Domain Archaea Research Articles

Equilibrium and Kinetics of Adsorption of Mn2+ by Haloarchaeon Halobacterium sp. GUSF (MTCC3265)

The coastal waters of countries bordering on an ocean show increases in manganese pollution due to runoff from mining activity and from industries dealing with production of ferroalloys, steel, iron, petrochemicals, and fertilizers. One gram of dried cells of haloarchaeon Halobacterium sp. GUSF (MTCC3265) adsorbed 99% Mn2+ in 60 min at pH 6.8 and 30ºC on contact with 109.54 mg Mn2+ per liter in saline solution. Adsorbed Mn2+ was quantified by atomic absorption spectrometry and demonstrated on the cell surface by SEM-EDX. Mn2+ adsorbed to functional groups of the adsorbent was studied by FTIR. The adsorption process of Mn2+ showed saturation and followed pseudo–second-order kinetics; was consistent with the homogeneity of the Langmuir model (R2 of 0.99); exhibited a Qmax of 62.5 mg g−1 and a binding energy of 0.018 L mg−1. The Mn2+adsorption was also consistent with the heterogeneity of the Freundlich model by exhibiting a Kf of 1.0 mg g−1 with an n value of 1.1. Adsorption efficiency of 99% was retained even after a third adsorption-desorption cycle. This is the first report on metal ion adsorption, using Mn2+ as an example, by the haloarchaeon Halobacterium sp. GUSF (MTCC3265) in the domain Archaea.

Genome stability: recent insights in the topoisomerase reverse gyrase and thermophilic DNA alkyltransferase.

Repair and defence of genome integrity from endogenous and environmental hazard is a primary need for all organisms. Natural selection has driven the evolution of multiple cell pathways to deal with different DNA damaging agents. Failure of such processes can hamper cell functions and induce inheritable mutations, which in humans may cause cancerogenicity or certain genetic syndromes, and ultimately cell death. A special case is that of hyperthermophilic bacteria and archaea, flourishing at temperatures higher than 80°C, conditions that favor genome instability and thus call for specific, highly efficient or peculiar mechanisms to keep their genome intact and functional. Over the last few years, numerous studies have been performed on the activity, function, regulation, physical and functional interaction of enzymes and proteins from hyperthermophilic microorganisms that are able to bind, repair, bypass damaged DNA, or modify its structure or conformation. The present review is focused on two enzymes that act on DNA catalyzing unique reactions: reverse gyrase and DNA alkyltransferase. Although both enzymes belong to evolutionary highly conserved protein families present in organisms of the three domains (Eucarya, Bacteria and Archaea), recently characterized members from hyperthermophilic archaea show both common and peculiar features.

Potential use of highly insoluble carbonates as carbon sources by methanogens in the subsurface of Mars

Methanogens, microorganisms in the domain Archaea, have been studied as life forms that might inhabit the subsurface of Mars. These organisms can use carbon dioxide as a carbon source, a compound that is abundant in the martian atmosphere. But if they exist in the deep subsurface where the carbon dioxide may not penetrate, they would have to rely on another source of carbon. Magnesium carbonate and calcium carbonate have been detected at the martian surface, and there is no reason to believe that they would not be in the subsurface as well. In the research reported here, we asked if these carbonates could possibly serve as carbon sources for four species of methanogens. Methanothermobacter wolfeii, Methanobacterium formicicum and Methanococcus maripaludis were able to produce a small amount of methane (approximately 0.4–0.8% headspace gas) when either carbonate was the carbon source available while Methanosarcina barkeri only produced significant methane (also 0.4–0.8%) when calcium carbonate was the carbon source. The amounts produced were dependent on methanogenic species, carbonate used and pH. At equilibrium, a small amount of carbon dioxide (approximately 0.05–0.15% headspace gas as well as in liquid media) was generated by these carbonates, and this carbon dioxide was most likely the carbon compound that was being metabolized. Background carbon dioxide from the atmosphere was not sufficient for measureable methane production.

Molecular characterization of anaerobic sulfur-oxidizing microbial communities in up-flow anaerobic sludge blanket reactor treating municipal sewage

A novel wastewater treatment system consisting of an up-flow anaerobic sludge blanket (UASB) reactor and a down-flow hanging sponge (DHS) reactor with sulfur-redox reaction was developed for treatment of municipal sewage under low-temperature conditions. In the UASB reactor, a novel phenomenon of anaerobic sulfur oxidation occurred in the absence of oxygen, nitrite and nitrate as electron acceptors. The microorganisms involved in anaerobic sulfur oxidation have not been elucidated. Therefore, in this study, we studied the microbial communities existing in the UASB reactor that probably enhanced anaerobic sulfur oxidation. Sludge samples collected from the UASB reactor before and after sulfur oxidation were used for cloning and terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes of the bacterial and archaeal domains. The microbial community structures of bacteria and archaea indicated that the genus Smithella and uncultured bacteria within the phylum Caldiserica were the dominant bacteria groups. Methanosaeta spp. was the dominant group of the domain archaea. The T-RFLP analysis, which was consistent with the cloning results, also yielded characteristic fingerprints for bacterial communities, whereas the archaeal community structure yielded stable microbial community. From these results, it can be presumed that these major bacteria groups, genus Smithella and uncultured bacteria within the phylum Caldiserica, probably play an important role in sulfur oxidation in UASB reactors.

Evolution of the first genetic cells and the universal genetic code: A hypothesis based on macromolecular coevolution of RNA and proteins

A qualitative hypothesis based on coevolution of protein and nucleic acid macromolecules was developed to explain the evolution of the first genetic cells, from the likely organic chemical-rich environment of early earth, through to the Last Universal Common Ancestor (LUCA). The evolution of the first genetic cell was divided into three phases, proto-genetic cells I, II and III, and the transition to each milestone is described, based on development of chemical cross-catalysis, bio-cross-catalysis, and the universal genetic code, respectively. Selection of macromolecular properties of both peptides and nucleic acids, in response to environmental factors, was likely to be a key aspect of early evolution. The development of hereditable nucleic acids with various key functions; translation, transcription and replication, is described. These functions are envisaged to have coevolved with protein enzymes, from simple organic precursors. Genetically heritable nucleotides may have developed after the local earth environment had cooled below 63°C. Around this temperature G–C bases would have been preferentially utilized for nucleotide synthesis. Under these conditions RNA type nucleotides were then likely selected from a range of different types of nucleotide backbones through template-based synthesis. Initial development of the genetic coding system was simplified by the availability of proto-messenger RNA sequences that contained only G and C bases, and the need to encode only four amino acids. The step-wise addition of further amino acids to the code was predicted to parallel the growing metabolic complexity of the proto-genetic cell. On completion of this evolutionary process the proto-genetic cell is envisaged to have become the LUCA, the last common ancestor of bacteria, eukaryote and archaea domains. Key issues addressed by the model include: (a) the transition from non-hereditable random sequences of peptides and nucleic acids to specific proteins coded by hereditable nucleotide sequences, (b) the origin of homochiral amino acids and sugars, and (c) the mutation limits on the sizes of early nucleic acid genomes. The first genome was limited to a size of about 200 base pairs.

The pivotal regulatory landscape of RNA modifications.

Posttranscriptionally modified nucleosides in RNA play integral roles in the cellular control of biological information that is encoded in DNA. The modifications of RNA span all three phylogenetic domains (Archaea, Bacteria, and Eukarya) and are pervasive across RNA types, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and (less frequently) small nuclear RNA (snRNA) and microRNA (miRNA). Nucleotide modifications are also one of the most evolutionarily conserved properties of RNAs, and the sites of modification are under strong selective pressure. However, many of these modifications, as well as their prevalence and impact, have only recently been discovered. Here, we examine both labile and permanent modifications, from simple methylation to complex transcript alteration (RNA editing and intron retention); detail the models for their processing; and highlight remaining questions in the field of the epitranscriptome.

Characterization of the RnfB and RnfG subunits of the Rnf complex from the archaeon Methanosarcina acetivorans.

Rnf complexes are redox-driven ion pumps identified in diverse species from the domains Bacteria and Archaea, biochemical characterizations of which are reported for two species from the domain Bacteria. Here, we present characterizations of the redox-active subunits RnfG and RnfB from the Rnf complex of Methanosarcina acetivorans, an acetate-utilizing methane-producing species from the domain Archaea. The purified RnfG subunit produced in Escherichia coli fluoresced in SDS-PAGE gels under UV illumination and showed a UV-visible spectrum typical of flavoproteins. The Thr166Gly variant of RnfG was colorless and failed to fluoresce under UV illumination confirming a role for Thr166 in binding FMN. Redox titration of holo-RnfG revealed a midpoint potential of −129 mV for FMN with n = 2. The overproduced RnfG was primarily localized to the membrane of E. coli and the sequence contained a transmembrane helix. A topological analysis combining reporter protein fusion and computer predictions indicated that the C-terminal domain containing FMN is located on the outer aspect of the cytoplasmic membrane. The purified RnfB subunit produced in E. coli showed a UV-visible spectrum typical of iron-sulfur proteins. The EPR spectra of reduced RnfB featured a broad spectral shape with g values (2.06, 1.94, 1.90, 1.88) characteristic of magnetically coupled 3Fe-4S and 4Fe-4S clusters in close agreement with the iron and acid-labile sulfur content. The ferredoxin specific to the aceticlastic pathway served as an electron donor to RnfB suggesting this subunit is the entry point of electrons to the Rnf complex. The results advance an understanding of the organization and biochemical properties of the Rnf complex and lay a foundation for further understanding the overall mechanism in the pathway of methane formation from acetate.

Sa1164 Exclusive Enteral Nutrition Optimizes Growth Outcomes Versus Corticosteroid Therapy for Pediatric Crohn's Disease

Background: The pathogenesis of IBD involves a genetically-determined dysregulation of mucosal immunity in response to environmental factors such as the gut microbiota. Multiple studies have shown the bacterial microbiota to be dysbiotic with an increase in Proteobacteria and a decrease in taxonomic richness. Serologic evidence in patients with IBD as well as mechanistic studies in murine models suggests that gut fungi, collectively referred to as the mycobiome, may also play a role in the pathogenesis of IBD. In this study, we utilized recently described analytic platforms to compare members of the gut microbiota from all three domains of life, Bacteria, Archaea, and Eukaryota in patients with IBD to healthy human subjects. Methods: A single stool sample was collected from pediatric patients with either Crohn's disease (CD) or ulcerative colitis (UC). DNA was extracted using the PSP DNA extraction kit. Pyrosequencing was carried out using barcoded primers. Domainspecific16S rRNA gene primers were used to analyze bacteria and archaea and ITS primers were used to analyze fungi. Sequences obtained were decoded using the QIIME pipeline. The results were compared to a cohort of pediatric control subjects from a previously published study (Hoffmann C. et al. PloS ONE 2013 8(6):e66019). In the IBD cohort, clinical records were obtained and disease activity was measured by the Pediatric Crohn Disease Activity Index (PCDAI). Results: Stool samples were collected from 32 pediatric IBD patients. The majority of these patients (81%) had CD. Four patients had UC and 2 patients had indeterminate colitis. Similar to previously published studies, IBD patients demonstrated decreased bacterial diversity. Although ITS sequencing showed that fecal DNA from patients with IBD and healthy subjects had a similar number of fungal reads, the two groups clustered separately on a principal coordinate analysis (Figure 1) suggesting differences in the mycobiome. Both Pichia jadinii and Candida parapsilosis were significantly more abundant in IBD patients (p = 0.0034 and P=0.00038, respectively). By contrast, an unclassified Candida taxon (OTU EU490138) was more abundant in healthy subjects (p=0.0025). There were no statistically significant differences in the archaeal microbiota. Within the CD patients, age, race, current medications, and PCDAI were not correlated with bacterial microbiota composition. Conclusions: Pediatric IBD is associated with an alteration in the gut mycobiota with increased proportions of both Pichia jadinii and Candida parapsilosis. Although some species within the Pichia genus are known to be pathogenic in immunocompromised hosts, additional studies will be needed to determine whether or not they play a role in the pathogenesis of IBD in humans.

Sa1163 Its Gene Sequencing Reveals a Unique Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease

Background: The pathogenesis of IBD involves a genetically-determined dysregulation of mucosal immunity in response to environmental factors such as the gut microbiota. Multiple studies have shown the bacterial microbiota to be dysbiotic with an increase in Proteobacteria and a decrease in taxonomic richness. Serologic evidence in patients with IBD as well as mechanistic studies in murine models suggests that gut fungi, collectively referred to as the mycobiome, may also play a role in the pathogenesis of IBD. In this study, we utilized recently described analytic platforms to compare members of the gut microbiota from all three domains of life, Bacteria, Archaea, and Eukaryota in patients with IBD to healthy human subjects. Methods: A single stool sample was collected from pediatric patients with either Crohn's disease (CD) or ulcerative colitis (UC). DNA was extracted using the PSP DNA extraction kit. Pyrosequencing was carried out using barcoded primers. Domainspecific16S rRNA gene primers were used to analyze bacteria and archaea and ITS primers were used to analyze fungi. Sequences obtained were decoded using the QIIME pipeline. The results were compared to a cohort of pediatric control subjects from a previously published study (Hoffmann C. et al. PloS ONE 2013 8(6):e66019). In the IBD cohort, clinical records were obtained and disease activity was measured by the Pediatric Crohn Disease Activity Index (PCDAI). Results: Stool samples were collected from 32 pediatric IBD patients. The majority of these patients (81%) had CD. Four patients had UC and 2 patients had indeterminate colitis. Similar to previously published studies, IBD patients demonstrated decreased bacterial diversity. Although ITS sequencing showed that fecal DNA from patients with IBD and healthy subjects had a similar number of fungal reads, the two groups clustered separately on a principal coordinate analysis (Figure 1) suggesting differences in the mycobiome. Both Pichia jadinii and Candida parapsilosis were significantly more abundant in IBD patients (p = 0.0034 and P=0.00038, respectively). By contrast, an unclassified Candida taxon (OTU EU490138) was more abundant in healthy subjects (p=0.0025). There were no statistically significant differences in the archaeal microbiota. Within the CD patients, age, race, current medications, and PCDAI were not correlated with bacterial microbiota composition. Conclusions: Pediatric IBD is associated with an alteration in the gut mycobiota with increased proportions of both Pichia jadinii and Candida parapsilosis. Although some species within the Pichia genus are known to be pathogenic in immunocompromised hosts, additional studies will be needed to determine whether or not they play a role in the pathogenesis of IBD in humans.

Microbial uncultured community of bottom sediments from the bays of Gydan and Yenisei of the Kara Sea

Using methods of molecular biology (PCR and cloning), we studied the diversity of microorganisms in the surface layers of bottom sediments from the bays of Gydan and Yenisei of the Kara Sea, which have different component composition of the pore water and mineralization level. Representatives of the domains Bacteria and Archaea were identified based on the analysis of the 16S rRNA gene fragment nucleotide sequences. The composition of the community of microorganisms in the bottom sediments changed with the changing salinity gradient of the pore waters. The phylogenetic analysis of the nucleotide sequences showed that the composition of the microbial communities in the southern parts of these bays was affected by fresh-water flows from rivers and streams from the lakes within the catchment area, whereas that in the northern parts was influenced by sea waters. The results indicate the presence of bacteria in the bottom sediments that are capable of using a wide range of substrates as a carbon source including hydrocarbons and organochlorine and aromatic compounds. These data can also indicate the presence of different pollutants in the sediments of these areas and the potential ability of bacteria to degrade chemical compounds that enter the waters and bottom sediments of the Kara Sea.

Recent studies in microbial degradation of petroleum hydrocarbons in hypersaline environments.

Many hypersaline environments are often contaminated with petroleum compounds. Among these, oil and natural gas production sites all over the world and hundreds of kilometers of coastlines in the more arid regions of Gulf countries are of major concern due to the extent and magnitude of contamination. Because conventional microbiological processes do not function well at elevated salinities, bioremediation of hypersaline environments can only be accomplished using high salt-tolerant microorganisms capable of degrading petroleum compounds. In the last two decades, there have been many reports on the biodegradation of hydrocarbons in moderate to high salinity environments. Numerous microorganisms belonging to the domain Bacteria and Archaea have been isolated and their phylogeny and metabolic capacity to degrade a variety of aliphatic and aromatic hydrocarbons in varying salinities have been demonstrated. This article focuses on our growing understanding of bacteria and archaea responsible for the degradation of hydrocarbons under aerobic conditions in moderate to high salinity conditions. Even though organisms belonging to various genera have been shown to degrade hydrocarbons, members of the genera Halomonas Alcanivorax, Marinobacter, Haloferax, Haloarcula, and Halobacterium dominate the published literature. Despite rapid advances in understanding microbial taxa that degrade hydrocarbons under aerobic conditions, not much is known about organisms that carry out similar processes in anaerobic conditions. Also, information on molecular mechanisms and pathways of hydrocarbon degradation in high salinity is scarce and only recently there have been a few reports describing genes, enzymes and breakdown steps for some hydrocarbons. These limited studies have clearly revealed that degradation of oxygenated and non-oxygenated hydrocarbons by halophilic and halotolerant microorganisms occur by pathways similar to those found in non-halophiles.

Effect of a 10 °C-elevated temperature under different water contents on the microbial community in a tea orchard soil

Tea (Camellia sinensis) is an important cash crop in China. However the response of the microbial communities in tea orchard soil to high temperature induced by climate change remains poorly understood. An incubation experiment where the soil was taken from a tea field, involving two temperatures (25 °C and 35 °C) and three levels of water saturation (30%, 55% and 80% water-filled pore space (WFPS)) was conducted. The abundance of the three microbial domains (bacteria, archaea and fungi) and functional genes related to the transformation of nitrogen were studied by real-time PCR. The response of microbial communities to different treatments were monitored by Terminal Restriction Fragment Length Polymorphism (T-RFLP) of PCR amplified rRNA gene sequences or internal transcribed spacer (ITS) sequence fragments. High temperature limited the transformation of ammonium to nitrate, increased the pH and repressed all analyzed genes except for the fungal marker genes (ITS) at 30% and 55% WFPS. However, at 80% WFPS, all genes at 35 °C, except bacterial amoA, increased and exceeded their abundance at 25 °C at the end of incubation. High temperature and soil moisture significantly influenced the abundance and diversity of all three domains because of a change in the relative abundance of dominant T-RFs or selection of new dominant T-RFs. The response of all three domains to temperature and different water regimes increased over time. Overall the study demonstrates the profound effects of an elevated temperature on the abundance of genes involved in the nitrogen cycle and the diversity of the dominant microbial community members.

Microbial Ecology of Thailand Tsunami and Non-Tsunami Affected Terrestrials

The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species.

System analysis of synonymous codon usage biases in archaeal virus genomes

Recent studies of geothermally heated aquatic ecosystems have found widely divergent viruses with unusual morphotypes. Archaeal viruses isolated from these hot habitats usually have double-stranded DNA genomes, linear or circular, and can infect members of the Archaea domain. In this study, the synonymous codon usage bias (SCUB) and dinucleotide composition in the available complete archaeal virus genome sequences have been investigated. It was found that there is a significant variation in SCUB among different Archaeal virus species, which is mainly determined by the base composition. The outcome of correspondence analysis (COA) and Spearman׳s rank correlation analysis shows that codon usage of selected archaeal virus genes depends mainly on GC richness of genome, and the gene׳s function, albeit with smaller effects, also contributes to codon usage in this virus. Furthermore, this investigation reveals that aromaticity of each protein is also critical in affecting SCUB of these viral genes although it was less important than that of the mutational bias. Especially, mutational pressure may influence SCUB in SIRV1, SIRV2, ARV1, AFV1, and PhiCh1 viruses, whereas translational selection could play a leading role in HRPV1׳s SCUB. These conclusions not only can offer an insight into the codon usage biases of archaeal virus and subsequently the possible relationship between archaeal viruses and their host, but also may help in understanding the evolution of archaeal viruses and their gene classification, and more helpful to explore the origin of life and the evolution of biology.

Degradation of high concentrations of nonionic surfactant (linear alcohol ethoxylate) in an anaerobic fluidized bed reactor

The removal and degradation of the nonionic surfactant linear alcohol ethoxylate (LAE)Genapol® C-100 in an anaerobic fluidized bed reactor were evaluated with 4.7mgLAE/L to 107.4mgLAE/L added to the synthetic substrate (535±121mg/L to 882±126mg/L of organic matter). High removal efficiencies of the COD (chemical oxygen demand) (88%) and LAE (98%) were observed even at high surfactant concentrations during the 492days of operation. The absence of sucrose in the synthetic substrate modified the microbial community. Similarity coefficients between the phases with sucrose and without sucrose were 74% and 59% for the Archaea and Bacteria domains, respectively. The higher LAE removal (98%) was obtained for the 97.9mgLAE/L influent in the absence of the co-substrate, as well as the greater diversity of volatile fatty acid. At the end of the reactor operation 2.05mg of LAE was adsorbed in the biomass and 98.5% was biodegraded.

CRISPR-Cas functional module exchange in Escherichia coli.

ABSTRACTClustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (cas) genes constitute the CRISPR-Cas systems found in the Bacteria and Archaea domains. At least in some strains they provide an efficient barrier against transmissible genetic elements such as plasmids and viruses. Two CRISPR-Cas systems have been identified in Escherichia coli, pertaining to subtypes I-E (cas-E genes) and I-F (cas-F genes), respectively. In order to unveil the evolutionary dynamics of such systems, we analyzed the sequence variations in the CRISPR-Cas loci of a collection of 131 E. coli strains. Our results show that the strain grouping inferred from these CRISPR data slightly differs from the phylogeny of the species, suggesting the occurrence of recombinational events between CRISPR arrays. Moreover, we determined that the primary cas-E genes of E. coli were altogether replaced with a substantially different variant in a minor group of strains that include K-12. Insertion elements play an important role in this variability. This result underlines the interchange capacity of CRISPR-Cas constituents and hints that at least some functional aspects documented for the K-12 system may not apply to the vast majority of E. coli strains.

Effects of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on abundance and activity of ammonia oxidizers in soil

Recent evidence from several environments suggest that besides autotrophic ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) are also able to perform the oxidation of NH4 + to NO2 −, although the relative importance of AOA in nitrification, compared to AOB, and their differential susceptibility to inhibitory compounds remains unclear. Experimental microcosms were set up to evaluate the effect of the addition of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) combined with a cattle effluent as organic fertilizer on the abundance and expression of ammonia oxidizers, denitrifiers, and non-target microbial populations using reverse transcription–real-time PCR, as well as on the diversity of metabolically active soil bacterial and archaeal communities by terminal restriction fragment length polymorphism. While no significant changes in soil mineral N concentrations or amoA gene copies could be detected between treatments, short-term changes in transcriptional activity revealed that DMPP impaired both bacterial and archaeal amoA mRNA, being significant at every time point for AOB and at one time point for AOA. Our findings revealed that, despite the different cellular biochemistry and metabolism existing between bacteria and archaea domains, DMPP exerts its inhibitory effect against both soil bacterial and archaeal ammonia-oxidizing transcriptional activity.

The thermal limits to life on Earth

AbstractLiving organisms on Earth are characterized by three necessary features: a set of internal instructions encoded in DNA (software), a suite of proteins and associated macromolecules providing a boundary and internal structure (hardware), and a flux of energy. In addition, they replicate themselves through reproduction, a process that renders evolutionary change inevitable in a resource-limited world. Temperature has a profound effect on all of these features, and yet life is sufficiently adaptable to be found almost everywhere water is liquid. The thermal limits to survival are well documented for many types of organisms, but the thermal limits to completion of the life cycle are much more difficult to establish, especially for organisms that inhabit thermally variable environments. Current data suggest that the thermal limits to completion of the life cycle differ between the three major domains of life, bacteria, archaea and eukaryotes. At the very highest temperatures only archaea are found with the current high-temperature limit for growth being 122 °C. Bacteria can grow up to 100 °C, but no eukaryote appears to be able to complete its life cycle above ∼60 °C and most not above 40 °C. The lower thermal limit for growth in bacteria, archaea, unicellular eukaryotes where ice is present appears to be set by vitrification of the cell interior, and lies at ∼−20 °C. Lichens appear to be able to grow down to ∼−10 °C. Higher plants and invertebrates living at high latitudes can survive down to ∼−70 °C, but the lower limit for completion of the life cycle in multicellular organisms appears to be ∼−2 °C.

Language‐like behavior of protein length distribution in proteomes

In this study, to demonstrate the language‐like behavior of protein length distribution in proteomes, a quantitative linguistic distribution model, Menzerath–Altmann model, was adopted. A total of 10 proteomes from completely sequenced representative organisms (archaea, bacteria, and eukarya domains) were examined. The results showed that the protein length distribution in the complete set of proteomic proteins, or at least in a wide range for each proteome, can be described reasonably well using the distribution model without considering any complex underlying mechanisms. The deliberation of the model parameters confirmed the evolutionary trend and the model parameters were observed to be related to organismal complexity. © 2014 Wiley Periodicals, Inc. Complexity 20: 12–21, 2014

Diversity of the DNA replication system in the Archaea domain.

The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the specialized replication proteins are observed. Indeed, Archaea possess specific features unique to this domain. Moreover, even though the general pattern of the replicative system is the same in all archaea, a great deal of variation exists between specific groups.