Physiology of halobacteriaceae

Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea

The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria-Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia, and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.

A comprehensive history of motility and Archaellation in Archaea

Each of the three Domains of life, Eukarya, Bacteria and Archaea, have swimming structures that were all originally called flagella, despite the fact that none were evolutionarily related to either of the other two. Surprisingly, this was true even in the two prokaryotic Domains of Bacteria and Archaea. Beginning in the 1980s, evidence gradually accumulated that convincingly demonstrated that the motility organelle in Archaea was unrelated to that found in Bacteria, but surprisingly shared significant similarities to type IV pili. This information culminated in the proposal, in 2012, that the 'archaeal flagellum' be assigned a new name, the archaellum. In this review, we provide a historical overview on archaella and motility research in Archaea, beginning with the first simple observations of motile extreme halophilic archaea a century ago up to state-of-the-art cryo-tomography of the archaellum motor complex and filament observed today. In addition to structural and biochemical data which revealed the archaellum to be a type IV pilus-like structure repurposed as a rotating nanomachine (Beeby et al. 2020), we also review the initial discoveries and subsequent advances using a wide variety of approaches to reveal: complex regulatory events that lead to the assembly of the archaellum filaments (archaellation); the roles of the various archaellum proteins; key post-translational modifications of the archaellum structural subunits; evolutionary relationships; functions of archaella other than motility and the biotechnological potential of this fascinating structure. The progress made in understanding the structure and assembly of the archaellum is highlighted by comparing early models to what is known today.

Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition

Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. In contrast, the last Haloarchaea common ancestor gained a large number of genes and expanded its aerobic respiration and salt/UV resistance gene repertoire. Our results suggest that complex and gradual patterns of gain and loss shaped the methanogen-to-halophile transition.

Metabolic capabilities and systems fluctuations in Haloarcula marismortui revealed by integrative genomics and proteomics analyses

The 1310 Haloarcula marismortui proteins identified from mid-log and late-log phase soluble and membrane proteomes were analyzed in metabolic and cellular process networks to predict the available systems and systems fluctuations upon environmental stresses. When the connected metabolic reactions with identified proteins were examined, the availability of a number of metabolic pathways and a highly connected amino acid metabolic network were revealed. Quantitative spectral count analyses suggested 300 or more proteins might have expression changes in late-log phase. Among these, integrative network analyses indicated approximately 106 were metabolic proteins that might have growth-phase dependent changes. Interestingly, a large proportion of proteins in affected biomodules had the same trend of changes in spectral counts. Disregard the magnitude of changes, we had successfully predicted and validated the expression changes of nine genes including the rimK, gltCP, rrnAC0132, and argC in lysine biosynthesis pathway which were downregulated in late-log phase. This study had not only revealed the expressed proteins but also the availability of biological systems in two growth phases, systems level changes in response to the stresses in late-log phase, cellular locations of identified proteins, and the likely regulated genes to facilitate further analyses in the postgenomic era.

Genetic transformation of a halophilic archaebacterium with a gas vesicle gene cluster restores its ability to float

The halophilic archaebacterium, Halobacterium halobium, and many other aquatic bacteria synthesize gas-filled vesicles for flotation. We recently identified a cluster of 13 genes (gvpMLKJIHGFEDACN) on a 200-kb H. halobium plasmid, pNRC100, involved in gas vesicle synthesis. We have cloned and reconstructed the gvp gene cluster on an H. halobium-E. coli shuttle plasmid. Transformation of H. halobium Vac- mutants lacking the entire gas vesicle gene region with the gvp gene cluster results in restoration of their ability to float. These results open the way toward further genetic analysis of gas vesicle gene functions and directed flotation of other microorganisms with potential biotechnological applications.

Structure and organization of the gas vesicle gene cluster on the Halobacterium halobium plasmid pNRC100

Halobacterium halobium strain NRC-1 contains intracellular gas-filled vesicles (GVs) that confer buoyancy to the cells. Cloning of the major GV protein (GvpA)-encoding gene, gvpA, and analysis of GV-deficient mutants (Vac-) of H. halobium led to the identification of a region of a 200-kb plasmid, pNRC100, important for GV synthesis. We report here the nucleotide sequence of an 8520-bp region which, including gvpA, contains twelve open reading frames (ORFs) that are organized into two divergent transcription units, gvpAC oriented rightward, and gvpD, E, F, G, H, I, J, K, L, and M located upstream from gvpAC and oriented leftward. Insertions into the gvpA promoter and gvpD and E resulted in the Vac- phenotype. The overall gene organization is highly compact with the end of one ORF overlapping with the beginning of the next in most cases. The gene cluster is bracketed by two ISH8 element copies in inverted orientation, an organization suggestive of a composite transposon. Comparison of predicted amino acid sequences showed homology between GvpA, and the gvpJ and gvpM putative gene products. The putative gvpC gene product contains eight copies of an imperfectly repeated sequence with similarity to repeats in a cyanobacterial GvpC plus a highly acidic C-terminal region not found in the cyanobacterial homologue.

Construction and use of halobacterial shuttle vectors and further studies on Haloferax DNA gyrase

We report here on advances made in the construction of plasmid shuttle vectors suitable for genetic manipulations in both Escherichia coli and halobacteria. Starting with a 20.4-kb construct, pMDS1, new vectors were engineered which were considerably smaller yet retained several alternative cloning sites. A restriction barrier observed when plasmid DNA was transferred into Haloferax volcanii cells was found to operate via adenine methylation, resulting in a 10(3) drop in transformation efficiency and the loss of most constructs by incorporation of the resistance marker into the chromosome. Passing shuttle vectors through E. coli dam mutants effectively avoided this barrier. Deletion analysis revealed that the gene(s) for autonomous replication of pHK2 (the plasmid endogenous to Haloferax strain Aa2.2 and used in the construction of pMDS1) was located within a 4.2-kb SmaI-KpnI fragment. Convenient restriction sites were identified near the termini of the novobiocin resistance determinant (gyrB), allowing the removal of flanking sequences (including gyrA). These deletions did not appear to significantly affect transformation efficiencies or the novobiocin resistance phenotype of halobacterial transformants. Northern blot hybridization with strand- and gene-specific probes identified a single gyrB-gyrA transcript of 4.7 kb. This is the first demonstration in prokaryotes that the two subunits of DNA gyrase may be cotranscribed.

Halobacterium halobium strains lysogenic for phage phi H contain a protein resembling coliphage repressors

DNA-binding proteins such as bacteriophage repressors belong to the helix-turn-helix family. Ionic interactions drive DNA binding, which means that repressors bind DNA most tightly at low salt concentrations. This raises the question of who gene expression might be regulated in obligate halophiles, which maintain internal salt concentrations of about 5 M. As a model system we have investigated the phage phi H, which infects the archaebacterium Halobacterium halobium. Previous genetic data and transcriptional mapping had suggested a region of the phage genome where a repressor might bind. A modified electrophoretic mobility shift assay was used to identify an activity, present only in lysogens, that specifically binds this region. Methylation interference and DNA sequencing were used to identify four similar binding sites, which are arranged so that two copies of a dimer might bind on one face of the DNA helix. Binding of a protein at these sites could block RNA polymerase from initiating a transcript found only during lytic growth. A nearby divergent promoter produces a lysogen-specific transcript, T6, which encodes a member of the helix-turn-helix family of DNA-binding proteins. By expressing the gene in Escherichia coli, we confirmed that T6 specifies the DNA binding activity detected biochemically. The data show that the basic DNA-binding motif of repressors can be adapted even for the unfavorable conditions of high salt concentration.

Transcriptional induction of purple membrane and gas vesicle synthesis in the archaebacterium Halobacterium halobium is blocked by a DNA gyrase inhibitor

We have investigated the expression of the bacteriorhodopsin gene (bop) and the gas vesicle protein gene (gvpA) in the extremely halophilic archaebacterium Halobacterium halobium, using primer-directed reverse transcription of RNA to quantify message levels. The level of gvpA gene transcript was found to increase about 5-fold from early to mid-logarithmic growth phase, while the level of bop gene transcript increased about 20-fold from mid-logarithmic to stationary phase. Transcriptional induction of both the gvpA and bop genes was significantly reduced by aeration and almost completely blocked by the DNA gyrase inhibitor novobiocin.

A rapid population method for action spectra applied to Halobacterium halobium

We have developed a simple and rapid technique for measuring the action spectra for phototaxis of populations of microorganisms and applied it to halobacteria. A microscope with a dark-field condenser was used to illuminate the cell suspension in a sealed chamber with light of wavelength greater than 750 nm; in this region of the spectrum, the halobacteria show no phototactic response. A 150-micron spot of light from a xenon arc lamp, whose wavelength and intensity can be varied, was projected through the objective lens into the center of the dark field. The objective lens imaged this measuring spot through a 780-nm cut-off filter on an aperture in front of a photomultiplier. The intensity of the scattered 750-nm light, and therefore the photomultiplier current, is proportional to the number of cells in the measuring spot. A third lamp provided background light of variable wavelength and intensity through the dark-field condenser. To minimize secondary effects due to large changes in cell density, we recorded the initial changes in the photomultiplier current over 1 min after the actinic light had been switched on. By plotting the rate of change against wavelength, we obtained action spectra after the proper corrections for changes in light intensity with wavelength were applied and saturation effects were avoided.

Sodium ion transport decarboxylases and other aspects of sodium ion cycling in bacteria

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Purification, reconstitution and polymorphic transition of halobacterial flagella

Flagellar filaments of Halobacterium halobium have been purified by dissociation and reconstitution. Three different protein bands (23,500, 26,500 and 31,500 apparent molecular weight) are seen on sodium dodecyl sulphate/polyacrylamide gels, thus confirming that all three proteins are intrinsic to the flagellar structure. We designate them as flagellin Fla I (23,500), Fla II (26,500) and Fla III (31,500). Polymorphic transitions from normal to a curly, a ring and a straight form are induced by different pH values and heat treatments.

Survival strategies of microorganisms in extreme saline environments

Halophilic representatives are found in all main lines of evolutionary descendence of microbes: in archaebacteria, Gram-negative and Gram-positive eubacteria, and also in eucaryotes. In principle all halophilic microorganisms have to adapt their surface and membrane structures to their highly ionic environments. Concerning their intracellular compartment two different strategies have been developed: Inorganic ions are largely excluded in some microorganisms while such ions are actively accumulated in others. In particular the second group of organisms has to adapt the whole metabolic machinery to the highly ionic conditions of several molar salts, whereas in the first group only the outer surface of the cytoplasmic membrane and the extracytoplasmic structures are in contact with high concentrations of inorgainic ions. In this latter group, a variety of organic solutes is accumulated in response to increases of the salinity of the environment.

Morphology, function and isolation of halobacterial flagella

Halobacterium halobium has right-handed helical flagella. During the logarithmic phase of growth, cells are predominantly monopolar, whereas in the stationary phase they are mostly bipolarly flagellated. The flagellar bundle consists of several filaments. Halobacteria swim forward by clockwise and backwards by counterclockwise rotation of their flagella. The flagellar bundle does not fly apart when the sense of rotation changes. In addition to the flagella attached to the cells, large amounts of loose flagella, which aggregate into thick super-flagella, can be observed at all phases of growth. During stationary phase, the production of these super-flagella, which are generally 10 to 20 times longer than the cell body, is significantly higher. Dissociation and association by high temperature and differential centrifugation allow the isolation of pure flagella. Three different protein bands, of 23,500, 26,500 and 31,500 apparent molecular weights, are seen on sodium dodecyl sulphate/polyacrylamide gels. Antibodies against halobacterial flagella were produced in chicken; these antibodies interact with the flagella even in 4 M-NaCl. Rotation of tethered cells demonstrates that Halobacteria move due to the rotation of the flagella.

Phototrophic growth of halobacteria and its use for isolation of photosynthetically-deficient mutants

Phototrophic growth conditions for halobacteria in complex and synthetic media have been established, demonstrating the photosynthetic capacity of this class of archaebacteria. Mutagenesis, 5-bromo-2'-deoxyuridine selection and screening techniques are described which are useful tools in the elucidation of the structure-function relationship of retinal proteins in halobacteria.

Anaerobic growth of halobacteria

An energy-transducing pathway in halobacteria is described. Arginine mediates substrate level phosphorylation and allows the cells to grow anaerobically. Bacteriorhodopsin plus light can function as an alternative energy source under these conditions, provided the cells contain the pigment when transferred to the anaerobic environment. Therefore the selection of mutants functionally defective in ATP synthase or bacteriorhodopsin becomes possible.

Enzyme activities in concentrated solutions of glycinebetaine and other solutes

The activities of a number of enzymes in concentrated solutions of glycinebetaine and other solutes have been studied. Glycinebetaine, in contrast to electrolytes such as NaCl, was found to be noninhibitory up to 500 mM. This is compatible with the postulated role of glycinebetaine in cytoplasmic osmoregulation. Partial protection against NaCl inhibition was afforded by glycinebetaine in some cases. More detailed studies on glycinebetaine -NaCl-enzyme interactions were carried out using malate dehydrogenase (decarboxylating) from Hordeum vulgare.