Cell Size Control in Yeast

Cell size is an important adaptive trait that influences nearly all aspects of cellular physiology. Despite extensive characterization of the cell-cycle regulatory network, the molecular mechanisms coupling cell growth to division, and thereby controlling cell size, have remained elusive. Recent work in yeast has reinvigorated the size control field and suggested provocative mechanisms for the distinct functions of setting and sensing cell size. Further examination of size-sensing models based on spatial gradients and molecular titration, coupled with elucidation of the pathways responsible for nutrient-modulated target size, may reveal the fundamental principles of eukaryotic cell size control

Fueling the Cycle: CDKs in Carbon and Energy Metabolism

Cyclin-dependent kinases (CDKs) are the central regulators of the eukaryotic cell cycle, and are conserved across eukaryotes. Their main and well-studied function lies in the regulation and the time-keeping of cell cycle entry and progression. Additionally, more and more non canonical functions of CDKs are being uncovered. One fairly recently discovered role of CDKs is the coordination of carbon and energy metabolism with proliferation. Evidence from different model organisms is accumulating that CDKs can directly and indirectly control fluxes through metabolism, for example by phosphorylating metabolic enzymes. In this mini-review, we summarize the emerging role of CDKs in regulating carbon and energy metabolism and discuss examples in different models from yeast to cancer cells

Mass spectrometry-based metabolomics:a guide for annotation, quantification and best reporting practices

Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography– and gas chromatography–mass spectrometry-based metabolomics-derived data.</p

Engineering Genetically Encoded Nanosensors for Real-Time In Vivo Measurements of Citrate Concentrations

Citrate is an intermediate in catabolic as well as biosynthetic pathways and is an important regulatory molecule in the control of glycolysis and lipid metabolism. Mass spectrometric and NMR based metabolomics allow measuring citrate concentrations, but only with limited spatial and temporal resolution. Methods are so far lacking to monitor citrate levels in real-time in-vivo. Here, we present a series of genetically encoded citrate sensors based on Förster resonance energy transfer (FRET). We screened databases for citrate-binding proteins and tested three candidates in vitro. The citrate binding domain of the Klebsiella pneumoniae histidine sensor kinase CitA, inserted between the FRET pair Venus/CFP, yielded a sensor highly specific for citrate. We optimized the peptide linkers to achieve maximal FRET change upon citrate binding. By modifying residues in the citrate binding pocket, we were able to construct seven sensors with different affinities spanning a concentration range of three orders of magnitude without losing specificity. In a first in vivo application we show that E. coli maintains the capacity to take up glucose or acetate within seconds even after long-term starvation

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses

Softening the donor set for light-emitting electrochemical cells : [Ir(ppy)(2)(N boolean AND N)](+), [Ir(ppy)(2)(P boolean AND P)](+) and [Ir(ppy)(2)(P boolean AND S)](+) salts

The syntheses and solution characterizations of [Ir(ppy)(2)(1)[PF6] (1 =4,4`-di(2-furany1)-6,6`-dimethy12,2`-bipyridine), [Ir(ppy)(2)(dppe)1[PF6] (dppe =1,2-bis(diphenylphosphino)ethane), [Ir(ppy)(2)(2)][PF6] (2 =1,2-bis(diphenylphosphino)benzene) and [Ir(PPY)2(3)1[PF6] (3 = 2-diphenylphosphinothioanisole) are reported. Solutions of the iridium(Ill) complexes incorporating 1, 2 and dppe are photoluminescent, but [Ir(ppy)(2)(3)][PF6] is non-emissive. The single crystal structures of [Ir(ppy)(2)(1)][PF6]center dot 2CH(2)Cl(2). [Ir-(ppy)(2)(dppe)][PF6]. 4[1r(ppy)(2)(2][PF6]center dot 3CH(2)Cl(2) and [Ir(ppy)(2)(3)][PF6] have been determined, and the role of inter-ligand face-to-face It-stacking (a means of suppressing emission quenching) in the [Ir(ppy)(2)(ppy)(2)(dppe)](+), [Ir(ppy)(2)(2)](+) and [Ir(ppy)(2)(3)](+) cations is assessed

Restricting the geometrical relaxation in four-coordinate copper(I) complexes using face-to-face and edge-to-face pi-interactions

A series of [Cu(N,N)(P,P)](+), [Cu(N,N)(P,S)](+), [Cu(N,N)(2)](+) and [Cu(P,S)(2)](+) complexes incorporating the ligands 2,2`-bipyridine, 1,10-phenanthroline, 1,2-bis(diphenylphosphino)ethane, bis(2-(diphenylphosphino)phenyl)ether (1), 2-diphenylphosphinothioanisole (3) and 2-methyl-6`-phenyl-2,2`- bipyridine (4) has been synthesized and structurally characterized. We have assessed the degree of distortion of two bidentate ligands away from an ideal tetrahedral arrangement about the copper(I) ion using the White model. The greatest distortion along a pathway towards square planar coordination is observed in [Cu(4)(2)][PF6] and is a result of intra-cation pi-stacking between phenyl and bpy domains. Each of the complexes which contain the P,S-chelating ligand 3 exhibits significant `rocking` or `wagging` distortions which are associated with intra-cation CHmethyl...pi interactions. The extent of this distortion can also be assessed using a less rigorous approach by measuring the S-Cu-X and P-Cu-X angles where the S and P atoms belong to ligand 3, and X is the midpoint of the backbone of the second ligand. [Cu(3)(2)][PF6] and [Cu(1)(3)][PF6] exhibit embraces between the phenyl substituents that result in the copper(I) ion being sterically protected, and the room temperature H-1 NMR solution spectrum of [Cu(1)(3)][PF6] reveals hindered rotation of the phenyl rings of ligand