Haloferax volcanii cells lacking the flagellin FlgA2 are hypermotile

TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii

Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme-coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum, TrmB-dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name trmB suppressor, or TbsP (a.k.a. "tablespoon"). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild-type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose-dependent transcription of gapII, which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii.

The Fate of Duplicated Enzymes in Prokaryotes: The Case of Isomerases

The isomerases are a unique enzymatic class of enzymes that carry out a great diversity of chemical reactions at the intramolecular level. This class comprises about 300 members, most of which are involved in carbohydrate and terpenoid/polyketide metabolism. Along with oxidoreductases and translocases, isomerases are one of the classes with the highest ratio of paralogous enzymes. Due to its relatively small number of members, it is plausible to explore it in greater detail to identify specific cases of gene duplication. Here, we present an analysis at the level of individual isomerases and identify different members that seem to be involved in duplication events in prokaryotes. As was suggested in a previous study, there is no homogeneous distribution of paralogs, but rather they accumulate into a few subcategories, some of which differ between Archaea and Bacteria. As expected, the metabolic processes with more paralogous isomerases have to do with carbohydrate metabolism but also with RNA modification (a particular case involving an rRNA-modifying isomerase is thoroughly discussed and analyzed in detail). Overall, our findings suggest that the most common fate for paralogous enzymes is the retention of the original enzymatic function, either associated with a dosage effect or with differential expression in response to changing environments, followed by subfunctionalization and, to a much lesser degree, neofunctionalization, which is consistent with what has been reported elsewhere.

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.

Mutations Affecting HVO_1357 or HVO_2248 Cause Hypermotility in Haloferax volcanii, Suggesting Roles in Motility Regulation

Motility regulation plays a key role in prokaryotic responses to environmental stimuli. Here, we used a motility screen and selection to isolate hypermotile Haloferax volcanii mutants from a transposon insertion library. Whole genome sequencing revealed that hypermotile mutants were predominantly affected in two genes that encode HVO_1357 and HVO_2248. Alterations of these genes comprised not only transposon insertions but also secondary genome alterations. HVO_1357 contains a domain that was previously identified in the regulation of bacteriorhodopsin transcription, as well as other domains frequently found in two-component regulatory systems. The genes adjacent to hvo_1357 encode a sensor box histidine kinase and a response regulator, key players of a two-component regulatory system. None of the homologues of HVO_2248 have been characterized, nor does it contain any of the assigned InterPro domains. However, in a significant number of Haloferax species, the adjacent gene codes for a chemotaxis receptor/transducer. Our results provide a foundation for characterizing the root causes underlying Hfx. volcanii hypermotility.

Haloferax volcanii Immersed Liquid Biofilms Develop Independently of Known Biofilm Machineries and Exhibit Rapid Honeycomb Pattern Formation

The ability to form biofilms is shared by many microorganisms, including archaea. Cells in a biofilm are encased in extracellular polymeric substances that typically include polysaccharides, proteins, and extracellular DNA, conferring protection while providing a structure that allows for optimal nutrient flow. In many bacteria, flagella and evolutionarily conserved type IV pili are required for the formation of biofilms on solid surfaces or floating at the air-liquid interface of liquid media. Similarly, in many archaea it has been demonstrated that type IV pili and, in a subset of these species, archaella are required for biofilm formation on solid surfaces. Additionally, in the model archaeon Haloferax volcanii, chemotaxis and AglB-dependent glycosylation play important roles in this process. H. volcanii also forms immersed biofilms in liquid cultures poured into petri dishes. This study reveals that mutants of this haloarchaeon that interfere with the biosynthesis of type IV pili or archaella, as well as a chemotaxis-targeting transposon and aglB deletion mutants, lack obvious defects in biofilms formed in liquid cultures. Strikingly, we have observed that these liquid-based biofilms are capable of rearrangement into honeycomb-like patterns that rapidly form upon removal of the petri dish lid, a phenomenon that is not dependent on changes in light or oxygen concentration but can be induced by controlled reduction of humidity. Taken together, this study demonstrates that H. volcanii requires novel, unidentified strategies for immersed liquid biofilm formation and also exhibits rapid structural rearrangements.IMPORTANCE This first molecular biological study of archaeal immersed liquid biofilms advances our basic biological understanding of the model archaeon Haloferax volcanii Data gleaned from this study also provide an invaluable foundation for future studies to uncover components required for immersed liquid biofilms in this haloarchaeon and also potentially for liquid biofilm formation in general, which is poorly understood compared to the formation of biofilms on surfaces. Moreover, this first description of rapid honeycomb pattern formation is likely to yield novel insights into the underlying structural architecture of extracellular polymeric substances and cells within immersed liquid biofilms.

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii, we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.

Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum

Halophilic archaea from the genus Halorubrum possess two extraordinarily diverged archaellin genes, flaB1 and flaB2. To clarify roles for each archaellin, we compared two natural Halorubrum lacusprofundi strains: One of them contains both archaellin genes, and the other has the flaB2 gene only. Both strains synthesize functional archaella; however, the strain, where both archaellins are present, is more motile. In addition, we expressed these archaellins in a Haloferax volcanii strain from which the endogenous archaellin genes were deleted. Three Hfx. volcanii strains expressing Hrr. lacusprofundi archaellins produced functional filaments consisting of only one (FlaB1 or FlaB2) or both (FlaB1/FlaB2) archaellins. All three strains were motile, although there were profound differences in the efficiency of motility. Both native and recombinant FlaB1/FlaB2 filaments have greater thermal stability and resistance to low salinity stress than single‐component filaments. Functional supercoiled Hrr. lacusprofundi archaella can be composed of either single archaellin: FlaB2 or FlaB1; however, the two divergent archaellin subunits provide additional stabilization to the archaellum structure and thus adaptation to a wider range of external conditions. Comparative genomic analysis suggests that the described combination of divergent archaellins is not restricted to Hrr. lacusprofundi, but is occurring also in organisms from other haloarchaeal genera.

Haloferax volcanii for biotechnology applications: challenges, current state and perspectives

Haloferax volcanii is an obligate halophilic archaeon with its origin in the Dead Sea. Simple laboratory culture conditions and a wide range of genetic tools have made it a model organism for studying haloarchaeal cell biology. Halophilic enzymes of potential interest to biotechnology have opened up the application of this organism in biocatalysis, bioremediation, nanobiotechnology, bioplastics and the biofuel industry. Functionally active halophilic proteins can be easily expressed in a halophilic environment, and an extensive genetic toolkit with options for regulated protein overexpression has allowed the purification of biotechnologically important enzymes from different halophiles in H. volcanii. However, corrosion mediated damage caused to stainless-steel bioreactors by high salt concentrations and a tendency to form biofilms when cultured in high volume are some of the challenges of applying H. volcanii in biotechnology. The ability to employ expressed active proteins in immobilized cells within a porous biocompatible matrix offers new avenues for exploiting H. volcanii in biotechnology. This review critically evaluates the various application potentials, challenges and toolkits available for using this extreme halophilic organism in biotechnology.

Limited Cross-Complementation Between Haloferax volcanii PilB1-C1 and PilB3-C3 Paralogs

Type IV pili are evolutionarily conserved cell surface filaments that promote surface adhesion and cell aggregation providing bacteria and archaea protection from a variety of stress conditions. In fact, prokaryotic genomes frequently contain several copies of the core biosynthesis genes, pilB and pilC, encoding an ATPase and membrane anchor, respectively. Recent phylogenetic analyses suggest that in haloarchaea, a subset of pilB-C paralogs, such as the Haloferax volcanii pilB1-C1, were gained via horizontal transfer from the crenarchaea, while the co-regulated type IV pilus subunits, the pilins, evolved by duplication, followed by diversification of the ancestral euryarchaeal pilins. Here, we report the identification of an H. volcanii pilB1 transposon mutant that exhibits an adhesion defect in defined media. A similar defect observed in an H. volcanii ∆pilB1-C1 strain can be rescued by expressing pilB1-C1 in trans. However, these proteins cannot rescue the severe adhesion defect of a previously reported ∆pilB3-C3 strain. Conversely, pilB3-C3, which are not predicted to have been laterally transferred, expressed in trans can rescue the adhesion defect of a ∆pilB1-C1 strain. This cross-complementation supports the proposed hybrid origin of the operon containing pilB1-C1 and shows that at least certain euryarchaeal PilB paralogs can work with different pilin sets. Efficient recognition of the euryarchaeal pilins by the crenarchaeal PilB1-C1 may have required some degree of pilin modification, but perhaps the modifications were minor enough that PilB3 recognition of these pilins was not precluded, resulting in modular evolution and an extensive combinatorial diversity that allows for adaptation to a variety of stress conditions and attachment to varied surfaces.

Salt-dependent regulation of archaellins in Haloarcula marismortui

Microorganisms require a motility structure to move towards optimal growth conditions. The motility structure from archaea, the archaellum, is fundamentally different from its bacterial counterpart, the flagellum, and is assembled in a similar fashion as type IV pili. The archaellum filament consists of thousands of copies of N‐terminally processed archaellin proteins. Several archaea, such as the euryarchaeon Haloarcula marismortui, encode multiple archaellins. Two archaellins of H. marismortui display differential stability under various ionic strengths. This suggests that these proteins behave as ecoparalogs and perform the same function under different environmental conditions. Here, we explored this intriguing system to study the differential regulation of these ecoparalogous archaellins by monitoring their transcription, translation, and assembly into filaments. The salt concentration of the growth medium induced differential expression of the two archaellins. In addition, this analysis indicated that archaellation in H. marismortui is majorly regulated on the level of secretion, by a still unknown mechanism. These findings indicate that in archaea, multiple encoded archaellins are not completely redundant, but in fact can display subtle functional differences, which enable cells to cope with varying environmental conditions.

Cross-kymography analysis to simultaneously quantify the function and morphology of the archaellum

In many microorganisms helical structures are important for motility, e.g., bacterial flagella and kink propagation in Spiroplasma eriocheiris. Motile archaea also form a helical-shaped filament called the ‘archaellum’ that is functionally equivalent to the bacterial flagellum, but structurally resembles type IV pili. The archaellum motor consists of 6–8 proteins called fla accessory genes, and the filament assembly is driven by ATP hydrolysis at catalytic sites in FlaI. Remarkably, previous research using a dark-field microscopy showed that right-handed filaments propelled archaeal cells forwards or backwards by clockwise or counterclockwise rotation, respectively. However, the shape and rotational rate of the archaellum during swimming remained unclear, due to the low signal and lack of temporal resolution. Additionally, the structure and the motor properties of the archaellum and bacterial flagellum have not been precisely determined during swimming because they move freely in three-dimensional space. Recently, we developed an advanced method called “cross-kymography analysis”, which enables us to be a long-term observation and simultaneously quantify the function and morphology of helical structures using a total internal reflection fluorescence microscope. In this review, we introduce the basic idea of this analysis, and summarize the latest information in structural and functional characterization of the archaellum motor.

The Archaellum: An Update on the Unique Archaeal Motility Structure

Each of the three domains of life exhibits a unique motility structure: while Bacteria use flagella, Eukarya employ cilia, and Archaea swim using archaella. Since the new name for the archaeal motility structure was proposed, in 2012, a significant amount of new data on the regulation of transcription of archaella operons, the structure and function of archaellum subunits, their interactions, and cryo-EM data on in situ archaellum complexes in whole cells have been obtained. These data support the notion that the archaellum is evolutionary and structurally unrelated to the flagellum, but instead is related to archaeal and bacterial type IV pili and emphasize that it is a motility structure unique to the Archaea.

Structure and function of the archaeal response regulator CheY

Motility is a central feature of many microorganisms and provides an efficient strategy to respond to environmental changes. Bacteria and archaea have developed fundamentally different rotary motors enabling their motility, termed flagellum and archaellum, respectively. Bacterial motility along chemical gradients, called chemotaxis, critically relies on the response regulator CheY, which, when phosphorylated, inverses the rotational direction of the flagellum via a switch complex at the base of the motor. The structural difference between archaellum and flagellum and the presence of functional CheY in archaea raises the question of how the CheY protein changed to allow communication with the archaeal motility machinery. Here we show that archaeal CheY shares the overall structure and mechanism of magnesium-dependent phosphorylation with its bacterial counterpart. However, bacterial and archaeal CheY differ in the electrostatic potential of the helix α4. The helix α4 is important in bacteria for interaction with the flagellar switch complex, a structure that is absent in archaea. We demonstrated that phosphorylation-dependent activation, and conserved residues in the archaeal CheY helix α4, are important for interaction with the archaeal-specific adaptor protein CheF. This forms a bridge between the chemotaxis system and the archaeal motility machinery. Conclusively, archaeal CheY proteins conserved the central mechanistic features between bacteria and archaea, but differ in the helix α4 to allow binding to an archaellum-specific interaction partner.

Versatile cell surface structures of archaea

Archaea are ubiquitously present in nature and colonize environments with broadly varying growth conditions. Several surface appendages support their colonization of new habitats. A hallmark of archaea seems to be the high abundance of type IV pili (T4P). However, some unique non T4 filaments are present in a number of archaeal species. Archaeal surface structures can mediate different processes such as cellular surface adhesion, DNA exchange, motility and biofilm formation and represent an initial attachment site for infecting viruses. In addition to the functionally characterized archaeal T4P, archaeal genomes encode a large number of T4P components that might form yet undiscovered surface structures with novel functions. In this review, we summarize recent advancement in structural and functional characterizations of known archaeal surface structures and highlight the diverse processes in which they play a role.

Screening of a Haloferax volcanii Transposon Library Reveals Novel Motility and Adhesion Mutants

Archaea, like bacteria, use type IV pili to facilitate surface adhesion. Moreover, archaeal flagella—structures required for motility—share a common ancestry with type IV pili. While the characterization of archaeal homologs of bacterial type IV pilus biosynthesis components has revealed important aspects of flagellum and pilus biosynthesis and the mechanisms regulating motility and adhesion in archaea, many questions remain. Therefore, we screened a Haloferax volcanii transposon insertion library for motility mutants using motility plates and adhesion mutants, using an adapted air–liquid interface assay. Here, we identify 20 genes, previously unknown to affect motility or adhesion. These genes include potential novel regulatory genes that will help to unravel the mechanisms underpinning these processes. Both screens also identified distinct insertions within the genomic region lying between two chemotaxis genes, suggesting that chemotaxis not only plays a role in archaeal motility, but also in adhesion. Studying these genes, as well as hypothetical genes hvo_2512 and hvo_2876—also critical for both motility and adhesion—will likely elucidate how these two systems interact. Furthermore, this study underscores the usefulness of the transposon library to screen other archaeal cellular processes for specific phenotypic defects.

Identification of Haloferax volcanii Pilin N-Glycans with Diverse Roles in Pilus Biosynthesis, Adhesion, and Microcolony Formation

N-Glycosylation is a post-translational modification common to all three domains of life. In many archaea, the oligosacharyltransferase (AglB)-dependent N-glycosylation of flagellins is required for flagella assembly. However, whether N-glycosylation is required for the assembly and/or function of the structurally related archaeal type IV pili is unknown. Here, we show that of six Haloferax volcanii adhesion pilins, PilA1 and PilA2, the most abundant pilins in pili of wild-type and ΔaglB strains, are modified under planktonic conditions in an AglB-dependent manner by the same pentasaccharide detected on H. volcanii flagellins. However, unlike wild-type cells, which have surfaces decorated with discrete pili and form a dispersed layer of cells on a plastic surface, ΔaglB cells have thick pili bundles and form microcolonies. Moreover, expressing PilA1, PilA2, or PilA6 in ΔpilA[1-6]ΔaglB stimulates microcolony formation compared with their expression in ΔpilA[1-6]. Conversely, expressing PilA3 or PilA4 in ΔpilA[1-6] cells results in strong surface adhesion, but not microcolony formation, and neither pilin stimulates surface adhesion in ΔpilA[1-6]ΔaglB cells. Although PilA4 assembles into pili in the ΔpilA[1-6]ΔaglB cells, these pili are, unlike wild-type pili, curled, perhaps rendering them non-functional. To our knowledge, this is the first demonstration of a differential effect of glycosylation on pilus assembly and function of paralogous pilins. The growth of wild-type cells in low salt media, a condition that decreases AglB glycosylation, also stimulates microcolony formation and inhibits motility, supporting our hypothesis that N-glycosylation plays an important role in regulating the transition between planktonic to sessile cell states as a response to stress.

Production of halophilic proteins using Haloferax volcanii H1895 in a stirred-tank bioreactor

The success of biotechnological processes is based on the availability of efficient and highly specific biocatalysts, which can satisfy industrial demands. Extreme and remote environments like the deep brine pools of the Red Sea represent highly interesting habitats for the discovery of novel halophilic and thermophilic enzymes. Haloferax volcanii constitutes a suitable expression system for halophilic enzymes obtained from such brine pools. We developed a batch process for the cultivation of H. volcanii H1895 in controlled stirred-tank bioreactors utilising knockouts of components of the flagella assembly system. The standard medium Hv-YPC was supplemented to reach a higher cell density. Without protein expression, cell dry weight reaches 10 g L(-1). Two halophilic alcohol dehydrogenases were expressed under the control of the tryptophanase promoter p.tna with 16.8 and 3.2 mg gCDW (-1), respectively, at a maximum cell dry weight of 6.5 g L(-1). Protein expression was induced by the addition of L-tryptophan. Investigation of various expression strategies leads to an optimised two-step induction protocol introducing 6 mM L-tryptophan at an OD650 of 0.4 followed by incubation for 16 h and a second induction step with 3 mM L-tryptophan followed by a final incubation time of 4 h. Compared with the uncontrolled shaker-flask cultivations used until date, dry cell mass concentrations were improved by a factor of more than 5 and cell-specific enzyme activities showed an up to 28-fold increased yield of the heterologous proteins.

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.

Archaeal membrane-associated proteases: insights on Haloferax volcanii and other haloarchaea

The function of membrane proteases range from general house-keeping to regulation of cellular processes. Although the biological role of these enzymes in archaea is poorly understood, some of them are implicated in the biogenesis of the archaeal cell envelope and surface structures. The membrane-bound ATP-dependent Lon protease is essential for cell viability and affects membrane carotenoid content in Haloferax volcanii. At least two different proteases are needed in this archaeon to accomplish the posttranslational modifications of the S-layer glycoprotein. The rhomboid protease RhoII is involved in the N-glycosylation of the S-layer protein with a sulfoquinovose-containing oligosaccharide while archaeosortase ArtA mediates the proteolytic processing coupled-lipid modification of this glycoprotein facilitating its attachment to the archaeal cell surface. Interestingly, two different signal peptidase I homologs exist in H. volcanii, Sec11a and Sec11b, which likely play distinct physiological roles. Type IV prepilin peptidase PibD processes flagellin/pilin precursors, being essential for the biogenesis and function of the archaellum and other cell surface structures in H. volcanii.

The archaellum: how Archaea swim

Recent studies on archaeal motility have shown that the archaeal motility structure is unique in several aspects. Although it fulfills the same swimming function as the bacterial flagellum, it is evolutionarily and structurally related to the type IV pilus. This was the basis for the recent proposal to term the archaeal motility structure the "archaellum." This review illustrates the key findings that led to the realization that the archaellum was a novel motility structure and presents the current knowledge about the structural composition, mechanism of assembly and regulation, and the posttranslational modifications of archaella.

Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer

BACKGROUND

Archaea share a similar microbial lifestyle with bacteria, and not surprisingly then, also exist within matrix-enclosed communities known as biofilms. Advances in biofilm biology have been made over decades for model bacterial species, and include characterizations of social behaviors and cellular differentiation during biofilm development. Like bacteria, archaea impact ecological and biogeochemical systems. However, the biology of archaeal biofilms is only now being explored. Here, we investigated the development, composition and dynamics of biofilms formed by the haloarchaeon Haloferax volcanii DS2.

RESULTS

Biofilms were cultured in static liquid and visualized with fluorescent cell membrane dyes and by engineering cells to express green fluorescent protein (GFP). Analysis by confocal scanning laser microscopy showed that H. volcanii cells formed microcolonies within 24 h, which developed into larger clusters by 48 h and matured into flake-like towers often greater than 100 μm in height after 7 days. To visualize the extracellular matrix, biofilms formed by GFP-expressing cells were stained with concanavalin A, DAPI, Congo red and thioflavin T. Stains colocalized with larger cellular structures and indicated that the extracellular matrix may contain a combination of polysaccharides, extracellular DNA and amyloid protein. Following a switch to biofilm growth conditions, a sub-population of cells differentiated into chains of long rods sometimes exceeding 25 μm in length, compared to their planktonic disk-shaped morphology. Time-lapse photography of static liquid biofilms also revealed wave-like social motility. Finally, we quantified gene exchange between biofilm cells, and found that it was equivalent to the mating frequency of a classic filter-based experimental method.

CONCLUSIONS

The developmental processes, functional properties and dynamics of H. volcanii biofilms provide insight on how haloarchaeal species might persist, interact and exchange DNA in natural communities. H. volcanii demonstrates some biofilm phenotypes similar to bacterial biofilms, but also has interesting phenotypes that may be unique to this organism or to this class of organisms, including changes in cellular morphology and an unusual form of social motility. Because H. volcanii has one of the most advanced genetic systems for any archaeon, the phenotypes reported here may promote the study of genetic and developmental processes in archaeal biofilms.

The temperature gradient-forming device, an accessory unit for normal light microscopes to study the biology of hyperthermophilic microorganisms

To date, the behavior of hyperthermophilic microorganisms in their biotope has been studied only to a limited degree; this is especially true for motility. One reason for this lack of knowledge is the requirement for high-temperature microscopy-combined, in most cases, with the need for observations under strictly anaerobic conditions-for such studies. We have developed a custom-made, low-budget device that, for the first time, allows analyses in temperature gradients up to 40°C over a distance of just 2 cm (a biotope-relevant distance) with heating rates up to ∼5°C/s. Our temperature gradient-forming device can convert any upright light microscope into one that works at temperatures as high as 110°C. Data obtained by use of this apparatus show how very well hyperthermophiles are adapted to their biotope: they can react within seconds to elevated temperatures by starting motility-even after 9 months of storage in the cold. Using the temperature gradient-forming device, we determined the temperature ranges for swimming, and the swimming speeds, of 15 selected species of the genus Thermococcus within a few months, related these findings to the presence of cell surface appendages, and obtained the first evidence for thermotaxis in Archaea.

A conserved type IV pilin signal peptide H-domain is critical for the post-translational regulation of flagella-dependent motility

In many bacteria and archaea, type IV pili facilitate surface adhesion, the initial step in biofilm formation. Haloferax volcanii has a specific set of adhesion pilins (PilA1-A6) that, although diverse, contain an absolutely conserved signal peptide hydrophobic (H) domain. Data presented here demonstrate that these pilins (PilA1-A6) also play an important role in regulating flagella-dependent motility, which allows cells to rapidly transition between planktonic and sessile states. Cells lacking adhesion pilins exhibit a severe motility defect, however, expression of any one of the adhesion pilins in trans can rescue the motility and adhesion. Conversely, while deleting pilB3-C3, genes required for PilA pilus biosynthesis, results in cells lacking pili and having an adhesion defect, it does not affect motility, indicating that motility regulation requires the presence of pilins, but not assembled pili. Mutagenesis studies revealed that the pilin-dependent motility regulatory mechanism does not require the diverse C-terminal region of the PilA pilins but specifically involves the conserved H-domain. This novel post-translational regulatory mechanism, which employs components that promote biofilm formation to inhibit motility, can provide a rapid response to changing environmental conditions. A model for this regulatory mechanism, which may also be present in other prokaryotes, is discussed.

Haloarcula marismortui archaellin genes as ecoparalogs

The genome of haloarchaeon Haloarcula marismortui contains two archaellin genes-flaA2 and flaB. Earlier we isolated and characterized two H. marismortui strains in that archaella consisting of FlaA2 archaellin (with a minor FlaB fraction) or of FlaB only. Both the FlaA2 and FlaB strains were motile and produced functional helical archaella. Thus, it may seem that the FlaA2 archaellin is redundant. In this study we investigated the biological roles of archaellin redundancy and demonstrated that FlaA2 archaellin is better adapted to more severe conditions of high temperature/low salinity, while FlaB has an advantage with increasing salinity. We used the thermodynamic data and bioinformatics sequence analysis to demonstrate that archaella formed by FlaA2 are more stable than those formed by FlaB. Our combined data indicate that the monomer FlaA2 archaellin is more flexible and leads to more compact and stable formation of filamentous structures. The difference in response to environmental stress indicates that FlaA2 and FlaB replace each other under different environmental conditions and can be considered as ecoparalogs.