Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families

The microbes that inhabit particular environments must be able to perform molecular functions that provide them with a competitive advantage to thrive in those environments. As most molecular functions are performed by proteins and are conserved between related proteins, we can expect that organisms successful in a given environmental niche would contain protein families that are specific for functions that are important in that environment. For instance, the human gut is rich in polysaccharides from the diet or secreted by the host, and is dominated by Bacteroides, whose genomes contain highly expanded repertoire of protein families involved in carbohydrate metabolism. To identify other protein families that are specific to this environment, we investigated the distribution of protein families in the currently available human gut genomic and metagenomic data. Using an automated procedure, we identified a group of protein families strongly overrepresented in the human gut. These not only include many families described previously but also, interestingly, a large group of previously unrecognized protein families, which suggests that we still have much to discover about this environment. The identification and analysis of these families could provide us with new information about an environment critical to our health and well being.     

Fluoride inhibition of enolase: crystal structure and thermodynamics

Enolase is a dimeric metal-activated metalloenzyme which uses two magnesium ions per subunit: the strongly bound conformational ion and the catalytic ion that binds to the enzyme-substrate complex inducing catalysis. The crystal structure of the human neuronal enolase-Mg2F2P(i) complex (enolase fluoride/phosphate inhibitory complex, EFPIC) determined at 1.36 A resolution shows that the combination of anions effectively mimics an intermediate state in catalysis. The phosphate ion binds in the same site as the phosphate group of the substrate/product, 2-phospho-D-glycerate/phosphoenolpyruvate, and induces binding of the catalytic Mg2+ ion. One fluoride ion bridges the structural and catalytic magnesium ions while the other interacts with the structural magnesium ion and the ammonio groups of Lys 342 and Lys 393. These fluoride ion positions correspond closely to the positions of the oxygen atoms of the substrate's carboxylate moiety. To relate structural changes resulting from fluoride, phosphate, and magnesium ions binding to those that are induced by phosphate and magnesium ions alone, we also determined the structure of the human neuronal enolase-Mg2P(i) complex (enolase phosphate inhibitory complex, EPIC) at 1.92 A resolution. It shows the closed conformation in one subunit and a mixture of open and semiclosed conformations in the other. The EPFIC dimer is essentially symmetric while the EPIC dimer is asymmetric. Isothermal titration calorimetry data confirmed binding of four fluoride ions per dimer and yielded Kb values of 7.5 x 10(5) +/- 1.3 x 10(5), 1.2 x 10(5) +/- 0.2 x 10(5), 8.6 x 10(4) +/- 1.6 x 10(4), and 1.6 x 10(4) +/- 0.7 x 10(4) M(-1). The different binding constants indicate negative cooperativity between the subunits; the asymmetry of EPIC supports such an interpretation.     

Biocidal effect of (<Emphasis Type="Italic">E</Emphasis>)-anethole on the cyanobacterium <Emphasis Type="Italic">Aphanizomenon gracile</Emphasis> Lemmermann

Biocidal natural substances of botanical origin offer a promising ecofriendly option for controlling toxic cyanobacteria. Herein, we study 11 essential oils and some of their major components for their activity on Aphanizomenon gracile. On the basis of our results we support that Origanum vulgare and O. dictamnus, Ocimum basilicum, Eucalyptus meliodora, Melissa officinalis, and Pimpinella anisum exhibited the strongest activities, and the IC_50/1d values of the extracts were calculated to be between 168.43 and 241.97 μg mL^?1. When the major components of the biocidal essential oils were tested individually, (E)-anethole was found active, exhibiting an IC_50/1d value of 71.35 μg mL^?1. On the other hand, the half-life (t _1/2 ) of (E)-anethole was calculated at 1 h. A preliminary attempt of (E)-anethole microencapsulation was conducted, in order to slowly release this biocidal agent, increasing the residual life under open air conditions and thus the biological activity. Results were promising since the microencapsulated product exhibited better activity than did the non-formulated (E)-anethole. This is a first report on the biocidal activity of EOs and (E)-anethole on A. gracile and a preliminary indication of the microencapsulated (E)-anethole potential use as a natural biocidal in fresh waters.

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Graphical abstract Filaments of Aphanizomenon gracile capable of bloom forming (strain SAG 31.79, in a batch culture) and (E)-anethole

     

Solitary terminal cells of Aphanizomenon gracile (Cyanobacteria,Nostocales) can divide and renew trichomes

An attempt was made to find evidence that morphologically distinct terminal cells of filamentous cyanobacterium Aphanizomenon gracile strain CCALA 8 are capable of dividing and forming trichomes. Based on our current knowledge, the division of morphologically diversified terminal cells is possible in nostocalean cyanobacteria. However, this process has been observed only in a few species. Terminal cells of A. gracile differ morphologically from other vegetative cells of a trichome, as they are not hyaline and can sometimes be found as solitary cells in cultures. Hence, it was reasonable for us to suspect that these cells are capable of dividing and forming trichomes. We observed terminal cells under a light and transmission electron microscope. Microscopic observations revealed that the septum formed in both solitary terminal cells and in terminal cells attached to trichomes. Our study is the first to demonstrate division and renewal of trichomes in terminal cells of A. gracile. Previously, such mode of reproduction was described only for another nostocalean cyanobacterium Raphidiopsis mediterranea. Moreover, our findings further emphasize the variability among members that belong to the genus Aphanizomenon , in which a type species (A. flos‐aquae) has hyaline cells incapable of dividing and renewing trichomes, while A. gracile can additionally propagate by solitary terminal cells division. This additional feature distinguishing A. gracile from typical species of Aphanizomenon, such as A. flos‐aquae, might be valuable for resolving taxonomic position of the species considering ambiguous genetic relationship between A. gracile and A. flos‐aquae.     

Setae thickening in <Emphasis Type="Italic">Daphnia magna</Emphasis> alleviates the food stress caused by the filamentous cyanobacteria

It is assumed that daphnids adjust the filter screen morphology in order to minimize the interference with cyanobacterial filaments. The aim of this study was to investigate the impact of filamentous cyanobacteria (Aphanizomenon gracile Lemmermann, Cylindrospermopsis raciborskii Woloszynska Seenaya et Subba Raju) on the thickness and length of setae of the third pair of thoracic limbs of Daphnia magna. The second objective was to assess whether the setae modifications could improve the performance of daphnids in the presence of cyanobacteria. Three clones of Daphnia magna Straus were cultured with: green algae; green algae with filaments of Cylindrospermopsis; and green algae with filaments of Aphanizomenon. The size and age of animals in the first reproduction cycle as well as the number of offspring were recorded. Setae thickness and length were measured in the central part of each endopodite. Additionally, we analyzed how the changes in setae morphology affect the fitness of experimental animals using the intrinsic rate of population increase calculated with the Euler–Lotka equation. The results showed that the thickness and length of setae increased in the presence of filamentous cyanobacteria. Moreover, cyanobacteria-induced setae thickening was positively correlated to the fitness of daphnids, which may indicate setae thickening as a phenotypic adaptation to cope with food stress caused by filamentous cyanobacteria.     

Susceptibility of Asian citrus psyllid, <Emphasis Type="Italic">Diaphorina citri</Emphasis> (Hemiptera: Liviidae), to the insecticide afidopyropen: a new and potent modulator of insect transient receptor potential channels

A relatively new insecticide chemistry for controlling sucking insects, afidopyropen, was investigated for toxicity against Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae). We evaluated the mortality of D. citri eggs, nymphs, and adults treated with afidopyropen using both laboratory-reared and field populations. We also quantified the effects of sublethal doses of afidopyropen on D. citri feeding, host choice selection, and fecundity. For laboratory susceptible adults, the contact LC₅₀, topical application LD₅₀, and leaf dip LC₅₀ were 2.13, 2.00, and 3.08 ng/µL, respectively. For adults collected from a commercially managed citrus grove in Florida, the contact LC₅₀, topical application LD₅₀, and leaf dip LC₅₀ were 1.37, 1.92, and 4.89 ng/µL, respectively. Egg hatch was significantly reduced following exposure to afidopyropen at 100 ng/µL. Furthermore, afidopyropen reduced D. citri nymph survival and adult emergence at concentrations ranging between 0.01 and 100 ng/µL. Diaphorina citri adult feeding decreased on citrus leaves treated with afidopyropen in a concentration-dependent manner as measured indirectly by honeydew excretion, and appeared almost completely inhibited after treatment with 10 and 100 ng/µL solutions of afidopyropen. In choice tests, significantly fewer D. citri adults settled on afidopyropen-treated plants than on control plants at 24, 48, and 72 h after release, with no differences in settling between males and females. Afidopyropen reduced the fecundity of D. citri in a concentration-dependent manner. Collectively, the results suggest that afidopyropen could contribute to the integrated management of D. citri and may therefore be useful in rotational programs to improve resistance management.     

Effects of Daphnia exudates and sodium octyl sulphates on filament morphology and cell wall thickness of Aphanizomenon gracile (Nostocales), Cylindrospermopsis raciborskii (Nostocales) and Planktothrix agardhii (Oscillatoriales)

Grazing is recognized as one of the selective factors shaping the morphology and physiology of cyanobacteria. A recent study has shown that the filamentous cyanobacterium Aphanizomenon gracile strain SAG 31.79 thickened in the presence of Daphnia (Cladocera) and its exudates. The aims of our study were: (1) to determine whether this type of response to Daphnia cues is common for other strains of A. gracile, and other species of filamentous cyanobacteria, (2) to test whether the response is due to nutrients recycled by Daphnia, or kairomone induced, and (3) whether it is related to toxin production. Prior to the experiment, cyanobacterial strains were inspected using chromatographic methods for the presence of two toxins, cylindrospermopsin (CYN) and three homologues of microcystin (MC-RR, MC-YR, MC-LR). HPLC analyses showed that all strains were free of cylindrospermopsin, whereas microcystins were detected only in one strain (Planktothrix agardhii). We then tested whether Daphnia exudates can cause thickening of cyanobacterial filaments, which would suggest the morphological changes in cyanobacterial filaments are caused by recycled nutrients. Cyanobacteria were also exposed to sodium octyl sulphate (a commercially available Daphnia kairomone). Transmission electron microscopy (TEM) was used to check whether Daphnia exudates and sodium octyl sulphate trigger thickening of cyanobacterial cell walls, which would be a defence mechanism against grazing. The TEM analysis revealed no significant effect of either Daphnia exudates or kairomone (sodium octyl sulphate) on the cell wall thickness of cyanobacteria. However, our study showed that Daphnia exudates triggered filament thickening in nostocalean cyanobacteria, while filaments of the oscillatorialean strain P. agardhii did not show this response. It was also demonstrated that sodium octyl sulphate alone can also cause filament thickening, which suggests that this might be a specific defence response to the presence of grazers.     

Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production

Background

Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways.

Results

A comprehensive metagenomic approach was used to compare seven environmental communities, originating from an agricultural biogas plant, cattle-associated samples, a lowland bog, sewage sludge from a wastewater treatment plant and sediments from an ancient gold mine. In addition to the native consortia, two laboratory communities cultivated on maize silage as the sole substrate were also analyzed. Results showed that all anaerobic communities harbored genes of all known methanogenesis pathways, but their abundance varied greatly between environments and that genes were encoded by different methanogens. Identification of microorganisms directly involved in different stages of methane production revealed that hydrogenotrophic methanogens, such as Methanoculleus, Methanobacterium, Methanobrevibacter, Methanocorpusculum or Methanoregula, predominated in most native communities, whereas acetoclastic Methanosaeta seemed to be the key methanogen in the wastewater treatment plant. Furthermore, in many environments, the methylotrophic pathway carried out by representatives of Methanomassiliicoccales, such as Candidatus Methanomethylophilus and Candidatus Methanoplasma, seemed to play an important role in methane production. In contrast, in stable laboratory reactors substrate versatile Methanosarcina predominated.

Conclusions

The metagenomic approach presented in this study allowed for deep exploration and comparison of nine environments in which methane production occurs. Different abundance of methanogenesis-related functions was observed and the functions were analyzed in the phylogenetic context in order to identify microbes directly involved in methane production. In addition, a comparison of two metagenomic analytical tools, MG-RAST and MetAnnotate, revealed that combination of both allows for a precise characterization of methanogenic communities.

     

A possible Fourier transform infrared‐based plasma fingerprint of angiotensin‐converting enzyme inhibitor‐induced reversal of endothelial dysfunction in diabetic mice

Angiotensin‐converting enzyme inhibitors (ACE‐I) display vasoprotective activity and represent the cornerstone in the treatment of cardiovascular diseases. In this study, we tested whether Fourier transform infrared (FTIR)‐based analysis of blood plasma is sensitive to detect vasoprotective effects of treatment with perindopril including reversal of endothelial dysfunction in diabetes. For this purpose, plasma samples were collected from untreated db/db mice, db/db mice treated with 2 or 10 mg/kg perindopril and db+ mice. The effect of perindopril on endothelial function was examined in ex vivo aortic rings; 10 mg/kg but not 2 mg/kg of perindopril reversed endothelial dysfunction. In plasma of db/db mice, the balance between conformations of plasma proteins was noted, and treatment with perindopril at a high dose but not at a low dose reversed this effect. This was revealed by amide II/amide I ratio attributed to increased β‐sheet formation. Spectral markers at 3010, 1520/1238 cm^?1, representative for unsaturation degree of lipids and phosphorylation of tyrosine, respectively, were also affected by perindopril treatment. In conclusion, although metabolic abnormalities associated with type 2 diabetes mellitus such as hypertriglyceridemia and hyperglycemia strongly affected spectral FTIR profile of diabetic plasma, we identified FTIR features that seem to be associated with the vasoprotective activity of ACE‐I.