Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti.
To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids o...
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2009-03-01
|
| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC2669436?pdf=render |
| _version_ | 1818150661393481728 |
|---|---|
| author | Arjan de Groot Rémi Dulermo Philippe Ortet Laurence Blanchard Philippe Guérin Bernard Fernandez Benoit Vacherie Carole Dossat Edmond Jolivet Patricia Siguier Michael Chandler Mohamed Barakat Alain Dedieu Valérie Barbe Thierry Heulin Suzanne Sommer Wafa Achouak Jean Armengaud |
| author_facet | Arjan de Groot Rémi Dulermo Philippe Ortet Laurence Blanchard Philippe Guérin Bernard Fernandez Benoit Vacherie Carole Dossat Edmond Jolivet Patricia Siguier Michael Chandler Mohamed Barakat Alain Dedieu Valérie Barbe Thierry Heulin Suzanne Sommer Wafa Achouak Jean Armengaud |
| author_sort | Arjan de Groot |
| collection | DOAJ |
| description | To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown function. The alliance of proteomics and genomics high-throughput techniques allowed identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced genes, ddrC and ddrH, and identification in D. deserti of supplementary genes involved in manganese import extend our knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a photolyase) were also identified and found to be expressed under standard growth conditions, and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient import and DNA repair genes are likely important for survival and adaptation of D. deserti to its nutrient-poor, dry, and UV-exposed extreme environment. |
| first_indexed | 2024-12-11T13:26:29Z |
| format | Article |
| id | doaj.art-1e343726ecab43afa2bf86cde54652f4 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-11T13:26:29Z |
| publishDate | 2009-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-1e343726ecab43afa2bf86cde54652f42022-12-22T01:05:30ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042009-03-0153e100043410.1371/journal.pgen.1000434Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti.Arjan de GrootRémi DulermoPhilippe OrtetLaurence BlanchardPhilippe GuérinBernard FernandezBenoit VacherieCarole DossatEdmond JolivetPatricia SiguierMichael ChandlerMohamed BarakatAlain DedieuValérie BarbeThierry HeulinSuzanne SommerWafa AchouakJean ArmengaudTo better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown function. The alliance of proteomics and genomics high-throughput techniques allowed identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced genes, ddrC and ddrH, and identification in D. deserti of supplementary genes involved in manganese import extend our knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a photolyase) were also identified and found to be expressed under standard growth conditions, and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient import and DNA repair genes are likely important for survival and adaptation of D. deserti to its nutrient-poor, dry, and UV-exposed extreme environment.http://europepmc.org/articles/PMC2669436?pdf=render |
| spellingShingle | Arjan de Groot Rémi Dulermo Philippe Ortet Laurence Blanchard Philippe Guérin Bernard Fernandez Benoit Vacherie Carole Dossat Edmond Jolivet Patricia Siguier Michael Chandler Mohamed Barakat Alain Dedieu Valérie Barbe Thierry Heulin Suzanne Sommer Wafa Achouak Jean Armengaud Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genetics |
| title | Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. |
| title_full | Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. |
| title_fullStr | Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. |
| title_full_unstemmed | Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. |
| title_short | Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. |
| title_sort | alliance of proteomics and genomics to unravel the specificities of sahara bacterium deinococcus deserti |
| url | http://europepmc.org/articles/PMC2669436?pdf=render |
| work_keys_str_mv | AT arjandegroot allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT remidulermo allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT philippeortet allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT laurenceblanchard allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT philippeguerin allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT bernardfernandez allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT benoitvacherie allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT caroledossat allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT edmondjolivet allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT patriciasiguier allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT michaelchandler allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT mohamedbarakat allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT alaindedieu allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT valeriebarbe allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT thierryheulin allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT suzannesommer allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT wafaachouak allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti AT jeanarmengaud allianceofproteomicsandgenomicstounravelthespecificitiesofsaharabacteriumdeinococcusdeserti |