A key element during the flow of genetic information in living systems is fidelity. The accuracy of DNA replication influences the genome size as well as the rate of genome evolution. The large amount of energy invested in gene expression implies that fidelity plays a major role in fitness. On the other hand, an increase in fidelity generally coincides with a decrease in velocity. Hence, an important determinant of the evolution of life has been the establishment of a delicate balance between fidelity and variability. This paper reviews the current knowledge on quality control in archaeal information processing. While the majority of these processes are homologous in Archaea, Bacteria, and Eukaryotes, examples are provided of nonorthologous factors and processes operating in the archaeal domain. In some instances, evidence for the existence of certain fidelity mechanisms has been provided, but the factors involved still remain to be identified.

Bart de Koning

Fabian Blombach

Stan J. J. Brouns

John van der Oost

Fidelity in Archaeal Information Processing

Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to put this knowledge into the context of their unique energy metabolism.

Michael Rother

Joseph A. Krzycki

Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea

In eukarya and bacteria, lysine methylation is relatively rare and is catalysed by sequence-specific lysine methyltransferases that typically have only a single-protein target. Using RNA polymerase purified from the thermophilic crenarchaeum <i>Sulfolobus solfataricus</i>, we identified 21 methyllysines distributed across 9 subunits of the enzyme. The modified lysines were predominantly in <svg     style="vertical-align:-0.1638pt;width:9.7749996px;" id="M1" height="7.9499998" version="1.1" viewBox="0 0 9.7749996 7.9499998" width="9.7749996"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,7.675)"><path id="x1D6FC" d="M545 106q-67 -118 -134 -118q-24 0 -40 37.5t-30 129.5h-2q-47 -72 -103 -119.5t-108 -47.5q-47 0 -76 45.5t-29 119.5q0 113 85 204t174 91q47 0 70 -33.5t43 -119.5h3q32 47 80 140l55 13l10 -9q-47 -80 -138 -201q17 -99 27.5 -136t22.5 -37q23 0 69 61zM333 204&#xA;q-14 98 -31 149.5t-50 51.5q-49 0 -94 -70t-45 -164q0 -55 15.5 -86t40.5 -31q70 0 164 150z" /></g>

		
	
</svg>-helices and showed no conserved sequence context. A limited survey of the <i  >Thermoproteus tenax</i> proteome revealed widespread modification with 52 methyllysines in 30 different proteins. These observations suggest the presence of an unusual lysine methyltransferase with relaxed specificity in the crenarchaea. Since lysine methylation is known to enhance protein thermostability, this may be an adaptation to a thermophilic lifestyle. The implications of this modification for studies and applications of recombinant crenarchaeal enzymes are discussed.

Catherine H. Botting

Paul Talbot

Sonia Paytubi

Malcolm F. White

Extensive Lysine Methylation in Hyperthermophilic Crenarchaea: Potential Implications for Protein Stability and Recombinant Enzymes

Many archaeal proteins undergo posttranslational modifications. S-layer proteins and flagellins have been used successfully to study a variety of these modifications, including N-linked glycosylation, signal peptide removal and lipid modification. Use of these well-characterized reporter proteins in the genetically tractable model organisms, <i>Haloferax volcanii, Methanococcus voltae</i>  and <i>Methanococcus maripaludis,</i>  has allowed dissection of the pathways and characterization of many of the enzymes responsible for these modifications. Such studies have identified archaeal-specific variations in signal peptidase activity not found in the other domains of life, as well as the enzymes responsible for assembly and biosynthesis of novel N-linked glycans.  In vitro assays for some of these enzymes have already been developed.  N-linked glycosylation is not essential for either <i>Hfx. volcanii</i>  or the <i>Methanococcus</i>  species, an observation that allowed researchers to analyze the role played by glycosylation in the function of both S-layers and flagellins, by generating mutants possessing these reporters with only partial attached glycans or lacking glycan altogether.  In future studies, it will be possible to consider questions related to the heterogeneity associated with given modifications, such as differential or modulated glycosylation.

Ken F. Jarrell

Gareth M. Jones

Lina Kandiba

Divya B. Nair

Jerry Eichler

S-Layer Glycoproteins and Flagellins: Reporters of Archaeal Posttranslational Modifications

Proteasomes are composed of 20S core particles (CPs) of <svg     style="vertical-align:-0.1638pt;width:9.7749996px;" id="M1" height="7.9499998" version="1.1" viewBox="0 0 9.7749996 7.9499998" width="9.7749996"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,7.675)"><path id="x1D6FC" d="M545 106q-67 -118 -134 -118q-24 0 -40 37.5t-30 129.5h-2q-47 -72 -103 -119.5t-108 -47.5q-47 0 -76 45.5t-29 119.5q0 113 85 204t174 91q47 0 70 -33.5t43 -119.5h3q32 47 80 140l55 13l10 -9q-47 -80 -138 -201q17 -99 27.5 -136t22.5 -37q23 0 69 61zM333 204&#xA;q-14 98 -31 149.5t-50 51.5q-49 0 -94 -70t-45 -164q0 -55 15.5 -86t40.5 -31q70 0 164 150z" /></g>

		
	
</svg>- and <svg     style="vertical-align:-3.56265pt;width:10px;" id="M2" height="16.6625" version="1.1" viewBox="0 0 10 16.6625" width="10"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,12.162)"><path id="x1D6FD" d="M558 587q0 -32 -14 -61t-40 -53.5t-48.5 -41t-54.5 -36.5q144 -51 144 -174q0 -55 -43.5 -108t-104.5 -87q-77 -42 -131 -42q-31 0 -54 20t-31 47l11 18q48 -29 108 -29q79 0 119.5 43t40.5 109t-44.5 107.5t-119.5 50.5l22 47q34 1 65 21q96 61 96 157q0 42 -24 67.5&#xA;t-62 25.5q-24 0 -43.5 -9t-35 -29.5t-27 -44t-22.5 -63t-19.5 -75.5t-18.5 -91q-57 -294 -68 -380q-26 -190 -35 -200q-26 -31 -97 -37l-4 26q19 9 48 170l77 413q23 121 52.5 187.5t83.5 114.5q70 62 148 62q51 0 88.5 -34t37.5 -91z" /></g>

		
	
</svg>-type subunits that associate with regulatory particle AAA ATPases such as the proteasome-activating nucleotidase (PAN) complexes of archaea. In this study, the roles and additional sites of post-translational modification of proteasomes were investigated using the archaeon <i  >Haloferax volcanii</i> as a model. Indicative of phosphorylation, phosphatase-sensitive isoforms of <svg     style="vertical-align:-0.1638pt;width:17.9375px;" id="M3" height="11.125" version="1.1" viewBox="0 0 17.9375 11.125" width="17.9375"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,10.862)"><use xlink:href="#x1D6FC"/></g><g transform="matrix(.017,-0,0,-.017,9.718,10.862)"><path id="x31" d="M384 0h-275v27q67 5 81.5 18.5t14.5 68.5v385q0 38 -7.5 47.5t-40.5 10.5l-48 2v24q85 15 178 52v-521q0 -55 14.5 -68.5t82.5 -18.5v-27z" /></g>

		
	
</svg> and <svg     style="vertical-align:-0.1638pt;width:17.9375px;" id="M4" height="11.125" version="1.1" viewBox="0 0 17.9375 11.125" width="17.9375"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,10.862)"><use xlink:href="#x1D6FC"/></g><g transform="matrix(.017,-0,0,-.017,9.718,10.862)"><path id="x32" d="M412 140l28 -9q0 -2 -35 -131h-373v23q112 112 161 170q59 70 92 127t33 115q0 63 -31 98t-86 35q-75 0 -137 -93l-22 20l57 81q55 59 135 59q69 0 118.5 -46.5t49.5 -122.5q0 -62 -29.5 -114t-102.5 -130l-141 -149h186q42 0 58.5 10.5t38.5 56.5z" /></g>

		
	
</svg> were detected by 2-DE immunoblot. To map these and other potential sites of post-translational modification, proteasomes were purified and analyzed by tandem mass spectrometry (MS/MS). Using this approach, several phosphosites were mapped including <svg     style="vertical-align:-0.1638pt;width:17.9375px;" id="M5" height="11.125" version="1.1" viewBox="0 0 17.9375 11.125" width="17.9375"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,10.862)"><use xlink:href="#x1D6FC"/></g><g transform="matrix(.017,-0,0,-.017,9.718,10.862)"><use xlink:href="#x31"/></g>

		
	
</svg> Thr147, <svg     style="vertical-align:-0.1638pt;width:9.7749996px;" id="M6" height="7.9499998" version="1.1" viewBox="0 0 9.7749996 7.9499998" width="9.7749996"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,7.675)"><use xlink:href="#x1D6FC"/></g>

		
	
</svg>2 Thr13/Ser14 and PAN-A Ser340. Multiple methylation sites were also mapped to <svg     style="vertical-align:-0.1638pt;width:17.9375px;" id="M7" height="11.125" version="1.1" viewBox="0 0 17.9375 11.125" width="17.9375"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,10.862)"><use xlink:href="#x1D6FC"/></g><g transform="matrix(.017,-0,0,-.017,9.718,10.862)"><use xlink:href="#x31"/></g>

		
	
</svg>, thus, revealing a new type of proteasomal modification. Probing the biological role of <svg     style="vertical-align:-0.1638pt;width:17.9375px;" id="M8" height="11.125" version="1.1" viewBox="0 0 17.9375 11.125" width="17.9375"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,10.862)"><use xlink:href="#x1D6FC"/></g><g transform="matrix(.017,-0,0,-.017,9.718,10.862)"><use xlink:href="#x31"/></g>

		
	
</svg> and PAN-A phosphorylation by site-directed mutagenesis revealed dominant negative phenotypes for cell viability and/or pigmentation for <svg     style="vertical-align:-0.1638pt;width:17.9375px;" id="M9" height="11.125" version="1.1" viewBox="0 0 17.9375 11.125" width="17.9375"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,10.862)"><use xlink:href="#x1D6FC"/></g><g transform="matrix(.017,-0,0,-.017,9.718,10.862)"><use xlink:href="#x31"/></g>

		
	
</svg> variants including Thr147Ala, Thr158Ala and Ser58Ala. An <i  >H. volcanii</i> Rio1p Ser/Thr kinase homolog was purified and shown to catalyze autophosphorylation and phosphotransfer to <svg     style="vertical-align:-0.1638pt;width:17.9375px;" id="M10" height="11.125" version="1.1" viewBox="0 0 17.9375 11.125" width="17.9375"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,10.862)"><use xlink:href="#x1D6FC"/></g><g transform="matrix(.017,-0,0,-.017,9.718,10.862)"><use xlink:href="#x31"/></g>

		
	
</svg>. The <svg     style="vertical-align:-0.1638pt;width:17.9375px;" id="M11" height="11.125" version="1.1" viewBox="0 0 17.9375 11.125" width="17.9375"  xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg">
	
		
			<g transform="matrix(.017,-0,0,-.017,.062,10.862)"><use xlink:href="#x1D6FC"/></g><g transform="matrix(.017,-0,0,-.017,9.718,10.862)"><use xlink:href="#x31"/></g>

		
	
</svg> variants in Thr and Ser residues that displayed dominant negative phenotypes were significantly reduced in their ability to accept phosphoryl groups from Rio1p, thus, providing an important link between cell physiology and proteasomal phosphorylation.

Matthew A. Humbard

Christopher J. Reuter

Kheir Zuobi-Hasona

Guangyin Zhou

Julie A. Maupin-Furlow

Phosphorylation and Methylation of Proteasomal Proteins of the Haloarcheon <i>Haloferax volcanii</i>

Although archaea have a similar cellular organization as other prokaryotes, the lipid composition of their membranes and their cell surface is unique. Here we discuss recent developments in our understanding of the archaeal protein secretion mechanisms, the assembly of macromolecular cell surface structures, and the release of S-layer-coated vesicles from the archaeal membrane.

Albert F. Ellen

Behnam Zolghadr

Arnold M. J. Driessen

Sonja-Verena Albers

Shaping the Archaeal Cell Envelope

Archaea SRP is composed of an SRP RNA molecule and two bound proteins named SRP19 and SRP54. Regulated by the binding and hydrolysis of guanosine triphosphates, the RNA-bound SRP54 protein transiently associates not only with the hydrophobic signal sequence as it emerges from the ribosomal exit tunnel, but also interacts with the membrane-associated SRP receptor (FtsY). Comparative analyses of the archaea genomes and their SRP component sequences, combined with structural and biochemical data, support a prominent role of the SRP RNA in the assembly and function of the archaea SRP. The 5e motif, which in eukaryotes binds a 72 kilodalton protein, is preserved in most archaea SRP RNAs despite the lack of an archaea SRP72 homolog. The primary function of the 5e region may be to serve as a hinge, strategically positioned between the small and large SRP domain, allowing the elongated SRP to bind simultaneously to distant ribosomal sites. SRP19, required in eukaryotes for initiating SRP assembly, appears to play a subordinate role in the archaea SRP or may be defunct. The N-terminal A region and a novel C-terminal R region of the archaea SRP receptor (FtsY) are strikingly diverse or absent even among the members of a taxonomic subgroup.

Christian Zwieb

Shakhawat Bhuiyan

Archaea Signal Recognition Particle Shows the Way

In <i>Haloferax volcanii</i>, AglD adds the final hexose to the N-linked pentasaccharide decorating the S-layer glycoprotein. Not knowing the natural substrate of the glycosyltransferase, together with the challenge of designing assays compatible with hypersalinity, has frustrated efforts at biochemical characterization of AglD activity. To circumvent these obstacles, an in vivo assay designed to identify amino acid residues important for AglD activity is described. In the assay, restoration of AglD function in an <i>Hfx. volcanii aglD</i> deletion strain transformed to express plasmid-encoded versions of AglD, generated through site-directed mutagenesis at positions encoding residues conserved in archaeal homologues of AglD, is reflected in the behavior of a readily detectable reporter of N-glycosylation. As such  Asp110 and Asp112 were designated as elements of the DXD motif of AglD, a motif that interacts with metal cations associated with nucleotide-activated sugar donors, while Asp201 was predicted to be the catalytic base of the enzyme.

Lina Kaminski

Identification of Residues Important for the Activity of <i>Haloferax volcanii</i> AglD, a Component of the Archaeal N-Glycosylation Pathway

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<p><em>Archaea</em> publishes original research articles as well as review articles dealing with all aspects of archaea, providing a unique venue for exchanging information about these extraordinary prokaryotes.</p>


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Archaea publishes original research articles as well as review articles dealing with all aspects of archaea, providing a unique venue for exchanging information about these extraordinary prokaryotes.

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