A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
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* Corresponding author: Eugene V Koonin koonin@ncbi.nlm.nih.gov
Biology Direct 2006, 1:7 doi:10.1186/1745-6150-1-7
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BioMed Central: 21 citations
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Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs Rudi F Vogel, Melanie Pavlovic, Matthias A Ehrmann, Arnim Wiezer, Heiko Liesegang, Stefanie Offschanka, Sonja Voget, Angel Angelov, Georg Böcker, Wolfgang Liebl Microbial Cell Factories 2011, 10(Suppl 1):S6 (30 August 2011) |
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Kira S Makarova, L Aravind, Yuri I Wolf, Eugene V Koonin Biology Direct 2011, 6:38 (14 July 2011) |
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Kounthéa Phok, Annick Moisan, Dana Rinaldi, Nicolas Brucato, Agamemnon J Carpousis, Christine Gaspin, Béatrice Clouet-d'Orval BMC Genomics 2011, 12:312 (13 June 2011) |
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Taming of the shrewd: novel eukaryotic genes from RNA viruses Eugene V Koonin BMC Biology 2010, 8:2 (12 January 2010) Eugene Koonin comments on the recent finding that integrated copies of non-retroviral RNA virus genes are widely spread in fungal genomes and proposes a role for these acquired genes in antiviral immunity.
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Is evolution Darwinian or/and Lamarckian? Eugene V Koonin, Yuri I Wolf Biology Direct 2009, 4:42 (11 November 2009) This article is part of a collection on Evolutionary Biology 150... Darwinian and Lamarckian mechanisms are both important for evolution and seem to belong to different parts of the broad range of complex interactions between genotypes and environment.
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Hypothesis for heritable, anti-viral immunity in crustaceans and insects Timothy W Flegel Biology Direct 2009, 4:36 (1 October 2009) |
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Kira S Makarova, Yuri I Wolf, John van der Oost, Eugene V Koonin Biology Direct 2009, 4:29 (25 August 2009) |
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Community-wide analysis of microbial genome sequence signatures Gregory J Dick, Anders F Andersson, Brett J Baker, Sheri L Simmons, Brian C Thomas, A Pepper Yelton, Jillian F Banfield Genome Biology 2009, 10:R85 (21 August 2009) Genome signatures are used to identify and cluster sequences de novo from an acid biofilm microbial community metagenomic dataset, revealing information about the low-abundance community members. |
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Shin-ichi Yokobori, Takashi Itoh, Shigeo Yoshinari, Norimichi Nomura, Yoshihiko Sako, Akihiko Yamagishi, Tairo Oshima, Kiyoshi Kita, Yoh-ichi Watanabe BMC Evolutionary Biology 2009, 9:198 (11 August 2009) |
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Fumito Maruyama, Mitsuhiko Kobata, Ken Kurokawa, Keishin Nishida, Atsuo Sakurai, Kazuhiko Nakano, Ryota Nomura, Shigetada Kawabata, Takashi Ooshima, Kenta Nakai, Masahira Hattori, Shigeyuki Hamada, Ichiro Nakagawa BMC Genomics 2009, 10:358 (5 August 2009) |
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Muktak Aklujkar, Julia Krushkal, Genevieve DiBartolo, Alla Lapidus, Miriam L Land, Derek R Lovley BMC Microbiology 2009, 9:109 (27 May 2009) |
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Jimmy H Saw, Bruce W Mountain, Lu Feng, Marina V Omelchenko, Shaobin Hou, Jennifer A Saito, Matthew B Stott, Dan Li, Guang Zhao, Junli Wu, Michael Y Galperin, Eugene V Koonin, Kira S Makarova, Yuri I Wolf, Daniel J Rigden, Peter F Dunfield, Lei Wang, Maqsudul Alam Genome Biology 2008, 9:R161 (17 November 2008) Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation. |
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Shaobin Hou, Kira S Makarova, Jimmy HW Saw, Pavel Senin, Benjamin V Ly, Zhemin Zhou, Yan Ren, Jianmei Wang, Michael Y Galperin, Marina V Omelchenko, Yuri I Wolf, Natalya Yutin, Eugene V Koonin, Matthew B Stott, Bruce W Mountain, Michelle A Crowe, Angela V Smirnova, Peter F Dunfield, Lu Feng, Lei Wang, Maqsudul Alam Biology Direct 2008, 3:26 (1 July 2008) Genome sequence of a methanotrophic member of the bacterial phylum Verrucomicrobia reveals adaptations to the methane utilization under acidic conditions and supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a superphylum
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Kira S Makarova, Alexander V Sorokin, Pavel S Novichkov, Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:33 (27 November 2007) |
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Hitting bacteria at the heart of the central dogma: sequence-specific inhibition Louise Rasmussen, Hans Sperling-Petersen, Kim Mortensen Microbial Cell Factories 2007, 6:24 (10 August 2007) |
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Charles Bland, Teresa L Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos C Kyrpides, Philip Hugenholtz BMC Bioinformatics 2007, 8:209 (18 June 2007) |
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Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel BMC Bioinformatics 2007, 8:172 (23 May 2007) |
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Evolutionary conservation of sequence and secondary structures in CRISPR repeats Victor Kunin, Rotem Sorek, Philip Hugenholtz Genome Biology 2007, 8:R61 (18 April 2007) The categorisation and structural analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) sequences from 195 microbial genomes show that repeats from diverse organisms can be grouped based on sequence similarity, and that some groups have pronounced secondary structures with compensatory base changes. |
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PILER-CR: Fast and accurate identification of CRISPR repeats Robert C Edgar BMC Bioinformatics 2007, 8:18 (20 January 2007) |
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The ancient Virus World and evolution of cells Eugene V Koonin, Tatiana G Senkevich, Valerian V Dolja Biology Direct 2006, 1:29 (19 September 2006) |
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Lakshminarayan M Iyer, A Maxwell Burroughs, L Aravind Genome Biology 2006, 7:R60 (19 July 2006) A systematic analysis of prokaryotic ubiquitin-related beta-grasp fold proteins provides new insights into the Ubiquitin family functional history. |