Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways.

Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3- supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.

NuA4 and H2A.Z control environmental responses and autotrophic growth in Arabidopsis.

Nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, but remains poorly characterized in plants. Here, we describe Arabidopsis homologs of the NuA4 scaffold proteins Enhancer of Polycomb-Like 1 (AtEPL1) and Esa1-Associated Factor 1 (AtEAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors, suggesting that NuA4 activates nuclear plastid genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished genome-wide in Atepl1, while another active chromatin mark, H3K9 acetylation (H3K9ac), is locally enhanced. Expression of many chloroplast-related genes depends on NuA4, as they are downregulated with loss of H4ac and H2A.Zac. Finally, we demonstrate that NuA4 promotes H2A.Z deposition and by doing so prevents spurious activation of stress response genes.

Metagenomic insights into mixotrophic denitrification facilitated nitrogen removal in a full-scale A2/O wastewater treatment plant.

Wastewater treatment plants (WWTPs) are important for pollutant removal from wastewater, elimination of point discharges of nutrients into the environment and water resource protection. The anaerobic/anoxic/oxic (A2/O) process is widely used in WWTPs for nitrogen removal, but the requirement for additional organics to ensure a suitable nitrogen removal efficiency makes this process costly and energy consuming. In this study, we report mixotrophic denitrification at a low COD (chemical oxygen demand)/TN (total nitrogen) ratio in a full-scale A2/O WWTP with relatively high sulfate in the inlet. Nitrogen and sulfur species analysis in different units of this A2/O WWTP showed that the internal sulfur cycle of sulfate reduction and reoxidation occurred and that the reduced sulfur species might contribute to denitrification. Microbial community analysis revealed that Thiobacillus, an autotrophic sulfur-oxidizing denitrifier, dominated the activated sludge bacterial community. Metagenomics data also supported the potential of sulfur-based denitrification when high levels of denitrification occurred, and sulfur oxidation and sulfate reduction genes coexisted in the activated sludge. Although most of the denitrification genes were affiliated with heterotrophic denitrifiers with high abundance, the narG and napA genes were mainly associated with autotrophic sulfur-oxidizing denitrifiers. The functional genes related to nitrogen removal were actively expressed even in the unit containing relatively highly reduced sulfur species, indicating that the mixotrophic denitrification process in A2/O could overcome not only a shortage of carbon sources but also the inhibition by reduced sulfur of nitrification and denitrification. Our results indicate that a mixotrophic denitrification process could be developed in full-scale WWTPs and reduce the requirement for additional carbon sources, which could endow WWTPs with more flexible and adaptable nitrogen removal.

Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates.

Phototrophic eukaryotes have evolved mainly by the primary or secondary uptake of photosynthetic organisms. A return to heterotrophy occurred multiple times in various protistan groups such as Chrysophyceae, despite the expected advantage of autotrophy. It is assumed that the evolutionary shift to mixotrophy and further to heterotrophy is triggered by a differential importance of nutrient and carbon limitation. We sequenced the genomes of 16 chrysophyte strains and compared them in terms of size, function, and sequence characteristics in relation to photo-, mixo- and heterotrophic nutrition. All strains were sequenced with Illumina and partly with PacBio. Heterotrophic taxa have reduced genomes and a higher GC content of up to 59% as compared to phototrophic taxa. Heterotrophs have a large pan genome, but a small core genome, indicating a differential specialization of the distinct lineages. The pan genome of mixotrophs and heterotrophs taken together but not the pan genome of the mixotrophs alone covers the complete functionality of the phototrophic strains indicating a random reduction of genes. The observed ploidy ranges from di- to tetraploidy and was found to be independent of taxonomy or trophic mode. Our results substantiate an evolution driven by nutrient and carbon limitation.

Untargeted Metabolomics Unveil Changes in Autotrophic and Mixotrophic Galdieria sulphuraria Exposed to High-Light Intensity.

The thermoacidophilic red alga Galdieria sulphuraria has been optimizing a photosynthetic system for low-light conditions over billions of years, thriving in hot and acidic endolithic habitats. The growth of G. sulphuraria in the laboratory is very much dependent on light and substrate supply. Here, higher cell densities in G. sulphuraria under high-light conditions were obtained, although reductions in photosynthetic pigments were observed, which indicated this alga might be able to relieve the effects caused by photoinhibition. We further describe an extensive untargeted metabolomics study to reveal metabolic changes in autotrophic and mixotrophic G. sulphuraria grown under high and low light intensities. The up-modulation of bilayer lipids, that help generate better-ordered lipid domains (e.g., ergosterol) and keep optimal membrane thickness and fluidity, were observed under high-light exposure. Moreover, high-light conditions induced changes in amino acids, amines, and amide metabolism. Compared with the autotrophic algae, higher accumulations of osmoprotectant sugars and sugar alcohols were recorded in the mixotrophic G. sulphuraria. This response can be interpreted as a measure to cope with stress due to the high concentration of organic carbon sources. Our results indicate how G. sulphuraria can modulate its metabolome to maintain energetic balance and minimize harmful effects under changing environments.

Molecular understanding of autotrophic CO2-fixing bacterial communities in composting based on RuBisCO genes analysis.

The CO2 fixation by autotrophic microbes has an important significance for improving carbon sequestration in composting. In this work, the succession of autotrophic CO2-fixing bacterial communities was investigated using quantitative PCR and high-throughput sequencing of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes (cbbL and cbbM). The results presented that the number of autotrophic CO2-fixing bacteria was comparable to that in the soil, and most species have not been classified into known bacterial groups, only part of them was assigned into Proteobacteria and Actinobacteria. Phylogenetic analysis displayed that the dominant known cbbL-containing bacteria were Allochromatium vinosum, Rhodobacter sphaeroides, Nitrobacter winogradskyi, Paracoccus yeei and Porphyrobacter sp. CACIAM 03H1, while the dominant known cbbM-containing bacteria were Sulfuritalea hydrogenivorans, Pseudomonas resinovorans, Achromobacter xylosoxidans, Sphingopyxis macrogoltabida and Thermomonospora curvata. In addition, canonical correspondence analysis showed that the evolution of autotrophic CO2-fixing bacterial communities was greatly affected by physico-chemical parameters such as temperature, C/N and pH.

Autotrophic carbon fixation pathways along the redox gradient in oxygen-depleted oceanic waters.

Anoxic marine zones (AMZs), also known as 'oxygen-deficient zones', contribute to the loss of fixed nitrogen from the ocean by anaerobic microbial processes. While these microbial processes associated with the nitrogen cycle have been extensively studied, those linked to the carbon cycle in AMZs have received much less attention, particularly the autotrophic carbon fixation - a crucial component of the carbon cycle. Using metagenomic and metatranscriptomic data from major AMZs, we report an explicit partitioning of the marker genes associated with different autotrophic carbon fixation pathways along the redox gradient (from oxic to anoxic conditions) present in the water column of AMZs. Sequences related to the Calvin-Benson-Bassham cycle were found along the entire gradient, while those related to the reductive Acetyl-CoA pathway were restricted to suboxic and anoxic waters. Sequences putatively associated with the 3-hydroxypropionate/4-hydroxybutyrate cycle dominated in the upper and lower oxyclines. Genes related to the reductive tricarboxylic acid cycle were represented from dysoxic to anoxic waters. The taxonomic affiliation of the sequences is consistent with the presence of microorganisms involved in crucial steps of biogeochemical cycles in AMZs, such as the gamma-proteobacteria sulfur oxidisers, the anammox bacteria Candidatus Scalindua and the thaumarcheota ammonia oxidisers of the Marine Group I.

Systems biology approach identifies functional modules and regulatory hubs related to secondary metabolites accumulation after transition from autotrophic to heterotrophic growth condition in microalgae.

Heterotrophic growth mode is among the most promising strategies put forth to overcome the low biomass and secondary metabolites productivity challenge. To shedding light on the underlying molecular mechanisms, transcriptome meta-analysis was integrated with weighted gene co-expression network analysis (WGCNA), connectivity analysis, functional enrichment, and hubs identification. Meta-analysis and Functional enrichment analysis demonstrated that most of the biological processes are up-regulated at heterotrophic growth condition, which leads to change of genetic architectures and phenotypic outcomes. WGNCA analysis of meta-genes also resulted four significant functional modules across logarithmic (LG), transition (TR), and production peak (PR) phases. The expression pattern and connectivity characteristics of the brown module as a non-preserved module vary across LG, TR, and PR phases. Functional analysis identified Carotenoid biosynthesis, Fatty acid metabolism and Methane metabolism as enriched pathways in the non-preserved module. Our integrated approach was applied here, identified some hubs, such as a serine hydroxymethyltransferase (SHMT1), which is the best candidate for development of metabolites accumulating strains in microalgae. Current study provided a new insight into underlying metabolite accumulation mechanisms and opens new avenue for the future applied studies in the microalgae field.

Hybrid Cyanobacterial-Tobacco Rubisco Supports Autotrophic Growth and Procarboxysomal Aggregation.

Much of the research aimed at improving photosynthesis and crop productivity attempts to overcome shortcomings of the primary CO2-fixing enzyme Rubisco. Cyanobacteria utilize a CO2-concentrating mechanism (CCM), which encapsulates Rubisco with poor specificity but a relatively fast catalytic rate within a carboxysome microcompartment. Alongside the active transport of bicarbonate into the cell and localization of carbonic anhydrase within the carboxysome shell with Rubisco, cyanobacteria are able to overcome the limitations of Rubisco via localization within a high-CO2 environment. As part of ongoing efforts to engineer a ß-cyanobacterial CCM into land plants, we investigated the potential for Rubisco large subunits (LSU) from the ß-cyanobacterium Synechococcus elongatus (Se) to form aggregated Rubisco complexes with the carboxysome linker protein CcmM35 within tobacco (Nicotiana tabacum) chloroplasts. Transplastomic plants were produced that lacked cognate Se Rubisco small subunits (SSU) and expressed the Se LSU in place of tobacco LSU, with and without CcmM35. Plants were able to form a hybrid enzyme utilizing tobacco SSU and the Se LSU, allowing slow autotrophic growth in high CO2 CcmM35 was able to form large Rubisco aggregates with the Se LSU, and these incorporated small amounts of native tobacco SSU. Plants lacking the Se SSU showed delayed growth, poor photosynthetic capacity, and significantly reduced Rubisco activity compared with both wild-type tobacco and lines expressing the Se SSU. These results demonstrate the ability of the Se LSU and CcmM35 to form large aggregates without the cognate Se SSU in planta, harboring active Rubisco that enables plant growth, albeit at a much slower pace than plants expressing the cognate Se SSU.

The Microalga Nannochloropsis during Transition from Quiescence to Autotrophy in Response to Nitrogen Availability.

The marine microalgae Nannochloropsis oceanica (CCMP1779) is a prolific producer of oil and is considered a viable and sustainable resource for biofuel feedstocks. Nitrogen (N) availability has a strong impact on the physiological status and metabolism of microalgal cells, but the exact nature of this response is poorly understood. To fill this gap we performed transcriptomic profiling combined with cellular and molecular analyses of N. oceanica CCMP1779 during the transition from quiescence to autotrophy. N deprivation-induced quiescence was accompanied by a strong reorganization of the photosynthetic apparatus and changes in the lipid homeostasis, leading to accumulation of triacylglycerol. Cell cycle activation and re-establishment of photosynthetic activity observed in response to resupply of the growth medium with N were accompanied by a rapid degradation of triacylglycerol stored in lipid droplets (LDs). Besides observing LD translocation into vacuoles, we also provide evidence for direct interaction between the LD surface protein (NoLDSP) and AUTOPHAGY-RELATED8 (NoATG8) protein and show a role of microlipophagy in LD turnover in N. oceanica CCMP1779. This knowledge is crucial not only for understanding the fundamental mechanisms controlling the cellular energy homeostasis in microalgal cells but also for development of efficient strategies to achieve higher algal biomass and better microalgal lipid productivity.

DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters.

Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira Here, we hypothesized that these nonclassical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subjected to a continuous supply of NH4+ or NO2- in the presence of 13C-HCO3- (labeled) or 12C-HCO3- (unlabeled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonia oxidation in the biofilter community. A total of 78 (8 by RNA-SIP and 70 by DNA-SIP) and 96 (25 by RNA-SIP and 71 by DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO3- uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, and Acidovorax under conditions that favored ammonia oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia-oxidizing taxa was not detected in the SIP fractions. This study provides the first in situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome.IMPORTANCE With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H13CO3- uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer in other environments.

Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity.

Nutrient availability is critical for growth of algae and other microbes used for generating valuable biochemical products. Determining the optimal levels of nutrient supplies to cultures can eliminate feeding of excess nutrients, lowering production costs and reducing nutrient pollution into the environment. With the advent of omics and bioinformatics methods, it is now possible to construct genome-scale models that accurately describe the metabolism of microorganisms. In this study, a genome-scale model of the green alga Chlorella vulgaris (iCZ946) was applied to predict feeding of multiple nutrients, including nitrate and glucose, under both autotrophic and heterotrophic conditions. The objective function was changed from optimizing growth to instead minimizing nitrate and glucose uptake rates, enabling predictions of feed rates for these nutrients. The metabolic model control (MMC) algorithm was validated for autotrophic growth, saving 18% nitrate while sustaining algal growth. Additionally, we obtained similar growth profiles by simultaneously controlling glucose and nitrate supplies under heterotrophic conditions for both high and low levels of glucose and nitrate. Finally, the nitrate supply was controlled in order to retain protein and chlorophyll synthesis, albeit at a lower rate, under nitrogen-limiting conditions. This model-driven cultivation strategy doubled the total volumetric yield of biomass, increased fatty acid methyl ester (FAME) yield by 61%, and enhanced lutein yield nearly 3 fold compared to nitrogen starvation. This study introduces a control methodology that integrates omics data and genome-scale models in order to optimize nutrient supplies based on the metabolic state of algal cells in different nutrient environments. This approach could transform bioprocessing control into a systems biology-based paradigm suitable for a wide range of species in order to limit nutrient inputs, reduce processing costs, and optimize biomanufacturing for the next generation of desirable biotechnology products.

Perspectives for the biotechnological production of biofuels from CO2 and H2 using Ralstonia eutropha and other 'Knallgas' bacteria.

With global CO2 emissions at their highest in several years, mitigation and possibly reduction of greenhouse gas buildup and concomitant production of renewable fuel molecules for growing transportation fuel needs are urgent challenges for renewable energy scientists and engineers. Knallgas bacteria provide a biocatalyst platform for utilization of CO2 and production of diverse and some high-energy density biofuel molecules, requisite for drop-in transportation fuels. The most well-studied Knallgas bacterium, Ralstonia eutropha, has been engineered to produce n-butanol, isobutanol, and terpene molecules under chemolithoautotrophic conditions. There are other representatives of this group of bacteria that potentially have the capabilities for CO2-based fuel molecule synthesis. In principle, fermentative production of biofuel from CO2 could rival the "power-to-gas" (non-biological production of fuels using CO2 and H2) production methods. However, challenges remain for both methods in order to compete with currently priced petroleum-based fuels. With continued streamlining of processes and attention to Industrial Ecology principles, biofuel synthesis by Knallgas bacteria could represent a viable part of a nation's energy portfolio.

A metatranscriptomics-based assessment of small-scale mixing of sulfidic and oxic waters on redoxcline prokaryotic communities.

Lateral intrusions of oxygen caused by small-scale mixing are thought to shape microbial activity in marine redoxclines. To examine the response of prokaryotes to such mixing events we employed a shipboard mixing experiment in the euxinic central Baltic Sea: oxic, nitrate containing and sulfidic water samples without detectable oxygenized substances were incubated directly or after mixing. While nitrate, nitrite and ammonium concentrations stayed approximately constant in all incubations, we observed a decrease of sulfide after the contact with oxygen in the sulfide containing incubations. The transcription of marker genes from chemolithoauthotrophic key players including archaeal nitrifiers as well as gammaproteobacterial and campylobacterial autotrophic organisms that couple denitrification with sulfur-oxidation were followed at four time points within 8.5 h. The temporally contrasting transcriptional profiles of gammaproteobacterial and campylobacterial denitrifiers that depend on the same inorganic substrates pointed to a niche separation. Particular archaeal and campylobacterial marker genes involved in nitrification, denitrification and sulfur oxidation, which depend on oxidized substrates, were highly upregulated in the anaerobic sulfidic samples. We suggest that, despite the absence of measurable oxygenated compounds in the sulfidic water, frequent intermittent small-scale intrusions stimulate the permanent upregulation of genes involved in nitrification, denitrification and sulfur oxidation.

De novo assembly and transcriptome of Pfaffia glomerata uncovers the role of photoautotrophy and the P450 family genes in 20-hydroxyecdysone production.

Pfaffia glomerata is a medically important species because it produces the phytoecdysteroid 20-hydroxyecdysone (20-E). However, there has been no ready-to-use transcriptome data available in the literature for this plant. Here, we present de novo transcriptome sequencing of RNA from P. glomerata in order to investigate the 20-E production as well as to understand the biochemical pathway of secondary metabolites in this non-model species. We then analyze the effect of photoautotrophy on the production of 20-E genes phylogenetically identified followed by expression analysis. For this, total messenger RNA (mRNA) from leaves, stems, roots, and flowers was used to construct indexed mRNA libraries. Based on the similarity searches against plant non-redundant protein database, gene ontology, and eukaryotic orthologous groups, 164,439 transcripts were annotated. In addition, the effect of photoautotrophy in two genes putatively involved in the 20-E synthesis pathway was analyzed. The Phantom gene (CYP76C), a precursor of the route, showed increased expression in P. glomerata plants cultured under photoautotrophic conditions. This was accompanied by increased production of this metabolite indicating a putative involvement in 20-E synthesis. This work reveals that several genes in the P. glomerata transcriptome are related to secondary metabolism and stresses, that genes of the P450 family participate in the 20-E biosynthesis route, and that plants cultured under photoautotrophic conditions promote an upregulated Phantom gene and enhance the productivity of 20-E. The data will be used for future investigations of the 20-E synthesis pathway in P. glomerata while offering a better understanding of the metabolism of the species.

Optimization of carbon and energy utilization through differential translational efficiency.

Control of translation is vital to all species. Here we employ a multi-omics approach to decipher condition-dependent translational regulation in the model acetogen Clostridium ljungdahlii. Integration of data from cells grown autotrophically or heterotrophically revealed that pathways critical to carbon and energy metabolism are under strong translational regulation. Major pathways involved in carbon and energy metabolism are not only differentially transcribed and translated, but their translational efficiencies are differentially elevated in response to resource availability under different growth conditions. We show that translational efficiency is not static and that it changes dynamically in response to mRNA expression levels. mRNAs harboring optimized 5'-untranslated region and coding region features, have higher translational efficiencies and are significantly enriched in genes encoding carbon and energy metabolism. In contrast, mRNAs enriched in housekeeping functions harbor sub-optimal features and have lower translational efficiencies. We propose that regulation of translational efficiency is crucial for effectively controlling resource allocation in energy-deprived microorganisms.

Insights into the carbonic anhydrases and autotrophic carbon dioxide fixation pathways of high CO2 tolerant Rhodovulum viride JA756.

Biofixation of CO2 is being extensively investigated to solve the global warming problem. Purple non-sulfur bacteria are fast growers that consume CO2 and produce beneficial biomass. Better the growth at higher CO2 levels, more efficient are the strains for biofixation. Nine among fifty strains that were analyzed at elevated CO2 levels responded with better growth. Considering its enhanced growth at high CO2 and metabolic versatility, Rhodovulum viride strain JA756 was chosen to make further studies. Strain JA756 tolerates up to 50% (v/v) CO2 with its optimum between 20-40% (v/v), yielding a biomass of 3.4 g. L-1. The pattern of specific enzyme activity of carbonic anhydrase corresponded well with that of its growth. To gain insights into the genomic composition and genes related to carbonic anhydrases and CO2 fixation, draft genome sequencing of JA756 was carried out which revealed the presence of two non-homologous genes encoding for ß and γ carbonic anhydrases, both of which are assumed to be implicated in maintaining intracellular inorganic carbon concentration at equilibrium. Most of the genes involved in the Calvin pathway, reductive tricarboxylic acid pathway, 3-hydroxypropionate bicycle and C4 pathways were found in the draft genome. While the experimental determinations of active roles of two of these pathways are still underway, the expression of key genes of Calvin and C4 pathway suggest their functional role in the organism. Owing to its metabolic versatility, JA756 can be advantageous for biological CO2 assimilation facilities located by the coastline, inland and also at wide ranges of CO2 concentrations.

Structural and functional studies of histidine biosynthesis in Acanthamoeba spp. demonstrates a novel molecular arrangement and target for antimicrobials.

Acanthamoeba is normally free-living, but sometimes facultative and occasionally opportunistic parasites. Current therapies are, by necessity, arduous and yet poorly effective due to their inabilities to kill cyst stages or in some cases to actually induce encystation. Acanthamoeba can therefore survive as cysts and cause disease recurrence. Herein, in pursuit of better therapies and to understand the biochemistry of this understudied organism, we characterize its histidine biosynthesis pathway and explore the potential of targeting this with antimicrobials. We demonstrate that Acanthamoeba is a histidine autotroph, but with the ability to scavenge preformed histidine. It is able to grow in defined media lacking this amino acid, but is inhibited by 3-amino-1,2,4-triazole (3AT) that targets Imidazoleglycerol-Phosphate Dehydratase (IGPD) the rate limiting step of histidine biosynthesis. The structure of Acanthamoeba IGPD has also been determined in complex with 2-hydroxy-3-(1,2,4-triazol-1-yl) propylphosphonate [(R)-C348], a recently described novel inhibitor of Arabidopsis thaliana IGPD. This compound inhibited the growth of four Acanthamoeba species, having a 50% inhibitory concentration (IC50) ranging from 250-526 nM. This effect could be ablated by the addition of 1 mM exogenous free histidine, but importantly not by physiological concentrations found in mammalian tissues. The ability of 3AT and (R)-C348 to restrict the growth of four strains of Acanthamoeba spp. including a recently isolated clinical strain, while not inducing encystment, demonstrates the potential therapeutic utility of targeting the histidine biosynthesis pathway in Acanthamoeba.

Genome Reports: Contracted Genes and Dwarfed Plastome in Mycoheterotrophic Sciaphila thaidanica (Triuridaceae, Pandanales).

With a reduced need for photosynthesis, the plastome of parasitic and mycoheterotrophic plants degrades. In the tiny, fully mycoheterotrophic plant Sciaphila thaidanica, we find one of the smallest plastomes yet encountered. Its size is just 12,780 bp and it contains only 20 potentially functional housekeeping genes. Thus S. thaidanica fits the proposed model of gene loss in achlorophyllous plants. The most astonishing feature of the plastome is its extremely compact nature, with more than half of the genes having overlapping reading frames. Additionally, intergenic sequences have been reduced to a bare minimum, and the retained genes have been reduced in length both compared with the orthologous genes in another mycoheterotrophic species of Sciaphila and in the autotrophic relative Carludovica.

Reaction engineering analysis of the autotrophic energy metabolism of Clostridium aceticum.

Acetogenesis with CO2:H2 or CO via the reductive acetyl-CoA pathway does not provide any net ATP formation in homoacetogenic bacteria. Autotrophic energy conservation is coupled to the generation of chemiosmotic H+ or Na+ gradients across the cytoplasm membrane using either a ferredoxin:NAD+ oxidoreductase (Rnf), a ferredoxin:H+ oxidoreductase (Ech) or substrate-level phosphorylation via cytochromes. The first isolated acetogenic bacterium Clostridium aceticum shows both cytochromes and Rnf complex, putting it into an outstanding position. Autotrophic batch processes with continuous gas supply were performed in fully controlled stirred-tank bioreactors to elucidate energy metabolism of C. aceticum. Varying the initial Na+ concentration in the medium showed sodium-dependent growth of C. aceticum with a growth optimum between 60 and 90 mM Na+. The addition of the Na+-selective ionophore ETH2120 or the protonophore CCCP or the H+/cation-antiporter monensin revealed that an H+ gradient is used as primary energy conservation mechanism, which strengthens the exceptional position of C. aceticum as acetogenic bacterium showing an H+-dependent energy conservation mechanism as well as Na+-dependent growth.