Summary of Major Differentiating Features Among Bacteria, Archaea, and Eucarya
Characteristic Bacteria Archaea Eucarya
Membrane-bound nucleus Absent Absent Present
Cell Wall Muramic Acid present Muramic Acid present Muramic Acid present
Membrane lipids Ester-linked Ether-linked Ester-linked
Ribosomes 70S 70S 80S (70S organelles)
Initiator tRNA Formyl-methionine Methionine Methionine
Introns in tRNA genes Rare Yes Yes
Operons Yes Yes No
Capping and poly-A tailing of mRNA No No Yes
Plasmids Common Yes Rare
Protein synthesis sensitive to diptheria toxin No Yes Yes
RNA polymerases One-type (4 subunits) Several (8-12 subunits) 3 (12-14 subunits)
Sensitivity to chloramphenicol, streptomycin, kanamycin Yes No No
Methanogenesis No Yes No
Reduction of S0 to H2S Yes Yes No
Nitrogen fixation Yes Yes No
Chlorophyll-based photosynthesis Yes No Yes (chloroplasts)

FONT>G + C CONTENT

Section I: 35 to 71 mol% G + C

Section III 40 to 67 mol% G + C

Sections II, IV and V: 38 to 47 mol% G + C

All bacteria: 29 to 74 mol% G + C

GENOME SIZE

Section I 3000 to 10,000 kbp (Mean: 4450)

Section II 5100 to 7900 kbp (Mean: 6200)

Section III 4100 to 10,000 kbp

Section IV 5300 to 14,000 kbp

Section V 6000 to 8600 kbp

It has been suggested that genomes may have evolved by a series of fusions of smaller genomes (each about 2000 kbp) to form genomes containing 4000 kbp, 6000 kbp, 8000 kbp and 12,000 kbp

Synechocystis sp. PCC 6803

Unicellular, non-nitrogen fixing, heavy capsule

Freshwater

Naturally transformable

Capable of dark heterotrophic growth on glucose

Prefers lower light intensity, Topt ~34°C; optimum doubling time = ~12 hours

Synechococcus sp. PCC 7002

Unicellular (probably a natural short-chain mutant of a Phormidium), non-nitrogen fixing, light capsule

Marine/euryhaline (brackish water)

Naturally transformable

Capable of dark heterotrophic growth on glycerol

High-light tolerant; Topt ~39°C; optimum doubling time = 3.5 hours

Synechocystis sp. PCC 6803 Genome

G + C Content = 47.7%

3168 potential protein coding sequences

145 (4.6%) genes already reported and characterized

933 (29.4%) homologs of known genes

324 (10.2%) similarity to known genes

340 (10.8%) similarity to hypothetical genes

1,426 (45%) no significant similarity to any known gene

87% of Genome was coding sequence (1 gene per 1.1 kb)

Smallest protein: 28 aa Largest potential protein: 4,199 aa

Average protein = 326 amino acids

99 ORFs with similarity to transposases

Stable RNAs

Two rrn clusters identified, which were identical in sequence

42 tRNA genes were identified

rnpB (RNA component of RNase P)


A FEW POTENTIALLY INTERESTING OBSERVATIONS

Although some evidence for operons is observed, clustering of related genes is not very extensive. This differs from E. coli, B. subtilis, etc. Similar observations being made in other sequenced genomes.

Photosynthesis ~4% of genome

Gene regulation ~4% of genome (2% 2-comp.)

Insertion sequences, etc. ~3% of genome

Sigma Factors 9 total identified 1 Group 1

4 Group 2

4 Group 3 (3 RpoE-like)

No RpoN, RpoH, or RpoS

Twitching Motility (Type IV Pili) and Chemotaxis genes present.

Several protein classes found in eucaryotes (e.g., kinases, WD repeat proteins, phytochrome-like proteins, "cyanoglobin" )

Only one set of sec genes was found. Suggests thylakoid lumen and periplasmic space are topographically identical. However, two LepB's and one LspA.

3 DnaKs, 2 GroELs, 4 DnaJs, 3 NifSs

Multiple ndh genes for ndhF (4) and ndhD (5)

Multiple petC genes (Rieske Fe-S protein) (3)

Three oxidases: cydBD genes (putative plastoquinol oxidase), and two cytochrome oxidase gene sets; also genes with similarity to succinate dehydrogenase, fumarate reductase, and uptake hydrogenase. 5 presumed 2Fe-2S Ferredoxins

Two DNA polymerases (Polymerases I and III).

WHY SO MANY GENES??

Developmentally among the most complex procaryotes known

Heterocysts Anaerobic cells for N2 fixation

terminally differentiated cells with a specified pattern (like a tissue)

Akinetes Resting cells

Hormogonia Swarmer cells for dispersal; formed upon akinete germination

Relationships Among Genomes

66% of the H. influenzae genes (1130 of 1703 sequences) have E. coli homologs

>50% of the H. pylori genes (more than 800 of 1590 sequences) have hits in E. coli

51.5% of the A. aeolicus genes (777 of 1508 sequences) have hits in E. coli (~38% similarity on average)

25% of the A. aeolicus genes (379 of 1508 sequences) have hits in M. jannaschii (~35% similarity on average)

21% of the Synechocystis sp. PCC 6803 genes (675 of 3168 sequences) have hits in E. coli

13% of the M. jannaschii genes have hits to E. coli (231 of 1738 sequences) have hits in E. coli

~13% of the Synechocystis sp. PCC 6803 genes have hits in M. jannaschii (407 of 3168)

4.3% of the Saccharomyces cerevisiae proteins (254 of 5885 sequences) have hits in E. coli Ɛ뺎p#KS,+A"NPY9=?/gwZ[_*\j.tZ_Rh2zfgdz^rsU~`~XuJԴSEgӵ]F(#0d^/]QWU