Nitrate Respiration in <i>Thermus thermophilus</i> NAR1: from Horizontal Gene Transfer to Internal Evolution
Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus <i>Thermus</i>, but only in few strains of the species <i>Thermus thermophilus</i> has the pathway been studied to a certain detail. Here, we review the e...
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MDPI AG
2020-11-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/11/11/1308 |
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| author | Mercedes Sánchez-Costa Alba Blesa José Berenguer |
| author_facet | Mercedes Sánchez-Costa Alba Blesa José Berenguer |
| author_sort | Mercedes Sánchez-Costa |
| collection | DOAJ |
| description | Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus <i>Thermus</i>, but only in few strains of the species <i>Thermus thermophilus</i> has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in <i>T. thermophilus</i> 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 O<sub>2</sub> 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 <i>cd1</i> 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. |
| first_indexed | 2024-03-10T15:05:35Z |
| format | Article |
| id | doaj.art-eb3d0f9c856a43de8a76081904c8c8a1 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T15:05:35Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-eb3d0f9c856a43de8a76081904c8c8a12023-11-20T19:48:01ZengMDPI AGGenes2073-44252020-11-011111130810.3390/genes11111308Nitrate Respiration in <i>Thermus thermophilus</i> NAR1: from Horizontal Gene Transfer to Internal EvolutionMercedes Sánchez-Costa0Alba Blesa1José Berenguer2Center for Molecular Biology Severo Ochoa (CBMSO), Autonomous University of Madrid-Spanish National Research Council (UAM-CSIC), 28049 Madrid, SpainDepartment of Biotechnology, Faculty of Experimental Sciences, Francisco de Vitoria University, 28223 Madrid, SpainCenter for Molecular Biology Severo Ochoa (CBMSO), Autonomous University of Madrid-Spanish National Research Council (UAM-CSIC), 28049 Madrid, SpainGenes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus <i>Thermus</i>, but only in few strains of the species <i>Thermus thermophilus</i> has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in <i>T. thermophilus</i> 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 O<sub>2</sub> 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 <i>cd1</i> 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.https://www.mdpi.com/2073-4425/11/11/1308denitrificationevolutionthermophilehorizontal gene transfernitrate respirationPacBio sequencing |
| spellingShingle | Mercedes Sánchez-Costa Alba Blesa José Berenguer Nitrate Respiration in <i>Thermus thermophilus</i> NAR1: from Horizontal Gene Transfer to Internal Evolution Genes denitrification evolution thermophile horizontal gene transfer nitrate respiration PacBio sequencing |
| title | Nitrate Respiration in <i>Thermus thermophilus</i> NAR1: from Horizontal Gene Transfer to Internal Evolution |
| title_full | Nitrate Respiration in <i>Thermus thermophilus</i> NAR1: from Horizontal Gene Transfer to Internal Evolution |
| title_fullStr | Nitrate Respiration in <i>Thermus thermophilus</i> NAR1: from Horizontal Gene Transfer to Internal Evolution |
| title_full_unstemmed | Nitrate Respiration in <i>Thermus thermophilus</i> NAR1: from Horizontal Gene Transfer to Internal Evolution |
| title_short | Nitrate Respiration in <i>Thermus thermophilus</i> NAR1: from Horizontal Gene Transfer to Internal Evolution |
| title_sort | nitrate respiration in i thermus thermophilus i nar1 from horizontal gene transfer to internal evolution |
| topic | denitrification evolution thermophile horizontal gene transfer nitrate respiration PacBio sequencing |
| url | https://www.mdpi.com/2073-4425/11/11/1308 |
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