Nature 442, 868 (24 August 2006) | doi:10.1038/442868c; Published online 23 August 2006

A positive definition of prokaryotes

William Martin1 and Eugene V. Koonin2

  1. Institute of Botany, University of Düsseldorf, 40225 Düsseldorf, Germany
  2. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA


In his Concepts essay, Norman R. Pace argues that the concept of prokaryotes is misleading and proposes that the word 'prokaryote' be banned from the scientific literature1. We disagree.

Pace contends that the term prokaryote refers to the lack of a nucleus and that it is hence a "negative and therefore scientifically invalid description" of cell organization, because "no one can define what is a prokaryote". The former is a matter of opinion, and the latter is arguably incorrect.

Prokaryotes are cells with co-transcriptional translation on their main chromosomes; they translate nascent messenger RNAs into protein. The presence of this character distinguishes them from cells that possess a nucleus and do not translate nascent transcripts on their main chromosomes2. Although historically founded on a negative trait (lacking a nucleus), the term prokaryote does indeed specifically designate organisms that are defined by a positive character.

Pace proposes that we should speak only of archaea and bacteria instead of prokaryotes, and that if a collective term is needed to designate those cells that are not eukaryotes, the term 'microbe' should be used. That suggestion, too, is unacceptable, because many eukaryotes are microbes.

Regardless of what any gene tree might suggest and regardless of what anyone might believe about early evolution, modern cells lacking spliceosomal introns and spliceosomes2, a nucleus, and mitochondria3 do possess transcriptionally coupled translation — they are prokaryotes4.



  1. Pace, N. R. Nature 441, 289 (2006). | Article | PubMed | ChemPort |
  2. Martin, W. & Koonin, E. V. Nature 440, 41–45 (2006). | Article | PubMed | ChemPort |
  3. Embley, T. M. & Martin, W. Nature 440, 623–630 (2006). | Article | PubMed | ChemPort |
  4. Walsh, D. A. & Doolittle, W. F. Curr. Biol. 15, R237–R240 (2005). | Article | PubMed | ChemPort |

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