Evolutionary analysis and quality assessment of ζ-carbonic anhydrase sequences from environmental microbiome.

Carbonic anhydrase (CA) is one of the most vital enzymes in living cells. This study has been performed due to the significance of this metalloenzyme for life and the novelty of some CA families like ζ-CA to evaluate evolutionary processes and quality check their sequences. In this study, bioinformatics methods revealed the presence of ζ-CA in some eukaryotic and prokaryotic microorganisms. Notably, it has not been previously reported in prokaryotes. The coexistence of ß- and ζ-CAs in some microorganisms is also a novel finding as well. Also, our analysis identified several CA proteins with 6-14 amino acid intervals between histidine and cysteine in the second highly conserved motif, which can be classified as the novel ζ-CA subfamily members that emerged under the Zn deficiency of aquatic ecosystems and selection pressure in these environments. There is also a possibility that the achieved results are rooted in the contamination of samples from the environmental microbiome genome with genomes of diatom species and the occurrence of errors was observed in the DNA sequencing outcomes. Combining of all results from evolutionary analysis to quality control of ζ-CA DNA sequences is the incentive motivation to explore more the hidden aspects of ζ-CAs.

Temperature and Monsoon Tango in a Tropical Stalagmite: Last Glacial-Interglacial Climate Dynamics.

High-resolution paleoclimate data on stable isotopes in a stalagmite were coupled to glycerol dialkyl glycerol tetraethers (GDGTs). The Indian Summer Monsoon (ISM) transitioned from limited rainfall during the Last Glacial Maximum (LGM) to intense precipitation during early Holocene (22 to 6 ka). This was associated with changes in stalagmite growth, abundance of branched (br) and isoprenoid (iso) GDGTs, as well as δ18O, δ13C, Sr/Ca and GDGT-derived signals providing both temperature and moisture information. The reconstructed mean annual air temperature (MAAT) of the most modern stalagmite sample at ~19 °C, matches the surface and cave MAAT, but was ~4 °C lower during LGM. Warming at the end of LGM occurred before ISM strengthened and indicate 6 ka lag consistent with sea surface temperature records. The isotope records during the Younger Dryas show rapid progressions to dry conditions and weak monsoons, but these shifts are not coupled to TEX86. Moreover, change to wetter and stronger ISM, along with warmer Holocene conditions are not continuous indicating a decoupling of local temperatures from ISM.

Molecular dynamics simulation study of the effect of glycerol dialkyl glycerol tetraether hydroxylation on membrane thermostability.

Archaeal tetraether membrane lipids span the whole membrane width and present two C40 isoprenoid chains bound by two glycerol groups (or one glycerol and calditol). These lipids confer stability and maintain the membrane fluidity in mesophile to extremophile environments, making them very attractive for biotechnological applications. The isoprenoid lipid composition in archaeal membranes varies with temperature, which has placed these lipids in the focus of paleo-climatological studies for over a decade. Non-hydroxylated isoprenoid archaeal lipids are typically used as paleo-thermometry proxies, but recently identified hydroxylated (OH) derivatives have also been proposed as temperature proxies. The relative abundance of hydroxylated lipids increases at lower temperatures, but the physiological function of the OH moiety remains unknown. Here we present molecular dynamics simulations of membranes formed by the acyclic glycerol-dialkyl-glycerol-tetraether caldarchaeol (GDGT-0), the most widespread archaeal core lipid, and its mono-hydroxylated variant (OH-GDGT-0) to better understand the physico-chemical properties conferred to the membrane by this additional moiety. The molecular dynamics simulations indicate that the additional OH group forms hydrogen bonds mainly with the sugar moieties of neighbouring lipids and with water molecules, effectively increasing the size of the polar headgroups. The hydroxylation also introduces local disorder that propagates along the entire alkyl chains, resulting in a slightly more fluid membrane. These changes would help to maintain trans-membrane transport in cold environments, explaining why the relative abundance of hydroxylated Archaea lipids increases at lower temperatures. The in silico approach aids to understand the underlying physiological mechanisms behind the hydroxylated lipid based paleo-thermometer recently proposed.

The emergence of modern sea ice cover in the Arctic Ocean.

Arctic sea ice coverage is shrinking in response to global climate change and summer ice-free conditions in the Arctic Ocean are predicted by the end of the century. The validity of this prediction could potentially be tested through the reconstruction of the climate of the Pliocene epoch (5.33-2.58 million years ago), an analogue of a future warmer Earth. Here we show that, in the Eurasian sector of the Arctic Ocean, ice-free conditions prevailed in the early Pliocene until sea ice expanded from the central Arctic Ocean for the first time ca. 4 million years ago. Amplified by a rise in topography in several regions of the Arctic and enhanced freshening of the Arctic Ocean, sea ice expanded progressively in response to positive ice-albedo feedback mechanisms. Sea ice reached its modern winter maximum extension for the first time during the culmination of the Northern Hemisphere glaciation, ca. 2.6 million years ago.

Analytical considerations for the use of the paleothermometer tetraether index(86) and the branched vs isoprenoid tetraether index regarding the choice of cleanup and instrumental conditions.

The tetraether index of tetraethers consisting of 86 carbons (TEX(86)) is a novel proxy applied to obtain paleotemperature reconstructions from marine and lacustrine settings. It is usually applied alongside the branched vs isoprenoid tetraether (BIT) index, which provides paleoenvironmental information as well as information on the reliability of TEX(86). Both indices are calculated via the analysis of glycerol dialkyl glycerol tetraethers or GDGTs by means of high-performance liquid chromatography/atmospheric pressure chemical ionization-mass spectrometry (HPLC/APCI-MS). Here we test the performance of alternative methods for sample cleanup and instrumental analysis. In particular, we evaluate using alkaline hydrolysis as an alternative cleanup step to alumina column fractionation and show that the resulting TEX(86) and BIT are statistically equivalent. We also test two different adsorbents in the activated or deactivated state for preparative column fractionation and show that any of them can be used to measure TEX(86) but that a certain discrimination between GDGTs used in the BIT index can occur. Regarding the mass spectrometer design, an ion-trap is shown to be as precise as a quadrupole mass spectrometer for GDGT analysis. Some differences are observed for TEX(86) and especially for BIT values obtained from both MS designs. We provide evidence that the APCI conditions are at least partly responsible for these differences. We recommend caution when comparing BIT values among laboratories as this index seems to be especially sensitive to analytical conditions.

Acclimation of the diatom Stephanodiscus neoastraea and the cyanobacterium Planktothrix agardhii to simulated natural light fluctuations.

Functional and structural characteristics of the photosynthetic apparatus were studied in the diatom Stephanodiscus neoastraea and the cyanobacterium Planktothrix agardhii which were grown semi-continuously under constant irradiance or under simulated natural light fluctuations. The light fluctuations consisted of 24 oscillations of exponentially increasing and decreasing irradiance over a 12-h light period. Maximum irradiance was 1100 mumol photons m(-2) s(-1) with the ratio of maximum to minimum intensities being 100, simulating Langmuir circulations with a ratio of euphotic to mixing depth of 1. S. neoastraea acclimated to the light fluctuations by doubling the number and halving the size of photosynthetic units (PS II) while the amount of chlorophylls and carotenoids remained unchanged. The chlorophyll-specific maximum photosynthetic rate was enhanced while the slope of the photosynthesis versus irradiance curves was not influenced by the light fluctuations. Acclimation of P. agardhii was mainly characterized by an increase in chlorophyll content. Both photosystems showed only little changes in number and size. Maximum photosynthetic rate, saturating irradiance and initial slope of the photosynthesis versus irradiance curves did not vary. Although both high and low light were contained in the fluctuating light, an analogy to low or high light acclimation was not found for the diatom nor for the cyanobacterium acclimated to light fluctuations. We suggest that the acclimation to fluctuating light is a response type outside the known scheme of low and high light acclimation.