A putative RNA-interference-based immune system in prokaryotes: The epitome of prokaryotic genomic diversity

E. V. Koonin, K. S. Makarova, N. V. Grishin, Y. I. Wolf

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Abstract

INTRODUCTION The extreme diversity and plasticity of prokaryotic genomes, manifest both at the level of gene loss and acquisition via horizontal gene transfer and at the level of gene order rearrangement, are arguably among the major generalizations of comparative genomics (Coenye et al., 2005; Koonin & Galperin, 1997, 2002; Snel et al., 2002). Bacteria and archaea have numerous partially conserved operons, probably thanks, in part, to the ‘selfish’ behaviour of operons, but little conservation of genome organization is seen at large evolutionary distances beyond the operon level (Dandekar et al., 1998; Lawrence, 1999; Mushegian & Koonin, 1996; Watanabe et al., 1997; Wolf et al., 2001). To detect traces of such long-range conservation, specially designed computational methods for detecting ‘überoperons’, or partially conserved gene neighbourhoods, have been developed (Lathe et al., 2000; Rogozin et al., 2002). As a case study for testing the methods for conserved neighbourhood analysis that we have developed, we characterized an extensive gene set that included several proteins related to DNA or RNA metabolism and was, mostly, specific to thermophiles (Makarova et al., 2002). These genes comprise a complex array of overlapping neighbourhoods that are partially conserved but highly diversified, in terms of both gene composition and gene order, and are represented in all archaeal and many bacterial genomes. At the time, we hypothesized that these genes encoded an uncharacterized, versatile repair system, largely associated with the thermophilic lifestyle.

Original languageEnglish (US)
Title of host publicationProkaryotic Diversity: Mechanisms and Significance: Published for the Society for General Microbiology
PublisherCambridge University Press
Pages39-64
Number of pages26
ISBN (Print)9780511754913, 0521869358, 9780521869355
DOIs
StatePublished - Jan 1 2006

Fingerprint

RNA Interference
Immune System
Operon
Genes
Gene Order
Genome
Bacterial Genomes
Horizontal Gene Transfer
Gene Rearrangement
Archaea
Genomics
Life Style
RNA
Bacteria
DNA
Proteins

ASJC Scopus subject areas

  • Immunology and Microbiology(all)

Cite this

Koonin, E. V., Makarova, K. S., Grishin, N. V., & Wolf, Y. I. (2006). A putative RNA-interference-based immune system in prokaryotes: The epitome of prokaryotic genomic diversity. In Prokaryotic Diversity: Mechanisms and Significance: Published for the Society for General Microbiology (pp. 39-64). Cambridge University Press. https://doi.org/10.1017/CBO9780511754913.004

A putative RNA-interference-based immune system in prokaryotes : The epitome of prokaryotic genomic diversity. / Koonin, E. V.; Makarova, K. S.; Grishin, N. V.; Wolf, Y. I.

Prokaryotic Diversity: Mechanisms and Significance: Published for the Society for General Microbiology. Cambridge University Press, 2006. p. 39-64.

Research output: Chapter in Book/Report/Conference proceedingChapter

Koonin, EV, Makarova, KS, Grishin, NV & Wolf, YI 2006, A putative RNA-interference-based immune system in prokaryotes: The epitome of prokaryotic genomic diversity. in Prokaryotic Diversity: Mechanisms and Significance: Published for the Society for General Microbiology. Cambridge University Press, pp. 39-64. https://doi.org/10.1017/CBO9780511754913.004
Koonin EV, Makarova KS, Grishin NV, Wolf YI. A putative RNA-interference-based immune system in prokaryotes: The epitome of prokaryotic genomic diversity. In Prokaryotic Diversity: Mechanisms and Significance: Published for the Society for General Microbiology. Cambridge University Press. 2006. p. 39-64 https://doi.org/10.1017/CBO9780511754913.004
Koonin, E. V. ; Makarova, K. S. ; Grishin, N. V. ; Wolf, Y. I. / A putative RNA-interference-based immune system in prokaryotes : The epitome of prokaryotic genomic diversity. Prokaryotic Diversity: Mechanisms and Significance: Published for the Society for General Microbiology. Cambridge University Press, 2006. pp. 39-64
@inbook{7dca773fa84f4fb09f4a690d8836185d,
title = "A putative RNA-interference-based immune system in prokaryotes: The epitome of prokaryotic genomic diversity",
abstract = "INTRODUCTION The extreme diversity and plasticity of prokaryotic genomes, manifest both at the level of gene loss and acquisition via horizontal gene transfer and at the level of gene order rearrangement, are arguably among the major generalizations of comparative genomics (Coenye et al., 2005; Koonin & Galperin, 1997, 2002; Snel et al., 2002). Bacteria and archaea have numerous partially conserved operons, probably thanks, in part, to the ‘selfish’ behaviour of operons, but little conservation of genome organization is seen at large evolutionary distances beyond the operon level (Dandekar et al., 1998; Lawrence, 1999; Mushegian & Koonin, 1996; Watanabe et al., 1997; Wolf et al., 2001). To detect traces of such long-range conservation, specially designed computational methods for detecting ‘{\"u}beroperons’, or partially conserved gene neighbourhoods, have been developed (Lathe et al., 2000; Rogozin et al., 2002). As a case study for testing the methods for conserved neighbourhood analysis that we have developed, we characterized an extensive gene set that included several proteins related to DNA or RNA metabolism and was, mostly, specific to thermophiles (Makarova et al., 2002). These genes comprise a complex array of overlapping neighbourhoods that are partially conserved but highly diversified, in terms of both gene composition and gene order, and are represented in all archaeal and many bacterial genomes. At the time, we hypothesized that these genes encoded an uncharacterized, versatile repair system, largely associated with the thermophilic lifestyle.",
author = "Koonin, {E. V.} and Makarova, {K. S.} and Grishin, {N. V.} and Wolf, {Y. I.}",
year = "2006",
month = "1",
day = "1",
doi = "10.1017/CBO9780511754913.004",
language = "English (US)",
isbn = "9780511754913",
pages = "39--64",
booktitle = "Prokaryotic Diversity: Mechanisms and Significance: Published for the Society for General Microbiology",
publisher = "Cambridge University Press",

}

TY - CHAP

T1 - A putative RNA-interference-based immune system in prokaryotes

T2 - The epitome of prokaryotic genomic diversity

AU - Koonin, E. V.

AU - Makarova, K. S.

AU - Grishin, N. V.

AU - Wolf, Y. I.

PY - 2006/1/1

Y1 - 2006/1/1

N2 - INTRODUCTION The extreme diversity and plasticity of prokaryotic genomes, manifest both at the level of gene loss and acquisition via horizontal gene transfer and at the level of gene order rearrangement, are arguably among the major generalizations of comparative genomics (Coenye et al., 2005; Koonin & Galperin, 1997, 2002; Snel et al., 2002). Bacteria and archaea have numerous partially conserved operons, probably thanks, in part, to the ‘selfish’ behaviour of operons, but little conservation of genome organization is seen at large evolutionary distances beyond the operon level (Dandekar et al., 1998; Lawrence, 1999; Mushegian & Koonin, 1996; Watanabe et al., 1997; Wolf et al., 2001). To detect traces of such long-range conservation, specially designed computational methods for detecting ‘überoperons’, or partially conserved gene neighbourhoods, have been developed (Lathe et al., 2000; Rogozin et al., 2002). As a case study for testing the methods for conserved neighbourhood analysis that we have developed, we characterized an extensive gene set that included several proteins related to DNA or RNA metabolism and was, mostly, specific to thermophiles (Makarova et al., 2002). These genes comprise a complex array of overlapping neighbourhoods that are partially conserved but highly diversified, in terms of both gene composition and gene order, and are represented in all archaeal and many bacterial genomes. At the time, we hypothesized that these genes encoded an uncharacterized, versatile repair system, largely associated with the thermophilic lifestyle.

AB - INTRODUCTION The extreme diversity and plasticity of prokaryotic genomes, manifest both at the level of gene loss and acquisition via horizontal gene transfer and at the level of gene order rearrangement, are arguably among the major generalizations of comparative genomics (Coenye et al., 2005; Koonin & Galperin, 1997, 2002; Snel et al., 2002). Bacteria and archaea have numerous partially conserved operons, probably thanks, in part, to the ‘selfish’ behaviour of operons, but little conservation of genome organization is seen at large evolutionary distances beyond the operon level (Dandekar et al., 1998; Lawrence, 1999; Mushegian & Koonin, 1996; Watanabe et al., 1997; Wolf et al., 2001). To detect traces of such long-range conservation, specially designed computational methods for detecting ‘überoperons’, or partially conserved gene neighbourhoods, have been developed (Lathe et al., 2000; Rogozin et al., 2002). As a case study for testing the methods for conserved neighbourhood analysis that we have developed, we characterized an extensive gene set that included several proteins related to DNA or RNA metabolism and was, mostly, specific to thermophiles (Makarova et al., 2002). These genes comprise a complex array of overlapping neighbourhoods that are partially conserved but highly diversified, in terms of both gene composition and gene order, and are represented in all archaeal and many bacterial genomes. At the time, we hypothesized that these genes encoded an uncharacterized, versatile repair system, largely associated with the thermophilic lifestyle.

UR - http://www.scopus.com/inward/record.url?scp=84926960289&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84926960289&partnerID=8YFLogxK

U2 - 10.1017/CBO9780511754913.004

DO - 10.1017/CBO9780511754913.004

M3 - Chapter

AN - SCOPUS:84926960289

SN - 9780511754913

SN - 0521869358

SN - 9780521869355

SP - 39

EP - 64

BT - Prokaryotic Diversity: Mechanisms and Significance: Published for the Society for General Microbiology

PB - Cambridge University Press

ER -