Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium

Identifying all essential genomic components is critical for the assembly of minimal artificial life. In the genome-reduced bacterium Mycoplasma pneumoniae, we found that small ORFs (smORFs; < 100 residues), accounting for 10% of all ORFs, are the most frequently essential genomic components (53%), followed by conventional ORFs (49%). Essentiality of smORFs may be explained by their function as members of protein and/or DNA/RNA complexes. In larger proteins, essentiality applied to individual domains and not entire proteins, a notion we could confirm by expression of truncated domains. The fraction of essential non-coding RNAs (ncRNAs) non-overlapping with essential genes is 5% higher than of non-transcribed regions (0.9%), pointing to the important functions of the former. We found that the minimal essential genome is comprised of 33% (269,410 bp) of the M. pneumoniae genome. Our data highlight an unexpected hidden layer of smORFs with essential functions, as well as non-coding regions, thus changing the focus when aiming to define the minimal essential genome.     

Influence of cholesterol on equilibrium and dynamic bilayer structure of unsaturated acyl chain phosphatidylcholine vesicles as determined from higher order analysis of fluorescence anisotropy decay

The influence of cholesterol on equilibrium and dynamic bilayer structure in minimally to highly unsaturated phosphatidylcholine (PC) vesicles has been examined by characterization of the dynamic fluorescence properties of 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-[4-(trimethylammonio)phenyl]-6-phenyl-1,3,5-hexatriene (TMA-DPH). Large, unilamellar egg PC, palmitoyloleoyl-PC (POPC), dioleoyl-PC (DOPC), palmitoylarachidonoyl-PC (PAPC), and palmitoyldocosahexaenoyl-PC (P-22:6-PC) vesicles containing no cholesterol or approximately 15 or 30 mol % cholesterol have been examined. Equilibrium and dynamic DPH orientational properties were analyzed according to an orthogonal, bimodal orientational distribution function [Straume, M., & Litman, B.J. (1987) Biochemistry (preceding paper in this issue)]. The same mathematical formalism was applied to TMA-DPH except that probe orientational probability was permitted only in the distribution peak aligned parallel to the bilayer normal. TMA-DPH fluorescence lifetimes were consistently increased by incorporation of cholesterol into these vesicles. Greater acyl chain unsaturation and increasing temperature each promoted reduction of lifetimes in the presence or absence of cholesterol. DPH lifetimes were much less sensitive than those of TMA-DPH to changes in composition or temperature. This behavior is consistent with reduced water penetrability into liquid-crystalline bilayers as cholesterol content is increased and as acyl chain unsaturation and temperature are reduced. Cholesterol also induces substantial equilibrium ordering of the bilayer both at the hydrophobic core and at the bilayer-water interface. DPH orientational distributions were shifted in favor of alignment parallel to the acyl side chains. The distributions of both probes were narrowed in response to incorporation of cholesterol.(ABSTRACT TRUNCATED AT 250 WORDS)     

Coregulation of beta-galactoside uptake and hydrolysis by the hyperthermophilic bacterium Thermotoga neapolitana

Regulation of the beta-galactoside transport system in response to growth substrates in the extremely thermophilic anaerobic bacterium Thermotoga neapolitana was studied with the nonmetabolizable analog methyl-beta-D-thiogalactopyranoside (TMG) as the transport substrate. T. neapolitana cells grown on galactose or lactose accumulated TMG against a concentration gradient in an intracellular free sugar pool that was exchangeable with external galactose or lactose and showed induced levels of beta-galactosidase. Cells grown on glucose, maltose, or galactose plus glucose showed no capacity to accumulate TMG, though these cells carried out active transport of the nonmetabolizable glucose analog 2-deoxy-D-glucose. Glucose neither inhibited TMG uptake nor caused efflux of preaccumulated TMG; rather, glucose promoted TMG uptake by supplying metabolic energy. These data show that beta-D-galactosides are taken up by T. neapolitana via an active transport system that can be induced by galactose or lactose and repressed by glucose but which is not inhibited by glucose. Thus, the phenomenon of catabolite repression is present in T. neapolitana with respect to systems catalyzing both the transport and hydrolysis of beta-D-galactosides, but inducer exclusion and inducer expulsion, mechanisms that regulate permease activity, are not present. Regulation is manifest at the level of synthesis of the beta-galactoside transport system but not in the activity of the system.     

Measurement of neutron-induced genetic damage in mouse immature oocytes

Recent experimental evidence concerning the nature of radiosensitive targets in mouse immature (resting) oocytes has led to new experimental designs that permit measurement of radiation-induced genetic damage in these important cells. We have previously reported initial results of the detection of genetic damage in mouse immature oocytes using monoenergetic 0.43-MeV neutrons. Here we provide a full report of our data and compare the genetic sensitivity of immature oocytes with those measured by others for maturing oocytes. Until recently, all attempts to detect radiation-induced genetic damage in mouse immature oocytes had failed. This appears to have been because the radiation types and modes of dose delivery used in those studies did not sufficiently spare the hypersensitive lethality target (the plasma membrane) while at the same time deposit enough dose in DNA to produce detectable mutation. Recoil protons from 0.43-MeV neutrons produce short ionization tracks (2.6 micron mean) and can therefore deposit energy in the DNA without simultaneously traversing the plasma membrane. Using these particles, we have obtained dose-response relationships for both chromosome aberrations and dominant lethal mutations in oocytes from females irradiated 8-12 weeks earlier, when oocytes were immature. Results suggest that the intrinsic mutational sensitivity of mouse immature oocytes is not very different from that of maturing oocytes.     

Purification and some properties of sn-glycerol-3-phosphate dehydrogenase from Saccharomyces cerevisiae

An NAD-dependent glycerol-3-phosphate dehydrogenase (sn-glycerol-3-phosphate: NAD⁺ oxidoreductase, EC 1.1.1.8) has been isolated and purified from Saccharomyces cerevisiae by affinity and exclusion chromatography. The enzyme was purified 5100-fold to a specific activity of 158. It has a molecular weight of approximately 31,000, a pH optimum between 6.8 and 7.2, and is sensitive to high-ionic-strength salt solutions. The enzyme is most strongly inhibited by phosphate and chloride ions.     

The treatment of neonatal isoimmune thrombocytopenia with intravenous immunoglobin (IgG i.v.)

We present a report of the use of IgG i.v. to treat clinically manifest neonatal immune thrombocytopenia. The IgG i.v. was administered at a daily dosage of 0.4 g/kg body weight for 5 days. Treatment was started when the child was 3 days old and had a platelet count of 2 X 10(9)/l. Four days later the platelet count had risen to 200 X 10(9)/l. The diagnosis of immune thrombocytopenia was confirmed by platelet typing of the mother's and child's platelets and identification of anti-platelet antibodies in maternal serum.     

Longitudinal proxy measurements in multiple sclerosis: patient-proxy agreement on the impact of MS on daily life over a period of two years

Background  

The use of self-report measurements in clinical settings is increasing. However, in patients with limitations that interfere with reliable self-assessment such as cognitive impairment or mood disturbances, as may be the case in multiple sclerosis (MS), data collection might be problematic. In these situations, information obtained from proxy respondents (e.g. partners) may replace self-ratings. The aim of this study was to examine the value of proxy ratings at separate points in time and to assess patient-proxy agreement on possible changes in disease impact of MS.     

Recent data on intratumor estrogens in breast cancer

The contribution of local synthesis versus circulatory delivery of normal breast as well as breast cancer tissue estrogens has remained a controversial area for decades. Novel data on tissue estrogen levels confirm a positive normal breast tissue to plasma concentration gradient for estrone, and to a smaller extent estradiol. Remarkably, this gradient is similar for pre- and post-menopausal women. Together with pharmacokinetic data on estrogen disposition, these findings suggest plasma and breast tissue estrogens to rapidly equilibrate, with circulating estrogens being a major contributor to breast tissue estrone levels. A likely explanation to the concentration gradient could be the fact that non-polar estrogens easily dissolve into tissue fat compartments as compared to plasma. While intratumor estrone levels are low as compared to benign tissue concentrations, intratumor estradiol is elevated in ER+ tumors. The correlation between intratumor estradiol levels and expression levels of dehydrogenases reducing estrone into estradiol but also intratumor ER concentrations are consistent with intratumor estrogen activation but also a scavenger effect of the ER.