The Phylogeny of Prokaryotes

Abstract

For the first time a single experimental approach, 16 S ribosomal RNA sequence characterization, has been used to develop an overview of phylogenetic relationships in the bacterial world. The technique permits the tracing of relationships back to the common ancestor of all extant life. This first glimpse of bacterial phylogeny reveals a world whose roots appear to span more than 3 billion years. A deep phylogenetic split exists among the bacteria, which necessitates their division into two major lines of descent, the archaebacteria and the true bacteria (or eubacteria). It is a general finding that the most ancient bacterial phenotypes are anaerobic, and that aerobic phenotypes have arisen a number of times. Photosynthetic phenotypes are also extremely ancient. Many nonphotosynthetic groups appear to have arisen from photosynthetic ancestry, which is reason to question the generally held belief that the first bacteria were anaerobic heterotrophs. The two ultimate lines of bacterial descent are no more closely related to one another than either is to the cytoplasmic aspect of the eukaryotic cell. However, in that the eukaryotic cell is a phylogenetic chimera, it itself cannot be seen as a line of descent comparable to the two bacterial lines—although some of its individual parts can be so viewed. In this way, the chloroplast and perhaps the mitochondrion are each eubacterial, and at least one ribosomal protein is archaebacterial. A third line of descent that is neither eubacterial nor archaebacterial is represented in the 18 S ribosomal RNA.

The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species

“…Comparisons of SS-rRNA sequences have revolutionized the understanding of the diversity and phylogenetic relationships of all organisms, and in particular those of microorganisms (Fox et al 1980, Olsen 1988, Sogin 1989, Woese 1991, Woese 1987. Some of the reasons that SS-rRNA sequence comparisons have been so useful include: SS-rRNAs are present in, and have conserved sequence, structure, and function among, all known species of free-living organisms as well as mitochondria and chloroplasts , Woese 1987; genes encoding SS-rRNAs are relatively easy to clone and sequence even from uncharacterized or unculturable species (Eisen et al 1992, Lane et al 1985, Medlin et al 1988, Weisburg et al 1991; the conservation of some regions of primary structure and large sections of secondary structure aids alignment of SSrRNA sequences between species (Woese 1987); the evolutionary substitution rate between species varies greatly within the molecule allowing for this one molecule to be used to infer relationships among both close and distant relatives , Woese 1987; and it is generally considered unlikely that SS-rRNA genes have undergone lateral transfers between species ), thus the history of SS-rRNA genes should correspond to the history of the species from which they come.…”

Rapid discrimination of archaeal tetraether lipid cores by liquid chromatography-tandem mass spectrometry

“…A rchaea represent one of the three domains of life, phylogenetically distinct from the eukaryota and eubacteria [1]. They were originally thought to comprise exclusively extremophiles, with each of the three phyla of archaea known at the time (euryarchaeota, crenarchaeota, and korarchaeota) found to thrive in distinct ecological niches such as hot springs, mud volcanoes, and hypersaline lakes.…”

The chromosomal origin of replication(oriC)ofErwinia carotovora

“…To date, this has been done only for genes coding for specific proteins such as the trpA genes of E. coli and S. typhimurium (28), for 5S rRNA species (29) and 16S rRNA species (30), and for transcriptional control regions such as the trp operon operator-promoter region (31). The method of Kimura (32), which assumes nucleotide changes to be neutral in evolution, separately accounts for transition-type and transversion-type differences.…”