Structure of Prokaryotes: Bacteria and Archaea

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64 Structure of Prokaryotes: Bacteria and Archaea

By the end of this section, you will be able to do the following:

Describe the basic structure of a typical prokaryote
Describe important differences in structure between Archaea and Bacteria

There are many differences between prokaryotic and eukaryotic cells. The name “prokaryote” suggests that prokaryotes are defined by exclusion—they are not eukaryotes, or organisms whose cells contain a nucleus and other internal membrane-bound organelles. However, all cells have four common structures: the plasma membrane, which functions as a barrier for the cell and separates the cell from its environment; the cytoplasm, a complex solution of organic molecules and salts inside the cell; a double-stranded DNA genome, the informational archive of the cell; and ribosomes, where protein synthesis takes place. Prokaryotes come in various shapes, but many fall into three categories: cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped) (Figure 1).

Part a: The micrograph shows ball-shaped cocci about 0.9 microns long. Part b: The micrograph shows elongated, oval-shaped bacilli about 2 microns long. Part c: The micrograph shows corkscrew-shaped spirilli that are quite long and 2 microns in diameter. — **Figure 1:** Common prokaryotic cell types. Prokaryotes fall into three basic categories based on their shape, visualized here using scanning electron microscopy: (a) cocci, or spherical (a pair is shown); (b) bacilli, or rod-shaped; and (c) spirilli, or spiral-shaped. (credit a: modification of work by Janice Haney Carr, Dr. Richard Facklam, CDC; credit c: modification of work by Dr. David Cox; scale-bar data from Matt Russell)

The Prokaryotic Cell

Recall that prokaryotes are unicellular organisms that lack membrane-bound organelles or other internal membrane-bound structures (Figure 2). Their chromosome—usually single—consists of a piece of circular, double-stranded DNA located in an area of the cell called the nucleoid. Most prokaryotes have a cell wall outside the plasma membrane. The cell wall functions as a protective layer, and it is responsible for the organism’s shape. Some bacterial species have a capsule outside the cell wall. The capsule enables the organism to attach to surfaces, protects it from dehydration and attack by phagocytic cells, and makes pathogens more resistant to our immune responses. Some species also have flagella (singular, flagellum) used for locomotion, and pili (singular, pilus) used for attachment to surfaces including the surfaces of other cells. Plasmids, which consist of extra-chromosomal DNA, are also present in many species of bacteria and archaea.

Recall that prokaryotes are divided into two different domains, Bacteria and Archaea, which together with Eukarya, comprise the three domains of life (Figure 3).

The trunk of the phylogenetic tree is a universal ancestor. The tree forms two branches. One branch leads to the domain bacteria, which includes the phyla proteobacteria, chlamydias, spirochetes, cyanobacteria, and Gram-positive bacteria. The other branch branches again, into the eukarya and archaea domains. Domain archaea includes the phyla euryarchaeotes, crenarchaeotes, nanoarchaeotes, and korarchaeotea. — **Figure 3:** The three domains of living organisms. Bacteria and Archaea are both prokaryotes but differ enough to be placed in separate domains. An ancestor of modern Archaea is believed to have given rise to Eukarya, the third domain of life. Major groups of Archaea and Bacteria are shown.

Characteristics of bacterial phyla are described in Figure 4 and Figure 5. Major bacterial phyla include the Proteobacteria, the Chlamydias, the Spirochaetes, the photosynthetic Cyanobacteria, and the Gram-positive bacteria. The Proteobacteria are in turn subdivided into several classes, from the Alpha- to the Epsilon proteobacteria. Eukaryotic mitochondria are thought to be the descendants of alphaproteobacteria, while eukaryotic chloroplasts are derived from cyanobacteria. Archaeal phyla are described in Figure 6.

Characteristics of the five phyla of bacteria are described. The first phylum described is proteobacteria, which includes five classes, alpha, beta, gamma, delta and epsilon. Most species of Alpha Proteobacteria are photoautotrophic but some are symbionts of plants and animals, and others are pathogens. Eukaryotic mitochondria are thought be derived from bacteria in this group. Representative species include Rhizobium, a nitrogen-fixing endosymbiont associated with the roots of legumes, and Rickettsia, obligate intracellular parasite that causes typhus and Rocky Mountain Spotted Fever (but not rickets, which is caused by Vitamin C deficiency). A micrograph shows rod-shaped Rickettsia rickettsii inside a much larger eukaryotic cell. Beta Proteobacteria is a diverse group of bacteria. Some species play an important role in the nitrogen cycle. Representative species include Nitrosomas, which oxidize ammonia into nitrate, and Spirillum minus, which causes rat bite fever. A micrograph of spiral-shaped Spirillum minus is shown. Gamma Proteobacteria include many are beneficial symbionts that populate the human gut, as well as familiar human pathogens. Some species from this subgroup oxidize sulfur compounds. Representative species include Escherichia coli, normally beneficial microbe of the human gut, but some strains cause disease; Salmonella, certain strains of which cause food poisoning, and typhoid fever; Yersinia pestis–the causative agent of Bubonic plague; Psuedomonas aeruganosa– causes lung infections; Vibrio cholera, the causative agent of cholera, and Chromatium–sulfur producing bacteria bacteria that oxidize sulfur, producing H2S. Micrograph shows rod-shaped Vibrio cholera, which are about 1 micron long. Some species of delta Proteobacteria generate a spore-forming fruiting body in adverse conditions. Others reduce sulfate and sulfur. Representative species include Myxobacteria, which generate spore-forming fruiting bodies in adverse conditions and Desulfovibrio vulgaris, an aneorobic, sulfur-reducing bacterium. Micrograph shows a bent rod-shaped Desulfovibrio vulgaris bacterium with a long flagellum. Epsilon Proteobacteria includes many species that inhabit the digestive tract of animals as symbionts or pathogens. Bacteria from this group have been found in deep-sea hydrothermal vents and cold seep habitats. The next phylum described is chlamydias. All members of this group are obligate intracellular parasites of animal cells. Cells walls lack peptidoglycan. Micrograph shows a pap smear of cells infected with Chlamydia trachomatis. Chlamydia infection is the most common sexually transmitted disease and can lead to blindness. All members of the phylum Spirochetes have spiral-shaped cells. Most are free-living anaerobes, but some are pathogenic. Flagella run lengthwise in the periplasmic space between the inner and outer membrane. Representative species include Treponema pallidum, the causative agent of syphilis and Borrelia burgdorferi, the causative agent of Lyme disease Micrograph shows corkscrew-shaped Trepanema pallidum, about 1 micron across. Bacteria in the phylum Cyanobacteria, also known as blue-green algae, obtain their energy through photosynthesis. They are ubiquitous, found in terrestrial, marine, and freshwater environments. Eukaryotic chloroplasts are thought be derived from bacteria in this group. The cyanobacterium Prochlorococcus is believed to be the most abundant photosynthetic organism on earth, responsible for generating half the world’s oxygen. Micrograph shows a long, thin rod-shaped species called Phormidium. Gram-positive Bacteria have a thick cell wall and lack an outer membrane. Soil-dwelling members of this subgroup decompose organic matter. Some species cause disease. Representative species include Bacillus anthracis, which causes anthrax; Clostridium botulinum, which causes botulism; Clostridium difficile, which causes diarrhea during antibiotic therapy; Streptomyces, from which many antibiotics, including streptomyocin, are derived; and Mycoplasmas, the smallest known bacteria, which lack a cell wall. Some are free-living, and some are pathogenic. Micrograph shows Clostridium difficile, which are rod-shaped and about 3 microns long. — **Figure 4:** The Proteobacteria. Phylum Proteobacteria is one of up to 52 bacteria phyla. Proteobacteria is further subdivided into five classes, Alpha through Epsilon. (credit “Rickettsia rickettsia”: modification of work by CDC; credit “Spirillum minus”: modification of work by Wolframm Adlassnig; credit “Vibrio cholera”: modification of work by Janice Haney Carr, CDC; credit “Desulfovibrio vulgaris”: modification of work by Graham Bradley; credit “Campylobacter”: modification of work by De Wood, Pooley, USDA, ARS, EMU; scale-bar data from Matt Russell)

**Figure 5:** Other bacterial phyla. Chlamydia, Spirochetes, Cyanobacteria, and Gram-positive bacteria are described in this table. Note that bacterial shape is not phylum-dependent; bacteria within a phylum may be cocci, rod-shaped, or spiral. (credit “Chlamydia trachomatis”: modification of work by Dr. Lance Liotta Laboratory, NCI; credit “Treponema pallidum”: modification of work by Dr. David Cox, CDC; credit “Phormidium”: modification of work by USGS; credit “Clostridium difficile”: modification of work by Lois S. Wiggs, CDC; scale-bar data from Matt Russell)

Characteristics of the four phyla of archaea are described. Euryarchaeotes includes methanogens, which produce methane as a metabolic waste product, and halobacteria, which live in an extreme saline environment. Methanogens cause flatulence in humans and other animals. Halobacteria can grow in large blooms that appear reddish, due to the presence of bacterirhodopsin in the membrane. Bacteriorhodopsin is related to the retinal pigment rhodopsin. Micrograph shows rod shaped Halobacterium. Members of the ubiquitous Crenarchaeotes phylum play an important role in the fixation of carbon. Many members of this group are sulfur dependent extremophiles. Some are thermophilic or hyperthermophilic. Micrograph shows cocci shaped Sulfolobus, a genus which grows in volcanic springs at temperatures between 75 degrees and 80 degrees Celsius and at a lower case p upper case H between 2 and 3. The phylum Nanoarchaeotes currently contains only one species, Nanoarchaeum equitans, which has been isolated from the bottom of the Atlantic Ocean, and from the a hydrothermal vent at Yellowstone National Park. It is an obligate symbiont with Ignococcus, another species of archaebacteria. Micrograph shows two small, round N. equitans cells attached to a larger Ignococcus cell. Korarchaeotes are considered to be one of the most primitive forms of life and so far have only been found in the Obsidian Pool, a hot spring at Yellowstone National Park. Micrograph shows a variety of specimens from this group which vary in shape. — **Figure 6:** Archaeal phyla. Archaea are separated into four phyla: the Korarchaeota, Euryarchaeota, Crenarchaeota, and Nanoarchaeota. (credit “Halobacterium”: modification of work by NASA; credit “Nanoarchaeotum equitans”: modification of work by Karl O. Stetter; credit “Korarchaeota”: modification of work by Office of Science of the U.S. Dept. of Energy; scale-bar data from Matt Russell)

The Plasma Membrane of Prokaryotes

The prokaryotic plasma membrane is a thin lipid bilayer (6 to 8 nanometers) that completely surrounds the cell and separates the inside from the outside. Its selectively permeable nature keeps ions, proteins, and other molecules within the cell and prevents them from diffusing into the extracellular environment, while other molecules may move through the membrane. Recall that the general structure of a cell membrane is a phospholipid bilayer composed of two layers of lipid molecules. In archaeal cell membranes, isoprene (phytanyl) chains linked to glycerol replace the fatty acids linked to glycerol in bacterial membranes. Some archaeal membranes are lipid monolayers instead of bilayers (Figure 7).

This illustration compares phospholipids from Bacteria and Eukarya to those from Archaea. In Bacteria and Eukarya, fatty acids are attached to glycerol by an ester linkage, while in Archaea, isoprene chains are linked to glycerol by an ether linkage. In the ester linkage, the first carbon in the fatty acid chain has an oxygen double-bonded to it, whereas in the ether linkage, it does not. In Archaea, the isoprene chains have methyl groups branching off from them, whereas such branches are absent in Bacteria and Eukarya. Both types of phospholipids result in similar lipid bilayers. — **Figure 7:** Bacterial and archaeal phospholipids. Archaeal phospholipids differ from those found in Bacteria and Eukarya in two ways. First, they have branched phytanyl sidechains instead of linear ones. Second, an ether bond instead of an ester bond connects the lipid to the glycerol.

The Cell Wall of Prokaryotes

The cytoplasm of prokaryotic cells has a high concentration of dissolved solutes. Therefore, the osmotic pressure within the cell is relatively high. The cell wall is a protective layer that surrounds some cells and gives them shape and rigidity. It is located outside the cell membrane and prevents osmotic lysis (bursting due to increasing volume). The chemical composition of the cell wall varies between Archaea and Bacteria, and also varies between bacterial species.

Bacterial cell walls contain peptidoglycan, composed of polysaccharide chains that are cross-linked by unusual peptides containing both L- and D-amino acids including D-glutamic acid and D-alanine. (Proteins normally have only L-amino acids; as a consequence, many of our antibiotics work by mimicking D-amino acids and therefore have specific effects on bacterial cell-wall development.) There are more than 100 different forms of peptidoglycan. S-layer (surface layer) proteins are also present on the outside of cell walls of both Archaea and Bacteria.

Bacteria are divided into two major groups: Gram positive and Gram negative, based on their reaction to Gram staining. Note that all Gram-positive bacteria belong to one phylum; bacteria in the other phyla (Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria, and others) are Gram-negative. The Gram staining method is named after its inventor, Danish scientist Hans Christian Gram (1853–1938). The different bacterial responses to the staining procedure are ultimately due to cell wall structure. Gram-positive organisms typically lack the outer membrane found in Gram-negative organisms (Figure 8). Up to 90 percent of the cell-wall in Gram-positive bacteria is composed of peptidoglycan, and most of the rest is composed of acidic substances called teichoic acids. Teichoic acids may be covalently linked to lipids in the plasma membrane to form lipoteichoic acids. Lipoteichoic acids anchor the cell wall to the cell membrane. Gram-negative bacteria have a relatively thin cell wall composed of a few layers of peptidoglycan (only 10 percent of the total cell wall), surrounded by an outer envelope containing lipopolysaccharides (LPS) and lipoproteins. This outer envelope is sometimes referred to as a second lipid bilayer. The chemistry of this outer envelope is very different, however, from that of the typical lipid bilayer that forms plasma membranes.

VISUAL CONNECTION

The left illustration shows the cell wall of Gram-positive bacteria. The cell wall is a thick layer of peptidoglycan that exists outside the plasma membrane. A long, thin molecule called lipoteichoic acid anchors the cell wall to the cell membrane. The right illustration shows Gram-negative bacteria. In Gram-negative bacteria, a thin peptidoglycan cell wall is sandwiched between an outer and an inner plasma membrane. The space between the two membranes is called the periplasmic space. Lipoproteins anchor the cell wall to the outer membrane. Lipopolysaccharides protrude from the outer membrane. Porins are proteins in the outer membrane that allow entry of substances. — **Figure 8:** Cell walls in Gram-positive and Gram-negative bacteria. Bacteria are divided into two major groups: Gram positive and Gram negative. Both groups have a cell wall composed of peptidoglycan: in Gram-positive bacteria, the wall is thick, whereas in Gram-negative bacteria, the wall is thin. In Gram-negative bacteria, the cell wall is surrounded by an outer membrane that contains lipopolysaccharides and lipoproteins. Porins are proteins in this cell membrane that allow substances to pass through the outer membrane of Gram-negative bacteria. In Gram-positive bacteria, lipoteichoic acid anchors the cell wall to the cell membrane. (credit: modification of work by “Franciscosp2″/Wikimedia Commons)

Which of the following statements is true?

Gram-positive bacteria have a single cell wall anchored to the cell membrane by lipoteichoic acid.
Porins allow entry of substances into both Gram-positive and Gram-negative bacteria.
The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
Gram-negative bacteria have a cell wall made of peptidoglycan, whereas Gram-positive bacteria have a cell wall made of lipoteichoic acid.

^Answer:
^{Statement “a” is true.}

Archaean cell walls do not have peptidoglycan. There are four different types of archaean cell walls. One type is composed of pseudopeptidoglycan, which is similar to peptidoglycan in morphology but contains different sugars in the polysaccharide chain. The other three types of cell walls are composed of polysaccharides, glycoproteins, or pure protein. Other differences between Bacteria and Archaea are seen in Table 1. Note that features related to DNA replication, transcription and translation in Archaea are similar to those seen in eukaryotes.

Table 1: Differences and Similarities between Bacteria and Archaea
Structural Characteristic	Bacteria	Archaea
Cell type	Prokaryotic	Prokaryotic
Cell morphology	Variable	Variable
Cell wall	Contains peptidoglycan	Does not contain peptidoglycan
Cell membrane type	Lipid bilayer	Lipid bilayer or lipid monolayer
Plasma membrane lipids	Fatty acids-glycerol ester	Phytanyl-glycerol ethers
Chromosome	Typically circular	Typically circular
Replication origins	Single	Multiple
RNA polymerase	Single	Multiple
Initiator tRNA	Formyl-methionine	Methionine
Streptomycin inhibition	Sensitive	Resistant
Calvin cycle	Yes	No

Reproduction

Reproduction in prokaryotes is asexual and usually takes place by binary fission. (Recall that the DNA of a prokaryote is a single, circular chromosome.) Prokaryotes do not undergo mitosis; instead, the chromosome is replicated and the two resulting copies separate from one another, due to the growth of the cell. The prokaryote, now enlarged, is pinched inward at its equator and the two resulting cells, which are clones, separate. Binary fission does not provide an opportunity for genetic recombination or genetic diversity, but prokaryotes can share genes by three other mechanisms.

In transformation, the prokaryote takes in DNA shed by other prokaryotes into its environment. If a nonpathogenic bacterium takes up DNA for a toxin gene from a pathogen and incorporates the new DNA into its own chromosome, it too may become pathogenic. In transduction, bacteriophages, the viruses that infect bacteria, may move short pieces of chromosomal DNA from one bacterium to another. Transduction results in a recombinant organism. Archaea also have viruses that may translocate genetic material from one individual to another. In conjugation, DNA is transferred from one prokaryote to another by means of a pilus, which brings the organisms into contact with one another, and provides a channel for transfer of DNA. The DNA transferred can be in the form of a plasmid or as a composite molecule, containing both plasmid and chromosomal DNA. These three processes of DNA exchange are shown in Figure 9.

Reproduction can be very rapid: a few minutes for some species. This short generation time coupled with mechanisms of genetic recombination and high rates of mutation result in the rapid evolution of prokaryotes, allowing them to respond to environmental changes (such as the introduction of an antibiotic) very quickly.

Illustration A shows a small, circular piece of DNA being absorbed by a cell. Illustration C shows a bacteriophage injecting DNA into a prokaryotic cell. The DNA then gets incorporated in the genome. Illustration C shows two bacteria connected by a pilus. A small loop of DNA is transferred from one cell to another via the pilus. — **Figure 9:** Gene transfer mechanisms in prokaryotes. There are three mechanisms by which prokaryotes can exchange DNA. In (a) transformation, the cell takes up prokaryotic DNA directly from the environment. The DNA may remain separate as plasmid DNA or be incorporated into the host genome. In (b) transduction, a bacteriophage injects DNA into the cell that contains a small fragment of DNA from a different prokaryote. In (c) conjugation, DNA is transferred from one cell to another via a mating bridge, or pilus, that connects the two cells after the sex pilus draws the two bacteria close enough to form the bridge.

EVOLUTION CONNECTION

The Evolution of Prokaryotes

How do scientists answer questions about the evolution of prokaryotes? Unlike with animals, artifacts in the fossil record of prokaryotes offer very little information. Fossils of ancient prokaryotes look like tiny bubbles in rock. Some scientists turn to genetics and to the principle of the molecular clock, which holds that the more recently two species have diverged, the more similar their genes (and thus proteins) will be. Conversely, species that diverged long ago will have more genes that are dissimilar.

Scientists at the NASA Astrobiology Institute and at the European Molecular Biology Laboratory collaborated to analyze the molecular evolution of 32 specific proteins common to 72 species of prokaryotes.^¹ The model they derived from their data indicates that three important groups of bacteria—Actinobacteria, Deinococcus, and Cyanobacteria (collectively called Terrabacteria by the authors)—were the first to colonize land. Actinobacteria are a group of very common Gram-positive bacteria that produce branched structures like fungal mycelia, and include species important in decomposition of organic wastes. You will recall that Deinococcus is a genus of bacterium that is highly resistant to ionizing radiation. It has a thick peptidoglycan layer in addition to a second external membrane, so it has features of both Gram-positive and Gram-negative bacteria.

Cyanobacteria are photosynthesizers, and were probably responsible for the production of oxygen on the ancient earth. The timelines of divergence suggest that bacteria (members of the domain Bacteria) diverged from common ancestral species between 2.5 and 3.2 billion years ago, whereas the Archaea diverged earlier: between 3.1 and 4.1 billion years ago. Eukarya later diverged from the archaean line. The work further suggests that stromatolites that formed prior to the advent of cyanobacteria (about 2.6 billion years ago) photosynthesized in an anoxic environment and that because of the modifications of the Terrabacteria for land (resistance to drying and the possession of compounds that protect the organism from excess light), photosynthesis using oxygen may be closely linked to adaptations to survive on land.

Footnotes

1 Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land. BioMed Central: Evolutionary Biology 4 (2004): 44, doi:10.1186/1471-2148-4-44.

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