The molecular basis of salt adaptation in Methanosarcina mazei Gö1

Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress

Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at 1%. However, during gradual increase of salt up to 3% in a reactor over 12 weeks, the culture continued to oxidize methane. Using gene expression profiles and metabolomics, we identified a pathway for salt-stress response that produces the osmolyte of anaerobic methanotrophic archaea: N(ε)-acetyl-β-L-lysine. An extensive phylogenomic analysis on N(ε)-acetyl-β-L-lysine-producing enzymes revealed that they are widespread across both bacteria and archaea, indicating a potential horizontal gene transfer and a link to BORG extrachromosomal elements. Physicochemical analysis of bioreactor biomass further indicated the presence of sialic acids and the consumption of intracellular polyhydroxyalkanoates in anaerobic methanotrophs during salt stress.

The Lysine 299 Residue Endows the Multisubunit Mrp1 Antiporter with Dominant Roles in Na+ Resistance and pH Homeostasis in Corynebacterium glutamicum

Corynebacterium glutamicum is generally regarded as a moderately salt- and alkali-tolerant industrial organism. However, relatively little is known about the molecular mechanisms underlying these specific adaptations. Here, we found that the Mrp1 antiporter played crucial roles in conferring both environmental Na⁺ resistance and alkali tolerance whereas the Mrp2 antiporter was necessary in coping with high-KCl stress at alkaline pH. Furthermore, the Δmrp1 Δmrp2 double mutant showed the most-severe growth retardation and failed to grow under high-salt or alkaline conditions. Consistent with growth properties, the Na⁺/H⁺ antiporters of C. glutamicum were differentially expressed in response to specific salt or alkaline stress, and an alkaline stimulus particularly induced transcript levels of the Mrp-type antiporters. When the major Mrp1 antiporter was overwhelmed, C. glutamicum might employ alternative coordinate strategies to regulate antiport activities. Site-directed mutagenesis demonstrated that several conserved residues were required for optimal Na⁺ resistance, such as Mrp1A K²⁹⁹, Mrp1C I⁷⁶, Mrp1A H²³⁰, and Mrp1D E¹³⁶ Moreover, the chromosomal replacement of lysine 299 in the Mrp1A subunit resulted in a higher intracellular Na⁺ level and a more alkaline intracellular pH value, thereby causing a remarkable growth attenuation. Homology modeling of the Mrp1 subcomplex suggested two possible ion translocation pathways, and lysine 299 might exert its effect by affecting the stability and flexibility of the cytoplasm-facing channel in the Mrp1A subunit. Overall, these findings will provide new clues to the understanding of salt-alkali adaptation during C. glutamicum stress acclimatization.IMPORTANCE The capacity to adapt to harsh environments is crucial for bacterial survival and product yields, including industrially useful Corynebacterium glutamicum Although C. glutamicum exhibits a marked resistance to salt-alkaline stress, the possible mechanism for these adaptations is still unclear. Here, we present the physiological functions and expression patterns of C. glutamicum putative Na⁺/H⁺ antiporters and conserved residues of Mrp1 subunits, which respond to different salt and alkaline stresses. We found that the Mrp-type antiporters, particularly the Mrp1 antiporter, played a predominant role in maintaining intracellular nontoxic Na⁺ levels and alkaline pH homeostasis. Loss of the major Mrp1 antiporter had a profound effect on gene expression of other antiporters under salt or alkaline conditions. The lysine 299 residue may play its essential roles in conferring salt and alkaline tolerance by affecting the ion translocation channel of the Mrp1A subunit. These findings will contribute to a better understanding of Na⁺/H⁺ antiporters in sodium antiport and pH regulation.

Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family

The nearly 50,000 known Nudix proteins have a diverse array of functions, of which the most extensively studied is the catalyzed hydrolysis of aberrant nucleotide triphosphates. The functions of 171 Nudix proteins have been characterized to some degree, although physiological relevance of the assayed activities has not always been conclusively demonstrated. We investigated substrate specificity for eight structurally characterized Nudix proteins, whose functions were unknown. These proteins were screened for hydrolase activity against a 74-compound library of known Nudix enzyme substrates. We found substrates for four enzymes with kcat /Km values >10,000 M-1  s-1 : Q92EH0_LISIN of Listeria innocua serovar 6a against ADP-ribose, Q5LBB1_BACFN of Bacillus fragilis against 5-Me-CTP, and Q0TTC5_CLOP1 and Q0TS82_CLOP1 of Clostridium perfringens against 8-oxo-dATP and 3'-dGTP, respectively. To ascertain whether these identified substrates were physiologically relevant, we surveyed all reported Nudix hydrolytic activities against NTPs. Twenty-two Nudix enzymes are reported to have activity against canonical NTPs. With a single exception, we find that the reported kcat /Km values exhibited against these canonical substrates are well under 105 M-1  s-1 . By contrast, several Nudix enzymes show much larger kcat /Km values (in the range of 105 to >107 M-1  s-1 ) against noncanonical NTPs. We therefore conclude that hydrolytic activities exhibited by these enzymes against canonical NTPs are not likely their physiological function, but rather the result of unavoidable collateral damage occasioned by the enzymes' inability to distinguish completely between similar substrate structures. Proteins 2016; 84:1810-1822. © 2016 Wiley Periodicals, Inc.

The role of methanogens in acetic acid production under different salinity conditions

In this study, a fed-batch acidogenic reactor was operated at a 3 d hydraulic retention time (HRT) and fed with alkaline pre-treated sludge to investigate salinity effects on methanogens' abundance, activities and their consumption of produced acetic acid (HAc) and total volatile fatty acids (VFAs). The salinity concentration was increased step-wise by adding sodium chloride. At 3‰ (parts per thousand) salinity, the average produced volatile fatty acids (VFAs) concentration was 2410.16 ± 637.62 mg COD L(-1) and 2.70 ± 0.36 L methane was produced daily in the acidogenic reactor. Further batch tests indicated methanogens showed a HAc degradation rate of 3.81 mg COD g(-1) VSS h(-1) at initial HAc concentration of 1150 mg COD L(-1), and showed tolerance up to 16‰ salinity (3.76 g Na(+) L(-1)) as indicated by a constant HAc degradation rate. The microbiological study indicated this can be related to the predominance of acetate-utilizing Methanosarcinaceae and Methanomicrobiales in the reactor. However, with salinity increased to 20‰ and 40‰, increases in VFAs and HAc production and decreases in methane production, methanogens population, acidogenic bacteria population and acidification extent were observed. This study demonstrated presence of acetate-utilizing methanogens in an acidogenic reactor and their high tolerance to salinity, as well as their negative impacts on net VFAs production. The results would suggest the presence of methanogens in the acidogenic reactor should not be ignored and the recovery of methane from the acidogenic reactor needs to be considered to avoid carbon loss.

Co-digestion of molasses or kitchen waste with high-rate activated sludge results in a diverse microbial community with stable methane production

Kitchen waste and molasses are organic waste streams with high organic content, and therefore are interesting substrates for renewable energy production by means of anaerobic digestion. Both substrates, however, often cause inhibition of the anaerobic digestion process, when treated separately, hence, co-digestion with other substrates is required to ensure stable methane production. In this research, A-sludge (sludge harvested from a high rate activated sludge system) was used to stabilize co-digestion with kitchen waste or molasses. Lab-scale digesters were fed with A-sludge and kitchen waste or molasses for a total period of 105 days. Increased methane production values revealed a stabilizing effect of concentrated A-sludge on kitchen waste digestion. Co-digestion of molasses with A-sludge also resulted in a higher methane production. Volumetric methane production rates up to 1.53 L L(-1) d(-1) for kitchen waste and 1.01 L L(-1) d(-1) for molasses were obtained by co-digestion with A-sludge. The stabilizing effect of A-sludge was attributed to its capacity to supplement various nutrients. Microbial community results demonstrated that both reactor conditions and substrate composition determined the nature of the bacterial community, although there was no direct influence of micro-organisms in the substrate itself, while the methanogenic community profile remained constant as long as optimal conditions were maintained.

Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response

Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

The ability to adjust to changing osmotic conditions (osmoadaptation) is crucial to the survival of organisms across the tree of life. However, significant gaps still exist in our understanding of this important phenomenon. To help fill some of these gaps, we have produced high-quality draft genomes for 59 osmoadaptation “experts” (extreme halophiles of the euryarchaeal family Halobacteriaceae). We describe the dispersal of osmoadaptive protein families across the haloarchaeal evolutionary tree. We use this data to suggest a generalized model for haloarchaeal ion transport in response to changing osmotic conditions, including proposed new mechanisms for magnesium and chloride accumulation. We describe the evolutionary expansion and differentiation of haloarchaeal general transcription factor families and discuss their potential for enabling rapid adaptation to environmental fluxes. Lastly, we challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. This result highlights the power of our dataset for making evolutionary inferences, a feature which will make it useful to the broader evolutionary community. We distribute our genomic dataset through a user-friendly graphical interface.

Microbial ecology of anaerobic digesters: the key players of anaerobiosis

Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO₂. The conversions of complex organic compounds to CH₄ and CO₂ are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed.

Methanosarcina: the rediscovered methanogen for heavy duty biomethanation

Anaerobic digestion is an important technology in the framework of renewable energy production. The anaerobic digestion system is susceptible to perturbations due to the sensitivity of the methanogens towards environmental factors. Currently, technology is evolving from conventional waste treatment, i.e. the removal of pollutants, to very intensive biogas production from concentrated wastes, in the framework of bio-energy production. In the latter configuration Methanosarcina species appear to be of crucial importance. Methanosarcina sp. are, compared to other methanogens, quite robust towards different impairments. They are reported to be tolerant to total ammonium concentrations up to 7000 mg L(-1), salt concentrations up to 18,000 mg Na(+)L(-1), a pH shock of 0.8-1.0 units and acetate concentrations up to 15,000 mg CODL(-1). The possibilities of Methanosarcina sp. as key organisms in specific types of anaerobic digestion systems are demonstrated in this review.

Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales

The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.

Studying gene regulation in methanogenic archaea

Methanogenic archaea are a unique group of strictly anaerobic microorganisms characterized by their ability, and dependence, to convert simple C1 and C2 compounds to methane for growth. The major models for studying the biology of methanogens are members of the Methanococcus and Methanosarcina species. Recent development of sophisticated tools for molecular analysis and for genetic manipulation allows investigating not only their metabolism but also their cell cycle, and their interaction with the environment in great detail. One aspect of such analyses is assessment and dissection of methanoarchaeal gene regulation, for which, at present, only a handful of cases have been investigated thoroughly, partly due to the great methodological effort required. However, it becomes more and more evident that many new regulatory paradigms can be unraveled in this unique archaeal group. Here, we report both molecular and physiological/genetic methods to assess gene regulation in Methanococcus maripaludis and Methanosarcina acetivorans, which should, however, be applicable for other methanogens as well.

Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways

BACKGROUND

Pathways provide topical descriptions of cellular circuitry. Comparing analogous pathways reveals intricate insights into individual functional differences among species. While previous works in the field performed genomic comparisons and evolutionary studies that were based on specific genes or proteins, whole genomic sequence, or even single pathways, none of them described a genomic system level comparative analysis of metabolic pathways. In order to properly implement such an analysis one should overcome two specific challenges: how to combine the effect of many pathways under a unified framework and how to appropriately analyze co-evolution of pathways. Here we present a computational approach for solving these two challenges. First, we describe a comprehensive, scalable, information theory based computational pipeline that calculates pathway alignment information and then compiles it in a novel manner that allows further analysis. This approach can be used for building phylogenies and for pointing out specific differences that can then be analyzed in depth. Second, we describe a new approach for comparing the evolution of metabolic pathways. This approach can be used for detecting co-evolutionary relationships between metabolic pathways.

RESULTS

We demonstrate the advantages of our approach by applying our pipeline to data from the MetaCyc repository (which includes a total of 205 organisms and 660 metabolic pathways). Our analysis revealed several surprising biological observations. For example, we show that the different habitats in which Archaea organisms reside are reflected by a pathway based phylogeny. In addition, we discover two striking clusters of metabolic pathways, each cluster includes pathways that have very similar evolution.

CONCLUSION

We demonstrate that distance measures that are based on the topology and the content of metabolic networks are useful for studying evolution and co-evolution.

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation

The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. Salt adaptation was reflected by increased expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). The expression of genes involved in carbon metabolism, cell growth, and phage structures was decreased. Transcriptome profiles of D. vulgaris responses to salt adaptation were compared with transcriptome profiles of D. vulgaris responses to salt shock (short-term NaCl exposure). Metabolite assays showed that glutamate and alanine accumulated under salt adaptation conditions, suggesting that these amino acids may be used as osmoprotectants in D. vulgaris. Addition of amino acids (glutamate, alanine, and tryptophan) or yeast extract to the growth medium relieved salt-related growth inhibition. A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of D. vulgaris adaptation to elevated NaCl levels.

A novel limb in the osmoregulatory network of Methanosarcina mazei Gö1: N(epsilon)-acetyl-beta-lysine can be substituted by glutamate and alanine

N(epsilon)-acetyl-beta-lysine is a unique compatible solute found in methanogenic archaea grown at high salinities. Deletion of the genes that encode the lysine-2,3-aminomutase (ablA) and the beta-lysine acetyltransferase (ablB) abolished the production of N(epsilon)-acetyl-beta-lysine in Methanosarcina mazei Gö1. The mutant grew well at low and intermediate salinities. Interestingly, growth at high salt (800 mM NaCl) was only slowed down but not impaired demonstrating that in M. mazei Gö1 N(epsilon)-acetyl-beta-lysine is not essential for growth at high salinities. Nuclear magnetic resonance (NMR) analysis revealed an increased glutamate pool in the mutant. In addition to alpha-glutamate, a novel solute, alanine, was produced. The intracellular alanine concentration was as high as 0.36 +/- 0.05 micromol (mg protein)-1 representing up to 18% of the total solute pool at 800 mM NaCl. The cellular alanine concentration increased with the salinity of the medium and decreased in the presence of glycine betaine in the medium, indicating that alanine is used as compatible solute by M. mazei Gö1.