Protective role of S-adenosyl-l-methionine against hydrochloric acid stress in Saccharomyces cerevisiae

S-adenosyl-l-methionine (AdoMet, 1 mM) protects the stationary phase cells of Saccharomyces cerevisiae against the killing effect of acid (10 mM HCl, pH ∼ 2). Both the acid and the acid plus AdoMet treatment for 2 h increased the plasma membrane H⁺-ATPase activity; thereafter it decreased to the basal level. AdoMet partially recovered the intracellular pH (pH_in) that dropped in presence of acid. AdoMet treatment facilitated acid induced phospholipid biosynthesis as well as membrane proliferation, which was reflected in the cellular lipid composition.     

S-adenosylmethionine conformations in solution and in protein complexes: conformational influences of the sulfonium group

S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR and computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes with proteins. S-Methylmethionine and S-dimethylsulfonioproprionate adopt a variety of conformations in aqueous solution; a conformation with an electrostatic interaction between the sulfonium sulfur and the carboxylate group is not noticeably favored, in contrast to the preferred conformation found by in vacuo calculations. Nuclear Overhauser effect measurements and computational results for AdoMet indicate a predominantly anti conformation about the glycosidic bond with a variety of conformations about the methionyl C(alpha)-C(beta) and C(beta)-C(gamma) bonds. An AdoMet conformation in which the positively charged sulfonium sulfur is near an electronegative oxygen in the ribose ring is common. Comparisons of NMR results for AdoMet with those for the uncharged S-adenosylhomocysteine and 5'-methylthioadenosine, and the anionic ATP, indicate that the solution conformations are not dictated mainly by molecular charge. In 20 reported structures of AdoMet.protein complexes, both anti and syn glycosidic torsional angles are found. The methionyl group typically adopts an extended conformation in complexes with enzymes that transfer the methyl group from the sulfonium center, but is more folded in complexes with proteins that do not catalyze reactions involving the sulfur and which can use the sulfonium sulfur solely as a binding site. The conformational energies of AdoMet in these crystal structures are comparable to those found for AdoMet in solution. The sulfonium sulfur is in van der Waals contact with a protein heteroatom in the structures of four proteins, which reflects an energetically favorable contact. Interactions of the sulfonium with aromatic rings are rarely observed.     

Mutational analysis of vaccinia virus mRNA cap (guanine-N7) methyltransferase reveals essential contributions of the N-terminal peptide that closes over the active site

RNA guanine-N7 methyltransferase catalyzes the third step of eukaryal mRNA capping, the transfer of a methyl group from AdoMet to GpppRNA to form m⁷GpppRNA. Mutational and crystallographic analyses of cellular and poxvirus cap methyltransferases have yielded a coherent picture of a conserved active site and determinants of substrate specificity. Models of the Michaelis complex suggest a direct in-line mechanism of methyl transfer. Because no protein contacts to the guanine-N7 nucleophile, the AdoMet methyl carbon (Cε) or the AdoHcy sulfur (Sδ) leaving group were observed in ligand-bound structures of cellular cap methyltransferase, it was initially thought that the enzyme facilitates catalysis by optimizing proximity and geometry of the donor and acceptor. However, the structure of AdoHcy-bound vaccinia virus cap methyltransferase revealed the presence of an N-terminal “lid peptide” that closes over the active site and makes multiple contacts with the substrates, including the AdoMet sulfonium. This segment is disordered in the vaccinia apoenzyme and is not visible in the available structures of cellular cap methyltransferase. Here, we conducted a mutational analysis of the vaccinia virus lid peptide (⁵⁴⁵DKFRLNPEVSYFTNKRTRG⁵⁶³) entailing in vivo and in vitro readouts of the effects of alanine and conservative substitutions. We thereby identified essential functional groups that interact with the AdoMet sulfonium (Tyr555, Phe556), the AdoMet adenine (Asn550), and the cap triphosphate bridge (Arg560, Arg562). The results suggest that van der Waals contacts of Tyr555 and Phe556 to the AdoMet Sδ and Cε atoms, and the electron-rich environment around the sulfonium, serve to stabilize the transition state of the transmethylation reaction.     

Comparative studies on S-adenosyl-l-methionine binding sites of protein N-methyltransferases,using 8-azido-S-adenosyl-l-methionine as photoaffinity probe

Employing a photoaffinity labeling procedure with 8-azido-S-adenosyl-l-[methyl-³H]methionine (8-N₃-Ado[methyl-³H]Met), the binding sites for S-adenosyl-l-methionine (AdoMet) of three protein N-methyltransferases [AdoMet:myelin basic protein-arginine N-methyltransferase (EC2.1.1.23); AdoMet:histone-arginin N-methyltransferase (EC2.1.1.23); and AdoMet:cytochromec-lysine N-methyltransferase (EC2.1.1.59)] have been investigated. The incorporation of the photoaffinity label into the enzymes upon UV irradiation was highly specific. In order to define the AdoMet binding sites, the photolabeled enzymes were sequentially digested with trypsin, chymotrypsin, and endoproteinase Glu-C. After each proteolytic digestion, radiolabeled peptide from each enzyme was resolved on HPLC first by gradient elution and further purified by an isocratic elution. Retention times of the purified radiolabeled peptides from the three enzymes from the corresponding proteolysis were significantly different, indicating that their sizes and compositions were different. Amino acid composition analysis of these peptides confirmed further that the AdoMet binding sites of these protein N-methyltransferases are quite different.     

Molecular dynamics simulation of human interleukin-4: comparison with NMR data and effect of pH,counterions and force field on tertiary structure stability

The human protein interleukin-4 (IL-4) has been simulated at two different pH values 2 and 6, with different amounts of counterions present in the aqueous solution, and with two different force-field parameter sets using molecular dynamics simulation with the aim of validation of force field and simulation set-up by comparison to experimental nuclear magnetic resonance data, such as proton–proton nuclear Overhauser effect (NOE) distance bounds, ³ J(HN,HC_α) coupling constants and backbone N–H order parameters. Thirteen simulations varying in the length from 3 to 7 ns are compared.

At pH 6 both force-field parameter sets used do largely reproduce the NOE's and order parameters, the GROMOS 45A3 set slightly better than the GROMOS 53A6 set. ³ J values predicted from the simulation agree less well with experimental values. At pH 2 the protein unfolds, unless counterions are explicitly present in the system, but even then the agreement with experiment is worse than at pH 6. When simulating a highly charged protein, such as IL-4 at pH 2, the inclusion of counterions in the simulation seems mandatory.     

The epimerization of chiral half sandwich 2-phenylpyridine-based ruthenacycle

The reaction of a chiral terpenic 2-phenylpyridine with mercury (II) acetate afforded a new ortho-chloromercurated substrate, which was treated with [(η⁶-cymene)RuCl₂]₂ to afford two diastereomers of the corresponding half-sandwich cyclochlororuthenated terpenic ligand. The latter two complexes were successfully separated by conventional chromatography and their configurational stability investigated by ¹H NMR and CD spectroscopy. It was found that both isolated diastereomers displayed a fair configurational stability in CH₂Cl₂ while when dissolved in MeOH they epimerize. It was shown that the rate of epimerization is rather slow in pure MeOH, whereas in the presence of an excess of Lewis acid such as HgCl₂ it was notably accelerated suggesting that the decoordination of the chloride from the Ru(II) center is a key step in the epimerization process.     

The alpha beta epimerization of reduced nicotinamide adenine dinucleotide.

The proton magnetic resonance spectra of the dihydronicotinamide ring of αNADH³ and the nicotinamide ring of αNAD⁺ are reported and the proton absorptions assigned. The absolute assignment of the C4 methylene protons of αNADH is based on the generation of specifically deuterium-labeled (pro-S) B-deuterio-αNADH from enzymatically prepared B-deuterio-βNADH. The C4 proton absorption of αNAD⁺ is assigned by oxidation of B-deuterio-αNADH by the A specific, yeast alcohol dehydrogenase to yield 4-deuterio-αNAD⁺.The epimerization of either αNADH or βNADH yields an equilibrium ratio of approximately 9:1 βNADH to αNADH. The rate of epimerization of αNADH to βNADH at 38 °C in 0.05, pH 7.5, phosphate buffer is 3.1 × 10^?3 min^?1, corresponding to a half-life of 4 hr. Four related dehydrogenases, yeast and horse liver alcohol dehydrogenase and chicken M₄ and H₄ lactate dehydrogenase, are shown to oxidize αNADH to αNAD⁺ at rates three to four orders of magnitude slower than for βNADH. By using specifically labeled B-deuterio-αNADH the enzymatic oxidation by yeast alcohol dehydrogenase has been shown to occur with the identical stereospecificity as the oxidation of βNADH. The nonenzymatic epimerization of αNADH to βNADH and the enzymatic oxidation αNADH are discussed as a possible source of αNAD⁺in vivo.     

Production of S-adenosyl-l-methionine by Saccharomyces sake

In a study of the optimization of the culture conditions for the intracellular accumulation of S-adenosyl-l-methionine (AdoMet) by Saccharomyces sake Kyokai No. 6, a medium containing 10% sucrose, 1.8% urea, 1% yeast extract and 0.75–1.5% l-methionine as the main components was found to be suitable for the production. Addition of CaCl₂, biotin and glycylglycine to the medium increased the accumulation of AdoMet. Under optimal conditions in a 10-liter fermenter, the yeast produced 10.8 g L⁻¹ AdoMet (260 mg per g dry cells).In order to increase the recovery yield and purity of AdoMet, a new and efficient isolation procedure involving freezing and thawing of cells for the extraction of AdoMet and chromatographies on Amberlite IRA-45, XAD-2 and IRC-50 was developed.     

Kinetic and pH studies on human phenylethanolamine N-methyltransferase

Phenylethanolamine N-methyltransferase (PNMT) catalyzes the conversion of norepinephrine (noradrenaline) to epinephrine (adrenaline) while, concomitantly, S-adenosyl-l-methionine (AdoMet) is converted to S-adenosyl-l-homocysteine. This reaction represents the terminal step in catecholamine biosynthesis and inhibitors of PNMT have been investigated, inter alia, as potential antihypertensive agents. At various times the kinetic mechanism of PNMT has been reported to operate by a random mechanism, an ordered mechanism in which norepinephrine binds first, and an ordered mechanism in which AdoMet binds first. Here we report the results of initial velocity studies on human PNMT in the absence and presence of product and dead end inhibitors. These, coupled with isothermal titration calorimetry and fluorescence binding experiments, clearly shown that hPNMT operates by an ordered sequential mechanism in which AdoMet binds first. Although the log V pH-profile was not well defined, plots of log V/K versus pH for AdoMet and phenylethanolamine, as well as the pK_i versus pH for the inhibitor, SK&F 29661, were all bell-shaped indicating that a protonated and an unprotonated group are required for catalysis.     

Myosin light chain kinase binding to plastic

Methionine-81 and/or -8 of the transmembrane sialoglycoprotein, glycophorin A, have been specifically alkylated with ¹³CH₃I to produce the sulfonium ion derivatives [S-[¹³C]methylmethionine-8]glycophorin A and [S-[¹³C]methylmethionine-8 and -81]glycophorin A. ¹³C NMR spectra of these species show that the resonances of the methyl groups of the modified glycophorins occur at 26.1 ppm downfield from Me₄Si. A spin-lattice relaxation time of 0.4 was observed for the ¹³C-enriched methyl resonances of the sulfonium ion derivatives of Met-8 and -81, which corresponds to an effective correlation time of < 2× 10^?10 s. Demethylation of the 2 glycophorin A sulfonium ion species with 2-mercaptoethanol produces native glycophorin A which now has the ε-carbon of the methionine residue(s) 45% isotopically enriched. The ε-carbon of Met-8 was found to occur at 15.7 ppm downfield from Me₄Si whereas the ε-carbon of Met-81 exhibited an unusual chemical shift of 2.0 ppm downfield from Me₄Si. The spin-lattice relaxation time of both resonances was found to be ～0.3 s.     

S-Adenosylmethionine synthetase in bloodstream Trypanosoma brucei

S-adenosylmethionine synthetase was studied from bloodstream forms of Trypanosoma brucei brucei, the agent of African sleeping sickness. Two isoforms of the enzyme were evident from Eadie Hofstee and Hanes-Woolf plots of varying ATP or methionine concentrations. In the range 10–250 μM the K_m for methionine was 20 μM, and this changed to 200 μM for the range 0.5–5.0 mM. In the range 10–250 μM the K_m for ATP was 53 μM, and this changed to 1.75 mM for the range 0.5–5.0 mM. The trypanosome enzyme had a molecular weight of 145 kDa determined by agarose gel filtration. Methionine analogs including selenomethionine, L-2-amino-4-methoxy-cis but-3-enoic acid and ethionine acted as competitive inhibitors of methionine and as weak substrates when tested in the absence of methionine with [¹⁴C]ATP. The enzyme was not inducible in procyclic trypomastigotes in vitro, and the enzyme half-life was > 6 h. T. b. brucei AdoMet synthetase was inhibited by AdoMet (K_i 240 μM). The relative insensitivity of the trypanosome enzyme to control by product inhibition indicates it is markedly different from mammalian isoforms of the enzyme which are highly sensitive to AdoMet. Since trypanosomes treated with the ornithine decarboxylase antagonist DL-α-difluoromethylornithine accumulate AdoMet and dcAdoMet (final concentration ≈ 5 mM), this enzyme may be the critical drug target linking inhibition of polyamine synthesis to disruption of AdoMet metabolism.     

Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N-adenine]-methyltransferase is important for S-adenosyl-L-methionine binding

Comparison of the deduced amino acid sequences of DNA-[N⁶-adenine]-methyltransferases has revealed several conserved regions. All of these enzymes contain a DPPY-motif, or a variant of it. By site-directed mutagenesis of a cloned T4 dam gene, we have altered the first proline residue in this motif (located in conserved region IV of the T4 Dam-MTase) to alanine or threonine. The mutant enzymic forms, P172A and P172T, were overproduced and purified. Kinetic studies showed that compared to the wild-type (wt) the two mutant enzymic forms had: (i) an increased (6 and 23-fold, respectively) K_m for substrate, S-adenosyl-methionine (AdoMet) and an increased (6 and 23-fold) K_i for product, S-adenosyl-homocysteine (AdoHcy); (ii) a slightly reduced (1.5 and 3-fold lower) k_cat; (iii) a strongly reduced k_cat/K_m^AdoMet (10 and 80-fold); and (iv) the same K_m for substrate DNA. Equilibrium dialysis studies showed that the mutant enzymes had a reduced (3 and 7-fold lower) K_a for AdoMet; all forms bound two molecules of AdoMet. Taken together these data indicate that the P172A and P172T alterations resulted primarily in a reduced affinity for AdoMet. This suggests that the DPPY-motif is important for AdoMet-binding, and that region IV contains an AdoMet-binding site.     

In vitro and in vivo D2-dopamine receptor binding with [123I]S(−)iodobenzamide ([123I]IBZM) in rat and human brain

As a promising dopamine D2-receptor imaging agent for single photon emission computerized tomography (SPECT), [¹²³I](S)-(−)-2-hydroxy-3-iodo-6-methoxy-N [(1-ethyl-2-pyrrolidinyl)methyl]benzamide ([¹²³I]IBZM) has recently been synthesized in a modified way along with its precursor, S(−)BZM, and the stereoisomer R(+)BZM. The present study applied this new product to investigate in vitro and in vivo D2-receptor binding in rat brain and in postmortem human brain. In vitro saturation binding curves with [¹²³I]IBZM for rat crude striatal membrane preparations yielded an affinity constant (K_d) of 0.28 nM confirming data in the literature. Displacement curves revealed an order of increasing potency as follows: R(+)BZM < S(−)sulpiride = < S(−)BZM < S(−)IBZM. A similar order was obtained when [³H]spiperone was used as ligand. For human putamen and caudate nucleus membranes slightly higher K_d values (0.49 nM) were obtained. Rank order of displacing potency for the various drugs was similar to that found in the rat preparations. In vivo uptake of [¹²³I]IBZM in rat brain following injection of 50 μCi (12–16pmol) in the tail vein revealed an increase in the striatum-to-cerebellum ratio from 1.5 at 5 min to 6.9 at 2 h. The olfactory tubercle-to-cerebellum ratio was also raised from 1.6 to 3.3. Other brain regions tested failed to show statistically significant enhancements. Coinjection of 40 nmol S(-)IBZM, 4μ mol S(−)BZM or 200 nmol haloperidol displaced [¹²³I]IBMZ when tested at 90 min. The use of 4μ mol R(+)BZM resulted in minor displacement only, demonstrating that stereospecificity of the displacement was present in vivo and in vitro. Displacements were also observed in substantia nigra and pons-medulla oblongata, but not in hippocampus or frontal and occipital cortex. The data provide the required background needed in order to initiate in vivo binding studies for D2-receptors in basal ganglia of human patients using [¹²³I]IBZM in SPECT analyses.     

The stimulation of GABAB receptors increases serotonin release in the rat suprachiasmatic area

The action of γ-aminobutyric acid (GABA) and related compounds on the spontaneous release of newly synthesized [³H]5-hydroxytryptamine ([³H]5-HT) was studied in the suprachiasmatic area (SCA) using a superfusion system. GABA (10 μM) increased [³H]5-HT release from SCA by up to 190%. Bicuculline or picrotoxin (10 μM) failed to inhibit the stimulatory effect of GABA. Muscimol (10 μM), a GABA_A agonist, was ineffective, however β-p-chlorophenyl GABA, R(−)baclofen, enhanced over 200% the release of the indoleamine; this latter effect was stereospecific. RS baclofen was twice less potent than the R(−)isomer in increasing the [³H]5-HT release. S(+)baclofen failed to affect the release of the indoleamine, whereas it attenuated the effect of its enantiomer. The effect of R(−)baclofen was Ca²⁺ dependent and was abolished by tetrodotoxin (TTX).Taken together these results suggest that in the SCA, [³H]5-HT release is facilitated by the stimulation of GABA_B receptors. The possible localization of these receptors is discussed in the light of morphological data recently reported by Bosler et al. (1985) and results obtained after TTX application.     

Purification,characterization, sequencing and molecular cloning of a novel cysteine methyltransferase that regulates trehalose-6-phosphate synthase from Saccharomyces cerevisiae

Background

In Saccharomyces cerevisiae methylation at cysteine residue displayed enhanced activity of trehalose-6-phosphate synthase (TPS).

Methods

The cysteine methyltransferase (CMT) responsible for methylating TPS was purified and characterized. The amino acid sequence of the enzyme protein was determined by a combination of N-terminal sequencing and MALDI-TOF/TOF analysis. The nucleotide sequence of the CMT gene was determined, isolated from S. cerevisiae and expressed in E. coli. Targeted disruption of the CMT gene by PCR based homologous recombination in S. cerevisiae was followed by metabolite characterization in the mutant.

Results

The purified enzyme was observed to enhance the activity of TPS by a factor of 1.76. The 14 kDa enzyme was found to be cysteine specific. The optimum temperature and pH of enzyme activity was calculated as 30 °C and 7.0 respectively. The K_m V_max and K_cat against S-adenosyl-l-methionine (AdoMet) were 4.95 μM, 3.2 U/mg and 6.4 s^− 1 respectively. Competitive inhibitor S-Adenosyl-l-homocysteine achieved a K_i as 10.9 μM against AdoMet. The protein sequence contained three putative AdoMet binding motifs. The purified recombinant CMT activity exhibited similar physicochemical characteristics with the native counterpart. The mutant, Mataα, cmt:: kan^r exhibited almost 50% reduction in intracellular trehalose concentration.

Conclusion

A novel cysteine methyltransferase is purified, which is responsible for enhanced levels of trehalose in S. cerevisiae.

General significance

This is the first report about a cysteine methyltransferase which performs S methylation at cysteine residue regulating TPS activity by 50%, which resulted in an increase of the intercellular stress sugar, trehalose.     

Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

S-Adenosyl-l-methionine (AdoMet or SAM)-dependent methyltransferases (MTase) catalyze the transfer of the activated methyl group from AdoMet to specific positions in DNA, RNA, proteins and small biomolecules. This natural methylation reaction can be expanded to a wide variety of alkylation reactions using synthetic cofactor analogues. Replacement of the reactive sulfonium center of AdoMet with an aziridine ring leads to cofactors which can be coupled with DNA by various DNA MTases. These aziridine cofactors can be equipped with reporter groups at different positions of the adenine moiety and used for Sequence-specific Methyltransferase-Induced Labeling of DNA (SMILing DNA). As a typical example we give a protocol for biotinylation of pBR322 plasmid DNA at the 5’-ATCGAT-3’ sequence with the DNA MTase M.BseCI and the aziridine cofactor 6BAz in one step. Extension of the activated methyl group with unsaturated alkyl groups results in another class of AdoMet analogues which are used for methyltransferase-directed Transfer of Activated Groups (mTAG). Since the extended side chains are activated by the sulfonium center and the unsaturated bond, these cofactors are called double-activated AdoMet analogues. These analogues not only function as cofactors for DNA MTases, like the aziridine cofactors, but also for RNA, protein and small molecule MTases. They are typically used for enzymatic modification of MTase substrates with unique functional groups which are labeled with reporter groups in a second chemical step. This is exemplified in a protocol for fluorescence labeling of histone H3 protein. A small propargyl group is transferred from the cofactor analogue SeAdoYn to the protein by the histone H3 lysine 4 (H3K4) MTase Set7/9 followed by click labeling of the alkynylated histone H3 with TAMRA azide. MTase-mediated labeling with cofactor analogues is an enabling technology for many exciting applications including identification and functional study of MTase substrates as well as DNA genotyping and methylation detection.     

Synthesis and crystal structures of platinum (II) complexes with phosphine sulfide: cis-Dichloro[dimethylsulfoxide](triphenylphosphine sulfide) platinum (II) and (−)-cis-dichloro[(S)-methyl-p-tolylsulfoxide](triphenylphosphine sulfide) platinum (II)

The addition of triphenylphosphine sulfide (Ph₃PS) to bis-sulfoxide platinum (II) complexes [Pt(Me₂SO)₂Cl₂] and (−)-[Pt(Me-p-TolSO)₂Cl₂] yields mixed ligand complexes [Pt(Ph₃PS)(Me₂SO)Cl₂] (1) and (−)-[Pt(Ph₃PS)(Me-p-TolSO)Cl₂] (2), which are effective catalysts for hydrosilylation reaction. These mixed-ligand complexes were obtained in crystal state and analyzed by X-ray diffraction, ¹H, ³¹P and ¹⁹⁵Pt NMR; 2 was also studied by circular dichroism spectroscopy. Both complexes exist in CDCl₃ solution as a dynamic equilibrium of two geometric isomers with an approximate 1:10 ratio, but only cis-isomer is obtained on crystallization. The X-ray structures of the complexes have classical geometry, and phosphine sulfide and sulfoxides are coordinated via sulfur. The new structural data for simple platinum–Ph₃PS coordination bond, unaffected by chelation or bridging, were evaluated. The lengths of this bond are 2.300(4) Å in 1 and 2.305(3) Å in 2, respectively. PtSP angle equals 105.7(2)° in 1 and 104.05(13)° in 2, the PtSP plane is almost perpendicular to the coordination plane. The static trans-influence of Ph₃PS is estimated to be strong and close to that of S-coordinated Me₂SO. The complex 2 exhibits strong circular dichroism at a wavelength below 330 nm, caused both by inherent Me-p-TolSO stereogenic center and induced asymmetry of Ph₃PS.     

Novel biosynthesis of d-pinitol in simmondsia chinensis

Chase experiments with ¹⁴CO₂ and feeding experiments with labelled inositols showed that d-pinitol in leaves of Simmondsia chinensis arises via epimerization of d-ononitol. This finding represents an alternative pathway, since d-pinitol is formed in gymnosperms and other plants by epimerization of sequoyitol.     

Production and Consumption of Dimethylsulfoniopropionate in Marine Microbial Mats

The fate of dimethylsulfoniopropionate (DMSP), a major sulfonium compound in marine ecosystems, was examined in Microcoleus chthonoplastes-dominated microbial mats. Chemical decomposition of DMSP was observed under laboratory conditions at pH values higher than 10.0. pH profiles measured in situ showed that these highly alkaline conditions occurred in microbial mats. Axenic cultures of M. chthonoplastes contained 37.3 μmol of DMSP g of protein⁻¹, which was partially liberated when the cells were subjected to an osmotic shock. DMSP-amended mat slurries showed a rapid turnover of this compound. The addition of glutaraldehyde blocked DMSP decrease, indicating biological consumption. Populations of potential dimethyl sulfide consumers were found in the top 10 mm of the mat.     

Metal Ion Dependence of Cooperative Collapse Transitions in RNA

Positively charged counterions drive RNA molecules into compact configurations that lead to their biologically active structures. To understand how the valence and size of the cations influences the collapse transition in RNA, small-angle X-ray scattering was used to follow the decrease in the radius of gyration (R_g) of the Azoarcus and Tetrahymena ribozymes in different cations. Small, multivalent cations induced the collapse of both ribozymes more efficiently than did monovalent ions. Thus, the cooperativity of the collapse transition depends on the counterion charge density. Singular value decomposition of the scattering curves showed that folding of the smaller and more thermostable Azoarcus ribozyme is well described by two components, whereas collapse of the larger Tetrahymena ribozyme involves at least one intermediate. The ion-dependent persistence length, extracted from the distance distribution of the scattering vectors, shows that the Azoarcus ribozyme is less flexible at the midpoint of transition in low-charge-density ions than in high-charge-density ions. We conclude that the formation of sequence-specific tertiary interactions in the Azoarcus ribozyme overlaps with neutralization of the phosphate charge, while tertiary folding of the Tetrahymena ribozyme requires additional counterions. Thus, the stability of the RNA structure determines its sensitivity to the valence and size of the counterions.