Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon<i>Thermococcus kodakarensis</i>

Maruyama, Hugo; Shin, Minsang; Oda, Tsuneo; Matsumi, Rie; Ohniwa, Ryosuke L.; Itoh, Takehiko; Shirahige, Katsuhiko; Imanaka, Tadayuki; Atomi, Haruyuki; Yoshimura, Shige H.; Takeyasu, Kunio

doi:10.1091/mbc.e10-08-0668

Cited by 50 publications

(100 citation statements)

References 48 publications

(56 reference statements)

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“…For Tco. kodakarensis TrmBL2 (TK0471), a role as an abundant chromosomal protein, which forms fibrous, thick structures with DNA, was reported (489). TrmBL2 binds to coding and intergenic regions of the DNA and thus probably represses transcription by blocking RNAP recruitment.…”

Section: Fig 20mentioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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Section: Fig 20mentioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

View full text Add to dashboard Cite

show abstract

“…Band shift experiments revealed that it binds to the TGM sequence with low affinity but not exclusively [3]. For the highly homologous TK0471 protein from T. kodakarensis [8,9], it was shown to bind nonspecifically to DNA and impart on it the appearance of a thick, stiff fiber.…”

Section: Discussionmentioning

confidence: 99%

“…This staggered arrangement of the dimers on the DNA ensures a larger coverage of the DNA surface that, along with its nonspecific binding mode, could hinder access to various DNA modifying enzymes [8].…”

Section: Discussionmentioning

confidence: 99%

“…The phospholipase D-like domains are also found in endonucleases, toxins and as structural components of pox virus envelope [23,24]. In case of TrmBL2, the C-terminal domain seems to function as a tetramerization domain and could in principle also act as a scaffold for protein-protein interactions [8].…”

Section: Structural Homologs Of the Trmbl2 Ctdmentioning

confidence: 99%

“…Apart from acting as a transcriptional regulator, it was observed that TrmBL2 associates nonspecifically to the chromatin forming thick fibrous structures [8]. The appearance of these thick fibrous structures only in the log phase suggests that TrmBL2 exerts its effect on the chromatin in a growth-phase-dependent manner.…”

Section: Introductionmentioning

confidence: 99%

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Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein

Ahmad

Waege

Hausner

et al. 2015

Journal of Molecular Biology

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The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix (HTH) domains binding to successive major grooves of the DNA. However, in TrmBL2, the two dimers are arranged at a mutual displacement of approximately 2 bp so that they associate with the DNA along the double-helical axis at an angle of approximately 80°.While the deoxyribose phosphate groups of the double-stranded DNA (dsDNA) used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The HTH domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent.This hitherto unseen mode of DNA binding by TrmBL2 seems to arise from nonoptimal protein-DNA contacts made by its four HTH domains resulting in a low-affinity, nonspecific binding to DNA.

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Sa‐Lrp from Sulfolobus acidocaldarius is a versatile, glutamine‐responsive, and architectural transcriptional regulator

et al. 2012

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Sa-Lrp is a member of the leucine-responsive regulatory protein (Lrp)-like family of transcriptional regulators in Sulfolobus acidocaldarius. Previously, we demonstrated the binding of Sa-Lrp to the control region of its own gene in vitro. However, the function and cofactor of Sa-Lrp remained an enigma. In this work, we demonstrate that glutamine is the cofactor of Sa-Lrp by inducing the formation of octamers and increasing the DNA-binding affinity and sequence specificity. In vitro protein-DNA interaction assays indicate that Sa-Lrp binds to promoter regions of genes with a variety of functions including ammonia assimilation, transcriptional control, and UV-induced pili synthesis. DNA binding occurs with a specific affinity for AT-rich binding sites, and the protein induces DNA bending and wrapping upon binding, indicating an architectural role of the regulator. Furthermore, by analyzing an Sa-lrp deletion mutant, we demonstrate that the protein affects transcription of some of the genes of which the promoter region is targeted and that it is an important determinant of the cellular aggregation phenotype. Taking all these results into account, we conclude that Sa-Lrp is a glutamine-responsive global transcriptional regulator with an additional architectural role.

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Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeonThermococcus kodakarensis

Cited by 50 publications

References 48 publications

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein

Sa‐Lrp from Sulfolobus acidocaldarius is a versatile, glutamine‐responsive, and architectural transcriptional regulator

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