Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C

Abstract

Temperature is one of the defining parameters of an ecological niche. Most organisms thrive within a temperature range that rarely exceeds ~30 °C, but the deep subsurface bacterium Kosmotoga olearia can grow over a temperature range of 59 °C (20–79 °C). To identify genes correlated with this flexible phenotype, we compared transcriptomes of K. olearia cultures grown at its optimal 65 °C to those at 30, 40, and 77 °C. The temperature treatments affected expression of 573 of 2224 K. olearia genes. Notably, this transcriptional response elicits re-modeling of the cellular membrane and changes in metabolism, with increased expression of genes involved in energy and carbohydrate metabolism at high temperatures and up-regulation of amino acid metabolism at lower temperatures. At sub-optimal temperatures, many transcriptional changes were similar to those observed in mesophilic bacteria at physiologically low temperatures, including up-regulation of typical cold stress genes and ribosomal proteins. Comparative genomic analysis of additional Thermotogae genomes indicates that one of K. olearia’s strategies for low-temperature growth is increased copy number of some typical cold response genes through duplication and/or lateral acquisition. At 77 °C one-third of the up-regulated genes are of hypothetical function, indicating that many features of high-temperature growth are unknown.Electronic supplementary materialThe online version of this article (doi:10.1007/s00792-017-0956-9) contains supplementary material, which is available to authorized users.

Genomic analysis of the mesophilic Thermotogae genus Mesotoga reveals phylogeographic structure and genomic determinants of its distinct metabolism

“…3). Both genes were transcribed at moderate levels in M. prima grown with thiosulfate (RPKM 341 and 243 respectively), whereas the K. olearia homologues (Kole_1827, Kole_1828) were highly expressed under similar conditions (RPKM > 1000; Pollo et al, 2017). SudAB complexes, however, are not known to be involved in thiosulfate reduction.…”

“…Fadhlaoui et al (2017) suggested that Mesotoga's inability to ferment sugars is mainly due to its lack of a bifurcating hydrogenase. However, K. olearia also lacks this enzyme and ferments pyruvate, producing large amounts of hydrogen using the homologue of M. prima's only Fe-hydrogenase (Pollo et al, 2017). In the model in Fig.…”

“…RNA isolation from a culture of M. prima (grown at 45 C for 73 h in 0.5% yeast extract, 0.01 M thiosulfate and 0.5% xylose) and subsequent sequencing as one of five barcoded libraries were performed as described by (Pollo et al, 2017). RNAseq analysis was carried out in CLC Genomics Workbench version 7.0.4 as described by (Pollo et al, 2017). The transcriptome has been submitted to GenBank's SRA archive with accession number PRJNA495810.…”

Genomic analysis of the mesophilic Thermotogae genusMesotogareveals phylogeographic structure and genomic determinants of its distinct metabolism

“…(Fadhlaoui 425 et al, 2017) suggested that Mesotoga's inability to ferment sugars is mainly due to its 426 lack of a bifurcating hydrogenase. However, K. olearia also lacks this enzyme and 427 ferments pyruvate, producing large amounts of hydrogen using the homolog of M. 428 prima's only Fe-hydrogenase (Pollo et al, 2017). In the model in Fig.…”

“…534 Recombinant fragments between lineages were detected using LikeWind Version 1.0 535 (Archibald and Roger, 2002) on the concatenated MAUVE alignment (above), using a 536 sliding window of 1000 bp with 100-bp increments. 537 538 RNAseq analysis 539RNA isolation from a culture of M. prima (grown at 45ºC for 73 h in 0.5% yeast extract, 540 0.01 M thiosulfate and 0.5% xylose) and subsequent sequencing as one of five barcoded 541 libraries were performed as described by(Pollo et al, 2017). RNAseq analysis was 542 carried out in CLC Genomics Workbench version 7.0.4 as described by(Pollo et al, 543 2017).…”