The Genome of
 Thermosipho africanus
 TCF52B: Lateral Genetic Connections to the
 Firmicutes
 and
 Archaea

Nesbø, Camilla; Bapteste, Éric; Curtis, Bruce A.; Dahle, Helge K.; Lopez, Philippe; MacLeod, D. P.; Dlutek, Marlena; Bowman, Sharen; Zhaxybayeva, Olga; Birkeland, Nils-Kåre; Doolittle, W. Ford

doi:10.1128/jb.01448-08

Cited by 33 publications

(33 citation statements)

References 22 publications

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“…maritima had their best matches to proteins from archaeal species whereas *21% of the proteins were most similar to the Firmicutes (Nelson et al 1999). However, the closest blast hits are often not the nearest neighbours (Koski and Golding 2001) and recent analyses on Thermotogae genomes have led to significant changes in the numbers of closest blast hits that are observed for the Archaea (*10%) and the Firmicute (*45%) taxa (Zhaxybayeva et al 2009;Nesbo et al 2009). Nevertheless, these studies suggested that many genes in the Tt.…”

Section: Introductionmentioning

confidence: 92%

Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups

Gupta

Bhandari

2011

Antonie van Leeuwenhoek

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Thermotogae species are currently identified mainly on the basis of their unique toga and distinct branching in the rRNA and other phylogenetic trees. No biochemical or molecular markers are known that clearly distinguish the species from this phylum from all other bacteria. The taxonomic/evolutionary relationships within this phylum, which consists of a single family, are also unclear. We report detailed phylogenetic analyses on Thermotogae species based on concatenated sequences for many ribosomal as well as other conserved proteins that identify a number of distinct clades within this phylum. Additionally, comprehensive analyses of protein sequences from Thermotogae genomes have identified >60 Conserved Signature Indels (CSI) that are specific for the Thermotogae phylum or its different subgroups. Eighteen CSIs in important proteins such as PolI, RecA, TrpRS and ribosomal proteins L4, L7/L12, S8, S9, etc. are uniquely present in various Thermotogae species and provide molecular markers for the phylum. Many CSIs were specific for a number of Thermotogae subgroups. Twelve of these CSIs were specific for a clade consisting of various Thermotoga species except Tt. lettingae, which was separated from other Thermotoga species by a long branch in phylogenetic trees; Fourteen CSIs were specific for a clade consisting of the Fervidobacterium and Thermosipho genera and eight additional CSIs were specific for the genus Thermosipho. In addition, the existence of a clade consisting of the deep branching species Petrotoga mobilis, Kosmotoga olearia and Thermotogales bacterium mesG1 was supported by seven CSIs. The deep branching of this clade was also supported by a number of CSIs that were present in various Thermotogae species, but absent in this clade and all other bacteria. Most of these clades were strongly supported by phylogenetic analyses based on two datasets of protein sequences and they identify potential higher taxonomic grouping (viz. families) within this phylum. We also report 16 CSIs that are shared by either some or all Thermotogae species and some species from other taxa such as Archaea, Aquificae, Firmicutes, Proteobacteria, Deinococcus, Fusobacteria, Dictyoglomus, Chloroflexi and eukaryotes. The shared presence of some of these CSIs could be due to lateral gene transfers between these groups. However, no clear preference for any particular group was observed in this regard. The molecular probes based on different genes/proteins, which contain these Thermotogae-specific CSIs, provide novel and highly specific means for identification of both known as well as previously unknown Thermotogae species in different environments. Additionally, these CSIs also provide valuable tools for genetic and biochemical studies that could lead to discovery of novel properties that are unique to these bacteria.

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Section: Introductionmentioning

confidence: 92%

Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups

Gupta

Bhandari

2011

Antonie van Leeuwenhoek

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“…When the genome of T. maritima MSB8 was first sequenced (Nelson et al 1999), 24% of its open reading frames (ORFs) showed greatest similarity to sequences from Archaea, suggesting that these genes have been acquired from these distantly related organisms that inhabit the same environment. Comparative genomic analyses of additional Thermotogae genomes have confirmed an influx of genes from Archaea (albeit the total number dropped to 10%-11% of the ORFs, due to increased number of bacterial homologs in GenBank) and an even larger fraction of Firmicutes genes in these genomes (Mongodin et al 2005;Nesbø et al 2009;Zhaxybayeva et al 2009Zhaxybayeva et al , 2012. Phylogenetic analysis of all the ORFs in the M. prima genome suggests this lineage has undergone extensive gene exchange with diverse mesophilic lineages and that LGT has aided its transition from a thermophilic to a mesophilic lifestyle (Zhaxybayeva et al 2012).…”

Section: Role Of Lgt In Temperature Adaptation: Acquisition Of Alreadmentioning

confidence: 99%

“…Thus, as a major force that has shaped the genomes of the Thermotogae, LGT may have also been important for the acquisition and development of the temperature ranges of the various Thermotogae lineages. Most of the acquired genes in Thermotogae (including M. prima) are involved in carbohydrate metabolism (Mongodin et al 2005;Nesbø et al 2009;Zhaxybayeva et al 2009Zhaxybayeva et al , 2012. However, M. prima has additionally acquired genes involved in signal transduction mechanisms, secondary metabolite biosynthesis, and amino acid transport and metabolism (Zhaxybayeva et al 2012), suggesting the potential importance of genes from these functional categories for life at lower temperatures.…”

Section: Role Of Lgt In Temperature Adaptation: Acquisition Of Alreadmentioning

confidence: 99%

Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae

2015

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Thermophiles are extremophiles that grow optimally at temperatures >45°C. To survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperature (mesophiles). At the cellular level, thermophiles have mechanisms for maintaining their membranes, nucleic acids, and other cellular structures. At the protein level, each of their proteins remains stable and retains activity at temperatures that would denature their mesophilic homologs. Conversely, cellular structures and proteins from thermophiles may not function optimally at moderate temperatures. These differences between thermophiles and mesophiles presumably present a barrier for evolutionary transitioning between the 2 lifestyles. Therefore, studying closely related thermophiles and mesophiles can help us determine how such lifestyle transitions may happen. The bacterial phylum Thermotogae contains hyperthermophiles, thermophiles, mesophiles, and organisms with temperature ranges wide enough to span both thermophilic and mesophilic temperatures. Genomic, proteomic, and physiological differences noted between other bacterial thermophiles and mesophiles are evident within the Thermotogae. We argue that the Thermotogae is an ideal group of organisms for understanding of the response to fluctuating temperature and of long-term evolutionary adaptation to a different growth temperature range.Key words: lateral gene transfer, Kosmotoga, Mesotoga, thermostability, stress response. Résumé :Les thermophiles sont des extrémophiles dont la température optimale de croissance se situe au-delà de 45°C. Pour survivre et permettre à leurs biomolécules de bien fonctionner, ils doivent se doter de caractéristiques qu'on ne retrouve pas chez des organismes se développant à des températures intermédiaires (mésophiles). Sur le plan cellulaire, les thermophiles ont des mécanismes permettant de préserver leurs membranes, acides nucléiques et autres structures cellulaires. Au chapitre des protéines, chacune d'entre elles demeure stable et active à des températures qui dénatureraient leurs homologues mésophiles. En revanche, les structures et protéines cellulaires des thermophiles pourraient ne pas fonctionner de manière optimale à des températures intermédiaires. De telles différences entre les thermophiles et les mésophiles auraient tendance à se dresser en travers d'une transition évolutive entre ces deux modes de vie. Par conséquent, l'étude de thermophiles et de mésophiles fortement apparentés pourrait nous permettre d'établir comment surviendraient de telles transitions du mode de vie. Le phylum bactérien Thermotogae regroupe des hyperthermophiles, des thermophiles, des mésophiles et des organismes dont l'intervalle de températures chevauche les plages thermophiles et mésophiles. On observe parmi les Thermotogae des différences sur le plan génomique, protéomique, et physiologique qu'on relève également entre d'autres thermophiles et méso-philes bactériens. Nous soutenons que les Thermot...

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“…The order Thermotogales is an enigmatic taxon that is highly susceptible to lateral gene transfer from members of the Firmicutes and Archaea (Nelson et al, 1999;Nesbø et al, 2009). However, it is not known how the toga is related to the susceptibility of these micro-organisms to lateral gene transfer.…”

mentioning

confidence: 99%

Thermosipho globiformans sp. nov., an anaerobic thermophilic bacterium that transforms into multicellular spheroids with a defect in peptidoglycan formation

Kuwabara

Kawasaki

Uda

et al. 2011

International Journal of Systematic and Evolutionary Microbiology

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An anaerobic rod-shaped thermophile was isolated from a hydrothermal vent at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean, and was named strain MN14 T. The rods were Gram-negative-staining, non-motile without flagella, 2-4 mm long and 0.5 mm wide, and divided by binary fission in the mid-exponential phase. The cells were surrounded by a sheath-like structure (toga) and occurred singly or in chains. Spheroids containing multiple cells were observed not only in the stationary phase, as previously observed for species of the order Thermotogales, but also from the early exponential phase. Transmission electron microscopy revealed that the peptidoglycan in rods partly disintegrated in the early growth phases and that the outer membrane of the spheroids was not completely lined with peptidoglycan. These findings suggested that the spheroids were formed from rods by the disintegration of peptidoglycan and subsequent inflation of the outer membrane. The spheroids eventually generated tiny cells in the periplasmic space, indicating a viviparous mode of proliferation in addition to binary fission. Strain MN14 T grew at 40-75 6C, pH 5.0-8.2 and with 0.25-5.20 % (w/v) NaCl, with optimal growth occurring at 68 6C, pH 6.8 and with 2.5 % NaCl. The shortest doubling time was 24 min, assuming that the strain propagated only by binary fission. Elemental sulfur enhanced growth, but was not essential. Thiosulfate was not an electron acceptor for growth. The strain was a chemo-organotroph that grew on yeast extract as the sole growth substrate. Tryptone and starch supported its growth in the presence of yeast extract. The G+C content of the genomic DNA was 31.7 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Thermosipho. No significant DNA-DNA hybridization was observed between the genomic DNA of strain MN14 T and phylogenetically related species of the genus Thermosipho. Based on this evidence, strain MN14 T is proposed to represent a novel species, named Thermosipho globiformans sp. nov. The species epithet globiformans reflects the formation of multicellular and reproductive spheroids by the novel strain. The type strain of this species is MN14 T (5JCM 15059 T 5DSM 19918 T).

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The Genome of Thermosipho africanus TCF52B: Lateral Genetic Connections to the Firmicutes and Archaea

Cited by 33 publications

References 22 publications

Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups

Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups

Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae

Thermosipho globiformans sp. nov., an anaerobic thermophilic bacterium that transforms into multicellular spheroids with a defect in peptidoglycan formation

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