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Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

Published on May 1, 1999in Nature 41.58
· DOI :10.1038/20601
Karen E. Nelson71
Estimated H-index: 71
(J. Craig Venter Institute),
Rebecca A. Clayton15
Estimated H-index: 15
(J. Craig Venter Institute)
+ 26 AuthorsClaire M. Fraser-Liggett95
Estimated H-index: 95
(J. Craig Venter Institute)
Abstract
The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T.maritima has the highest percentage (24%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.
  • References (44)
  • Citations (1261)
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References44
Newest
Published on Dec 1, 1998in Nucleic Acids Research 11.56
Yi-Ping Huang1
Estimated H-index: 1
(University of Arizona),
Junetsu Ito12
Estimated H-index: 12
(University of Arizona)
Bacterial DNA polymerase III (family C DNA polymerase), the principal chromosomal replicative enzyme, is known to occur in at least three distinct forms which have provisionally been classified as class I ( Escherichia coli DNA pol C-type), class II ( Bacillus subtilis DNA pol C-type) and class III (cyanobacteria DNA pol C-type). We have identified two family C DNA polymerase sequences in the hyperthermophilic bacterium Thermotoga maritima. One DNA polymerase consisting of 842 amino acid residue...
19 Citations Source Cite
Published on Nov 1, 1998in Nature 41.58
Stewart T. Cole93
Estimated H-index: 93
,
Roland Brosch61
Estimated H-index: 61
+ 39 AuthorsClifton E. Barry74
Estimated H-index: 74
(National Institutes of Health)
Countless millions of people have died from tuberculosis, a chronic infectious disease caused by the tubercle bacillus. The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve our understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions. The genome comprises 4,411,529 base pairs, contains around 4,000 genes, and has a very...
6,257 Citations Source Cite
Published on Sep 1, 1998in Gene 2.50
Steven L. Salzberg120
Estimated H-index: 120
(Johns Hopkins University),
Alan J. Salzberg2
Estimated H-index: 2
(KPMG)
+ 1 AuthorsJean Francois Tomb8
Estimated H-index: 8
Abstract The putative origin of replication in prokaryotic genomes can be located by a new method that finds short oligomers whose orientation is preferentially skewed around the origin. The skewed oligomer method is shown to work for all bacterial genomes and one of three archaeal genomes sequenced to date, confirming known or predicted origins in most cases and in three cases ( H. pylori , M. thermoautotrophicum , and Synechocystis sp.), suggesting origins that were previously unknown. In many...
155 Citations Source Cite
Published on Sep 1, 1998in Nature 41.58
Madeline Vargas9
Estimated H-index: 9
(College of the Holy Cross),
Kazem Kashefi10
Estimated H-index: 10
(University of Massachusetts Amherst)
+ 1 AuthorsDerek R. Lovley140
Estimated H-index: 140
(University of Massachusetts Amherst)
It is generally considered1 that sulphur reduction was one of the earliest forms of microbial respiration, because the known microorganisms that are most closely related to the last common ancestor of modern life are primarily anaerobic, sulphur-reducing hyperthermophiles2,3,4. However, geochemical evidence indicates that Fe(III) is more likely than sulphur to have been the first external electron acceptor of global significance in microbial metabolism5,6,7. Here we show that Archaea and Bacteri...
374 Citations Source Cite
Published on Jul 17, 1998in Science 41.06
Claire M. Fraser-Liggett95
Estimated H-index: 95
(J. Craig Venter Institute),
Steven J. Norris7
Estimated H-index: 7
(University of Texas Health Science Center at Houston)
+ 30 AuthorsKaren A. Ketchum21
Estimated H-index: 21
(J. Craig Venter Institute)
The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential...
836 Citations Source Cite
Published on Jun 1, 1998in Microbiology and Molecular Biology Reviews 13.44
Christoph J. Hueck1
Estimated H-index: 1
Various gram-negative animal and plant pathogens use a novel, sec-independent protein secretion system as a basic virulence mechanism. It is becoming increasingly clear that these so-called type III secretion systems inject (translocate) proteins into the cytosol of eukaryotic cells, where the translocated proteins facilitate bacterial pathogenesis by specifically interfering with host cell signal transduction and other cellular processes. Accordingly, some type III secretion systems are activat...
2,048 Citations
Published on Mar 1, 1998in Nature 41.58
Gerard Deckert1
Estimated H-index: 1
,
Patrick V. Warren2
Estimated H-index: 2
+ 12 AuthorsMonette Aujay1
Estimated H-index: 1
Aquifex aeolicus was one of the earliest diverging, and is one of the most thermophilic, bacteria known. It can grow on hydrogen, oxygen, carbon dioxide, and mineral salts. The complex metabolic machinery needed for A. aeolicus to function as a chemolithoautotroph (an organism which uses an inorganic carbon source for biosynthesis and an inorganic chemical energy source) is encoded within a genome that is only one-third the size of the E. coli genome. Metabolic flexibility seems to be reduced as...
954 Citations Source Cite
Published on Jan 1, 1998in DNA Research 5.42
Yutaka Kawarabayasi31
Estimated H-index: 31
(National Institute of Technology and Evaluation),
Mituhiro Sawada1
Estimated H-index: 1
(National Institute of Technology and Evaluation)
+ 28 AuthorsAkira Hosoyama16
Estimated H-index: 16
(National Institute of Technology and Evaluation)
The complete sequence of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3, has been determined by assembling the sequences of the physical map-based contigs of fosmid clones and of long polymerase chain reaction (PCR) products which were used for gap-filling. The entire length of the genome was 1,738,505 bp. The authenticity of the entire genome sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As...
632 Citations Source Cite
Published on Jan 1, 1998in Nucleic Acids Research 11.56
Steven L. Salzberg120
Estimated H-index: 120
(Johns Hopkins University),
Arthur L. Delcher47
Estimated H-index: 47
(Loyola University Maryland)
+ 1 AuthorsOwen White84
Estimated H-index: 84
This paper describes a new system, GLIMMER, for finding genes in microbial genomes. In a series of tests on Haemophilus influenzae , Helicobacter pylori and other complete microbial genomes, this system has proven to be very accurate at locating virtually all the genes in these sequences, outperforming previous methods. A conservative estimate based on experiments on H.pylori and H. influenzae is that the system finds >97% of all genes. GLIMMER uses interpolated Markov models (IMMs) as a framewo...
863 Citations Source Cite
Published on Dec 1, 1997in Microbiology and Molecular Biology Reviews 13.44
J R Brown1
Estimated H-index: 1
,
W F Doolittle1
Estimated H-index: 1
Since the late 1970s, determining the phylogenetic relationships among the contemporary domains of life, the Archaea (archaebacteria), Bacteria (eubacteria), and Eucarya (eukaryotes), has been central to the study of early cellular evolution. The two salient issues surrounding the universal tree of life are whether all three domains are monophyletic (i.e., all equivalent in taxanomic rank) and where the root of the universal tree lies. Evaluation of the status of the Archaea has become key to an...
384 Citations
Cited By1261
Newest
Published on May 1, 2019in Ecological Modelling 2.51
Alexandra I. Klimenko (Novosibirsk State University), Yury G. Matushkin (Novosibirsk State University)+ 1 AuthorsSergey A. Lashin (Novosibirsk State University)
Abstract There are two evolutionary trends in genome organization among microbes: towards either amplification or reduction. Which evolutionary scenario overcomes depends on environmental conditions and the complexity of gene networks determining phenotypic traits such as metabolic features of cells. In this simulation study, we have shown that the habitats characterized by nutrient gradients allow spatial subdivision of evolutionary trends depending on the distance to the nutrient source. We ha...
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Published on Apr 26, 2019in Frontiers in Microbiology 4.02
Bradley Gary Lusk (United States Naval Research Laboratory)
Approximately four billion years ago, the first microorganisms to thrive on earth were anaerobic chemoautotrophic thermophiles, a specific group of extremophiles that survive and operate at temperatures 50 - 125°C and do not use molecular oxygen (O2) for respiration. Instead, these microorganisms performed respiration via dissimilatory metal reduction by transferring their electrons extracellularly to insoluble electron acceptors. Genetic evidence suggests that Gram-positive thermophilic bacteri...
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Published on Apr 9, 2019in bioRxiv
Alex Salazar5
Estimated H-index: 5
(Delft University of Technology),
Arthur R. Gorter de Vries5
Estimated H-index: 5
(Delft University of Technology)
+ 5 AuthorsThomas Abeel22
Estimated H-index: 22
(Delft University of Technology)
Background: The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for S. cerevisiae chromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies of S. pastorianus strains are inc...
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Published on Mar 1, 2019
Ratna Prabha7
Estimated H-index: 7
(Indian Council of Agricultural Research),
Dhananjaya P. Singh10
Estimated H-index: 10
(Indian Council of Agricultural Research)
Phylogenetic studies based on a definite set of marker genes usually reconstruct evolutionary relationships among the prokaryotic species. Based on specific target sequences, such studies represent variations and allow identification of similarities or dissimilarities in organisms. With the advent of completely sequenced genomes and accumulation of information on whole prokaryotic genomes, phylogenetic reconstructions should be considered more reliable if they are ideally based on entire genomes...
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Published on Mar 1, 2019in Frontiers in Microbiology 4.02
Jiyu Liang1
Estimated H-index: 1
(Shandong University),
Haiyan Huang (Academy of Medical Sciences, United Kingdom), Shuning Wang11
Estimated H-index: 11
(Shandong University)
NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) is an electron-bifurcating enzyme first discovered in the strict anaerobes Clostridium kluyveri and Moorella thermoacetica. In vivo, Nfn catalyzes the endergonic reduction of NADP+ with NADH coupled to the exergonic reduction of NADP+ with reduced ferredoxin. Most Nfn homologs consist of two subunits, although in certain species Nfn homologs are fused. In contrast to other electron-bifurcating enzymes, Nfn possess a simpler structure. ...
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Published on Jan 21, 2019
Alba Blesa5
Estimated H-index: 5
,
Mercedes Sanchez7
Estimated H-index: 7
+ 3 AuthorsJosé Berenguer28
Estimated H-index: 28
A high level of transposon-mediated genome rearrangement is a common trait among microorganisms isolated from thermal environments, probably contributing to the extraordinary genomic plasticity and horizontal gene transfer (HGT) observed in these habitats. In this work, active and inactive insertion sequences (ISs) spanning the sequenced members of the genus Thermus were characterized, with special emphasis on three T. thermophilus strains: HB27, HB8, and NAR1. A large number of full ISs and fra...
1 Citations Source Cite
Published on Jan 20, 2019in bioRxiv
Rida Assaf2
Estimated H-index: 2
(University of Chicago),
Fangfang Xia15
Estimated H-index: 15
(Argonne National Laboratory),
Rick Stevens41
Estimated H-index: 41
(University of Chicago)
Horizontal Gene Transfer(HGT) is the main source of adaptability for bacteria, allowing it to obtain genes from different sources like bacteria, archaea, viruses, and eukaryotes. This promotes the rapid spread of genetic information across lineages, typically in the form of clusters of genes referred to as genomic islands(GIs). There are different types of GIs, often classified by the content of their cargo genes or their means of integration and mobility. Different computational methods have be...
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Published on Jan 1, 2019in Gene 2.50
Bashir Salim9
Estimated H-index: 9
(University of Khartoum),
Mutaz Amin3
Estimated H-index: 3
(University of Khartoum)
+ 5 AuthorsRyo Nakao12
Estimated H-index: 12
(Hokkaido University)
Abstract Heartwater is an economically important disease of ruminants caused by the tick-borne bacterium Ehrlichia ruminantium . The disease is present throughout sub-Saharan Africa as well as on several islands in the Caribbean, where it poses a risk of spreading onto the American mainland. The dominant immune response of infected animals is directed against the variable outer membrane proteins of E. ruminantium encoded by a polymorphic multigene family. Here, we examined the full-length sequen...
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Published on Jan 1, 2019
Hugo Maruyama3
Estimated H-index: 3
(Osaka Dental University),
Nicholas A. Kent20
Estimated H-index: 20
(Cardiff University)
+ 1 AuthorsTaku Oshima2
Estimated H-index: 2
(Toyama Prefectural University)
It is well known that horizontally transferred genes (HTGs) contribute to the adaptation of archaea to their living environment. Archaea have acquired HTGs not only from other archaea but also from bacteria. HTGs should be integrated into the host archaeal transcriptional networks to become functional. In bacteria, the nucleoid proteins, such as H-NS and Lsr2, are well known as the major factors to enhance horizontal transfer of foreign DNAs into the bacterial cells by silencing the expression o...
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