scholarly journals Nitrate Respiration in Thermus Thermophilus NAR1: From Horizontal Gene Transfer to Internal Evolution

2020 ◽  
Author(s):  
Mercedes Sánchez-Costa ◽  
Alba Blesa ◽  
José Berenguer
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nadh Dehydrogenase ◽  
Thermus Thermophilus ◽  
Nitrate Respiration ◽  
Small Plasmid ◽  
Nitrite Reductases ◽  
Nitrite Respiration ◽  
Nitrate And Nitrite ◽  
Internal Evolution

Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species T. thermophilus the pathway has been studied to a certain detail. Here, we review the enzymes involved in this pathway present in T. thermophilus NAR1, a strain extensively employed as a model for nitrate respiration, on the light of its full sequence recently assembled through a combination of PacBio and Illumina technologies in order to counteract the systematic errors introduced by the former technique. The genome of this strain is divided in four replicons, a chromosome of 2,021,843 pb, two megaplasmids of 370,865 and 77,135 bp and a small plasmid of 9,799 pb. Nitrate respiration is encoded in the largest megaplasmid, pTTHNP4, within a region that includes operons for O2 and nitrate sensory systems, a nitrate reductase, nitrate and nitrite transporters and a nitrate specific NADH dehydrogenase, in addition to multiple insertion sequences (IS), suggesting its mobility-prone nature. Despite nitrite is the final product of nitrate respiration in this strain, the megaplasmid encodes two putative nitrite reductases of the cd1 and Cu-containing types, apparently inactivated by IS. No nitric oxide reductase genes have been found within this region, although the NorR sensory gene, needed for its expression, is found near the inactive nitrite respiration system. These data clearly support that partial denitrification in this strain is the consequence of recent deletions and IS insertions in genes involved in nitrite respiration. Based on these data, the capability of this strain to transfer or acquire denitrification clusters by horizontal gene transfer is discussed.

scholarly journals Nitrate Respiration in Thermus thermophilus NAR1: from Horizontal Gene Transfer to Internal Evolution

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1308
Author(s):  
Mercedes Sánchez-Costa ◽  
Alba Blesa ◽  
José Berenguer
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nadh Dehydrogenase ◽  
Thermus Thermophilus ◽  
Nitrate Respiration ◽  
Small Plasmid ◽  
Nitrite Reductases ◽  
Nitrite Respiration ◽  
Nitrate And Nitrite ◽  
Internal Evolution

Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species Thermus thermophilus has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in T. thermophilus NAR1, a strain extensively employed as a model for nitrate respiration, in the light of its full sequence recently assembled through a combination of PacBio and Illumina technologies in order to counteract the systematic errors introduced by the former technique. The genome of this strain is divided in four replicons, a chromosome of 2,021,843 bp, two megaplasmids of 370,865 and 77,135 bp and a small plasmid of 9799 pb. Nitrate respiration is encoded in the largest megaplasmid, pTTHNP4, within a region that includes operons for O2 and nitrate sensory systems, a nitrate reductase, nitrate and nitrite transporters and a nitrate specific NADH dehydrogenase, in addition to multiple insertion sequences (IS), suggesting its mobility-prone nature. Despite nitrite is the final product of nitrate respiration in this strain, the megaplasmid encodes two putative nitrite reductases of the cd1 and Cu-containing types, apparently inactivated by IS. No nitric oxide reductase genes have been found within this region, although the NorR sensory gene, needed for its expression, is found near the inactive nitrite respiration system. These data clearly support that partial denitrification in this strain is the consequence of recent deletions and IS insertions in genes involved in nitrite respiration. Based on these data, the capability of this strain to transfer or acquire denitrification clusters by horizontal gene transfer is discussed.

scholarly journals Two Nitrate/Nitrite Transporters Are Encoded within the Mobilizable Plasmid for Nitrate Respiration of Thermus thermophilus HB8

2000 ◽  
Vol 182 (8) ◽  
pp. 2179-2183 ◽  
Author(s):  
Sandra Ramírez ◽  
Renata Moreno ◽  
Olga Zafra ◽  
Pablo Castán ◽  
Cristina Vallés ◽  
...  
Keyword(s):  
Nitrate Reductase ◽  
Average Distance ◽  
Thermus Thermophilus ◽  
Major Facilitator Superfamily ◽  
Nitrate Respiration ◽  
Mobilizable Plasmid ◽  
Excretion Rates ◽  
Major Facilitator ◽  
Nitrate And Nitrite

ABSTRACT Thermus thermophilus HB8 can grow anaerobically by using a membrane-bound nitrate reductase to catalyze the reduction of nitrate as a final electron acceptor in respiration. In contrast to other denitrifiers, the nitrite produced does not continue the reduction pathway but accumulates in the growth medium after its active extrusion from the cell. We describe the presence of two genes,narK1 and narK2, downstream of the nitrate reductase-encoding gene cluster (nar) that code for two homologues to the major facilitator superfamily of transporters. The sequences of NarK1 and NarK2 are 30% identical to each other, but whereas NarK1 clusters in an average-distance tree with putative nitrate transporters, NarK2 does so with putative nitrite exporters. To analyze whether this differential clustering was actually related to functional differences, we isolated derivatives with mutations of one or both genes. Analysis revealed that single mutations had minor effects on growth by nitrate respiration, whereas a double narK1 narK2 mutation abolished this capability. Further analysis allowed us to confirm that the double mutant is completely unable to excrete nitrite, while single mutants have a limitation in the excretion rates compared with the wild type. These data allow us to propose that both proteins are implicated in the transport of nitrate and nitrite, probably acting as nitrate/nitrite antiporters. The possible differential roles of these proteins in vivo are discussed.

scholarly journals Genome Signature Difference between Deinococcus radiodurans and Thermus thermophilus

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Hiromi Nishida ◽  
Reina Abe ◽  
Taishi Nagayama ◽  
Kentaro Yano
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Common Ancestor ◽  
Deinococcus Radiodurans ◽  
Thermophilic Bacteria ◽  
Thermus Thermophilus ◽  
Genomic Signatures ◽  
Genome Signature ◽  
Gc Contents

The extremely radioresistant bacteria of the genus Deinococcus and the extremely thermophilic bacteria of the genus Thermus belong to a common taxonomic group. Considering the distinct living environments of Deinococcus and Thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. Their guanine-cytosine (GC) contents are similar; however, we hypothesized that their genomic signatures would be different. Our findings indicated that the genomes of Deinococcus radiodurans and Thermus thermophilus have different tetranucleotide frequencies. This analysis showed that the genome signature of D. radiodurans is most similar to that of Pseudomonas aeruginosa, whereas the genome signature of T. thermophilus is most similar to that of Thermanaerovibrio acidaminovorans. This difference in genome signatures may be related to the different evolutionary backgrounds of the 2 genera after their divergence from a common ancestor.

Biochemical and regulatory properties of a respiratory island encoded by a conjugative plasmid in the extreme thermophile Thermus thermophilus

2006 ◽  
Vol 34 (1) ◽  
pp. 97-100 ◽  
Author(s):  
F. Cava ◽  
J. Berenguer
Keyword(s):  
Nadh Dehydrogenase ◽  
Current Knowledge ◽  
Thermus Thermophilus ◽  
Thermophilic Bacterium ◽  
Conjugative Plasmid ◽  
Nitrate Respiration ◽  
Final Electron ◽  
New Type ◽  
Regulatory Properties ◽  
Final Electron Acceptor

In the present paper, we summarize the current knowledge on the first step of the denitrification pathway in the ancestral extreme thermophilic bacterium Thermus thermophilus. In this organism, nitrate respiration is performed by a mobilizable respiratory island that encodes a new type of respiratory NADH dehydrogenase as electron donor, a tetrameric membrane nitrate reductase as final electron acceptor, two nitrate/nitrite transporters and the transcription factors required for their expression in response to nitrate and anoxia.

scholarly journals Extensive Phenotypic Changes Associated with Large-scale Horizontal Gene Transfer

2013 ◽  
Author(s):  
Kevin Dougherty ◽  
Brian A Smith ◽  
Autum F Moore ◽  
Shannon Maitland ◽  
Chris Fanger ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Large Scale ◽  
Pseudomonas Stutzeri ◽  
Transfer Event ◽  
Small Plasmid ◽  
Phenotypic Changes ◽  
Evolutionary Trajectories ◽  
Evolutionary Consequences

Horizontal gene transfer often leads to phenotypic changes within recipient organisms independent of any immediate evolutionary benefits. While secondary phenotypic effects of horizontal transfer (i.e. changes in growth rates) have been demonstrated and studied across a variety of systems using relatively small plasmid and phage, little is known about how size of the acquired region affects the magnitude or number of such costs. Here we describe an amazing breadth of phenotypic changes which occur after a large-scale horizontal transfer event (~1Mb megaplasmid) within Pseudomonas stutzeri including sensitization to various stresses as well as changes in bacterial behavior. These results highlight the power of horizontal transfer to shift pleiotropic relationships and cellular networks within bacterial genomes. They also provide an important context for how secondary effects of transfer can bias evolutionary trajectories and interactions between species. Lastly, these results and system provide a foundation to investigate evolutionary consequences in real time as newly acquired regions are ameliorated and integrated into new genomic contexts.

scholarly journals Lateral Transfer of the Denitrification Pathway Genes amongThermus thermophilusStrains

2010 ◽  
Vol 77 (4) ◽  
pp. 1352-1358 ◽  
Author(s):  
Laura Alvarez ◽  
Carlos Bricio ◽  
Manuel José Gómez ◽  
José Berenguer
Keyword(s):  
Nitric Oxide ◽  
Genetic Linkage ◽  
Sequence Data ◽  
Thermus Thermophilus ◽  
Draft Genome ◽  
Specific Property ◽  
Lateral Transfer ◽  
Regulatory Control ◽  
Nitrate Respiration ◽  
Nitrite Respiration

ABSTRACTNitrate respiration is a common and strain-specific property inThermus thermophilusencoded by the nitrate respiration conjugative element (NCE) that can be laterally transferred by conjugation. In contrast, nitrite respiration and further denitrification steps are restricted to a few isolates of this species. These later steps of the denitrification pathway are under the regulatory control of an NCE-encoded transcription factor, but nothing is known about their coding sequences or its putative genetic linkage to the NCE. In this study we examine the genetic linkage between nitrate and nitrite respiration through lateral gene transfer (LGT) assays and describe a cluster of genes encoding the nitrite-nitric oxide respiration inT. thermophilusPRQ25. We show that the whole denitrification pathway can be transferred from the denitrificant strain PRQ25 to an aerobic strain, HB27, and that the genes coding for nitrite and nitric oxide respiration are encoded near the NCE. Sequence data from the draft genome of PRQ25 confirmed these results and allowed us to describe the most compactnor-nircluster known thus far and to demonstrate the expression and activities of the encoded enzymes in the HB27 denitrificant derivatives obtained by LGT. We conclude that this NCEnor-nirsupercluster constitutes a whole denitrification island that can be spread by lateral transfer amongThermus thermophilusstrains.

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