TABLE 4.
Prokaryotic species with relevance to top-down, system-level studies toward construction of minimal or simpler cells
| Category and species | Genome size | Special feature(s) (reference[s]) |
|---|---|---|
| Mollicutes | Usually parasites without a cell wall; these were the first genomes to be analyzed by global transposon mutagenesis (M. genitalium and M. pneumoniae) (26); the same methodology was applied to Mycoplasma pulmonis (214); defined media have been described for both M. genitalium and M. pneumoniae (24); different species have been compared at the system level for the genome (203), proteome (43), complete sets of tRNA isoacceptors (tRNomics) and tRNA/rRNA modification enzymes (modomics) (39), and methylome (40) | |
| Mycoplasma genitalium G37 | 580 kbp | Second genome to be fully sequenced (13) and still the autonomously replicating culturable species with the smallest genome; the full genome was analyzed early by global transposon mutagenesis for essential genes (26); a later expt concluded that 387 protein-encoding and 43 structural RNA genes were essential (27); genome-scale metabolic reconstruction (72) and an integrative whole-cell computational model (170) are available |
| Mycoplasma pneumoniae M129 | 816 kbp | A genome-scale in vivo assay was performed for this bacterium to determine essential genes for mouse infection, which identified 194 genes (215); the proteome (45, 216), transcriptome (48), and metabolic network (24) have been analyzed at the cell level; it seems to have a larger fraction of multifunctional enzymes than other bacteria (24); the transcriptome was shown to be remarkably dynamic and complex (including antisense transcripts, alternative transcripts, and multiple regulators) and more similar to those of eukaryotes than to those of other bacteria (48) |
| “Candidatus Phytoplasma mali” AT | 602 kbp | Insect-transmitted plant pathogen that represents an economically important disease of apple (217); one of its most distinctive characteristics is its linear chromosome (218) |
| Obligate endosymbionts of insects | Usually the smallest and most GC-poor genomes reported, with the exception of Hodgkinia (219); genomes indicate functional convergence during evolution (220) | |
| “Candidatus Tremblaya princeps” PCVAL | 138 kbp | Smallest genome of an endosymbiont; genes for synthesis of nucleotides and cofactors, energy production, transport, and cell wall biogenesis are absent; only part of the replication machinery is preserved (221); ability to synthesize most of the amino acids is still encoded; it is a primary insect endosymbiont with a secondary endosymbiont (221) |
| Buchnera aphidicola APS | 656 kbp | Model bacterium for extremely reduced prokaryotic genomes of obligate endosymbionts of insects (71, 128, 162, 222, 223); there are no reports of cultures without insect cells (70, 223) |
| “Candidatus Hodgkinia cicadicola” Dsem | 144 kbp | Unprecedented combination of an extremely small genome (144 kb), a GC-biased base composition (58.4%), and a coding reassignment of the UGA codon from stop to tryptophan (219) |
| “Candidatus Carsonella ruddii” PV | 160 kbp | Symbiont that appears to be present in all species of phloem sap-feeding insects; more than half of the ORFs are devoted to translation and amino acid metabolism (21) |
| “Candidatus Sulcia muelleri” | The most ancient and widely distributed insect nutritional symbiont; the cells can be very large with an elongated shape, often >30 μm in length (224); it is present in a large group of related insects, which supports the ancient acquisition of the symbiont by a shared ancestor, dating the original infection to at least 260 million yr ago (224); together with other endosymbionts, it forms dual-symbiont systems that allow collective production of the 10 amino acids not synthesized by the host (220) | |
| DMIN | 244 kbpa | |
| GWSS | 246 kbpb | |
| Other obligate endosymbionts | ||
| “Candidatus Vesicomyosocius okutanii” HA | 1.02 Mbp | Thioautotrophic primary endosymbiont of a deep-sea clam; this is the smallest genome reported for autotrophic bacteria (225); it contains genes for thioautotrophy and for synthesis of almost all amino acids and various cofactors but apparently lacks several transporters of these substances to the host cell and several other genes that are essential in E. coli, mainly the ftsZ genes and related genes for cytokinesis (225) |
| Free-living prokaryotes with the smallest genomes | ||
| Pelagibacter ubique SAR11 HTCC1062 | 1.31 Mbp | Heterotrophic prokaryote supposed to be the most abundant species on Earth (226); it has the smallest genome encoding the smallest no. of predicted ORFs of all free-living microorganisms (227); in contrast to other genome-reduced prokaryotes, it has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors; no pseudogenes, introns, transposons, extrachromosomal elements, or inteins are known; it has few paralogs and the shortest intergenic spacers observed for any cell (227); noncanonical metabolic rearrangements in defined media have been reported (226); an analysis of the proteome covering 65% of the ORFs confirmed remodeling of expression during adaptation to stationary phase (228) |
| Prochlorococcus marinus MED4 | 1.66 Mbp | Smallest genome and cell size of an oxygenic phototroph; it is believed to be the most abundant photosynthetic organism on Earth (227); the two genomes spanning the largest phylogenetic distance in the genus were compared, revealing genomic dynamics and small proportions of regulatory genes (229); the no. of noncoding RNAs relative to the genome size is comparable to that found in other bacteria (230); simplified regulation of nitrogen utilization was reported (231) |
| Model bacteria relevant for industry | ||
| Escherichia coli K-12 MG1655 | 4.64 Mbp | Model Gram-negative bacterium with the highest species knowledge index for a prokaryote (112); different genome-scale gene essentiality assays concluded that 620 genes (150) and, later, 303 genes (204) were essential; using the lambda red recombination system, genome reductions of up to 15% (103), 22% (102, 106), and 29.7% (125) of the original genome size were reported; another procedure combining Tn5 transposon mutagenesis with the Cre/loxP excision system and phage P1 transduction achieved a smaller but faster reduction of ∼7% (127) |
| Bacillus subtilis subsp. subtilis 168 | 4.21 Mbp | Model Gram-positive bacterium; an early estimation of the no. of essential genes based on 79 chromosomal deletions extrapolated that 562 kbp would be sufficient to sustain a minimal cell based on this species (232); a later assay concluded that 271 genes were indispensable for growth (149); 7.7% of the genome was deleted by removing prophages and AT-rich islands using plasmid-based chromosomal integration-excision systems, which resulted in B. subtilis strain Δ6 (233); another project, the MG1 M strain, deleted about 25% (991 kbp) of the genome (101); later, strain MBG874 was reported, with a deletion of 874 kb (20%), and showed enhanced protein productivity; this was the first report demonstrating that genome reduction could contribute to the creation of a bacterial cell with application in industry (105) |
| Archaea | ||
| Nanoarchaeum equitans Kin4-M | 491 kbp | The only known archaeal parasite; it is an obligate symbiont of another archaeon (Ignicoccus sp.); unlike the small genomes of bacteria undergoing reductive evolution, N. equitans has very small regions of noncoding DNA (234); the genome encodes the machinery for information processing and repair but lacks genes for lipid, cofactor, amino acid, or nucleotide biosynthesis |