MCB3020 Chapter 4: Archaeal Cell Structure PDF

4 Archaeal Cell Structure ©Ingram Publishing Cows and Buffaloes and Sheep, Oh My! Readiness Check: T ✓ Summarize the structures observed in bacterial cells and their he next time you drive or walk through the countryside, count the number of domesticated ruminants you see—dairy cows, beef cattl...

4 Archaeal Cell Structure ©Ingram Publishing Cows and Buffaloes and Sheep, Oh My! Readiness Check: T ✓ Summarize the structures observed in bacterial cells and their he next time you drive or walk through the countryside, count the number of domesticated ruminants you see—dairy cows, beef cattle, sheep, and goats, among others. It is estimated that there are about 3 billion head worldwide. These animals are important because they are a substantial protein source. But they do something else that is noteworthy: Each year they exhale about 200 million metric tons of methane, a potent greenhouse gas (GHG). The manure these and other domesticated animals produce is thought to release another 18 million metric tons of methane. As detailed in chapter 28, carbon dioxide is an important GHG and is considered to be a significant contributor to global warming. Methane and nitrous oxide are also GHGs. Carbon dioxide is the dominant GHG in the atmosphere. However, methane has about 30 times the heat-retaining capacity of carbon dioxide. Thus, although the contribution of methane by domesticated ruminants and their manure represents only about 5% of the total GHG emissions worldwide each year, the impact of these emissions is of concern. But don’t blame the animals; they are not directly responsible for generating methane. Rather, it is a unique group of archaea— the methanogens—that make methane from hydrogen gas, carbon dioxide, and acetate. Furthermore, these substrates arise in the animals as their food is digested with the help of a complex community of microbes living in their rumen. For these animals, methane is a waste product; for farmers and ranchers, methane represents a loss in production. There is considerable interest in figuring out how to decrease methane production so that GHG emissions are lowered and farmers and ranchers can earn more from each animal. Methanogens are only one physiological group in domain Archaea. Other archaea have attracted attention because of their ability to live in extreme environments. All are of interest because of their chimeric natures: They have some features that are similar to bacteria and some that are similar to eukaryotes. Their cell structure is like that of bacteria; that is, they look like the canonical prokaryotic cell. However, the molecules used to construct their cell structures are often unique or are similar to those found in eukaryotes. As we describe in chapters 15 and 20, their physiologies exhibit this dichotomy. In general, the processes and molecules used to conserve energy are like those of bacteria, whereas the processes and molecules used to replicate and express their genomes are like those of eukaryotes. In this chapter, we describe some of the molecular and structural aspects of archaeal cells that set them apart. Based on what you have learned previously, you should be able to: molecular makeup (chapter 3) ✓ Describe the mechanisms used by bacteria to obtain nutrients (section 3.3) ✓ Describe the mechanisms used by bacteria to move in response to stimuli (section 3.8) 4.1 Archaea Are Diverse but Share Some Common Features After reading this section, you should be able to: a. Describe a typical archaeal cell b. Discuss key differences between bacteria and archaea Recall that for many years, archaea and bacteria had been lumped together and referred to as prokaryotes. Today Archaea and Bacteria are recognized as distinct taxa. The separation of bacteria and archaea into distinct taxa correlates with the observation that they each have unique and distinguishing characteristics. Some of these are summarized in table 4.1. Keep in mind that only a small subset of the archaea can be grown in the laboratory. Many archaea inhabit niches that constitute extreme environments from a human perspective. Their requirements for high temperature, low pH, or high salt present challenges for culturing them. Historically, environments dominated by archaea were not believed to support life. Once microbiologists broadened their exploration of earth’s microbial habitats, archaea have been found to be ubiquitous, but in small numbers. Surveys of nonextreme environments have established that archaea reside in most habitats—again, in small numbers. Most of the studies described in this chapter were performed on archaea that are readily grown in the lab. Methanogens (microbes that generate methane gas) are killed by exposure to oxygen, and must be handled in sealed containers. The names of these organisms begin with Methano-. Halophiles (salt-lovers) require high salt conditions and are named Halo-. Another commonly studied archaeon is Sulfolobus, which requires both high temperature and low pH for growth. Many archaea are known only in the sense that their 16S rRNA sequence or a partial genome sequence has been determined. Archaeal taxonomy is currently in a state of flux because of the vast 77 wil11886_ch04_077-086.indd 77 22/10/18 7:26 pm 78 CHAPTER 4 | Archaeal Cell Structure Table 4.1 Comparison of Bacterial and Archaeal Cells amount of genomic data that has identified new archaea. There is controversy over the taxonomic designations used for these new organisms, but three phyla are well established: Crenarchaeota, Euryarchaeota, and Thaumarchaeota. We begin our discussion of archaeal cells by considering overall cell morphology and organization and then specific cell structures. Shape, Arrangement, and Size Archaeal cells, like bacterial cells, exhibit a variety of shapes. Cocci and rods are common (figure 4.1a). Both usually exist singly, but some cocci form clusters and some rods form chains. Curved rods, spiral shapes, and pleomorphic (many shaped) archaea have also been observed. To date, no spirochete-like and mycelial archaea have been discovered. However, some archaea exhibit unique shapes, such as the branched form of Thermoproteus tenax (fig- ure 4.1b) and the flat, postage-stamp-shaped Haloquadratum walsbyi, an archaeon that lives in salt ponds and measures about 2 μm by 2 to 4 μm and only 0.25 μm thick. This shape has the advantage of greatly increasing the surface area-to-volume (S/V) ratio (see figure 3.5), which in turn increases efficiency of nutrient uptake, diffusion of molecules, and growth rate. Bacteria are diverse but share some common features (section 3.2) Archaeal cells also vary in size as much as in shape. Typical rods are 1 to 2 μm wide by 1 to 5 μm long; cocci are typically 1 to 3 μm in diameter. However, extremely small and extremely large archaea have been identified. Several free-living, acid-loving (acidophilic), mine-dwelling microbes measure a mere 0.2 to 0.4 μm in diameter. Also at the small end of the size continuum is the parasitic archaeon Nanoarchaeum equitans (0.4 μm in diameter). At the other extreme are two recently observed giant archaea that form long 1 µm (a) Methanosarcina mazei—a coccus that forms clusters (b) Thermoproteus tenax—a branched archaeal cell Figure 4.1 Archaeal Cell Morphology. (a) Scanning electron micrograph. Bar = 5 μm. (b) Transmission electron micrograph. From J.T. Staley, M.P. Bryant, N. Pfenning and J.G. Holt (Eds), Bergey’s Manual of Systematic Bacteriology, Vol. 3. ©1989 Williams and Wilkins Co., Baltimore wil11886_ch04_077-086.indd 78 22/10/18 7:26 pm 4.2 Archaeal Cell Envelopes Are Structurally Diverse 79 4.2 Archaeal Cell Envelopes Are Filamentous archaeon Structurally Diverse After reading this section, you should be able to: Bacterial biofilm a. Draw an archaeal cell envelope and identify the component layers b. Compare and contrast archaeal and bacterial cell envelopes in terms of their structure, molecular makeup, and functions c. Compare and contrast nutrient uptake mechanisms observed in bacteria and archaea 6 μm Figure 4.2 A Giant Archaeon. Candidatus Giganthauma karukerense forms long filaments that are covered with a bacterial biofilm. The bacteria may be symbionts of the host archaeon. ©Prof. Olivier Gros filaments up to 30 mm in length. For one archaeon, the filament is composed of numerous cells, each measuring 8 to 10 μm wide by 20 to 24 μm long. An interesting characteristic of this archaeon is that its filaments are coated with a biofilm formed by bacteria of a single species (figure 4.2). The nature of this interaction is not known, but it is thought that the archaeon is the host and the bacteria are symbionts. Cell Organization Structures observed in members of both Bacteria and Archaea are summarized and their differences noted in table 4.1. The archaeal plasma membrane is composed of strikingly different lipids than those found in bacterial membranes; in fact, the unusual lipids were one of the first pieces of evidence to suggest that these microbes are phylogenetically distinct from bacteria. Most archaea have a cell wall, but their walls are considerably more diverse than bacterial walls. Notably, archaeal cell walls lack peptidoglycan. Capsules are not widespread among archaea examined thus far. Within the archaeal cytoplasm, a nucleoid, ribosomes, and inclusions can be found. Finally, many archaea use flagella for locomotion and attachment, but these structures differ sufficiently from bacterial flagella so they have been named archaella (s., archaellum). In the remaining sections of this chapter, we describe the major structures observed in archaea in more detail, noting the aspects that distinguish them from the analogous bacterial structures. Understanding archaeal structures at the molecular level is an area of intense research because many archaea are found in extreme habitats. We note those structural adaptations that contribute to this lifestyle. However, the topic of survival in extreme habitats is considered more thoroughly in chapter 7. Environmental factors affect microbial growth (section 7.5) We define the cell envelope as the plasma membrane and any layers external to it. For bacteria, these extra layers include cell walls, S-layers, capsules, and slime layers. One of the most distinctive features of archaeal cells is the nature of their cell envelopes. Their uniqueness begins with their plasma membranes. Recall from chapter 3 that the fluid mosaic model describes membranes as lipid bilayers within which proteins float (see figure 3.7). The model is based on studies of eukaryotic and bacterial membranes and is well established. Imagine the surprise of microbiologists when they found that some archaea have monolayer membranes that function like bilayers. This structural difference is due to the presence of unique lipids in archaeal plasma membranes. Archaeal cell envelopes also differ in terms of organization. For many archaea, an S-layer is the major, and sometimes only, component of the cell wall. Slime layers have been observed in some archaea where they appear to mediate cellcell interactions, but little is known about their composition and regulation. Finally, capsules are relatively rare among archaea and thus are not discussed. Archaeal Plasma Membranes Are Composed of Unique Lipids but Function Like Bacterial Membranes Archaeal membranes are composed primarily of lipids that differ from bacterial and eukaryotic lipids in two ways. First, they contain hydrocarbons derived from isoprene units—five-carbon, branched molecules (figure 4.3). Thus the hydrocarbons are branched as shown in figure 4.4. This affects the way the lipids pack together, which in turn affects the fluidity and permeability of the membrane. This is especially important for extremophilic archaea for which membrane fluidity and permeability could be compromised by extreme conditions. Second, the hydrocarbons are attached to glycerol by ether links rather than ester links (figure 4.4a). Ether linkages are more resistant to chemical attack and heat than are ester links. Two major types of archaeal lipids have been identified: glycerol diethers and diglycerol tetraethers. Glycerol diether lipids are Comprehension Check 1. Which cell shapes are observed in members of both Bacteria and Archaea? Which are unique to bacteria? Which to archaea? 2. Archaea was first defined as a distinct taxon by comparisons of ribosomal RNA sequences. Identify two other molecules that could be used to determine if a microbe having a typical prokaryotic architecture is a bacterium or an archaeon. wil11886_ch04_077-086.indd 79 CH3 H2C C CH CH2 Isoprene Figure 4.3 Isoprene. This five-carbon, branched molecule is the building block of archaeal lipids. 22/10/18 7:26 pm 80 CHAPTER 4 | Archaeal Cell Structure Archaeal membranes Ether linkage O R′ C C R′ n Isoprene derived hydrocarbon (a) O CH2 O H 2C H 2C O C R HC O C R O O O O O 5 O O O OO O O O O O O Monolayers (a) Bilayer of C20 diethers (b) Monolayer of C40 tetraethers Figure 4.5 Examples of Archaeal Plasma Membranes. wil11886_ch04_077-086.indd 80 Fatty acid O CH2 4 3 O O 1 Head groups CH 2 (b) Bacterial membranes Ester linkage O O O O O O O OO O O O 6 O O O O Figure 4.4 Comparison of Archaeal and Bacterial Membranes. (a) Archaeal membrane lipids are attached to glycerol by ether linkages instead of ester linkages, as found in bacteria and eukaryotes. The stereochemistry also differs. In archaeal lipids, the stereoisomer of glycerol is sn-glycerol-1-phosphate; in bacterial lipids, the stereoisomer is sn-glycerol-3phosphate. Thus in archaeal lipids, the side chains are attached to carbons 2 and 3 of glycerol, and in bacterial lipids, the side chains are attached to carbons 1 and 2. (b) Examples of archaeal lipids are lipids 1, 2, and 3. Lipids 4, 5, and 6 are bacterial lipids. Note that some archaeal lipids form monolayers (figure 4.5), whereas all bacterial lipids form bilayers. O O O O Bilayers formed when two hydrocarbons are attached to glycerol (figure 4.4b, lipid 3). Usually, the hydrocarbon chains in glycerol diethers are 20 carbons in length. Diglycerol tetraether lipids are formed when two glycerol residues are linked by two long hydrocarbons that are 40 carbons in length (figure 4.4b, lipids 1 and 2). Tetraethers are more rigid lipids than diethers. Cells can adjust the overall length of the tetraethers by cyclizing the chains to form pentacyclic rings (figure 4.4b, lipid 2). Phosphorus-, sulfur-, amino-, and sugarcontaining groups can be attached to the glycerol moieties in the diethers and tetraethers, just like the phospholipids observed in bacterial and eukaryotic membranes. Despite the significant differences in membrane lipids, the basic design of archaeal membranes is similar to that of bacterial and eukaryotic membranes: There are two hydrophilic surfaces and a hydrophobic core. When C20 diethers are used, a typical bilayer membrane is formed (figure 4.5a). When the membrane is constructed of C40 tetraethers, a monolayer membrane with much more rigidity is formed (figure 4.5b). The addition of pentacyclic rings further increases this rigidity. As might be expected from their need for stability, the membranes of extreme thermophiles such as Sulfolobus spp., which grow best at temperatures over 85°C, are almost completely tetraether monolayers. Archaea that live in moderately hot environments such as 22/10/18 7:27 pm 4.2 Archaeal Cell Envelopes Are Structurally Diverse 81 Thermoplasma spp., have membranes containing some regions with monolayers and some with bilayers. Archaeal membranes are believed to include microdomains, as described in chapter 3 for bacterial membranes. Flotillin-like proteins have been identified in Pyrococcus membranes where they cluster into complexes as observed in both bacterial and eukaryotic membranes. As we discuss in chapter 3, organisms have several options for obtaining the nutrients they need from their environment. Importantly, microbes often find themselves in nutrient-poor environments and therefore must be able to accumulate nutrients in their cytoplasm at concentrations higher than the external milieu. Thus, although passive and facilitated diffusion have been observed, archaea primarily use active transport for nutrient uptake. Both primary (e.g., ABC transport) and secondary active transport systems (e.g., symport and antiport) have been identified in archaeal cells, often by searching an archaeon’s genome for the genes encoding components of these systems (i.e., genomic analysis). These systems tend to be similar to those seen in bacteria. The group translocation system phosphoenolpyruvate:sugar phosphotransferase system (PTS) also functions in some archaea. Bacteria use many mechanisms to bring nutrients into the cell (section 3.3) Microbial genomics (chapter 18) Protein sheath S-layer S-layer Plasma membrane Plasma membrane Cytoplasm (a) Cytoplasm (b) Methanochondroitin S-layer S-layer Plasma membrane Plasma membrane Cytoplasm Cytoplasm (c) Pseudomurein (d) Glycocalyx Polysaccharides Plasma membrane Plasma membrane Cytoplasm Cytoplasm (f) (e) Outer membrane Intermembrane compartment Plasma membrane Cytoplasm There Are Many Different Types of Archaeal Cell Walls Before they were distinguished as a unique domain of life, archaeal species were characterized as being either Gram positive or Gram negative based on their response to Gram staining. Thus, like all cells (even eukaryotic cells), they will stain either purple or pink when Gram stained. However, their staining reaction does not correlate reliably with a particular cell wall structure as it does for bacteria. Archaeal cell walls exhibit considerable variety in terms of their chemical makeup. Furthermore, their cell walls lack peptidoglycan. The most common type of archaeal cell wall is an S-layer composed of either glycoprotein or protein (figure 4.6a). The S-layer may be as thick as 70 nm. Some methanogens (Methanolobus and Methanococcus spp.), salt-loving archaea (Halobacterium spp.), and extreme thermophiles (Sulfolobus, Thermoproteus, and Pyrodictium spp.) have S-layer cell walls. Other archaea have additional layers of material outside the S-layer. For instance, Methanospirillum spp. have a protein sheath external to the S-layer (figure 4.6b). Other methanogens (Methanosarcina spp.) have a polysaccharide layer covering the S-layer (figure 4.6c). This material, called methanochondroitin, is similar to the chondroitin sulfate of animal connective tissue. In some archaea, the S-layer is the outermost layer and is separated from the plasma membrane by a peptidoglycan-like molecule called pseudomurein (figure 4.6d). Pseudomurein differs from peptidoglycan in that it has L-amino acids instead of Damino acids in its cross-links, N-acetyltalosaminuronic acid instead of N-acetylmuramic acid, and β(1→3) glycosidic bonds instead of β(1→4) glycosidic bonds (figure 4.7). These differences mean that lysozyme, penicillin, and other chemicals that wil11886_ch04_077-086.indd 81 (g) Figure 4.6 Archaeal Cell Envelopes. (a) Methanococcus, Halobacterium, Pyrodictium, Sulfolobus, and Thermoproteus spp. cell envelopes. (b) Methanospirillum spp. cell envelope. (c) Methanosarcina spp. cell envelope. (d) Methanothermus and Methanopyrus spp. cell envelopes. (e) Methanothermobacter, Methanosphaera, Methanobrevibacter, Halococcus, and Natronococcus spp. cell envelopes. For Methanothermobacter and Methanosphaera spp., the polysaccharide layer is composed of pseudomurein. (f) Thermoplasma cell envelope. (g) Ignicoccus hospitalis cell envelope. affect peptidoglycan structure and synthesis in bacterial cell walls have no effect on pseudomurein-containing archaeal cell walls. Cell walls and osmotic protection (section 3.4) Another type of archaeal cell wall consists of a single, thick homogeneous layer resembling that in Gram-positive bacteria (figure 4.6e). These archaea lack an S-layer and often stain Gram positive. Their wall chemistry varies from species to species but usually consists of complex polysaccharides such as pseudomurein. Some archaea lack any layer resembling a cell wall. For instance, members of the acidophilic genera Ferroplasma and Thermoplasma have envelopes consisting only of a plasma membrane covered by a layer of slime. The slime, which is referred to as a glycocalyx, may provide some of the protection needed for these archaea to survive in their acidic habitats (figure 4.6f). The most unique wall-less archaeon is Ignicoccus hospitalis. Its envelope consists only of the plasma membrane and an outer membrane, with an intermembrane compartment between them (figure 4.6g and figure 4.8). The outer membrane contains protein complexes that form pores, much like bacterial porin proteins create pores in the outer membrane of typical Gram-negative bacteria. 22/10/18 7:27 pm 82 CHAPTER 4 | Archaeal Cell Structure H O CH2OH O H OH β (1 → 3) H NHAc O OH H β (1 → 3) CO H H H H NHAc Glu H O H O β (1 →3) a. Compare and contrast the cytoplasm of bacterial and archaeal cells b. Discuss the organization of archaeal DNA and similarities to both bacteria and eukaryotes Ala Lys Glu Lys (Ala) Ala Glu (NH2) H H CO H β (1 →3) OH O O Hβ (1 →3) OH H O H NHAc H H NHAc H H β (1 →3) O O CH2OH N-acetyltalosaminuronic acid N-acetylglucosamine Figure 4.7 Pseudomurein. The amino acids and amino groups in parentheses are not always present. Ac, acetyl group. MICRO INQUIRY How is pseudomurein similar to peptidoglycan? How does it differ? Overall, the cytoplasm of archaeal cells is similar to that of bacteria. Within it can be found inclusions—polyhydroxyalkonates, polyphosphate granules, glycogen granules, and gas vacuoles; ribosomes; a nucleoid; and plasmids. Proteins that might form a cytoskeleton have also been identified, including FtsZ (tubulin homologue), MreB (actin homologue), and crenactin, an actin homologue unique to certain members of the Crenarchaeota. In those archaea having FtsZ, the protein participates in cell division, as it does in bacteria. Evidence suggests that the actin homologues MreB and crenactin are involved in conferring a rod shape. Interestingly, a tubulin homologue called CetZ is observed in some members of the Euryarchaeota. CetZ confers a rod shape to cells rather than functioning in cytokinesis as FtsZ does. Some structures found in the cytoplasm of archaeal cells have distinctive molecular makeup. In this section, we focus on those structures. Phylum Crenarchaeota (section 20.2); Phylum Euryarchaeota: methanogens, haloarchaea, and others (section 20.3) Archaeal Ribosomes Are the Same Size as Bacterial Ribosomes but Are Composed of Different Molecules V PM IMC Cy OM Figure 4.8 Cell Envelope of the Wall-less Archaeon Ignicoccus hospitalis. Cy, cytoplasm; IMC, intermembrane compartment; OM, outer membrane; PM, plasma membrane; V, periplasmic vesicles. Many archaeal energy conservation reactions occur in the space between the plasma membrane and the S-layer. This region of the cell is sometimes referred to as the pseudo-periplasm, by analogy to the structure in Gram-negative bacteria. Comprehension Check 1. Identify three features that distinguish archaeal plasma membranes from those of bacteria. 2. Both bacteria and archaea can have S-layers. How does their use within the cells differ? wil11886_ch04_077-086.indd 82 to Bacterial Cytoplasm After reading this section, you should be able to: (NH2) (Glu) 4.3 Archaeal Cytoplasm Is Similar Like bacterial cells, the ribosomes of archaeal cells are 70S in size and are constructed of a 50S and a 30S subunit. However, their shape is somewhat different and their component molecules are not the same. Both have ribosomal RNA (rRNA) molecules of similar size: 16S in the small subunit, and 23S and 5S in the large subunit. However, as we discuss in chapter 1, the differences in nucleotide sequences of these molecules were the initial basis for establishing the taxon Archaea. Furthermore, at least one archaeon has an additional rRNA, a 5.8S rRNA, in the large subunit. This is of interest because the large subunit of eukaryotic ribosomes contains both 5S and 5.8S rRNA molecules. The protein composition of bacterial and archaeal ribosomes also differs. Archaeal ribosomes have more proteins: about 68 rather than about 55. Archaeal ribosomal proteins can be sorted into three groups based on their similarity to proteins found in bacterial and eukaryotic ribosomes: (1) those observed in all three domains of life, (2) those unique to archaea, (3) those observed in both archaea and eukaryotes. There are only a few ribosomal proteins unique to archaea; the rest are about evenly divided between the other two groups. Importantly, all the ribosomal proteins present in both archaeal and bacterial ribosomes are also seen in eukaryotic ribosomes. Thus there are no ribosomal proteins that are present only in the ribosomes of archaea and bacteria. The difference in bacterial and archaeal ribosomes correlates with the fact that archaeal ribosomes are unaffected 22/10/18 7:27 pm 4.4 Many Archaea Have External Structures Used for Attachment and Motility 83 by antibiotics that bind and inhibit bacterial ribosomes tein synthesis inhibitors (section 9.4) Pro- 4.4 Many Archaea Have External Structures Used for Attachment and Motility Nucleoid The nucleoid provides another example of the difference between archaea and bacteria. This region in the cytoplasm contains the cell’s chromosome and numerous proteins. The chromosomes of all known archaea are circular, double-stranded deoxyribonucleic acid (DNA). Members of the Euryarchaeota are polyploid; that is, they have multiple copies of their chromosomes throughout their life cycles. In contrast, members of the Crenarchaeota are monoploid, with a single copy of the chromosome. It is believed that this difference reflects the mechanism for chromosome partitioning to daughter cells during cell division. Crenarchaeota have a highly regulated chromosome segregation mechanism, but the process appears to be random in the Euryarchaeota. Maintaining multiple copies of the genetic information is good insurance for an intact copy to end up in each daughter cell. Chromosome replication and partitioning (section 7.2) The problem of compacting a genome to fit into a cell is common to archaea and bacteria, and the solution is similar. Both supercoiling and the presence of nucleoid-associated proteins (NAPs) on the genomic DNA contribute to chromosome organization. As in bacteria, there is a variety of NAPs, but they bear little resemblance to bacterial NAPs. The common features of these proteins are small size and positive charge. Each archaeon contains at least two different NAPs that may act at different scales of chromosome structure. On short segments of DNA, certain NAPs bend or stiffen the chromosome; on a global level, other NAPs bridge nonadjacent regions of the chromosome. Many members of the Euryarchaeota have histones associated with their chromosomes. There is a strong correlation between the presence of histones and multiple chromosome copies, although it is not clear how the two features are related. These histones form nucleosomes that are related to the nucleosomes observed in eukaryotes (see figure 5.10). In Haloferax volcanii, the nucleosomes differ from eukaryotic nucleosomes in that they consist of four histones rather than eight and they organize a shorter length of DNA. In Thermococcus kodakarensis, however, histones assemble into various-sized complexes containing from two histones to more than a dozen. It is hypothesized that in thermophilic archaea, histones help prevent denaturation of the chromosomes. Nucleoid (section 3.6); Nucleus (section 5.5) Comprehension Check 1. Thus far, homologues of intermediate filaments have not been identified in archaea. Is it likely that they will be identified eventually? Explain your answer. 2. Archaea are often described as chimeric organisms having some features that are similar to bacteria and some that are similar to eukaryotes. Based on what you have just read in this section, provide two examples that illustrate the similarity of archaea to bacteria; list two examples of their similarity to eukaryotes. wil11886_ch04_077-086.indd 83 After reading this section, you should be able to: a. Compare and contrast bacterial and archaeal pili b. Compare and contrast bacterial and archaeal flagella in terms of their structure and function Like bacteria, many archaea have structures that extend beyond the cell envelope, namely pili and flagella. These external structures and their functions are discussed in this section. Pili Many archaea have pili, and these appendages are found in a range of lengths and diameters, some solid and others hollow. Pili are composed of many copies of single protein subunits termed pilins, but pilins are not related to one another, thus explaining the diversity in the structures observed. Methanococcus maripaludis makes a major pilin that comprises the bulk of its pilus, and several other less abundant pilins. Its genome encodes at least six other pilins, and changing the relative proportions of pilins may be a means of responding to environmental stimuli. Archaeal pili are type IV pili, which describes their mechanism of assembly within the cell envelope. Pilins are synthesized on ribosomes in the cytoplasm and then anchored to a protein complex in the plasma membrane. Pilin proteins are secreted through the complex to assemble the mature pilus structure. Pili perform a range of functions. Sulfolobus solfataricus can display at least two distinct types of pili. The archaeal adhesive pilus (Aap) is responsible for cell adhesion to surfaces under certain growth conditions. The ultraviolet (UV)–inducible pilus (Ups) is only produced following exposure of the cells to UV light. As UV light can damage DNA, the Ups mediates the aggregation of cells and promotes the transfer of DNA between cells. Bacterial pili and fimbriae (section 3.7) Two particular pili are noteworthy: cannulae and hami. Cannulae are hollow, tubelike structures observed on the surface of thermophilic archaea belonging to the genus Pyrodictium (figure 4.9). The function of cannulae is unknown, but it is known that daughter cells arising from a single round of cell division remain connected to each other by cannulae. After many rounds of cell division, a network of cells is formed. Hami are of particular interest because of their shape (figure 4.10). They look like tiny grappling hooks, which suggests they might function to attach cells to surfaces. Indeed, archaeal cells that produce hami are members of biofilm communities generally consisting of a hami-producing archaeon and a bacterium. Archaella and Motility Archaeal flagella, or archaella, have been studied in detail in only a few model archaea. They are superficially similar to 22/10/18 7:27 pm 84 CHAPTER 4 | Archaeal Cell Structure (a) Hami radiating from cell 1 µm Figure 4.9 Cannulae. Cannulae are tubular structures about 25 nm in diameter. They have only been observed on Pyrodictium spp. They connect daughter cells, ultimately forming a dense network of cells. SEM, bar = 1 µm. ©Karl O. Stetter Figure 4.10 Hami. (a) A coccus-shaped cell is in the center of the electron micrograph and about 100 hami are radiating out from the platinumshadowed cell. TEM, bar = 500 nm. (b) At the ends of the hami are grappling hook–like structures that are thought to allow cells to adhere to surfaces, including other cells. TEM, bar = 50 nm. (b) “Grappling hooks” at distal ends of hami their bacterial counterparts, but important differences have been identified. Archaella are thinner than bacterial flagella (10 to 14 nm ©Dr. Christine Moissl-Eichinger rather than 18 to 22 nm) and some are composed of more than one type of protein subunit (figure 4.11). The filament is not hollow. Assembly of the archaellum also differs from bacterial flagellum assembly. In a manner similar to the assembly of bacterial type IV pili, the archaellin proteins are exported through the motor complex (figure 4.11) and added to the base of the filament. Additional proteins anchor the archaellum to the S-layer. Cryotomography has revealed bundles of archaella at one pole of the cell, organized by a proteinaceous structure in the membrane. Bacterial flagella (section 3.7) Archaella from the two major phyla, Euryarchaeota and Crenarchaeota, have characteristic structural variations. Crenarchaeal filaments are composed of a single archaellin subunit. In contrast, euryarchaeal filaments have multiple archaellins, one of which is the primary subunit with S-layer others in lower abundance. Halophiles have been demonstrated to synthesize archaellins in different proportions under different culture conditions. It is not known how the filament properties vary with subunit composition. The motor complex also differs between these phyla, and it is believed that this variation is related to the presence of a bacterialFlaJ like chemotaxis system in Euryarchaeota. Archaella work in a manner similar to bacterial FlaH, FlaI flagella: Rotation propels the cell. Again, there are FlaB some important differences. First, rotation is powPlasma FlaF FlaC, FlaD/E membrane ered by ATP hydrolysis rather than by proton motive force. Second, when the direction of rotation Motor complex switches, it causes the cell to move in either the forward or reverse direction, just as is seen for some Figure 4.11 Structure of the Archaellum, Based on Pyrococcus. The archaellin protein FlaB bacteria having polar flagella. Thus far, alternation comprises the filament, and monomers are added through FlaJ. The motor complex is composed of multiple Fla proteins, and the FlaF protein anchors the rotating archaellum in the cell envelope. between runs and tumbles has not been observed. wil11886_ch04_077-086.indd 84 22/10/18 7:27 pm Key Concepts 85 Halobacterium salinarum flagellar movement is the best studied. In this archaeon, clockwise rotation of the flagella pushes the cell forward, and counterclockwise rotation pulls the cell (i.e., the flagella are in front of the cell as it moves). H. salinarum exhibits both chemotaxis and phototaxis. Phototaxis is used to position the archaeon properly to absorb light when carrying out rhodopsinbased phototrophy. Surprisingly, considering the difference in flagellar architecture, much of the machinery controlling chemotaxis and phototaxis in H. salinarum is homologous to that found in bacterial systems. The archaellum in Sulfolobus also switches rotational direction, but the switch appears to be a random event. Rhodopsin-based phototrophy (section 11.12) Archaea have been observed to engage in two types of swimming behaviors, termed a relocate-and-seek strategy. Fast speeds in a straight line (up to ~500 μm/sec) result in a rapid change of location. A slower zigzag motion (~50 to 100 μm/sec) constitutes the seek, a scan for favorable conditions. The fastest known swimmers, Methanocaldococcus villosus and M. jannaschii, can travel at about 500 body lengths per second (bps), compared to 20 bps for E. coli and 11 bps for humans. This extreme swimming behavior is an advantage in their deep sea hydrothermal vent environment. Temperature gradients force these microbes to inhabit a narrow space between the 400°C vent fluid and the surrounding 2°C seawater. When fast swimming identifies a suitable niche (50° to 90°C), the microbes use the archaella for attachment. In addition to their role in motility, archaella are involved in adhesion to substrates, the formation of bioflms, and cell-cell interactions. Comprehension Check 1. What observations about cannulae and hami suggest that they allow archaeal cells to adhere to surfaces, including other cells? 2. List three aspects of archaella and their motility that are similar to bacterial flagella and their motility. 3. Defend the proposal that the archaellum is a type of pilus. Key Concepts 4.1 " Archaea Are Diverse but Share Some Common Features ■ ■ ■ ■ Members of Bacteria and Archaea share a common cell architecture. However, they have characteristics that define them as distinct taxa. Table 4.1 summarizes some of the differences. Many archaea have been identified only through 16S rRNA or partial genome sequences. Rods and cocci are the most common archaeal shapes. Archaea also can be curved rods, spirals, branched, square, and pleomorphic (figure 4.1). Most archaea are similar in size to bacteria. Archaea that are extremely small or are extremely large have also been identified (figure 4.2). 4.3 Archaeal Cytoplasm Is Similar to Bacterial Cytoplasm ■ ■ ■ ■ 4.2 Archaeal Cell Envelopes Are Structurally Diverse ■ ■ ■ ■ The cell envelope consists of the plasma membrane and all external coverings, including cell walls and other layers. Archaeal cell envelopes usually consist of only the plasma membrane and the cell wall. Archaeal membranes are composed of glycerol diether and diglycerol tetraether lipids (figure 4.4). Membranes composed of glycerol diether are lipid bilayers. Membranes composed of diglycerol tetraethers are lipid monolayers. The overall structure of a monolayer membrane is similar to that of the bilayer membrane in that the membrane has a hydrophobic core and its surfaces are hydrophilic (figure 4.5). Archaea typically use active transport systems to obtain nutrients from their environment. Archaeal cell walls do not contain peptidoglycan, and they exhibit great diversity in their makeup. The most common type of cell wall is one consisting of an S-layer only (figure 4.6). wil11886_ch04_077-086.indd 85 Cytoskeletal proteins have been identified in archaeal cells. They include FtsZ (tubulin homologue), MreB (actin homologue), and crenactin (a unique archaeal actin homologue). Numerous inclusions are observed in archaeal cells, including gas vesicles. Bacterial and archaeal ribosomes are 70S in size but differ slightly in their morphology. They also differ in terms of their protein content, with many archaeal ribosomal proteins being more similar to those in eukaryotic ribosomes than to those in bacterial ribosomes. The genetic material of archaeal cells is located in the nucleoid, which is not enclosed by a membrane. All known archaeal chromosomes consist of a doublestranded, covalently closed, circular DNA molecule. In many archaea, the nucleoid contains a single chromosome. However, some archaea are polyploid, having more than one copy of their chromosome. Like bacteria, archaea use nucleoid-associated proteins (NAPs) to organize their chromosomes. 4.4 Many Archaea Have External Structures Used for Attachment and Motility ■ ■ ■ ■ Many archaea have pili, similar to bacterial type IV pili. Many archaea are motile by means of flagella called archaella, which are structurally related to bacterial type IV pili (figure 4.11). They are rigid helices that rotate, and the direction of rotation determines if the cell moves forward or backward. Rotation is powered by ATP hydrolysis. Motile archaea exhibit chemotaxis. Some are also phototactic. The archaeal taxis machinery is similar to that of bacteria. Archaea engage in relocate-and-seek swimming behaviors that may aid in positioning cells optimally in a temperature gradient. 22/10/18 7:27 pm 86 CHAPTER 4 | Archaeal Cell Structure Active Learning 1. Archaea with cell walls consisting of a thick, homogeneous layer of complex polysaccharides often retain crystal violet dye when stained using the Gram-staining procedure. Suggest a reason for this staining reaction. 2. Isoprene serves as a building block not only for the hydrocarbons observed in archaeal membranes but also for sterols, carotenoids, retinal, and quinones. Use any resources necessary to identify the function of these other isoprenebased molecules and to determine their distribution in nature. What does the use of isoprene to make this diverse array of molecules suggest about the nature of the last universal common ancestor (LUCA)? 3. As we note in section 4.3, archaeal ribosomal proteins can be divided into three classes: (1) those with homologues in all three domains of life, (2) those unique to archaea, and (3) those with homologues in eukaryotic ribosomes. Predict a class of archaeal ribosomal proteins that would refute the argument made by some microbiologists that the term prokaryote should be abandoned. 4. Consider the cell shape of Haloquadratum walsbyi, a rectangular prism with dimensions of 2 µm by 2 µm by 0.25 µm. Calculate the surface area and volume of a single wil11886_ch04_077-086.indd 86 cell with these dimensions and calculate the ratio of these values. Compare your results to the values given for a coccus in figure 3.5. 5. Identify some challenges to working with archaea in the laboratory, given their habitats in locations like salt ponds, acid mine drainage sites, and deep sea hydrothermal vents. 6. Scientists studying the human archaeome, the subset of the human microbiome that comprises archaea, found that some typical laboratory procedures bias the types of organisms detected. As you might expect, using techniques devised for working with bacteria resulted in those organisms being detected more frequently. The scientists developed strategies to survey the types of archaea present in several regions of the human body and documented archaeal populations among the resident microbes. Why might breaking open a mixture of microbial cells to extract genomic DNA be biased against archaeal cells? Why might procedures to determine the 16S rRNA sequences be biased against archaeal 16S rRNA sequences? Read the original paper: Koskinen, K., et al. 2017. First insights into the diverse human archaeome. mBio 8(6): e00824-17. 22/10/18 7:27 pm