Gene replacement in Haloarcula marismortui: construction of a strain with two of its three chromosomal rRNA operons deleted

Rft1 catalyzes lipid-linked oligosaccharide translocation across the ER membrane

The eukaryotic asparagine (N)-linked glycan is pre-assembled as a fourteen-sugar oligosaccharide on a lipid carrier in the endoplasmic reticulum (ER). Seven sugars are first added to dolichol pyrophosphate (PP-Dol) on the cytoplasmic face of the ER, generating Man5GlcNAc2-PP-Dol (M5GN2-PP-Dol). M5GN2-PP-Dol is then flipped across the bilayer into the lumen by an ER translocator. Genetic studies identified Rft1 as the M5GN2-PP-Dol flippase in vivo but are at odds with biochemical data suggesting Rft1 is dispensable for flipping in vitro. Thus, the question of whether Rft1 plays a direct or an indirect role during M5GN2-PP-Dol translocation has been controversial for over two decades. We describe a completely reconstituted in vitro assay for M5GN2-PP-Dol translocation and demonstrate that purified Rft1 catalyzes the translocation of M5GN2-PP-Dol across the lipid bilayer. These data, combined with in vitro results demonstrating substrate selectivity and rft1∆ phenotypes, confirm the molecular identity of Rft1 as the M5GN2-PP-Dol ER flippase.

The dark side of the ribosome life cycle

Thanks to genetics, biochemistry, and structural biology many features of the ribosome´s life cycles in models of bacteria, eukaryotes, and some organelles have been revealed to near-atomic details. Collectively, these studies have provided a very detailed understanding of what are now well-established prototypes for ribosome biogenesis and function as viewed from a 'classical' model organisms perspective. However, very important challenges remain ahead to explore the functional and structural diversity of both ribosome biogenesis and function across the biological diversity on earth. Particularly, the 'third domain of life', the archaea, and also many non-model bacterial and eukaryotic organisms have been comparatively neglected. Importantly, characterizing these additional biological systems will not only offer a yet untapped window to enlighten the evolution of ribosome biogenesis and function but will also help to unravel fundamental principles of molecular adaptation of these central cellular processes.

An Acidic Exopolysaccharide from Haloarcula hispanica ATCC33960 and Two Genes Responsible for Its Synthesis

A 1.1 × 10⁶ Da acidic exopolysaccharide (EPS) was purified from an extremely halophilic archaeon Haloarcula hispanica ATCC33960 with a production of 30 mg L^-1 when grown in AS-168 medium, which mainly composed of mannose and galactose with a small amount of glucose in a molar ratio of 55.9 : 43.2 : 0.9. Two glycosyltransferase genes (HAH_1662 and HAH_1667) were identified to be responsible for synthesis of the acidic EPS. Deletion of either HAH_1662 or HAH_1667 led to loss of the acidic EPS. The mutants displayed a different cell surface morphology, retarded growth in low salty environment, an increased adhesion, and swimming ability. Our results suggest that biosynthesis of the acidic EPS might act as an adaptable mechanism to protect the cells against harsh environments.

Expression and Function of Different Guanine-Plus-Cytosine Content 16S rRNA Genes in Haloarcula hispanica at Different Temperatures

The halophilic archaeon Haloarcula hispanica harbors three ribosomal RNA (rRNA) operons (rrnA, rrnB, and rrnC) that contain the 16S rRNA genes rrsA, rrsB, and rrsC, respectively. Although rrsB and rrsC (rrsBC) have almost identical sequences, the rrsA and rrsBC sequences differ by 5.4%, and they differ by 2.5% with respect to guanine-plus-cytosine content (P_GC). The strong correlation between the typical growth temperatures of archaea and P_GC of their 16S rRNA genes suggests that H. hispanica may harbor different 16S rRNA genes having different P_GC to maintain rapid growth in a wide range of temperatures. We therefore performed reverse transcription-coupled quantitative PCR to assess expression levels of rrsA (P_GC, 58.9%) and rrsBC (P_GC, 56.4-56.5%) at various temperatures. The expression ratio of rrsA to rrsBC increased with culture temperature. Mutants with complete deletions of one or two of the three rRNA operons were constructed and their growth rates at different temperatures compared to that of the wild-type. The growth characteristics of the rRNA operon single-mutant strains were indistinguishable from the wild-type. The rRNA operon double-mutant strains maintained the same temperature range as wild-type but displayed reduced growth rates. In particular, the double-mutant strains grew much slower than wild-type at low temperature related to minimum growth temperature of the wild-type. On the other hand, at physiologically high temperatures the wild-type and the double-mutant strain which harbors only rrnA with high-P_GCrrsA grew significantly faster than the double-mutant strain which harbors only rrnC with low-P_GCrrsC. These findings suggest the importance of 16S rRNAs transcribed from rrsA with high-P_GC in maintaining rapid growth of this halophilic archaeon at raised growth temperatures.

Flagella of halophilic archaea: differences in supramolecular organization

Archaeal flagella are similar functionally to bacterial flagella, but structurally they are completely different. Helical archaeal flagellar filaments are formed of protein subunits called flagellins (archaellins). Notwithstanding progress in studies of archaeal flagella achieved in recent years, many problems in this area are still unsolved. In this review, we analyze the formation of these supramolecular structures by the example of flagellar filaments of halophilic archaea. Recent data on the structure of the flagellar filaments demonstrate that their supramolecular organization differs considerably in different haloarchaeal species.

Overview of the genetic tools in the Archaea

This section provides an overview of the genetic systems developed in the Archaea. Genetic manipulation is possible in many members of the halophiles, methanogens, Sulfolobus, and Thermococcales. We describe the selection/counterselection principles utilized in each of these groups, which consist of antibiotics and their resistance markers, and auxotrophic host strains and complementary markers. The latter strategy utilizes techniques similar to those developed in yeast. However, Archaea are resistant to many of the antibiotics routinely used for selection in the Bacteria, and a number of strategies specific to the Archaea have been developed. In addition, examples utilizing the genetic systems developed for each group will be briefly described.

Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales

The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.

Alternative flagellar filament types in the haloarchaeon Haloarcula marismortui

Many Archaea use rotation of helical flagellar filaments for swimming motility. We isolated and characterized the flagellar filaments of Haloarcula marismortui, an archaeal species previously considered to be nonmotile. Two Haloarcula marismortui phenotypes were discriminated--their filaments are composed predominantly of either FlaB or FlaA2 flagellin, and the corresponding genes are located on different replicons. FlaB and FlaA2 filaments differ in antigenicity and thermostability. FlaA2 filaments are distinctly thicker (20-22 nm) than FlaB filaments (16-18 nm). The observed filaments are nearly twice as thick as those of other characterized euryarchaeal filaments. The results suggest that the helicity of Haloarcula marismortui filaments is provided by a mechanism different from that in the related haloarchaeon Halobacterium salinarum, where 2 different flagellin molecules present in comparable quantities are required to form a helical filament.

Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium

All members of the genera Haloarcula and Halomicrobium whose names have been validly published were surveyed for 16S rRNA gene polymorphism, and the transcription of the genes from two species was investigated during growth at different NaCl concentrations. The species of Haloarcula and Halomicrobium harbour at least two different 16S rRNA gene copies, and 18 new sequences of 16S rRNA genes were obtained. The type I and type II 16S rRNA genes of Haloarcula are divergent at 4.8-5.6% of their nucleotide positions. The type III and type IV 16S rRNA genes from Halomicrobium mukohataei JCM 9738(T) are 9.0% divergent, which represents the highest intraspecific divergent 16S rRNA genes so far seen. Phylogenetic analysis based on 16S rRNA genes indicated that all type I 16S rRNA genes were clustered, and the same was true for the type II 16S rRNA genes of Haloarcula species. The two clusters, respectively generated from type I and type II 16S rRNA genes, were sharply separated and their divergences (4.8-5.6%) are in the range of various divergence usually found between genera in the order Halobacteriales (about 5-10%). Results from reverse transcription-PCR showed that the type I and type II copies of Har. amylolytica BD-3(T) and type III and type IV copies of Hmc. mukohataei JCM 9738(T) were all transcribed to 16S rRNA molecules under different salt concentrations (15-28% NaCl).

Mutations outside the anisomycin-binding site can make ribosomes drug-resistant

Eleven mutations that make Haloarcula marismortui resistant to anisomycin, an antibiotic that competes with the amino acid side chains of aminoacyl tRNAs for binding to the A-site cleft of the large ribosomal unit, have been identified in 23S rRNA. The correlation observed between the sensitivity of H. marismortui to anisomycin and the affinity of its large ribosomal subunits for the drug indicates that its response to anisomycin is determined primarily by the binding of the drug to its large ribosomal subunit. The structures of large ribosomal subunits containing resistance mutations show that these mutations can be divided into two classes: (1) those that interfere with specific drug-ribosome interactions and (2) those that stabilize the apo conformation of the A-site cleft of the ribosome relative to its drug-bound conformation. The conformational effects of some mutations of the second kind propagate through the ribosome for considerable distances and are reversed when A-site substrates bind to the ribosome.

Genomics and functional genomics with haloarchaea

The first haloarchaeal genome was published in 2000 and today five genome sequences are available. Transcriptome and proteome analyses have been established for two and three haloarchaeal species, respectively, and more than 20 studies using these functional genomic approaches have been published in the last two years. These studies gave global overviews of metabolic regulation (aerobic and anaerobic respiration, phototrophy, carbon source usage), stress response (UV, X-rays, transition metals, osmotic and temperature stress), cell cycle-dependent transcript level regulation, and transcript half-lives. The only translatome analysis available for any prokaryotic species revealed that 10 and 20% of all transcripts are translationally regulated in Haloferax volcanii and Halobacterium salinarum, respectively. Very effective methods for the construction of in frame deletion mutants have been established recently for haloarchaea and are intensively used to unravel the biological roles of genes in this group. Bioinformatic analyses include both cross-genome comparisons as well as integration of genomic data with experimental results. The first systems biology approaches have been performed that used experimental data to construct predictive models of gene expression and metabolism, respectively. In this contribution the current status of genomics, functional genomics, and molecular genetics of haloarchaea is summarized and selected examples are discussed.

Genetic and biochemical characterization of the poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthase in Haloferax mediterranei

The haloarchaeon Haloferax mediterranei has shown promise for the economical production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), a desirable bioplastic. However, little is known at present about the genes involved in PHBV synthesis in the domain Archaea. In this study, we cloned the gene cluster (phaEC(Hme)) encoding a polyhydroxyalkanoate (PHA) synthase in H. mediterranei CGMCC 1.2087 via thermal asymmetric interlaced PCR. Western blotting revealed that the phaE(Hme) and phaC(Hme) genes were constitutively expressed, and both the PhaE(Hme) and PhaC(Hme) proteins were strongly bound to the PHBV granules. Interestingly, CGMCC 1.2087 could synthesize PHBV in either nutrient-limited medium (supplemented with 1% starch) or nutrient-rich medium, up to 24 or 18% (wt/wt) in shaking flasks. Knockout of the phaEC(Hme) genes in CGMCC 1.2087 led to a complete loss of PHBV synthesis, and only complementation with the phaEC(Hme) genes together (but not either one alone) could restore to this mutant the capability for PHBV accumulation. The known haloarchaeal PhaC subunits are much longer at their C termini than their bacterial counterparts, and the C-terminal extension of PhaC(Hme) was proven to be indispensable for its function in vivo. Moreover, the mixture of purified PhaE(Hme)/PhaC(Hme) (1:1) showed significant activity of PHA synthase in vitro. Taken together, our results indicated that a novel member of the class III PHA synthases, composed of PhaC(Hme) and PhaE(Hme), accounted for the PHBV synthesis in H. mediterranei.

Selection for intragenic suppressors of lethal 23S rRNA mutations in Escherichia coli identifies residues important for ribosome assembly and function

Mutations in several functionally important regions of the 23S rRNA of E. coli increase the levels of frameshifting and readthrough of stop codons. These mutations include U2555A, U2555G, DeltaA1916 and U2493C. The mutant rRNAs are lethal when expressed at high levels from a plasmid, in strains also expressing wild type rRNA from chromosomal rrn operons. The lethal phenotype can be suppressed by a range of second-site mutations in 23S rRNA. However, analysis of the functionality of the double mutant rRNAs in heterogeneous ribosome populations shows that in general, the second site mutations do not restore function. Instead, they prevent the assembly, or entry of the mutant 50S subunits into the functioning 70S ribosome and polysome pools, by affecting the competitiveness of the mutant subunits for association with 30S particles. The second-site mutations lie in regions of the 23S rRNA involved in subunit assembly, intersubunit bridge formation and interactions of the ribosome with tRNAs and factors. These second site suppressor mutations thus define functionally important rRNA nucleotides and this approach may be of general use in the functional mapping of large RNAs.

Molecular characterization of the phaECHm genes, required for biosynthesis of poly(3-hydroxybutyrate) in the extremely halophilic archaeon Haloarcula marismortui

Although many haloarchaea produce biodegradable polyhydroxyalkanoates (PHAs), the genes involved in PHA synthesis in the domain of Archaea have not yet been experimentally investigated yet. In this study, we revealed that Haloarcula marismortui was able to accumulate poly(3-hydroxybutyrate) (PHB) up to 21% of cellular dry weight when cultured in a minimal medium with excessive glucose and identified the phaE(Hm) and phaC(Hm) genes, probably encoding two subunits of a class III PHA synthase. These two genes were adjacent and directed by a single promoter located 26 bp upstream of the transcriptional start site and were constitutively expressed under both nutrient-rich and -limited conditions. Interestingly, PhaC(Hm) was revealed to be strongly bound with the PHB granules, but PhaE(Hm) seemed not to be. Introduction of either the phaE(Hm) or phaC(Hm) gene into Haloarcula hispanica, which harbors highly homologous phaEC(Hh) genes, could enhance the PHB synthesis in the recombinant strains, while coexpression of the both genes always generated the highest PHB yield. Significantly, knockout of the phaEC(Hh) genes in H. hispanica led to a complete loss of the PHA synthase activity. Complementation with phaEC(Hm) genes, but not a single one, restored the capability of PHB accumulation as well as the PHA synthase activity in this phaEC-deleted haloarchaeon. These results indicated that the phaEC genes are required for biosynthesis of PHB and might encode an active PHA synthase in the Haloarcula species.

From replication to cultivation: hot news from Haloarchaea

Haloarchaea have developed into model organisms that are utilized to study many biological processes. Examples are the mechanisms of chromosome maintenance, gene expression and its regulation, protein export and degradation, and motility and sensing. In addition to the analysis of model species like Halobacterium salinarum and Haloferax volcanii, natural communities have been characterized. Halophilic Archaea were found in low-salt environments and are thus more widespread than previously thought.