Archaeal flagella – Its Structure and Mechanism of Rotation

Overview of archeal flagella

Archaeal flagella, or archaella, have been studied in detail in only a few model archaea. They are superficially similar to their bacterial counterparts, but important differences have been identified. Archaella are thinner than bacterial flagella (10 to 14 nm rather than 18 to 22 nm) and some are composed of more than one type of protein subunit. The filament is not hollow. Assembly of the archaellum also differs from bacterial flagellum assembly

History of archaea 

In the 1970s, Carl Woese made significant contributions to the field of biology by utilizing sequence data from small subunit ribosomal ribonucleic acid (RNA) to classify all life forms. His work led to the establishment of the Archaea as a distinct domain of life, separate from both Bacteria and Eukarya (Woese and Fox, 1977). 

Archaea represent a prokaryotic lineage that has evolved independently from Bacteria and Eukarya, exhibiting unique characteristics exclusive to this domain. 

In 1996, Flagellation is a prevalent trait observed across all major subgroupings of the Archaea. This widespread occurrence underscores the significance of flagellar motility within this domain. However, it is important to note that the majority of our current understanding regarding the function, structure, and assembly of the archaeal flagellum stems from research conducted on the genera Methanococcus and Halobacterium.

Through extensive studies on Methanococcus and Halobacterium, researchers have made significant strides in unraveling the complexities of the archaeal flagellum. These investigations have shed light on the unique properties and functions of this motility apparatus, providing valuable insights into the biology of Archaea as a whole.

Structural Components of Archaeal Flagella 

  • Flagellar filament: The prominent part of archaeal flagella, exhibits a whip-like structure that enables movement. Composed of unique proteins, it contributes to the motility and function of the flagellum.
  • Hook: The connector between the filament and the motor The hook serves as a crucial connector between the flagellar filament and the motor complex. Its role is to transmit the rotational force generated by the motor to the filament, facilitating efficient movement.
  • Motor complex: Driving force behind flagellar rotation The motor complex, located at the base of the flagellum, acts as the powerhouse for flagellar rotation. It converts chemical energy into mechanical work, propelling the flagellar filament and enabling motility.
  • Basal body: Anchoring the flagellum to the cell membrane The basal body acts as the anchor, firmly attaching the flagellum to the cell membrane. It plays a pivotal role in maintaining the structural integrity of the flagella and ensuring efficient movement.

Composition of Archaeal Flagella

Archaeal flagella are composed of various protein components that contribute to their structure and function. These components play a crucial role in the motility and survival of Archaea in diverse environments.

Flagellin proteins

The archaeal flagellum is composed of multiple flagellin proteins. Different flagellins serve different functions. 


The major flagellins (FlaB1 and FlaB2) make up the bulk of the filament structure, while the minor flagellin (FlaB3) is concentrated at the base and forms the hook portion.

Flagellar Genes

Genes encoding archaeal flagellar components are localized within one genetic locus. The locus contains multiple flagellin genes arranged in tandem, followed by other conserved flagella-associated genes.

  • FlaHIJ: The flaHIJ clusters are highly conserved flagella-associated genes found in archaea. They are believed to be involved in flagellin export. FlaI and FlaJ have similarities to proteins in the bacterial type IV pili system.
  • FlaCDEFG: These genes are found between the flagellins and the flaHIJ genes in many flagellated archaea. Their exact roles in flagellation are still unknown.

Flagellin Glycosylation

Archaeal flagellins can undergo glycosylation, a post-translational modification where sugar groups are covalently linked to the protein. The attached glycans are required for the proper assembly of flagellins into functional flagella. Archaeal flagellin glycosylation involves N-linked glycosidic linkages, unlike bacterial glycosylated flagellins.

Role of Glycosylation in Archaeal Flagella

Glycosylated Flagellins: Archaeal flagellins are often glycosylated, with sugar molecules attached to specific amino acid residues. This glycosylation can provide stability to the flagellum and protect it from harsh environmental conditions.

Functional Significance

Glycosylation of flagellins can also modulate flagellar function. It may affect flagellar assembly, motility, adhesion, or the interaction of Archaea with their surroundings. The specific glycan structures and their interactions with other molecules determine the functional consequences of glycosylation.

Assembly of Archaeal Flagella

The assembly of archaeal flagella is a complex and tightly regulated process that involves the biosynthesis and organization of flagellum components.

Biosynthesis and Assembly of Flagellum Components

The various flagellum protein components, including flagellins, hook-associated proteins, and basal body proteins, are synthesized within the cell. They are produced in specific locations, such as the cytoplasm or specialized organelles.

Assembly Pathways: The assembly of flagellum components occurs in a stepwise manner. The flagellins from the filament, which is attached to the hook-associated proteins. The basal body proteins facilitate the integration of the flagellum with the cell membrane.

Regulation of Flagellum Assembly

Transcriptional Regulation: The expression of flagellum-related genes is regulated at the transcriptional level. Specific regulatory proteins control the activation or repression of these genes, depending on environmental cues and cellular needs.

Post-translational Modifications: Post-translational modifications, such as phosphorylation or acetylation, can regulate the activity and stability of flagellum proteins during assembly. These modifications are often mediated by protein kinases or other enzymes.

Secretion Systems Involved in Flagellum Assembly

Archaea employ various secretion systems to transport flagellum components to their proper locations during assembly.

  • Type III Secretion System: Some archaeal species use a type III secretion system to export flagellum proteins across the cell membrane. This system resembles the bacterial type III secretion system and is involved in the assembly of the basal body and filament.
  • Other Secretion Mechanisms: In addition to the type III secretion system, other secretion mechanisms may be employed by Archaea for the delivery of flagellum components. These mechanisms can vary among different archaeal species and remain an area of ongoing research.

Archaeal Flagellar Movement

The movement of archaeal flagella is essential for the motility and behavior of Archaea. It involves intricate mechanisms of rotation and response to environmental cues.

archaeal flagella structure
source image: VanDyke, D. J., M Ng, S. Y., Chaban, B., Wu, J., & Jarrell, K. F. Archaeal Flagella.

Mechanisms of Flagellar Rotation

  1. Motor Complex: The rotation of the archaeal flagellum is facilitated by a motor complex, which consists of several components, including the flaHIJ clusters.
  2. FlaI ATPase: FlaI is a key component of the motor complex and is a Walker box-containing protein. This protein is similar to ATPases involved in bacterial type IV pili extension and retraction. The presence of the Walker box suggests that FlaI utilizes ATP hydrolysis to generate the energy required for flagellar rotation.
  3. Interaction with FlaJ: FlaJ is an integral membrane protein that is thought to interact with FlaI. The exact nature of their interaction and the role of FlaJ in the rotation mechanism is not fully understood but may involve facilitating the function of FlaI.
  4. FlaH and its Function: FlaH is another component of the motor complex that contains a Walker box A motif. However, the specific function of FlaH in flagellar rotation is not well understood. Further research is needed to determine its exact role in the mechanism.
  5. Energy Generation: The FlaI ATPase, located within the motor complex, is proposed to be responsible for generating the energy required for flagellar rotation. This energy is obtained through the hydrolysis of ATP, which provides the necessary power to drive the rotation of the flagellum.
  6. ATP Hydrolysis and Flagellar Rotation: As ATP molecules are hydrolyzed by FlaI, the energy released is used to power the rotation of the flagellum. The exact mechanism by which this energy is converted into flagellar motion is not fully elucidated and requires further investigation.
  7. Regulation: The rotation of the flagellum in archaea is likely regulated by various factors, including environmental cues and cellular signals. Signal transduction systems, such as two-component systems, may be involved in sensing and responding to external stimuli, leading to changes in the rotational speed or direction of the flagellum.

Archaeal Taxis and Response to Environmental Cues

Archaea employ flagella to respond to various environmental cues and navigate their surroundings.

  • Chemotaxis: Archaeal flagella can mediate chemotaxis, allowing Archaea to move towards or away from specific chemical stimuli in their environment. This enables them to locate favorable conditions or avoid harmful substances.
  • Phototaxis and Aerotaxis: In addition to chemotaxis, Archaea can exhibit phototaxis (movement in response to light) or aerotaxis (movement in response to oxygen gradients). These responses are crucial for their survival and for optimizing their metabolic activities.

Flagellar Function in Archaea

Flagella in Archaea serves multiple important functions that extend beyond motility alone. They play critical roles in surface attachment, biofilm formation, and nutrient acquisition.

Role of Flagella in Archaeal Motility

  • Swimming Motility: Flagella allow Archaea to move through liquid environments, facilitating their dispersal, exploration, and colonization of new habitats.
  • Twitching Motility: Some Archaea exhibit twitching motility, which involves the extension and retraction of flagella to generate jerky movements on solid surfaces. This enables surface exploration and biofilm formation.

Flagellar Function in Surface Attachment and Biofilm Formation

  • Surface Attachment: Flagella can aid Archaea in attaching to surfaces, such as sediment particles or host tissues. This attachment promotes stable colonization and the formation of microbial communities.
  • Biofilm Formation: Biofilms are structured communities of microorganisms embedded in a matrix. Flagella are often involved in the initial stages of biofilm formation, allowing Archaea to anchor themselves and contribute to the development of complex biofilm structures.

Flagellar Function in Nutrient Acquisition

  • Nutrient Capture: Archaeal flagella can serve as sensory appendages, detecting and capturing nutrients from the surrounding environment. They can sense gradients of nutrients and guide Archaea towards favorable locations for growth and metabolism.
  • Extracellular Enzyme Secretion: Flagella can also be involved in the secretion of extracellular enzymes that aid in nutrient acquisition. These enzymes can break down complex substrates, enabling Archaea to access essential nutrients.


In conclusion, the composition of archaeal flagella involves various protein components, including flagellins, hook-associated proteins, and basal body proteins. The role of glycosylation in archaeal flagella provides structural stability and functional diversity. The assembly of archaeal flagella is a regulated process involving biosynthesis, assembly pathways, and secretion systems. Archaeal flagellar movement is driven by rotary motors, and Archaea exhibit unique movement patterns and responses to environmental cues. Flagella in Archaea serve multiple functions, including motility, surface attachment, biofilm formation, and nutrient acquisition. Understanding the mechanisms and functions of archaeal flagella enhances our knowledge of microbial diversity and their adaptation to different environments.


  • VanDyke, D. J., M Ng, S. Y., Chaban, B., Wu, J., & Jarrell, K. F. Archaeal Flagella.
  • Tortora, G. J., Funke, B. R., & Case, C. L. (2021). Microbiology: An introduction. Pearson Education Limited.
    Willey, J. M., Sandman, K. M., Wood, D. H., & Prescott, L. M. (2019). Prescott’s microbiology (11th ed.). McGraw Hill.
  • Morgan, D. G., & Khan, S. Bacterial Flagella.
Mubashir Iqbal
Mubashir Iqbal

Mubashir Iqbal is a highly dedicated and motivated Microbiologist with an MPhil in Microbiology from the University of Veterinary and Animal Sciences. Currently, he is researching the efficacy of commercially available SARS Cov-2 vaccines to neutralize the omicron variant in Pakistan. He holds a Bachelor's degree in Microbiology and has experience in chemical and microbiological analysis of water samples, managing SOPs and documents according to standard ISO 17025. Additionally, he has worked as an internee in BSL 3, Institute of Microbiology, UVAS, where he gained experience in RNA extraction, sample processing, and microscopy.

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