Draft Genome Sequence of the Thermoalkaliphilic Caldalkalibacillus thermarum Strain TA2.A1

Abstract

The genes and molecular machines that allow for a thermoalkaliphilic lifestyle have not been defined. To address this goal, we report on the improved high-quality draft genome sequence of Caldalkalibacillus thermarum strain TA2.A1, an obligately aerobic bacterium that grows optimally at pH 9.5 and 65 to 70°C on a wide variety of carbon and energy sources.Thermoalkaliphilic microorganisms are poorly understood as a group, and there is very little information available on the genes and molecular machines that allow for a thermoalkaliphilic lifestyle. To live at high pH and temperature, akin to a proton desert, these bacteria must overcome a number of thermodynamic challenges. These include capturing and retaining protons from an alkaline environment (pH 9.5) to drive endothermic reactions in the cell membrane (2), increased membrane permeability to protons at high temperature (16), and a low protonmotive force that appears to be suboptimal for growth (12). Studies of the membrane-bound F 1 F o -ATP synthase of Caldalkalibacillus thermarum strain TA2.A1 (formerly Bacillus sp. strain TA2.A1) have revealed a number of unique adaptations that enable this enzyme to function at extremes of pH and temperature by using protons as coupling ions (2,8,9,11,(13)(14)(15). Additionally, thermoalkaliphilic bacteria with a respiratory metabolism have an obligate growth requirement for iron (10). At alkaline pH, the solubility constant for iron decreases far below the requirement for living cells, and the concentration of bioavailable iron is estimated to be approximately 10 Ϫ23 M at pH 10 (3), suggesting that thermoalka-liphilic bacteria must possess powerful, yet undiscovered, mechanisms to sequester iron. Despite these apparent thermodynamic problems and the challenge of severe iron limitation, thermoalkaliphilic bacteria grow rapidly (doubling time Ͻ 60 min) under these conditions, demonstrating that these bacteria are superbly adapted to combat these challenges.

Crystal structure of type II NADH:quinone oxidoreductase from Caldalkalibacillus thermarum with an improved resolution of 2.15 Å

“…The aromatic ring of MD makes a distant edge-to-facestacking with the FAD cofactor, which is not observed for ubiquinone. This additional chemical interaction might confer higher affinity than ubiquinone species, which is consistent with the fact that menaquinone is the sole quinone species found in C. thermarum (Kalamorz et al, 2011). However, further experiments are required to prove this hypothesis.…”

Biophysical Characterization of a Thermoalkaliphilic Molecular Motor with a High Stepping Torque Gives Insight into Evolutionary ATP Synthase Adaptation

“…Bacterial Strains, Plasmids, and Growth Conditions-E. coli DH5␣ (71) was used for all cloning experiments, and E. coli DK8 (72) lacking the ATP synthase genes encoding the unc operon (⌬atp) was used to overproduce the TA2F 1 (63,73). For cloning and overexpression of TA2F 1 enzyme, the plasmid pTrc99A (Amersham Biosciences) was used.…”

Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation

“…The thermoalkaliphilic bacterium C. thermarum strain TA2.A1 contains a type II NADH dehydrogenase and genome analysis reveals a biosynthetic operon for menaquinone, but not ubiquinone, which is consistent with other species of bacilli that utilize menaquinone as the physiological electron acceptor for NDH-2 (Accession No. ZP_08531709.1) (Kalamorz et al, 2011). Bioinformatics analysis reveals that yeast Ndi1 and C. thermarum NDH-2 share 26% sequence identity (Fig.…”