Comparisons of Eubacteria, Archaea, and Eukaryotes

Characteristic Eubacteria Archaea


Cell wall gram +ve or gram -ve (structure) murein absent plasma membrane
Predominantly multicellularno no yes
Nucleus, membrane bound organelles no no yes
DNA circular circularlinear
Ribosome 70s 70s 80s
Membrane lipids ester-linked* yes no yes
Photosynthesis with chlorophyll yes no yes
Growth above 80o C yes yes no
Histone proteins present no yes yes
tRNA initiator fMet Met Met
Operons yes yes no
Introns in genome none some [a, 1, 2, 3, 4, 5, 6, 7, 8,] most
Capping and poly-A tailing of mRNA no no yes
Transcription factors required yes no yes
Methanogenesis no yes no
Nitrification yes no no
Denitrification yes yes no
Nitrogen Fixation yes yes no
Chemolithotrophy yes yes no
Gas vesicles present yes yes no
Sensitive to chloramphenicol, kanamycin and streptomycin yes no no
* Archaea membrane lipids are ether-linked
Adapted from here.
Property Eubacteria Archaea Eukarya
Cytological features
Nucleus No No Yes
Cytoskeleton No No Yes
Organelles (mitochondria, chloroplasts, Golgi apparatus, endoplasmic reticulum) No No Yes
Molecular features
DNA topology Negatively supercoiled Relaxed or positively supercoiled (in hyperthermophilic Archaea that contain reverse gyrase) Negatively supercoiled
Promoter structure Two conserved boxes at - 10 (TATAAT) and - 35 (TTGACA) from transcription start site TATA box and/or initiator element TATA box and/or initiator element
RNA polymerase One type; relatively simple subunit composition; binds directly to promoter (can be footprinted) One type; complex subunit structure (subunit pattern, genes, and serological properties similar to eukaryal RNA polymerase II); can be footprinted, but still requires basal transcription factors for promoter recognition [1, 2, 3,] Three types; complex subunit compositions; cannot be footprinted; require basal transcription factors for promoter recognition/binding
Basal transcription factors No TBP , TFIIB, and TIIS homologs of eucaryal RNA polymerase II-associated factors described thus far TBP, TAFs, TFIIA, TFIIB, TFIIE, TFIIF, TFIIH required for RNA polymerase II initiation; P-TEFb, TFIIS, TFIIF, elongin, and ELL required for elongation
Poly(A) tails in RNA Short Short (avg. 12 bases in length) Long
Chromatin No ? Yes

Table adapted from Archaeal chromatin: Virtual or real? Jordanka Zlatanova Proc. Natl. Acad. Sci. USA, Vol. 94, pp. 12251-12254, November 1997

For further features and references see the series of minireviews on Archaea published in the June 27, 1997, issue of Cell, and refs. 5 and 27.

 Cell walls of Prokaryotes  Electron acceptors for respiration and methanogenesis in prokaryotes  Glycolysis in bacteria  Lithotrophic prokaryotes  Gene Regulation in E.coli  Second Messengers  Cell signaling

Cell walls of Prokaryotes

Domain Eubacteria Archaea
membrane Glycerol-ester lipids Glycerol-ether lipids

Amphipathic molecules containing a backbone of glycerol connected to a hydrophilic head group and two hydrophobic long-chain fatty acids.

Fatty acids are attached to the glycerol backbone by ester bonds.

Isoprenoid side chain

Fatty acids are attached to the glycerol backbone by ether bonds.

In some extremophiles, C-40 hydrophobic chains attached to the glycerol backbone are twice normal length and pass completely through the membrane, attaching to a second backbone on the opposite side and adding stability.

chains linear branched

carbon rings

chirality of glycerol D-glycerol (R) L-glycerol (S)
lacking cell wall


(sterol-like compounds in cell membranes provide osmotic protection)

Thermoplasma, Picrophilaceae

In addition to differences in composition of the cell membrane, Eubacteria and Archaea differ in the composition of the cell wall. Cell walls are rigid to semi-rigid structures that enclose the protoplastic cell membrane, and which are found in bacteria, archaea, fungi, plants, and algae, but not in animals.

 Comparisons of Eubacteria, Archaea, and Eukaryotes

Cell Wall Gram +ve bacteria

Gram -ve bacteria

Gram +ve Archea Gram -ve Archaea
outer membrane

Lipoprotein-lipopolysaccharide-phospholipid (LPS) with porins.

Braun’s lipoprotein anchors outer membrane to peptidoglycan



teichoic acid

none none

pseudomurein or complex carbohydrate




patterned, surface layer of protein or glycoprotein

some bacteria

associated with the peptidoglycan

some bacteria

adheres directly to outer membrane

sole cell-wall component in Planctomyces

commonly constitutes cell wall

commonly constitutes cell wall

*Peptidoglycan comprises N-acetylglucosamine (NAG) bonded to N-acetyl muramic acid (NAM) by a 1,4 glycosidic bond. The N-acetylmuramic acid (NAM) in peptidoglycan is replaced by N-acetyl talosaminouronic acid acid (NAT) in pseudopeptidoglycan (pseudomurein) of Archaea (im). Each glycan is linked by 1,4 glycosidic bonds in peptidoglycan and by 1,3 glycosidic bonds in pseudomurein (NAT). Hyperthermophiles use branched glycerol tetraethers (single-layer membranes) to increase membrane fluidity, so they lack a cell wall. Psychrophiles have plasma membranes with lipids that contain mainly unsaturated fatty acids.

Electron acceptors for respiration and methanogenesis in prokaryotes

Electron acceptor Reduced end product Process Organism
O2 H2O aerobic respiration Escherichia, Streptomyces
NO3 NO2, NH3 or N2 denitrification Bacillus, Pseudomonas
SO4 S or H2S sulfate reduction Desulfovibrio
fumarate succinate anaerobic respiration

using an e- acceptor

CO2 CH4 methanogenesis Methanococcus

Glycolysis in bacteria

Bacterium Embden-Meyerhof pathway Phosphoketolase (heterolactic) pathway Entner-Doudoroff pathway
Acetobacter aceti absent present absent
Agrobacterium tumefaciens absent absent present
Azotobacter vinelandii absent absent present
Bacillus subtilis major minor absent
Escherichia coli present absent absent
Lactobacillus acidophilus present absent absent
Leuconostoc mesenteroides absent present absent
Pseudomonas aeruginosa absent absent present
Vibrio cholerae minor absent major
Zymomonas mobilis absent absent present

Lithotrophic prokaryotes

Physiological group Energy source Oxidized end product Lithotrophic organism
methanogens H2 H2O Methanobacterium
hydrogen bacteria H2 H2O Alcaligenes, Pseudomonas
carboxydobacteria CO CO2 Rhodospirillum, Azotobacter
nitrifying bacteria* NH3 NO2 Nitrosomonas
nitrifying bacteria* NO2 NO3 Nitrobacter
sulfur oxidizers H2S or S SO4 Thiobacillus, Sulfolobus
iron bacteria Fe ++ Fe+++ Gallionella, Thiobacillus
* The overall process of nitrification, conversion of NO3 to NH3, requires a consortium of microorganisms.
. . . since 10/06/06