A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans (2008)
Podar, Mircea, Anderson, Iain, Makarova, Kira S, Elkins, James G, Ivanova, Natalia, Wall, Mark A, ...
Abstract Background The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea....
Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks (2008)
Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group...
A highly conserved family of inactivated archaeal B family DNA polymerases (2008)
Rogozin, Igor B, Makarova, Kira S, Pavlov, Youri I, Koonin, Eugene V
Abstract A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms...
Hou, Shaobin, Makarova, Kira S, Saw, Jimmy HW, Senin, Pavel, Ly, Benjamin V, Zhou, Zhemin, ...
Abstract Background The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide...
Evolutionary primacy of sodium bioenergetics (2008)
Mulkidjanian, Armen Y, Galperin, Michael Y, Makarova, Kira S, Wolf, Yuri I, Koonin, Eugene V
Abstract Background The F- and V-type ATPases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of ATP. Both the...
Podar, Mircea, Wall, Mark A, Makarova, Kira S, Koonin, Eugene V
Abstract Intracellular vesicle traffic that enables delivery of proteins between the endoplasmic reticulum, Golgi and various endosomal subcompartments is one of the hallmarks of the eukaryotic cell....
Koonin, Eugene V, Makarova, Kira S, Elkins, James G
Abstract Although most of the key components of the transcription apparatus, and in particular, RNA polymerase (RNAP) subunits, are conserved between archaea and eukaryotes, no archaeal homologs of...
Makarova, Kira S, Sorokin, Alexander V, Novichkov, Pavel S, Wolf, Yuri I, Koonin, Eugene V
Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary...
Makarova, Kira S, Grishin, Nick V, Shabalina, Svetlana A, Wolf, Yuri I, Koonin, Eugene V
Abstract Background All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated ( cas ) genes that...
Omelchenko, Marina V, Wolf, Yuri I, Gaidamakova, Elena K, Matrosova, Vera Y, Vasilenko, Alexander, Zhai, Min, ...
Abstract Background Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is...
Koonin, Eugene V, Fedorova, Natalie D, Jackson, John D, Jacobs, Aviva R, Krylov, Dmitri M, Makarova, Kira S, ...
Abstract Background Sequencing the genomes of multiple, taxonomically diverse eukaryotes enables in-depth comparative-genomic analysis which is expected to help in reconstructing ancestral eukaryotic...
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ (2003)
Omelchenko, Marina V, Makarova, Kira S, Wolf, Yuri I, Rogozin, Igor B, Koonin, Eugene V
Abstract Background Shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. Under the 'selfish operon' hypothesis,...
Comparative genomics of archaea: how much have we learned in six years, and what's next? (2003)
Makarova, Kira S, Koonin, Eugene V
Abstract Archaea comprise one of the three distinct domains of life (with bacteria and eukaryotes). With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved...
Koonin, Eugene V, Makarova, Kira S, Rogozin, Igor B, Davidovic, Laetitia, Letellier, Marie-Claude, Pellegrini, Luca
Abstract Background The rhomboid family of polytopic membrane proteins shows a level of evolutionary conservation unique among membrane proteins. They are present in nearly all the sequenced genomes...
Koonin, Eugene V, Makarova, Kira S, Davidovic, Laetitia, Pellegrini, Luca
Abstract Background The rhomboid family consists of polytopic membrane proteins, which show a level of evolutionary conservation that is unique among membrane proteins. The rhomboids are present in...
Makarova, Kira S, Ponomarev, Vladimir A, Koonin, Eugene V
Abstract Background Ribosomal proteins are encoded in all genomes of cellular life forms and are, generally, well conserved during evolution. In prokaryotes, the genes for most ribosomal proteins are...
Conservation of the binding site for the arginine repressor in all bacterial lineages (2001)
Makarova, Kira S, Mironov, Andrey A, Gelfand, Mikhail S
Abstract Background The arginine repressor ArgR/AhrC is a transcription factor universally conserved in bacterial genomes. Its recognition signal (the ARG box), a weak palindrome, is also conserved...
Makarova, Kira S., Aravind, L., Wolf, Yuri I., Tatusov, Roman L., Minton, Kenneth W., Koonin, Eugene V., ...
The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D....
Nölling, Jörk, Breton, Gary, Omelchenko, Marina V., Makarova, Kira S., Zeng, Qiandong, Gibson, Rene, ...
The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has been determined by the shotgun approach. The genome consists of a 3.94-Mb chromosome and a 192-kb...
Makarova, Kira S., Aravind, L., Grishin, Nick V., Rogozin, Igor B., Koonin, Eugene V.
During a systematic analysis of conserved gene context in prokaryotic genomes, a previously undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in...
Aravind, L., Makarova, Kira S., Koonin, Eugene V.
Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. A detailed computer analysis of the structural and evolutionary relationships of HJRs and related nucleases suggests that the...
Connected gene neighborhoods in prokaryotic genomes
Rogozin, Igor B., Makarova, Kira S., Murvai, Janos, Czabarka, Eva, Wolf, Yuri I., Tatusov, Roman L., ...
A computational method was developed for delineating connected gene neighborhoods in bacterial and archaeal genomes. These gene neighborhoods are not typically present, in their entirety, in any...
Slesarev, Alexei I., Mezhevaya, Katja V., Makarova, Kira S., Polushin, Nikolai N., Shcherbinina, Olga V., Shakhova, Vera V., ...
We have determined the complete 1,694,969-nt sequence of the GC-rich genome of Methanopyrus kandleri by using a whole direct genome sequencing approach. This approach is based on unlinking of genomic...
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes
Rogozin, Igor B., Makarova, Kira S., Natale, Darren A., Spiridonov, Alexey N., Tatusov, Roman L., Wolf, Yuri I., ...
Prokaryotic genomes are considered to be ‘wall-to-wall’ genomes, which consist largely of genes for proteins and structural RNAs, with only a small fraction of the genomic DNA allotted to...
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
Liu, Yongqing, Zhou, Jizhong, Omelchenko, Marina V., Beliaev, Alex S., Venkateswaran, Amudhan, Stair, Julia, ...
Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain...
Koonin, Eugene V, Makarova, Kira S, Rogozin, Igor B, Davidovic, Laetitia, Letellier, Marie-Claude, Pellegrini, Luca
The near-universal presence of the rhomboid family in bacteria, archaea and eukaryotes appears to suggest that this protein is part of the heritage of the last universal common ancestor, phylogenetic...
Initial Proteome Analysis of Model Microorganism Haemophilus influenzae Strain Rd KW20
Kolker, Eugene, Purvine, Samuel, Galperin, Michael Y., Stolyar, Serg, Goodlett, David R., Nesvizhskii, Alexey I., ...
The proteome of Haemophilus influenzae strain Rd KW20 was analyzed by liquid chromatography (LC) coupled with ion trap tandem mass spectrometry (MS/MS). This approach does not require a gel...
Dufresne, Alexis, Salanoubat, Marcel, Partensky, Frédéric, Artiguenave, François, Axmann, Ilka M., Barbe, Valérie, ...
Prochlorococcus marinus, the dominant photosynthetic organism in the ocean, is found in two main ecological forms: high-light-adapted genotypes in the upper part of the water column and...
Comparative genomics of archaea: how much have we learned in six years, and what's next?
Makarova, Kira S, Koonin, Eugene V
With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved core of 313 genes that are represented in all sequenced archaeal genomes, plus a variable 'shell'...
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
Omelchenko, Marina V, Makarova, Kira S, Wolf, Yuri I, Rogozin, Igor B, Koonin, Eugene V
Comparative genomics and phylogenetic analysis have been used to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired...
Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes
Jordan, I. King, Makarova, Kira S., Spouge, John L., Wolf, Yuri I., Koonin, Eugene V.
Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution...
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
Koonin, Eugene V, Fedorova, Natalie D, Jackson, John D, Jacobs, Aviva R, Krylov, Dmitri M, Makarova, Kira S, ...
We examined functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs from seven eukaryotic genomes. The analysis reveals a conserved core of...
Identification and functional analysis of ‘hypothetical’ genes expressed in Haemophilus influenzae
Kolker, Eugene, Makarova, Kira S., Shabalina, Svetlana, Picone, Alex F., Purvine, Samuel, Holzman, Ted, ...
The progress in genome sequencing has led to a rapid accumulation in GenBank submissions of uncharacterized ‘hypothetical’ genes. These genes, which have not been experimentally characterized and...
Iyer, Lakshminarayan M., Makarova, Kira S., Koonin, Eugene V., Aravind, L.
Recently, it has been shown that a predicted P-loop ATPase (the HerA or MlaA protein), which is highly conserved in archaea and also present in many bacteria but absent in eukaryotes, has a...
Ettema, Thijs J. G., Makarova, Kira S., Jellema, Gera L., Gierman, Hinco J., Koonin, Eugene V., Huynen, Martijn A., ...
Despite the fact that phosphoenolpyruvate carboxylase (PEPC) activity has been measured and in some cases even purified from some Archaea, the gene responsible for this activity has not been...
Hou, Shaobin, Saw, Jimmy H., Lee, Kit Shan, Freitas, Tracey A., Belisle, Claude, Kawarabayasi, Yutaka, ...
We report the complete genome sequence of the deep-sea γ-proteobacterium, Idiomarina loihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on the Lōihi submarine volcano, Hawaii....
Kolker, Eugene, Picone, Alex F., Galperin, Michael Y., Romine, Margaret F., Higdon, Roger, Makarova, Kira S., ...
The γ-proteobacterium Shewanella oneidensis strain MR-1 is a metabolically versatile organism that can reduce a wide range of organic compounds, metal ions, and radionuclides. Similar to most other...
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
Makarova, Kira S., Wolf, Yuri I., Mekhedov, Sergey L., Mirkin, Boris G., Koonin, Eugene V.
Gene duplication is a crucial mechanism of evolutionary innovation. A substantial fraction of eukaryotic genomes consists of paralogous gene families. We assess the extent of ancestral paralogy,...
Omelchenko, Marina V, Wolf, Yuri I, Gaidamakova, Elena K, Matrosova, Vera Y, Vasilenko, Alexander, Zhai, Min, ...
Makarova, Kira S., Aravind, L., Wolf, Yuri I., Tatusov, Roman L., Minton, Kenneth W., Koonin, Eugene V., ...
The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D....
Nölling, Jörk, Breton, Gary, Omelchenko, Marina V., Makarova, Kira S., Zeng, Qiandong, Gibson, Rene, ...
The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has been determined by the shotgun approach. The genome consists of a 3.94-Mb chromosome and a 192-kb...
Makarova, Kira S., Aravind, L., Grishin, Nick V., Rogozin, Igor B., Koonin, Eugene V.
During a systematic analysis of conserved gene context in prokaryotic genomes, a previously undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in...
Aravind, L., Makarova, Kira S., Koonin, Eugene V.
Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. A detailed computer analysis of the structural and evolutionary relationships of HJRs and related nucleases suggests that the...
Connected gene neighborhoods in prokaryotic genomes
Rogozin, Igor B., Makarova, Kira S., Murvai, Janos, Czabarka, Eva, Wolf, Yuri I., Tatusov, Roman L., ...
A computational method was developed for delineating connected gene neighborhoods in bacterial and archaeal genomes. These gene neighborhoods are not typically present, in their entirety, in any...
Slesarev, Alexei I., Mezhevaya, Katja V., Makarova, Kira S., Polushin, Nikolai N., Shcherbinina, Olga V., Shakhova, Vera V., ...
We have determined the complete 1,694,969-nt sequence of the GC-rich genome of Methanopyrus kandleri by using a whole direct genome sequencing approach. This approach is based on unlinking of genomic...
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes
Rogozin, Igor B., Makarova, Kira S., Natale, Darren A., Spiridonov, Alexey N., Tatusov, Roman L., Wolf, Yuri I., ...
Prokaryotic genomes are considered to be ‘wall-to-wall’ genomes, which consist largely of genes for proteins and structural RNAs, with only a small fraction of the genomic DNA allotted to...
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
Liu, Yongqing, Zhou, Jizhong, Omelchenko, Marina V., Beliaev, Alex S., Venkateswaran, Amudhan, Stair, Julia, ...
Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain...
Koonin, Eugene V, Makarova, Kira S, Rogozin, Igor B, Davidovic, Laetitia, Letellier, Marie-Claude, Pellegrini, Luca
The near-universal presence of the rhomboid family in bacteria, archaea and eukaryotes appears to suggest that this protein is part of the heritage of the last universal common ancestor, phylogenetic...
Initial Proteome Analysis of Model Microorganism Haemophilus influenzae Strain Rd KW20
Kolker, Eugene, Purvine, Samuel, Galperin, Michael Y., Stolyar, Serg, Goodlett, David R., Nesvizhskii, Alexey I., ...
The proteome of Haemophilus influenzae strain Rd KW20 was analyzed by liquid chromatography (LC) coupled with ion trap tandem mass spectrometry (MS/MS). This approach does not require a gel...
Dufresne, Alexis, Salanoubat, Marcel, Partensky, Frédéric, Artiguenave, François, Axmann, Ilka M., Barbe, Valérie, ...
Prochlorococcus marinus, the dominant photosynthetic organism in the ocean, is found in two main ecological forms: high-light-adapted genotypes in the upper part of the water column and...
Comparative genomics of archaea: how much have we learned in six years, and what's next?
Makarova, Kira S, Koonin, Eugene V
With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved core of 313 genes that are represented in all sequenced archaeal genomes, plus a variable 'shell'...
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
Omelchenko, Marina V, Makarova, Kira S, Wolf, Yuri I, Rogozin, Igor B, Koonin, Eugene V
Comparative genomics and phylogenetic analysis have been used to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired...
Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes
Jordan, I. King, Makarova, Kira S., Spouge, John L., Wolf, Yuri I., Koonin, Eugene V.
Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution...
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
Koonin, Eugene V, Fedorova, Natalie D, Jackson, John D, Jacobs, Aviva R, Krylov, Dmitri M, Makarova, Kira S, ...
We examined functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs from seven eukaryotic genomes. The analysis reveals a conserved core of...
Identification and functional analysis of ‘hypothetical’ genes expressed in Haemophilus influenzae
Kolker, Eugene, Makarova, Kira S., Shabalina, Svetlana, Picone, Alex F., Purvine, Samuel, Holzman, Ted, ...
The progress in genome sequencing has led to a rapid accumulation in GenBank submissions of uncharacterized ‘hypothetical’ genes. These genes, which have not been experimentally characterized and...
Iyer, Lakshminarayan M., Makarova, Kira S., Koonin, Eugene V., Aravind, L.
Recently, it has been shown that a predicted P-loop ATPase (the HerA or MlaA protein), which is highly conserved in archaea and also present in many bacteria but absent in eukaryotes, has a...
Ettema, Thijs J. G., Makarova, Kira S., Jellema, Gera L., Gierman, Hinco J., Koonin, Eugene V., Huynen, Martijn A., ...
Despite the fact that phosphoenolpyruvate carboxylase (PEPC) activity has been measured and in some cases even purified from some Archaea, the gene responsible for this activity has not been...