Comparisons of Eubacteria, Archaea, and Eukaryotes

Characteristic	Eubacteria	Archaea	Eukaryotes
Cell wall	gram +ve or gram -ve (structure)	murein absent	plasma membrane
Predominantly multicellular	no	no	yes
Nucleus, membrane bound organelles	no	no	yes
DNA	circular	circular	linear
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
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	Mycoplasma (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
peptidoglycan*	thick teichoic acid	none	none pseudomurein or complex carbohydrate	none protein-glycoprotein
S-layer 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	Escherichia
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.