An archaellum filament composed of two alternating subunits

Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. In many species, several archaellin homologs are encoded in the same operon; however, previous structural studies indicated that archaellum filaments mainly consist of only one protein species. Here, we use electron cryo-microscopy to elucidate the structure of the archaellum from Methanocaldococcus villosus at 3.08 Å resolution. The filament is composed of two alternating archaellins, suggesting that the architecture and assembly of archaella is more complex than previously thought. Moreover, we identify structural elements that may contribute to the filament’s flexibility.

The archaellum is a molecular machine used by archaea to swim, consisting of an intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. Here, the authors use electron cryo-microscopy to elucidate the structure of an archaellum, and find that the filament is composed of two alternating archaellins.

Identification of a novel N-linked glycan on the archaellins and S-layer protein of the thermophilic methanogen, Methanothermococcus thermolithotrophicus

Motility in archaea is facilitated by a unique structure termed the archaellum. N-Glycosylation of the major structural proteins (archaellins) is important for their subsequent incorporation into the archaellum filament. The identity of some of these N-glycans has been determined, but archaea exhibit extensive variation in their glycans, meaning that further investigations can shed light not only on the specific details of archaellin structure and function, but also on archaeal glycobiology in general. Here we describe the structural characterization of the N-linked glycan modifications on the archaellins and S-layer protein of Methanothermococcus thermolithotrophicus, a methanogen that grows optimally at 65 °C. SDS-PAGE and MS analysis revealed that the sheared archaella are composed principally of two of the four predicted archaellins, FlaB1 and FlaB3, which are modified with a branched, heptameric glycan at all N-linked sequons except for the site closest to the N termini of both proteins. NMR analysis of the purified glycan determined the structure to be α-d-glycero-d-manno-Hep3OMe6OMe-(1-3)-[α-GalNAcA3OMe-(1-2)-]-β-Man-(1-4)-[β-GalA3OMe4OAc6CMe-(1-4)-α-GalA-(1-2)-]-α-GalAN-(1-3)-β-GalNAc-Asn. A detailed investigation by hydrophilic interaction liquid ion chromatography-MS discovered the presence of several, less abundant glycan variants, related to but distinct from the main heptameric glycan. In addition, we confirmed that the S-layer protein is modified with the same heptameric glycan, suggesting a common N-glycosylation pathway. The M. thermolithotrophicus archaellin N-linked glycan is larger and more complex than those previously identified on the archaellins of related mesophilic methanogens, Methanococcus voltae and Methanococcus maripaludis This could indicate that the nature of the glycan modification may have a role to play in maintaining stability at elevated temperatures.

Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia

Echoing the repeated convergent evolution of flight and vision in large eukaryotes, propulsive swimming motility has evolved independently in microbes in each of the three domains of life. Filamentous appendages – archaella in Archaea, flagella in Bacteria and cilia in Eukaryotes – wave, whip or rotate to propel microbes, overcoming diffusion and enabling colonization of new environments. The implementations of the three propulsive nanomachines are distinct, however: archaella and flagella rotate, while cilia beat or wave; flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force. These underlying differences reflect the tinkering required to evolve a molecular machine, in which pre-existing machines in the appropriate contexts were iteratively co-opted for new functions and whose origins are reflected in their resultant mechanisms. Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure. Here, we review the structure, assembly, mechanism and homologies of the three distinct solutions as a foundation to better understand how propulsive nanomachines evolved three times independently and to highlight principles of molecular evolution.

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.

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.

A way to identify archaellins in Halobacterium salinarum archaella by FLAG-tagging

In the current study, haloarchaea Halobacterium salinarum cells were transformed individually with each of the modified archaellin genes (flaA1, flaA2 and flaB2) containing an oligonucleotide insert encoding the FLAG peptide (DYKDDDDK). The insertion site was selected to expose the FLAG peptide on the archaella filament surface. Three types of transformed cells synthesizing archaella, containing A1, A2, or B2 archaellin modified with FLAG peptide were obtained. Electron microscopy of archaella has demonstrated that in each case the FLAG peptide is available for the specific antibody binding. It was shown for the first time that the B2 archaellin, like archaellins A1 and A2, is found along the whole filament length.

S-layer glycoproteins and flagellins: reporters of archaeal posttranslational modifications

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, Haloferax volcanii, Methanococcus voltae and Methanococcus maripaludis, 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 Hfx. volcanii or the Methanococcus 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.

Shaping the archaeal cell envelope

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.

The surprisingly diverse ways that prokaryotes move

Prokaryotic cells move through liquids or over moist surfaces by swimming, swarming, gliding, twitching or floating. An impressive diversity of motility mechanisms has evolved in prokaryotes. Movement can involve surface appendages, such as flagella that spin, pili that pull and Mycoplasma 'legs' that walk. Internal structures, such as the cytoskeleton and gas vesicles, are involved in some types of motility, whereas the mechanisms of some other types of movement remain mysterious. Regardless of the type of motility machinery that is employed, most motile microorganisms use complex sensory systems to control their movements in response to stimuli, which allows them to migrate to optimal environments.