Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes

Abstract

SUMMARY The presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. An alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. In this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryotes. They are believed to be descended from the most primitive organisms. Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria, and I suggest that this evolution occurred in response to antibiotic selection pressures. Evidence is presented that diderm prokaryotes (i.e., gram-negative bacteria), which have a bilayered cell wall, are derived from monoderm prokaryotes. Signature sequences in different proteins provide a means to define a number of different taxa within prokaryotes (namely, low G+C and high G+C gram-positive, Deinococcus-Thermus, cyanobacteria, chlamydia-cytophaga related, and two different groups of Proteobacteria) and to indicate how they evolved from a common ancestor. Based on phylogenetic information from indels in different protein sequences, it is hypothesized that all eukaryotes, including amitochondriate and aplastidic organisms, received major gene contributions from both an archaebacterium and a gram-negative eubacterium. In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes.

On the origin of genomes and cells within inorganic compartments

“…However, it finds support from theory [35] and experiments [34,[80][81][82], whereas the two current alternatives are more problematic. In one, Cavalier-Smith [10] argued that archaebacteria arose from actinobacteria (high-GC Gram-positive bacteria) w850 million years ago (Mya) and evolved an entirely new lipid membrane and cell wall biochemistry in response to thermophilic adaptation; independently, Gupta proposed that archaebacteria derive from low-GC Gram-positive bacteria [83]. The problems we see with these scenarios are that: (i) no known prokaryotes have demonstrably undergone any vaguely similar cataclysmic lipid transition; and (ii) to our knowledge, no genome-wide data implicate either actinobacteria or low-GC Grampositive bacteria as ancestors of archaebacteria.…”

A new α‐proteobacterial clade of Bdellovibrio‐like predators: implications for the mitochondrial endosymbiotic theory

“…The most accepted hypotheses concerning the origin of the eukaryotic cell suggest that it resulted from the integration of Bacteria and Archaea cells, probably through endosymbiotic acquisition (Gupta, 1998;Emelyanov, 2003;Embley and Martin, 2006;Martin and Koonin, 2006). However, prokaryotes were never observed to fuse their cytoplasms or to engulf other cells.…”

Evolutionary relationship of Rickettsiae and mitochondria

“…In contrast to SSU rRNA, intrinsic properties of Cpn60 make it a`smooth chronometer' perhaps the most appropriate for phylogenetic studies [9,11,15,16]. Fig.…”