Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125

Abstract

A considerable fraction of life develops in the sea at temperatures lower than 15°C. Little is known about the adaptive features selected under those conditions. We present the analysis of the genome sequence of the fast growing Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. We find that it copes with the increased solubility of oxygen at low temperature by multiplying dioxygen scavenging while deleting whole pathways producing reactive oxygen species. Dioxygen-consuming lipid desaturases achieve both protection against oxygen and synthesis of lipids making the membrane fluid. A remarkable strategy for avoidance of reactive oxygen species generation is developed by P. haloplanktis, with elimination of the ubiquitous molybdopterin-dependent metabolism. The P. haloplanktis proteome reveals a concerted amino acid usage bias specific to psychrophiles, consistently appearing apt to accommodate asparagine, a residue prone to make proteins age. Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome.[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to EMBL under accession nos. CR954246 and CR954247.

The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125

“…Although many cold-adapted marine species have been studied [1], we still have limited knowledge about molecular adaptations at low temperatures. The genome of the Antarctic marine eubacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) has been sequenced and annotated [2], shedding light on several molecular features that have selectively developed in cold environments. The genome contains multiple genes encoding three different truncated hemoglobins (Hbs) at distinct positions on chromosome I, namely PSHAa0030, PSHAa2217 and PSHAa0458, which exhibit a 2/2 a-helical fold [3].…”

Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913

“…Aside from its adaptability to cold temperatures, the deep-sea-specific features of SM9913 remain largely unknown. Pseudoalteromonas haloplanktis TAC125 which was isolated from the Antarctic coastal sea water and has already been sequenced by the whole genome shotgun method (Médigue et al, 2005) is closely related to SM9913. SM9913 and TAC125 are both psychrophilic strains with similar optimal growth temperatures, and both were isolated from permanently cold environments.…”

Proteomics of marine bacteria

“…Recently, the genome of another Pseudoalteromonas species, the Antarctic Pseudoalteromonas haloplanktis TAC125 isolate, has been completely sequenced [64]. On this basis, the cold-adapted metabolism of this fast-growing, culturable marine bacterium was investigated in a comprehensive proteomic approach, which includes a closer look at both cytoplasmic and periplasmic proteins (Wilmes et al in preparation).…”

“…The high abundance of TonB receptors might contribute to P. haloplanktis' high growth rates under nutrient-rich conditions by supporting the recruitment of essential substrates. This assumption is underlined by the fact that many of the TonB receptor proteins encoded in P. haloplanktis are missing in other, slowly growing psychrophilic bacteria [64]. A remarkably high abundance of ribosomal proteins was detected on the P. haloplanktis 2-D gels (13.3% of the total cytoplasmic proteome), which indicates that -despite the low temperatures -translation rates are high, allowing for short doubling times (Wilmes et al in preparation).…”

“…Besides its negative regulatory function in siderophore production, Fur could be shown to be a positive global regulator for genes involved in electron transport, the response to oxygen toxicity and adaptive stress responses [83]. Furthermore, S. oneidensis's metabolic responses to oxygen availability have been documented, showing that proteins involved in aerobic respiration, such as TCA cycle enzymes, are repressed under anaerobic conditions, while anaerobic respiration-related proteins like fumarate reductase are induced [64,84]. An LC-MS label-free approach using accurate mass and time (AMT) tags has been successfully applied for that purpose [39].…”