Complete Genome Sequence of the Thermophilic Bacterium Thermus sp. Strain CCB_US3_UF1

Teh, Beng Soon; Rahman, Azimah Abd; Saito, Jennifer A.; Hou, Shaobin; Alam, Maqsudul

doi:10.1128/jb.06589-11

Cited by 15 publications

(8 citation statements)

References 13 publications

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“…For example, the genome of T. aquaticus Y51MC23 contains two ! 30 complete and two residual prophages (Brumm et al, 2015), whereas Thermus strains RL, 2.9, and CCB_US3_UF1 each contain a prophage (Dwivedi et al, 2012;Navas et al, 2015;Teh et al, 2012). However, the ability of these prophages to excise and replicate has not been studied, and their involvement in specialized transduction is yet to be assayed.…”

Section: Transductionmentioning

confidence: 99%

Horizontal Gene Transfer in Thermus spp.

Blesa¹,

Averhoff²,

Berenguer³

2018

Current Issues in Molecular Biology

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The small amount of genetic content in thermophiles generally limits their adaptability to environmental changes. In Thermus spp., very active horizontal gene transfer (HGT) mechanisms allow the rapid spread of strain-specific adaptive gene modules among the entire population. Constitutive expression of a rather particular and highly efficient DNA transport apparatus (DTA) is at the center of this HGT-mediated enhanced adaptability. The function of the DTA is dependent on the integrity and longevity of the extracellular DNA (eDNA) being transformed, which can be improved by the production of extracellular vesicles (EV) through lysis of a fraction of the population. The DTA must also contend with the recipient cell's defensive barriers, namely restriction enzymes, a panoply of CRISPR-Cas systems, and the argonaute-like protein TtAgo, which may be bypassed by transjugation, a new class of bidirectional transformation-dependent conjugation. Efficient transjugation depends on the presence of the ICETh1, an integrative and conjugative element which promotes simultaneous, generalized DNA transfer from several points in the genome. Transjugation shows preference for genes located within a megaplasmid replicon, where the main strain-specific adaptive modules are located. Contribution of transformation, vesicle-mediated eDNAs, and transjugation to HGT in this genus is discussed.

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Section: Transductionmentioning

confidence: 99%

Horizontal Gene Transfer in Thermus spp.

Blesa¹,

Averhoff²,

Berenguer³

2018

Current Issues in Molecular Biology

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“…The GC content in some thermophiles is different from that of mesophiles, such as Thermus thermophilus ATCC 33923 with a GC content of 69.41% (38), Geobacillus kaustophilus with 52.1% (75), and Thermus sp. strain CCB_US3_UF1 with 68.6% (76). Muston et al, therefore, hypothesized that a high GC content contributes to the thermostability of the genome and is correlated with the OGT (57,58).…”

Section: Base Biases Of Thermophilic Genomesmentioning

confidence: 99%

The Survival Mechanisms of Thermophiles at High Temperatures: An Angle of Omics

2015

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Thermophiles are referred to as microorganisms with optimal growth temperatures of >60 °C. Over the past few years, a number of studies have been conducted regarding thermophiles, especially using the omics strategies. This review provides a systematic view of the survival physiology of thermophiles from an "omics" perspective, which suggests that the adaptive ability of thermophiles is based on a cooperative mode with multi-dimensional regulations integrating genomics, transcriptomics, and proteomics.

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“…RL [ 17 ], T. igniterrae ATCC 700962, T. oshimai JL-2 [ 18 ], Thermus sp. CCB US3 UF1 [ 19 ] and several others. Despite taxonomic diversity of these species that will be discussed below, we identified the same trends of accumulation of specific amino acids in proteins of extreme thermophiles compared to their orthologs in T. scotoductus (Figure 1 ) that we discovered before in a few T. thermophilus strains [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

Analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important Thermus species

2014

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BackgroundBacteria of genus Thermus inhabit both man-made and natural thermal environments. Several Thermus species have shown biotechnological potential such as reduction of heavy metals which is essential for eradication of heavy metal pollution; removing of organic contaminants in water; opening clogged pipes, controlling global warming among many others. Enzymes from thermophilic bacteria have exhibited higher activity and stability than synthetic or enzymes from mesophilic organisms.ResultsUsing Meiothermus silvanus DSM 9946 as a reference genome, high level of coordinated rearrangements has been observed in extremely thermophilic Thermus that may imply existence of yet unknown evolutionary forces controlling adaptive re-organization of whole genomes of thermo-extremophiles. However, no remarkable differences were observed across species on distribution of functionally related genes on the chromosome suggesting constraints imposed by metabolic networks. The metabolic network exhibit evolutionary pressures similar to levels of rearrangements as measured by the cross-clustering index. Using stratigraphic analysis of donor-recipient, intensive gene exchanges were observed from Meiothermus species and some unknown sources to Thermus species confirming a well established DNA uptake mechanism as previously proposed.ConclusionGlobal genome rearrangements were found to play an important role in the evolution of Thermus bacteria at both genomic and metabolic network levels. Relatively higher level of rearrangements was observed in extremely thermophilic Thermus strains in comparison to the thermo-tolerant Thermus scotoductus. Rearrangements did not significantly disrupt operons and functionally related genes. Thermus species appeared to have a developed capability for acquiring DNA through horizontal gene transfer as shown by the donor-recipient stratigraphic analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-813) contains supplementary material, which is available to authorized users.

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Complete Genome Sequence of the Thermophilic Bacterium Thermus sp. Strain CCB_US3_UF1

Cited by 15 publications

References 13 publications

Horizontal Gene Transfer in Thermus spp.

Horizontal Gene Transfer in Thermus spp.

The Survival Mechanisms of Thermophiles at High Temperatures: An Angle of Omics

Analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important Thermus species

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