 30–40 nm fibers. Major protein players are histone (Eukarya and Archaea), Alba (Archaea), and HU (Bacteria) for fundamental structural units of the genome. In Euryarchaeota, a major archaeal phylum, either histone or HTa (the bacterial HU homolog) were found to wrap DNA. This finding divides archaea into two groups: those that use DNA-wrapping as the fundamental step in genome folding and those that do not. Archaeal transcription factor-like protein TrmBL2 has been suggested to be involved in genome folding and repression of horizontally acquired genes, similar to bacterial H-NS protein. Evolutionarily divergent SMC proteins contribute to the establishment of higher-order structures. Recent results are presented, including the use of Hi-C technology to reveal that archaeal SMC proteins are involved in higher-order genome folding, and the use of single-molecule tracking to reveal the detailed functions of bacterial and eukaryotic SMC proteins. Here, we highlight the similarities and differences in the DNA-folding mechanisms in the three domains of life.

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Different Proteins Mediate Step-wise Chromosome Architectures inThermoplasma acidophilumandPyrobaculum calidifontis

Maruyama

Prieto

Nambu

et al. 2020

Preprint

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Archaeal species encode a variety of distinct lineage-specific chromosomal proteins. We have previously shown that in Thermococcus kodakarensis, histone, Alba, and TrmBL2 play distinct roles in chromosome organization. Although our understanding of individual archaeal chromosomal proteins has been advancing, how archaeal chromosomes are folded into higher-order structures and how they are regulated are largely unknown. Here, we investigated the primary and higher-order structures of archaeal chromosomes from different archaeal lineages. Atomic force microscopy of chromosome spreads out of Thermoplasma acidophilum and Pyrobaculum calidifontis cells revealed 10-nm fibers and 30–40-nm globular structures, suggesting the occurrence of higher-order chromosomal folding. Our results also indicated that chromosome compaction occurs toward the stationary phase. Micrococcal nuclease digestion indicated that fundamental structural units of the chromosome exist in T. acidophilum and T. kodakarensis but not in P. calidifontis or Sulfolobus solfataricus. In vitro reconstitution showed that, in T. acidophilum, the bacterial HU protein homolog HTa formed a 6-nm fiber by wrapping DNA, and that Alba was responsible for the formation of the 10-nm fiber by binding along the DNA without wrapping. Remarkably, Alba could form different higher-order complexes with histone or HTa on DNA in vitro. Mass spectrometry detected HTa in the T. acidophilum chromosome but not in other species. A putative transcriptional regulator of the AsnC/Lrp family (Pcal_1183) was detected on the P. calidifontis chromosome, but not on that of other species studied. Putative membrane-associated proteins were detected in the chromosomes of the three archaeal species studied, including T. acidophilum, P. calidifontis, and T. kodakarensis. Collectively, our data show that Archaea use different combinations of proteins to achieve chromosomal architecture and functional regulation.

show abstract

Functions of Archaeal Nucleoid Proteins: Archaeal Silencers are Still Missing

Cited by 4 publications

References 96 publications

Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis

Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis

Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life

Different Proteins Mediate Step-wise Chromosome Architectures inThermoplasma acidophilumandPyrobaculum calidifontis

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