Synthesis, Biochemical Characterization, and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family.

Lysine acetylation is a charge-neutralizing post-translational modification of proteins bound by bromodomains (Brds). A 1,2,4-triazole amino acid (ApmTri) was established as acetyllysine (Kac) mimic recruiting Brds of the BET family in contrast to glutamine commonly used for simulating this modification. Optimization of triazole substituents and side chain spacing allowed BET Brd recruitment to ApmTri-containing peptides with affinities similar to native substrates. Crystal structures of ApmTri-containing peptides in complex with two BET Brds revealed the binding mode which mirrored that of Kac ligands. ApmTri was genetically encoded and recombinant ApmTri-containing proteins co-enriched BRD3(2) from cellular lysates. This interaction was blocked by BET inhibitor JQ1. With genetically encoded ApmTri, biochemistry is now provided with a stable Kac mimic reflecting charge neutralization and Brd recruitment, allowing new investigations into BET proteins in vitro and in vivo.

A study on assessing the urban growth, population, and water resources of Bodrum Peninsula, Turkey.

In recent years, it has been difficult to establish a supply-demand balance between urban growth, increasing population, and existing water resources in many countries. In this study, the Bodrum Peninsula, which is an important tourism center for Turkey, was examined in terms of the relationship between the urban growth of the peninsula, population projections, the need for drinking and potable water, and the availability of the existing water resources. Using the Geographic Information System, it has been determined that the urban growth of the peninsula increased by 11.36% between 1985 and 2010. Urban growth is mostly concentrated in the coastal areas where 2 houses are densely built. The population is expected to increase approximately six times between 2010 and 2060. The amount of drinking and potable water required according to the population projection is 12.38, 26.50, 69.12, and 109.50 hm3/year for 2010, 2030, 2050, and 2060 respectively. The existing water resources of the peninsula will be able to meet the requirements until 2030. In order to meet the water needs of the peninsula until 2055, the Bozalan and Gökçeler dams located nearby as well as the Namnam dam located at mid-range to the peninsular should be built. It is not possible to meet the water needs of the peninsula in 2060 with just the near and medium distance water resources. However, by supplying water from the Akköprü dam located at a further distance, it is possible that 2060 water needs can be met.

Structural and enzymatic analysis of TarM glycosyltransferase from Staphylococcus aureus reveals an oligomeric protein specific for the glycosylation of wall teichoic acid.

Anionic glycopolymers known as wall teichoic acids (WTAs) functionalize the peptidoglycan layers of many Gram-positive bacteria. WTAs play central roles in many fundamental aspects of bacterial physiology, and they are important determinants of pathogenesis and antibiotic resistance. A number of enzymes that glycosylate WTA in Staphylococcus aureus have recently been identified. Among these is the glycosyltransferase TarM, a component of the WTA de novo biosynthesis pathway. TarM performs the synthesis of α-O-N-acetylglycosylated poly-5'-phosphoribitol in the WTA structure. We have solved the crystal structure of TarM at 2.4 Å resolution, and we have also determined a structure of the enzyme in complex with its substrate UDP-GlcNAc at 2.8 Å resolution. The protein assembles into a propeller-like homotrimer in which each blade contains a GT-B-type glycosyltransferase domain with a typical Rossmann fold. The enzymatic reaction retains the stereochemistry of the anomeric center of the transferred GlcNAc-moiety on the polyribitol backbone. TarM assembles into a trimer using a novel trimerization domain, here termed the HUB domain. Structure-guided mutagenesis experiments of TarM identify residues critical for enzyme activity, assign a putative role for the HUB in TarM function, and allow us to propose a likely reaction mechanism.

A study on the role and importance of irrigation management in integrated river basin management.

The purpose of this paper is to identify the role and the importance of irrigation management in integrated river basin management during arid and semi-arid conditions. The study has been conducted at Büyük Menderes Basin which is located in southwest of Turkey and where different sectors (irrigation, drinking and using, industry, tourism, ecology) related to the use and distribution of water sources compete with each other and also where the water demands for important ecological considerations is evaluated and where the river pollution has reached important magnitudes. Since, approximately 73% of the water resources of the basin are utilized for irrigation; as a result, irrigation management becomes important for basin management. Irrigation operations have an effect on basin soil resources, water users, and environmental and ecological conditions. Thus, the determination of the role and importance of irrigation management require an integrated and interdisciplinary approach. In the studies conducted in Turkey, usually the environmental reactions have been analyzed in the basin studies and so the other topics related to integrated river basin management have not been taken into account. Therefore, this study also is to address these existing gaps in the literature and practice.

Structure-Activity Relationship Study Reveals the Molecular Basis for Specific Sensing of Hydrophobic Amino Acids by the Campylobacter jejuni Chemoreceptor Tlp3.

Chemotaxis is an important virulence factor of the foodborne pathogen Campylobacter jejuni. Inactivation of chemoreceptor Tlp3 reduces the ability of C. jejuni to invade human and chicken cells and to colonise the jejunal mucosa of mice. Knowledge of the structure of the ligand-binding domain (LBD) of Tlp3 in complex with its ligands is essential for a full understanding of the molecular recognition underpinning chemotaxis. To date, the only structure in complex with a signal molecule is Tlp3 LBD bound to isoleucine. Here, we used in vitro and in silico screening to identify eight additional small molecules that signal through Tlp3 as attractants by directly binding to its LBD, and determined the crystal structures of their complexes. All new ligands (leucine, valine, α-amino-N-valeric acid, 4-methylisoleucine, ß-methylnorleucine, 3-methylisoleucine, alanine, and phenylalanine) are nonpolar amino acids chemically and structurally similar to isoleucine. X-ray crystallographic analysis revealed the hydrophobic side-chain binding pocket and conserved protein residues that interact with the ammonium and carboxylate groups of the ligands determine the specificity of this chemoreceptor. The uptake of hydrophobic amino acids plays an important role in intestinal colonisation by C. jejuni, and our study suggests that C. jejuni seeks out hydrophobic amino acids using chemotaxis.

Heterologous production, isolation, characterization and crystallization of a soluble fragment of the NADH:ubiquinone oxidoreductase (complex I) from Aquifex aeolicus.

The proton-pumping NADH:ubiquinone oxidoreductase (complex I) is the first enzyme complex of the respiratory chains in many bacteria and most eukaryotes. It is the least understood of all, due to its enormous size and unique energy conversion mechanism. The bacterial complex is in general made up of 14 different subunits named NuoA-N. Subunits NuoE, -F, and -G comprise the electron input part of the complex. We have cloned these genes from the hyperthermophilic bacterium Aquifex aeolicus and expressed them heterologously in Escherichia coli. A soluble subcomplex made up of NuoE and NuoF and containing the NADH binding site, the primary electron acceptor flavin mononucleotide (FMN), the binuclear iron-sulfur cluster N1a, and the tetranuclear iron-sulfur cluster N3 was isolated by chromatographic methods. The proteins were identified by N-terminal sequencing and mass spectrometry; the cofactors were characterized by UV/vis and EPR spectroscopy. Subunit NuoG was not produced in this strain. The preparation was thermostable and exhibited maximum NADH/ferricyanide oxidoreductase activity at 85 degrees C. Analytical size-exclusion chromatography and dynamic light scattering revealed the homogeneity of the preparation. First attempts to crystallize the preparation led to crystals diffracting more than 2 A.

Organic pollution of the Büyük Menderes River, Turkey and effects on aquaculture.

Water quality was measured at eight stations on the Buyuk Menderes River in Turkey (Adigüzel dam, Yenice regülator, Sarayköy bridge, Feslek regülator, Yenipazar bridge, Aydin bridge, Koçarli bridge, Söke regülator) between 2000 and 2013 in February, April, June, August, October and December. The resulting data were evaluated in terms of biochemical oxygen demand (BOD), chemical oxygen demand (COD), dissolved oxygen (DO), ammoniac-nitrogen (NH3-N), nitrite-nitrogen (NO2-N), nitrate-nitrogen (NO3-N) and orthophosphate (o-PO4) aquaculture. According to the analysis, while river water pollution generally varied during each year, samples from certain measurement points demonstrated high pollution levels throughout the year. In this study, water parameters were classified according to the "Turkish water pollution control regulation." The studied parameters are also compared with TS 266 and WHO guidelines. While levels at Sarayköy station were generally higher than other stations, values at Adigüzel dam were the lowest, giving it the best water quality of the eight stations. The highest values on a yearly basis were obtained in 2007 due to the severe drought in the Menderes basin within which irrigation water levels fell to 4255 m(3)/ha. The BOD, COD levels are the lowest in 2009 and highest in 2007; the DO level is lowest in 2007 and highest in 2009; NH3-N, NO2-N, and NO3-N parameters are the lowest in 2007 and highest in 2009; and the o-PO4 are at the lowest level in 2004 and seen as the highest in 2007. Analysis of the data was performed by SPSS 21 statistics program. One direction ANOVA was applied to the data, which were also subject to Tukey multiple comparison tests. Differences between groups were evaluated at p < 0.05. Box-plot graphs were used to demonstrate the data distribution. In the study, it was analyzed, the effect of fish species and pollution involved in the Büyük Menderes River so far on fish species.

Structure of the host-recognition device of Staphylococcus aureus phage ϕ11.

Phages play key roles in the pathogenicity and adaptation of the human pathogen Staphylococcus aureus. However, little is known about the molecular recognition events that mediate phage adsorption to the surface of S. aureus. The lysogenic siphophage ϕ11 infects S. aureus SA113. It was shown previously that ϕ11 requires α- or ß-N-acetylglucosamine (GlcNAc) moieties on cell wall teichoic acid (WTA) for adsorption. Gp45 was identified as the receptor binding protein (RBP) involved in this process and GlcNAc residues on WTA were found to be the key component of the ϕ11 receptor. Here we report the crystal structure of the RBP of ϕ11, which assembles into a large, multidomain homotrimer. Each monomer contains a five-bladed propeller domain with a cavity that could accommodate a GlcNAc moiety. An electron microscopy reconstruction of the ϕ11 host adhesion component, the baseplate, reveals that six RBP trimers are assembled around the baseplate core. The Gp45 and baseplate structures provide insights into the overall organization and molecular recognition process of the phage ϕ11 tail. This assembly is conserved among most glycan-recognizing Siphoviridae, and the RBP orientation would allow host adhesion and infection without an activation step.

An essential role for the baseplate protein Gp45 in phage adsorption to Staphylococcus aureus.

Despite the importance of phages in driving horizontal gene transfer (HGT) among pathogenic bacteria, the underlying molecular mechanisms mediating phage adsorption to S. aureus are still unclear. Phage ϕ11 is a siphovirus with a high transducing efficiency. Here, we show that the tail protein Gp45 localized within the ϕ11 baseplate. Phage ϕ11 was efficiently neutralized by anti-Gp45 serum, and its adsorption to host cells was inhibited by recombinant Gp45 in a dose-dependent manner. Flow cytometry analysis demonstrated that biotin-labelled Gp45 efficiently stained the wild-type S. aureus cell but not the double knockout mutant ΔtarM/S, which lacks both α- and ß-O-GlcNAc residues on its wall teichoic acids (WTAs). Additionally, adsorption assays indicate that GlcNAc residues on WTAs and O-acetyl groups at the 6-position of muramic acid residues in peptidoglycan are essential components of the ϕ11 receptor. The elucidation of Gp45-involved molecular interactions not only broadens our understanding of siphovirus-mediated HGT, but also lays the groundwork for the development of sensitive affinity-based diagnostics and therapeutics for S. aureus infection.

The environmental effects of salinity load in Great Menderes Basin irrigation schemes.

This study aimed to assess how poor planning for irrigation led to heavy salt loads, how those salt loads adversely affected the environment, and how to identify management practices to deal with these potential problems in the Great Menderes River Basin, Aydin Plain Irrigation Scheme of Turkey for the period between 2000 and 2006. In order to determine the effects on the environment; electrical conductivity, salinity load, total amount of water table salinity, inflow and outflow salinity were measured and calculated for the research area. There was no problem on account of water table fluctuations. The mean of area prevented the plant growth by high water table was 8.5%. The percentage of the area occurring water table salinity problem was 39.2. The total amount of salt transported to the Great Menderes River and accumulated in the soil of the research area was 211,609 and 246,565 tones respectively. Salt, 458,174 tones in total, had adverse effects on the environment.

The effects of the environment and ecology projects on lake management and water quality.

In this study, the characteristics, benefits, and effects of the environment and ecology project, which has been implemented in Turkey for the first time to restore the natural life that has been spoilt and the ecological balance of Lake Bafa located in Great Meander Basin, are searched. Moreover, the water samples taken from the stations that were spotted in the lake have been analyzed for the physical and chemical changes taking place in water quality before and after the project. The water cycle occurring as a result of giving water that was raised in Great Meander River by the Rubber regulator, which is the most important element of the project, through the Serçin inlet and feeder channel; and draining the saline and low-quality water to the river bed of the Great Meander, will improve the water quality, the natural life, and the ecological balance of the lake in time. Thanks to the water given to the lake within the scope of project, the salinity of the lake water decreased from 25,500 to 22,500 mmhos cm( - 1). The electrical conductivity, Na+, Mg+2, Ca+2, Cl(-), CO3(-2), HCO3(-), and the amount of the organic substances were found as over the appropriate values for fishery. Besides, the decreases in the amounts of NO3(-), HN3(-) and PO4(-3) affect the living beings in the lake negatively. In addition, the measures to take are specified, so that the natural life of the Lake and the ecological balance can renew themselves within a short time.

Effects on environment and agriculture of geothermal wastewater and boron pollution in great Menderes basin.

Boron toxicity is an important disorder that can be limit plant growth on soils of arid and semi arid environments through the world. High concentrations of Boron may occur naturally in the soil or in groundwater, or be added to the soil from mining, fertilizers, or irrigation water. Off all the potential resources, irrigation water is the most important contributor to high levels of soil boron, boron is often found in high concentrations in association with saline soil and saline well water. Although of considerable agronomic importance, our understanding of Boron toxicity is rather fragment and limited. In this study, Boron content of Great Menderes River and Basin was researched. Great Menderes Basin is one of the consequence basins having agricultural potential, aspect of water and soil resources in Turkey. Great Menderes River, water resource of the basin was to be polluted by geothermal wastewater and thermal springs including Boron element. Great Menderes Basin has abundant geothermal water resources which contain high amounts of Boron and these ground water are brought to surface and used for various purposes such as power generation, heating or thermal spring and than discharged to Great Menderes River. In order to prevent Boron pollution and hence unproductively in soils, it is necessary not to discharged water with Boron to irrigation water. According to results, it was obtained that Boron content of River was as high in particular Upper Basin where there was a ground thermal water reservoir. Boron has been accumulated more than plant requirement in this area irrigated by this water. Boron content of River was relatively low in rainy months and irrigation season while it was high in dry season. Boron concentration in the River was to decrease from upstream to downstream. If it is no taken measure presently, about 130,000 ha irrigation areas which was constructed irrigation scheme in the Great Menderes basin will expose the Boron pollution and salinity. Even though Boron concentration of river water is under 0.5 ppm limit value, Boron element will store in basin soils, decrease in crop yields, and occur problematic soils in basin.