Comparative Cataloging of 16S Ribosomal Ribonucleic Acid: Molecular Approach to Procaryotic Systematics

Fox, George E.; Pechman, Kenneth R.; Woese, Carl R.

doi:10.1099/00207713-27-1-44

Cited by 347 publications

(144 citation statements)

References 21 publications

Supporting

Mentioning

139

Contrasting

Unclassified

Order By: Relevance

“…In particular, informational genes including 16S rDNA (see Fig. 7) are particularly resistant to LGT (5,33), and cell wall and cell division proteins tend to be inherited vertically, and are therefore informative for high-level systematics of prokaryotes (31). However, high-level functional groupings of proteins encompass multiple biochemical processes that may have different degrees of susceptibility to LGT.…”

Section: Discussionmentioning

confidence: 99%

Highways of gene sharing in prokaryotes

Beiko

Harlow²,

Ragan³

2005

Proc. Natl. Acad. Sci. U.S.A.

452

510

View full text Add to dashboard Cite

The extent to which lateral genetic transfer has shaped microbial genomes has major implications for the emergence of community structures. We have performed a rigorous phylogenetic analysis of >220,000 proteins from genomes of 144 prokaryotes to determine the contribution of gene sharing to current prokaryotic diversity, and to identify ''highways'' of sharing between lineages. The inferred relationships suggest a pattern of inheritance that is largely vertical, but with notable exceptions among closely related taxa, and among distantly related organisms that live in similar environments.lateral genetic transfer ͉ microbial genomes ͉ molecular phylogeny B eginning in the 1980s, recognition of the 16S ribosomal RNA gene (rDNA) as a molecular chronometer (1), the development of automated sequencing technology and PCR, and improved phylogenetic methods (2) converged to yield a universal phylogenetic tree (1, 3) that was often interpreted as the ''tree of life.'' However, trees inferred from protein-coding genes or proteins are not always topologically congruent with the rDNA tree (4, 5) or with one another (6, 7). Instances of incongruence are often attributed to historical transfers of genetic information from one genealogical lineage to another (8). Mechanisms for lateral genetic transfer (LGT) are well characterized, and in a laboratory context underpin much of the biotechnology industry. At issue, however, is the extent to which LGT has contributed to the natural diversity of prokaryotes. If LGT has been rampant and consequential, there may in fact be no universal tree of life, and attempts to construct a phylogenetic classification of prokaryotes based on molecular sequence information will ultimately be futile (9).Least controversial among proposed LGT events are transfers that span relatively short evolutionary distances, where the donor and recipient organisms are members of the same species. DNA exchanges between close relatives are likely to be successful because of compatible methods of genetic exchange such as conjugation and the increased likelihood of homologous recombination between the donated DNA and the recipient genome (10). Linkage disequilibrium analysis of environmental samples has revealed extensive homologous recombination within many species of prokaryotes (11). Transfers between distantly related taxa are much less likely to succeed, because conjugation or viral transduction of genes between different species is less common (although not impossible), and foreign DNA must be integrated into the genome via illegitimate rather than homologous recombination (10). However, if organisms in the environment are subjected to a constant ''rain'' of DNA (12), then these rare processes will occur in evolutionary time, and will be fixed in a lineage especially if they confer a selective advantage on the recipient organism.LGT has tremendous implications for the genesis and evolution of microbial communities: if extensive LGT can occur among distantly related organisms, then processes such as niche inv...

show abstract

Section: Discussionmentioning

confidence: 99%

Highways of gene sharing in prokaryotes

Beiko

Harlow²,

Ragan³

2005

Proc. Natl. Acad. Sci. U.S.A.

452

510

View full text Add to dashboard Cite

show abstract

“…The development of nucleic acid hybridization methods (DNA-DNA and DNA-RNA) has allowed the indirect comparison of gene sequences. The introduction of the analysis of the 16S rRNA gene by cataloguing (Fox et al, 1977), reverse transcriptase-sequencing (Sanger et al, 1977;Lane et al, 1988) and finally PCR-based gene sequencing (Saiki et al, 1988) has provided a useful working hypothesis on which other elements may be compared when investigating the taxonomy and evolution of prokaryotes. It is realistic to assume that the recognition of novel taxa often centres on the use of 16S rRNA genebased techniques.…”

Section: Genetic-based Methodsmentioning

confidence: 99%

Notes on the characterization of prokaryote strains for taxonomic purposes

Tindall

Rosselló‐Móra

Busse

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

1,208

959

View full text Add to dashboard Cite

Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers. INTRODUCTIONThe characterization of a strain is a key element in prokaryote systematics. Although various new methodologies have been developed over the past 100 years, both the newer methodologies and those considered to be 'traditional' remain key elements in determining whether a strain belongs to a known taxon or constitutes a novel one. In the case of a known taxon, a selected set of tests may be used to determine whether a strain has been identified as a member of an existing taxon. However, in the case of a strain or set of strains shown to be novel taxa, they should be characterized as comprehensively as possible. The goal of this characterization is to place them within the hierarchical framework laid down by the Bacteriological Code (1990 revision) (Lapage et al., 1992), as well as to provide a description of the taxa. Strains should be allocated to species (and/or subspecies), but the nature of the 'species name' (a binomial or combination) dictates that it must also be assigned to a genus. The genus may be either an existing or a novel genus. The Bacteriological Code also recommends that the placement of a genus in a family should be mentioned, and this can be extended to the other hierarchical levels as these become defined. Although this approach may appear novel, with much emphasis currently being placed on the species, the advent of 16S rRNA gene sequencing forces us to choose between primers that are specific for members of the Archaea or for members of the Bacteria, so the first step in that direction is already routine in many laboratories. However, such a classification system is only possible if strains are comprehensively and properly characterized. A further key element is the way in which datasets are compared and it is here too that some degree of guidance and a discussion of the potential problems needs to be provided. In the case of species, various recommendations have been made with respect to the ways in which species may be delineated and it is important to consider these aspects when considering how new strains are to be placed in novel species. However, far too little attention has been paid to the way in which taxa above the rank of species should be characterized a...

show abstract

“…Comparative cataloging of TrRNase generated fragrnents of 16S-rRNAs has led to the concept that all living organisms can be classified into one of three major groups: the "urkingdoms" of the eubacteria, the archaebacteria a nd the eukaryotes Woese et al, 1978;Fox et al, 1977). Since then much additional evidence has been accumulated confirming the idea that there a re two groups of prokaryotes that are no more related to °ne another than either of them is related to the eucyta (i. e. the nuclear plus the cytoplasmic compartment of the e ukaryotes).…”

Section: Introductionmentioning

confidence: 99%

Homologies of components of DNA-dependent RNA polymerases of archaebacteria, eukaryotes and eubacteria

Gropp¹,

Reiter²,

Sentenac³

et al. 1986

Systematic and Applied Microbiology

View full text Add to dashboard Cite

SummaryUsing an immunochemical approach homologies between single components of DNA-dependent RNA polymerases from eubacteria, archaebacteria and eukaryotes were investigated. The largest components of all RNA polymerases included in this study are homologous to one another indicating a monophyletic origin of these proteins.Immunological crossreactions show that one of the large subunits present in the enzymes of sulfurdependent archaebacteria is split into two smaller components in methanogens and halophiles. One of these smaller components roughly corresponds to the second largest subunit of the three eukaryotic enzymes whereas the other one shares antigenic determinants with subunit ß of eubacterial RNA polymerases.Semi-quantitative evaluation of the data suggests that the three nuclear RNA polymerases of eukaryotes have evolved from an ancestral enzyme of the type that is found in sulfur-dependent archaebacteria.

show abstract

Comparative Cataloging of 16S Ribosomal Ribonucleic Acid: Molecular Approach to Procaryotic Systematics

Cited by 347 publications

References 21 publications

Highways of gene sharing in prokaryotes

Highways of gene sharing in prokaryotes

Notes on the characterization of prokaryote strains for taxonomic purposes

Homologies of components of DNA-dependent RNA polymerases of archaebacteria, eukaryotes and eubacteria

Contact Info

Product

Resources

About