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The archaellum (: archaella; formerly archaeal flagellum) is a unique structure on the cell surface of many archaea that allows for swimming motility. The archaellum consists of a rigid helix filament that is attached to the cell membrane by a molecular motor. This molecular motorcomposed of cytosolic, membrane, and pseudo-periplasmic proteinsis responsible for the assembly of the filament and, once assembled, for its rotation. The rotation of the filament propels archaeal cells in liquid medium, in a manner similar to the propeller of a boat. The bacterial analog of the archaellum is the flagellum, which is also responsible for their swimming motility and can also be compared to a rotating corkscrew. Although the movement of archaella and flagella is sometimes described as "whip-like", this is incorrect, as only Cilium from Eukaryotes move in this manner. Indeed, even "" (word derived from Latin meaning "whip") is a misnomer, as bacterial flagella also work as propeller-like structures.
Early studies on "archaeal flagella" identified several differences between archaella and flagella, although those differences were dismissed as a possible adaptation of archaella to the extreme ecological environments where archaea were at the time known to inhabit. When the first genomes of archaeal organisms were sequenced, it became obvious that archaea do not code for any of the proteins that are part of the flagellum, thus establishing that the motility system of archaea is fundamentally different from that of bacteria. In order to highlight the difference between these two organelles, the name archaellum was proposed in 2012 following studies that showed it to be evolutionarily and structurally different from the bacterial flagella and eukaryotic cilia.
Archaella are evolutionarily and structurally related to type IV filament systems (TFF). The TFF family seems to have originated in the last universal common ancestor, from where it diversified into archaella, Type IV Pili, Type II Secretion Systems, and the Tad pili.
During the 2010s, studies on the gene products of the arl operon allowed to establish the function of many of the "accessory" proteins of the archaellum, that is, proteins that compose the motor of this organelle. During this time, it was possible to define a minimal set of components necessary for a mature and functional archaellum: the archaellin (either a single type or several), the prepilin peptidase which cleaves the signal peptide off from the pre-archaellin, and the proteins ArlC/D/E/F/G/H/I/J. In the phyla Thermoproteota, the genes for the proteins ArlC/D/E are not found; instead, archaellated members of this phylum code for ArlX, thought to have a similar function to ArlC/D/E. Based on all the evidence that had accumulated on the unique nature of archaella, in 2012 Ken Jarrell and Sonja-Verena Albers proposed that this organelle should not be called "archaeal flagella", but rather "archaella". Despite some initial criticism, the name is now widely accepted in the scientific community, and as of 6 June 2021, a PubMed search for the terms "archaella" or "archaellum" retrieves more results in recent years than the terms "archaeal flagella" or "archaeal flagellum".
Research of archaella still continues, both related to the basic biology of this organelle, to its ecological roles, and even potential biotechnological applications. Some of the questions that remain open is: how is the expression of the arl operon regulated, how does the archaellum motor complex look like, and what is the role of some of the accessory components of the archaellum.
The archaellum operon used to be historically known as fla (from "flagellum"), but in order to avoid confusion with the bacterial flagellum and to be consistent with the remaining nomenclature (archaellum, archaellins), it has been recently proposed to be renamed to arl ( archae llin-related genes). Consequently, the name of the genes is also different (e.g., flaJ is now arlJ). Therefore, in the specialised literature, both nomenclatures can be found, with the arl nomenclature being increasingly more used since 2018.
Genetic analysis in different archaea revealed that each of these components is essential for assembly of the archaellum. The prepilin peptidase (called PibD in crenarchaeota and ArlK (formerly FlaK) in euryarchaeota) is essential for the maturation of the archaellins and is generally encoded elsewhere on the chromosome.
Functional characterization has been performed for ArlI, a Type II/IV secretion system ATPase super-family member and PibD/ArlK. ArlI forms a hexamer which hydrolyses ATP and most likely generates energy to assemble the archaellum and to power its rotation. PibD cleaves the N-terminus of the archaellins before they can be assembled. ArlH () has a RecA-like fold and inactive ATPase domains. This protein is a homolog of KaiC, a protein central for the regulation of the circadian rhythm in cyanobacteria. However, this function is not thought to be conserved; rather, ArlH also exhibits auto-phosphorylation which seems to modulate its interaction with the ATPase ArlI. Despite arlH deletion resulting in loss of motiliy, rendering this protein essential for archaellation, its role in the archaellum motor remains unknown. ArlI and ArlH interact and, possibly together with the predicted membrane-protein ArlJ, form the central motor complex. In Crenarchaeota, this motor complex might be surrounded by a scaffold formed by a ring composed of ArlX. In Euryarchaeotes, cryo-electron tomograms suggest that ArlCDE form a structure underneath the motor, possibly in the order (from top to bottom) ArlJ-ArlI-ArlH-ArlCDE. ArlF and ArlG possibly form the stator of this complex, providing a static surface against which the rotor can move, and also anchoring the motor to the cell envelope, thus preventing the membrane from rupturing due to archaellar rotation. The structure of ArlCDE is unknown, but this complex (or variations thereof) have been shown to link the chemotaxis machinery and the archaellum in Haloferax volcanii.
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