Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1

Pfeiffer, Friedhelm; Schuster, Stephan C.; Broicher, Alexander; Falb, Michaela; Palm, Peter; Rodewald, Karin; Ruepp, Andreas; Soppa, Jörg; Tittor, Jörg; Oesterhelt, Dieter

doi:10.1016/j.ygeno.2008.01.001

Cited by 127 publications

(159 citation statements)

References 48 publications

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“…salinarum NRC-1 (415) and Hbt. salinarum R1 (559), and a genetic system has also been developed (560). Some species are able to produce bacteriorhodopsin, one of the best-studied membrane proteins, and use sunlight as an energy source, which is, however, restricted to bright-light and lowoxygen conditions (for more details, see references 542, 543, and 561).…”

Section: Fig 27mentioning

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 27mentioning

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

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“…Recent advances in haloarchaeal genome sequencing (4,6,14,15) and the development of new genetic tools, such as the targeted and markerless deletion of chromosomal genes (1), have made this group of microbes ideal for providing insight into cell physiology.…”

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confidence: 99%

Proteasomal Components Required for Cell Growth and Stress Responses in the Haloarchaeon Haloferax volcanii

et al. 2008

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Little is known regarding the biological roles of archaeal proteases. The haloarchaeon Haloferax volcanii is an ideal model for understanding these enzymes, as it is one of few archaea with an established genetic system. In this report, a series of H. volcanii mutant strains with markerless and/or conditional knockouts in each known proteasome gene was systematically generated and characterized. This included single and double knockouts of genes encoding the 20S core ␣1 (psmA), ␤ (psmB), and ␣2 (psmC) subunits as well as genes (panA and panB) encoding proteasome-activating nucleotidase (PAN) proteins closely related to the regulatory particle triple-A ATPases (Rpt) of eukaryotic 26S proteasomes. Our results demonstrate that 20S proteasomes are required for growth. Although synthesis of 20S proteasomes containing either ␣1 or ␣2 could be separately abolished via gene knockout with little to no impact on growth, conditional depletion of either ␤ alone or ␣1 and ␣2 together rendered the cells inviable. In contrast, the PAN proteins were not essential based on the robust growth of the panA panB double knockout strain. Deletion of genes encoding either ␣1 or PanA did, however, render cells more sensitive to growth on organic versus inorganic nitrogen sources and hypo-osmotic stress and limited growth in the presence of L-canavanine. Abolishment of ␣1 synthesis also had a severe impact on the ability of cells to withstand thermal stress. This contrasted with what was seen for panA knockouts, which displayed enhanced thermotolerance. Together, these results provide new and important insight into the biological role of proteasomes in archaea.Detailed three-dimensional structures of archaeal proteasomes have provided a firm foundation for understanding how these elaborate nanocompartmentalized complexes mediate protein degradation (3, 11). While their thermostable properties make archaeal proteasomes ideal for structural studies, the optimum growth requirements of archaea, which often include extreme pH, salt, and/or temperature, have limited our fundamental knowledge of how these proteolytic enzymes work in the ubiquitin-free archaeal cell.Halophilic archaea or haloarchaea have developed into model organisms that are used to study many biological processes. Recent advances in haloarchaeal genome sequencing (4,6,14,15) and the development of new genetic tools, such as the targeted and markerless deletion of chromosomal genes (1), have made this group of microbes ideal for providing insight into cell physiology.Haloferax volcanii is a haloarchaeon which encodes at least five protein components associated with the proteasome system. These include the ␣1, ␤, and ␣2 proteins, encoded by psmA, psmB, and psmC, respectively, which form at least two 20S proteasome subtypes of differing subunit compositions (␣1␤ and ␣1␣2␤) (8,20). H. volcanii also encodes two proteasome-activating nucleotidase (PAN) proteins, PanA (panA) and PanB (panB), closely related to the regulatory particle triple A-ATPase (Rpt) proteins of eukaryal 26S pro...

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“…25 In H. salinarum NRC-1, reannotation based on R1 strain identified 10 IS1341-type transposases. 26 Five of these IS1341-type transposases are located adjacent to tnpA, 1 in divergent and 4 in convergent orientation ( Table 1).…”

Section: Resultsmentioning

confidence: 99%

Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea

et al. 2015

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The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS1341-type transposase (tnpB) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon Halobacterium salinarum NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS1341-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a H. salinarum intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved H. salinarum growth, indicating that these ncRNAs are functional.

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Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1

Cited by 127 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

Proteasomal Components Required for Cell Growth and Stress Responses in the Haloarchaeon Haloferax volcanii

Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea

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