Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium Deinococcus deserti

Abstract

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.

Mutagenic lesion bypass and two functionally different RecA proteins in Deinococcus deserti

“…As recAP1 and recAP3 code for identical proteins, these results indicate that recAP3 expression is weak compared with that of recAP1, at least under the experimental conditions used. This is in agreement with our previously reported RT-PCR data that indicated that recAP3 transcription levels are lower than that of recAP1 and recAC (de Groot et al, 2009). The promoter activities of recAP1 and recAP3 may be different: the first 72 bp upstream of their start codons is nearly identical (only one difference), but the sequences further upstream are different.…”

“…It has also three different recA genes (Deide_19450, Deide_1p01260 and Deide_3p00210, present on the chromosome, plasmid P1 and plasmid P3 respectively). Except for Deide_1p00180, transcription of all these genes was induced after exposure of D. deserti to UV, suggesting a role in the DNA damage response (de Groot et al, 2009).…”

“…The products of additional genes specifically conserved in Deinococcus are also involved in DNA repair and radiation tolerance. These include PprA (reported to stimulate ligase activity) (Narumi et al, 2004), DdrA (an oligomeric ring-forming protein involved in DNA extremity protection) (Harris et al, 2004;Gutsche et al, 2008), DdrB, DdrC and DdrD (functions unknown) de Groot et al, 2009) and IrrE (regulator of recA and pprA expression) (Earl et al, 2002a;Hua et al, 2003;Lu et al, 2009;Vujicic-Zagar et al, 2009). Homologues of DNA repair photolyases and specialized translesion synthesis (TLS) DNA polymerases have not been identified in D. radiodurans and D. geothermalis.…”

“…Recently, the genome of Deinococcus deserti, a bacterium isolated from surface sand of the Sahara desert (de Groot et al, 2005), was sequenced and analysed (de Groot et al, 2009). Its genome consists of a 2.8 Mb chromosome and three large plasmids of 324, 314 and 396 kb.…”

Functional distinctness in the exoproteomes of marine Synechococcus

“…NanoLC‐MS/MS experiments were performed using a LTQ‐Orbitrap XL hybrid mass spectrometer (ThermoFisher) coupled to an UltiMate 3000 LC system (Dionex‐LC Packings). Conditions used were those previously described (de Groot et al ., 2009). …”