Prokaryote structure

Generalized bacterium

1. pericytoplasmic space
2. cytoplasmic membrane
3. cell wall
4. capsule
5. pili
6. cytoplasm
7. cytoplasmic nucleoid
8. 70s ribosomes
9. plasmid
10. flagellum (monotrichous)
11. pore within pilus

Prokaryotes mostly possess one or two* chromosomes termed nucleoids (tem). Because prokaryotes lack a membrane enclosed nucleus their DNA is usually contained in circular structures located within the cytosol, but may be organized as linear strands that are typically attached to the cytoplasmic membrane. Plasmids are small circular, extrachromosomal genetic elements that can be transmitted from one bacterium to another through the pili during conjugation.

*for example, Vibrio cholerae and Deinococcus radiodurans

Cell wall

The Gram stain for bacteria allows differentiation according to thickness of the layer of peptidoglycan (murein, im) in the cell wall. Bacteria that stain heavily (Gram +ve) have a thick monolayer of peptidoglycan compared to the thin or absent layer of peptidoglycan in (bilayer) bacteria that do not take up the stain (Gram -ve). The cell walls of Archaeobacteria contain no peptidoglycan (murein), rather they contain pseudomurein, complex carbohydrates, or protein-glycoproteins.

S-layers comprise one of the most common surface structures on archaea and bacteria. These surface layers have now been identified in hundreds of different species belonging to all major phylogenetic groups of bacteria, and they represent a feature common to almost all archaea (recent compilation 133). S-layers are monomolecular crystalline arrays of proteinaceous subunits (125, 131, 132).

Tables  Cell walls of Prokaryotes  Comparisons of Eubacteria, Archaea, and Eukaryotes  Electron acceptors for respiration and methanogenesis in prokaryotes  Glycolysis in bacteria  Lithotrophic prokaryotes  Structure of bacteriochlorophylls  Comparison of plant and bacterial photosynthesis :

Diagrams: Eubacteria : peptidoglycan : gram + gram - peptidoglycan : Gram + : Gram - : P. aeruginosa comp-mod : gram -ve : antimicrobials gram + gram - : cell walls gram + gram - mycobacteria : comparison gram + / gram - cell walls : b-w g+ g- : Archaea : Gram positive archaeal cell wall : Gram negative archaeal cell wall : Unusual cell wall of Deinococcus radiodurans :

: S-layer Freeze etched sem :

The structure of secondary cell wall polymers: how Gram-positive bacteria stick their cell walls together.
The cell wall of Gram-positive bacteria has been a subject of detailed chemical study over the past five decades. Outside the cytoplasmic membrane of these organisms the fundamental polymer is peptidoglycan (PG), which is responsible for the maintenance of cell shape and osmotic stability. In addition, typical essential cell wall polymers such as teichoic or teichuronic acids are linked to some of the peptidoglycan chains. In this review these compounds are considered as 'classical' cell wall polymers. In the course of recent investigations of bacterial cell surface layers (S-layers) a different class of 'non-classical' secondary cell wall polymers (SCWPs) has been identified, which is involved in anchoring of S-layers to the bacterial cell surface. Comparative analyses have shown considerable differences in chemical composition, overall structure and charge behaviour of these SCWPs. This review discusses the progress that has been made in understanding the structural principles of SCWPs, which may have useful applications in S-layer-based 'supramolecular construction kits' in nanobiotechnology.
Schaffer C, Messner P. The structure of secondary cell wall polymers: how Gram-positive bacteria stick their cell walls together. (Free Full Text Article) Microbiology. 2005 Mar;151(Pt 3):643-51.

Molecular organization of selected prokaryotic S-layer proteins.
Regular crystalline surface layers (S-layers) are widespread among prokaryotes and probably represent the earliest cell wall structures. S-layer genes have been found in approximately 400 different species of the prokaryotic domains bacteria and archaea. S-layers usually consist of a single (glyco-)protein species with molecular masses ranging from about 40 to 200 kDa that form lattices of oblique, tetragonal, or hexagonal architecture. The primary sequences of hyperthermophilic archaeal species exhibit some characteristic signatures. Further adaptations to their specific environments occur by various post-translational modifications, such as linkage of glycans, lipids, phosphate, and sulfate groups to the protein or by proteolytic processing. Specific domains direct the anchoring of the S-layer to the underlying cell wall components and transport across the cytoplasma membrane. In addition to their presumptive original role as protective coats in archaea and bacteria, they have adapted new functions, e.g., as molecular sieves, attachment sites for extracellular enzymes, and virulence factors.
Claus H, Akca E, Debaerdemaeker T, Evrard C, Declercq JP, Harris JR, Schlott B, Konig H.
Molecular organization of selected prokaryotic S-layer proteins. Can J Microbiol. 2005 Sep;51(9):731-43.
Glycoproteins in prokaryotes. [Arch Microbiol. 1997] PMID: 9382700
Structural research on surface layers: a focus on stability, surface layer homology domains, and surface layer-cell wall interactions. [J Struct Biol. 1998] PMID: 10049812
Prokaryotic glycosylation. [Proteomics. 2001] PMID: 11680871
Glycobiology of surface layer proteins. [Biochimie. 2001] PMID: 11522387
Stress genes and proteins in the archaea. [Microbiol Mol Biol Rev. 1999] PMID: 10585970
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S-Layer proteins.
Cell walls are an important structural component of prokaryotic organisms and essential for many aspects of their life. Particularly, the diverse structures of the outermost boundary layers strongly reflect adaptations of organisms to specific ecological and environmental conditions (6).
Over the past 3 decades of research, it has become apparent that one of the most common surface structures on archaea and bacteria are monomolecular crystalline arrays of proteinaceous subunits termed surface layers or S-layers (125, 131, 132). Since S-layer-carrying organisms are ubiquitous in the biosphere and because S-layers represent one of the most abundant cellular proteins, it is now obvious that these metabolically expensive products must provide the organisms with an advantage of selection in very different habitats (133). This minireview provides a brief survey of the current state of our knowledge about S-layers with a particular focus on molecular biological and genetic aspects. Other recent reviews (5, 7, 127, 133, 135) are recommended for a more detailed introduction to and treatises on this subject.
Sara M, Sleytr UB. S-Layer proteins. (Free Full Text Article) J Bacteriol. 2000 Feb;182(4):859-68.

Prokaryotic glycosylation. [Proteomics. 2001] PMID: 11680871
Common history at the origin of the position-function correlation in transcriptional regulators in archaea and bacteria. [J Mol Evol. 2001] PMID: 11523004
[Homologous protein domains in superkingdoms Archaea, Bacteria, and Eukaryota and the problem of the origin of eukaryotes] [Izv Akad Nauk Ser Biol. 2005] PMID: 16212260
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Cell wall polymers in Archaea (Archaebacteria).
The distribution of the various cell wall and cell envelope (S-layer) polymers among the main lineages of the domain Archaea (Archaebacteria) and the chemical composition and primary structure of polymers forming rigid cell wall sacculi is described. Differences between bacteria and archaea in their sensitivity to antibiotics which inhibit cell wall synthesis in bacteria are discussed.
Kandler O, Konig H. Cell wall polymers in Archaea (Archaebacteria). Cell Mol Life Sci. 1998 Apr;54(4):305-8.

beta-Lactamases are absent from Archaea (archaebacteria). [Microb Drug Resist. 1996] PMID: 9158771
Structure of anionic carbohydrate-containing cell wall polymers in several representatives of the order actinomycetales. [Biochemistry (Mosc). 2000] PMID: 11092967
Anionic polymers in cell walls of gram-positive bacteria. [Biochemistry (Mosc). 1997] PMID: 9360295
The response of selected members of the archaea to the gram stain. [Microbiology. 1996] PMID: 8885405
Life's third domain (Archaea): an established fact or an endangered paradigm? [Theor Popul Biol. 1998] PMID: 9733652
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Taxonomy and Phylogeny

Taxonomy of the bacteria was historically based on phenotypical physical and chemical characteristics – phenetic taxonomy. According to "Bergey's Manual of Systematic Bacteriology", all bacteria can be classified into four divisions, or phyla according to the constituents of their cell walls. [flow chart for classification of obligate intracellular bacteria]

Each division was further subdivided into sections according to -
bacterial shapes1. Reaction to the Gram stain due to thick layer of peptidoglycan (Gram +ve) or thin layer of peptidoglycan (Gram -ve). The cell walls of Archaeobacteria contain no peptidoglycan.
2. Shape (left) – cocci (1), pleomorphic (2), bacillus (3), helical (4) 3. Arrangement of cells
4. Oxygen requirement – aerobic, anaerobic, or facultative anaerobe
5. Motility – flagellated, non-motile
6. Specific nutritional requirements
7. Trophic (metabolic) properties – autotrophic (chemical or photosynthetic), heterotrophic

The major subdivisions employed in general taxonomies are:
Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species. The mnemonic "Dashing King Philip Came Over From Greater Spain" applies.

These subdivisions may be further subdivided. It is common for bacteria to be subdivided into Divisions and further subdivided into Orders. The advent of genomics and examination of 16s ribosomal RNA has led to modifications in the classification of the prokaryotes, with the older nomenclatures revised into new classifications of Phyla.

endosymbiotic transfersRight - click to enlarge image: Proposed endosymbiotic transfer events between the three Domains and the six Kingdoms of Life. (below) Both the Eubacteria and Archaea are prokaryotes, while animals, fungi, plants, and protists are eukaryotes.

The yellow asterisk * indicates the last universal common ancestor (LUCA), or universal cenancestor, which is hypothesized as being at the ancestral root of all living organisms. Not the earliest or simplest living organism, and not necessarily the sole example of its type, this organism possessed the genetic material that diverged (about 3.5 Ga) into all current living organisms. A number of terms are employed to refer to the universal cenancestor – last universal ancestor (LUA), last common ancestor (LCA), or last universal common ancestor (LUCA).

Woese and Fox proposed the Three Domain system: Eubacteria, Archaea, and Eukaryotes.

The Five Kingdom system was proposed in 1969: Monera (prokaryotes), Protista, Plantae, Fungi, Animalia. Discovery of the Archaea added the sixth kingdom.

History of taxonomic concepts:
Linnaeus, 1735 – 2 Kingdoms – Animalia, Vegetabilia
Haeckel, 1866 – 3 Kingdoms – Protista, Plantae, Animalia. Image Haeckel's tree of life.
Chatton, 1937 – 2 Empires – Prokaryota, Eukaryota
Copeland, 1956 – 4 Kingdoms – Monera (prokaryotes), Protoctista, Plantae, Animalia
Whittaker, 1969 – Monera (prokaryotes), Fungi, Protista, Plantae, Animalia
Woese et al, 1977 – 6 Kingdom – Eubacteria, Archaea, Protista, Fungi, Plantae, Animalia
Woese and Fox, 1999 – 3 Domain system: Eubacteria, Archaea, and Eukaryotes

When Woese and Fox proposed the 3 Domain system, the term 'Urkaryotes' was proposed for ancestors of eukaryotes prior to their endosymbiotic acquisition of mitochondria and chloroplasts from prokaryotes. Margulis and Schwartz proposed that Kingdom Protista be replaced by Protoctista to reflect inclusion of multicellular organisms that did fit into the other three eukaryotic kingdoms.

"Misunderstanding the Bacteriological Code"

The Three Domain system is increasingly accepted. Free Full Text Article : Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Woese CR, Fox GE. Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088-90.

Archaea Eocyte Trees
According to the Tree of Life Web Project, two alternative views on the relationship of the major lineages (omitting viruses) are currently regarded as viable (right - click to enlarge image).

Horizontal Gene Transfer Left - click to enlarge image: Horizontal gene transfer - gene swapping - has blurred the evolutionary relationships (image) of prokaryotes, and continues to provide a mechanism for the sharing of antibiotic resistance between bacteria. See: Trees, vines and nets: Microbial evolution changes its face.

Phylogenetic separation into evolutionary relationships (clades), based on comparison of genomes is likely to supplant phenotypical (phenetic) taxonomies of the prokaryotes.


Classification based on 16s rRNALeft - click to enlarge image: Woese has proposed a scheme based on the 16s subunit of ribosomal RNA, which appears to better illustrate evolutionary relationships within the 3 domains.

Phylogenetic tree of organisms

Domain combinations in archaeal, eubacterial and eukaryotic proteomes.
There is a limited repertoire of domain families that are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products, and at the level of genes, duplication, recombination, fusion and fission are the processes that produce new genes. We attempt to gain an overview of these processes by studying the evolutionary units in proteins, domains, in the protein sequences of 40 genomes. The domain and superfamily definitions in the Structural Classification of Proteins Database are used, so that we can view all pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 783 out of the 859 superfamilies in SCOP in these genomes, and the 783 families occur in 1307 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour; 209 families do not make combinations with other families. This type of pattern can be described as a scale-free network. We also study the N to C-terminal orientation of domain pairs and domain repeats. The phylogenetic distribution of domain combinations is surveyed, to establish the extent of common and kingdom-specific combinations. Of the kingdom-specific combinations, significantly more combinations consist of families present in all three kingdoms than of families present in one or two kingdoms. Hence, we are led to conclude that recombination between common families, as compared to the invention of new families and recombination among these, has also been a major contribution to the evolution of kingdom-specific and species-specific functions in organisms in all three kingdoms. Finally, we compare the set of the domain combinations in the genomes to those in the RCSB Protein Data Bank, and discuss the implications for structural genomics.
Apic G, Gough J, Teichmann SA. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol. 2001 Jul 6;310(2):311-25.

Table  Comparisons of Eubacteria, Archaea, and Eukaryotes  Electron acceptors for respiration and methanogenesis in prokaryotes  Glycolysis in bacteria  Lithotrophic prokaryotes  Comparison of plant and bacterial photosynthesis - The Three Domains View Quicktime Movie - Genetic Data movie of phylogram construction - image cladogram - image Tree of Life— Lateral Gene Transfer Diagram - image uprooted tree - image 16S ribosomal RNA - image The "Shrub of Life" - image A comparison of key characteristics from the three domains of life - enlarged - Genomics Animations and Images - Proteins & Proteomics - Animations and Images – Evolution and Phylogenetics - Animations and Images - Biodiversity - Animations and Images – Microbial Diversity – Animations and Images – Emerging Infectious Diseases - Animations and Images – HIV & AIDS - Animations and Images :


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