Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.

PloS One
John F HeidelbergDevaki Bhaya

Abstract

CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B') as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B' genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B', but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as "viritopes" to emphasize their critical role in viral immunity) were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequ...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Dec 5, 1998·Microbiology and Molecular Biology Reviews : MMBR·D M WardM M Bateson
Mar 8, 2000·Microbiology and Molecular Biology Reviews : MMBR·K E Wommack, R R Colwell
Jan 11, 2000·Nucleic Acids Research·J D PetersonO White
Apr 16, 2002·Molecular Microbiology·Ruud JansenLeo M Schouls
Jul 23, 2003·Environmental Microbiology·R Thane PapkeDavid M Ward
Oct 7, 2003·Annual Review of Microbiology·Michael S Rappé, Stephen J Giovannoni
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Mar 29, 2005·Journal of Molecular Evolution·Francisco J M MojicaElena Soria
Jun 7, 2005·Trends in Microbiology·Mya Breitbart, Forest Rohwer
Jun 28, 2005·Current Opinion in Microbiology·Martin J Loessner
Aug 30, 2005·Trends in Microbiology·Vincent A Fischetti
Aug 1, 2006·Archaea : an International Microbiological Journal·Reidun K LillestølKim Brügger
Mar 24, 2007·Science·Rodolphe BarrangouPhilippe Horvath
Apr 20, 2007·Genome Biology·Victor KuninPhilip Hugenholtz
Jun 1, 2007·Nucleic Acids Research·Ibtissem GrissaChristine Pourcel
Sep 25, 2007·Research in Microbiology·Hans-W Ackermann, Andrew M Kropinski
Sep 27, 2007·Environmental Microbiology·Gene W Tyson, Jillian F Banfield
Dec 11, 2007·Journal of Bacteriology·Philippe HorvathRodolphe Barrangou
Dec 11, 2007·Journal of Bacteriology·Hélène DeveauSylvain Moineau
Dec 25, 2007·Nature Reviews. Microbiology·Rotem SorekPhilip Hugenholtz
Apr 29, 2008·Applied and Environmental Microbiology·Thomas SchoenfeldDavid Mead
May 17, 2008·The Journal of Biological Chemistry·Natalia BeloglazovaAlexander F Yakunin
May 24, 2008·Science·Anders F Andersson, Jillian F Banfield

❮ Previous
Next ❯

Citations

Jul 16, 2013·Archaea : an International Microbiological Journal·Joanne B EmersonJillian F Banfield
Mar 19, 2013·Annual Review of Biochemistry·Rotem SorekBlake Wiedenheft
Jun 10, 2010·Annual Review of Microbiology·Hélène DeveauSylvain Moineau
Nov 9, 2011·Annual Review of Genetics·Devaki BhayaRodolphe Barrangou
Jan 10, 2012·Annual Review of Food Science and Technology·Rodolphe Barrangou, Philippe Horvath
Feb 2, 2010·Applied and Environmental Microbiology·Valery A SorokinIrena I Artamonova
Feb 4, 2010·Nature Reviews. Genetics·Luciano A Marraffini, Erik J Sontheimer
Oct 12, 2010·PloS One·Nicole L HeldRachel J Whitaker
Mar 29, 2011·Cold Spring Harbor Perspectives in Biology·Matthijs M JoreJohn van der Oost
Jun 22, 2012·PLoS Genetics·Mina RhoYuzhen Ye
Mar 16, 2011·Yi chuan = Hereditas·Tie-Min Li, Bo Du
Dec 8, 2009·Science·Jillian F Banfield, Mark Young
Jan 9, 2010·Science·Philippe Horvath, Rodolphe Barrangou
Mar 20, 2010·Proceedings. Biological Sciences·Pedro F Vale, Tom J Little
Apr 28, 2012·Briefings in Functional Genomics·M Senthil Kumar, Kevin C Chen
Jul 12, 2016·Current Stem Cell Reports·Simon N WaddingtonHelen C O'Neill
Dec 19, 2012·Trends in Microbiology·Joshua S WeitzMichael E Hochberg
Mar 24, 2012·Current Opinion in Virology·Karyna Rosario, Mya Breitbart
Jan 17, 2016·Annual Review of Food Science and Technology·Rodolphe Barrangou, Edward G Dudley
Aug 4, 2009·Trends in Biochemical Sciences·John van der OostStan J J Brouns
Jul 25, 2015·Marine Genomics·Rimantas Kodzius, Takashi Gojobori
Mar 23, 2013·Wiley Interdisciplinary Reviews. RNA·Rodolphe Barrangou
Oct 13, 2012·Environmental Microbiology·Christine L SunJillian F Banfield
Jul 5, 2012·Evolution; International Journal of Organic Evolution·Lauren M ChildsJoshua S Weitz
Jul 2, 2011·EMBO Reports·Antonio GonzalezRob Knight
May 25, 2013·Environmental Microbiology·Nicole L HeldRachel J Whitaker
Oct 28, 2010·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Adi Stern, Rotem Sorek
Feb 6, 2010·Microbiology·C Díez-VillaseñorF J M Mojica
Jul 1, 2015·The ISME Journal·Bernhard TschitschkoRicardo Cavicchioli
Dec 20, 2014·The ISME Journal·Allan KonopkaJim Fredrickson
Jun 26, 2015·Journal of Biological Engineering·Kunal K MehtaJames R Swartz
Dec 14, 2011·Bacteriophage·Stephen T Abedon

❮ Previous
Next ❯

Methods Mentioned

BETA
electrophoresis

Software Mentioned

BLASTN Site
MUSCLE
BLASTX
TBLASTX
BLASTN
CRISPRfinder
BLASTP
ORFinder

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.

CRISPR for Genome Editing

Genome editing technologies enable the editing of genes to create or correct mutations. Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). Here is the latest research on the use of CRISPR-Cas system in gene editing.

Bacterial Cell Wall Structure (ASM)

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.

CRISPR Ribonucleases Deactivation

CRISPR-Cas system enables the editing of genes to create or correct mutations. This feed focuses on mechanisms that underlie deactivation of CRISPR ribonucleases. Here is the latest research.

Bacterial Cell Wall Structure

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.