Sequential folding of transfer RNA: A nuclear magnetic resonance study of successively longer tRNA fragments with a common 5′ end

Most folding studies on proteins and nucleic acids have been addressed to the transition between the folded and unfolded states of an intact molecule, where an entire residue sequence is present during the folding event. However, since these polymers are synthesized sequentially from one terminus to the other in vivo, their folding pathways may be influenced greatly by the sequential appearance of the residues as a function of time.The three-dimensional structure of yeast tRNA^Phe in the crystalline state is correlated with 360 MHz proton nuclear magnetic resonances from three fragments plus an intact molecule of the tRNA that share a common 5′ end and are in a solution condition similar to that of the crystal structure. This has allowed identification of folded structures present in the fragments and presumably present in the growing tRNA molecule as it is being synthesized from the 5′ end. The experiments show that only the correct stems are formed in the fragments; no additional or competing helical region is produced. This suggests that in the biosynthesis of this tRNA, correct folding of helical stems occurs before the entire molecule is formed. Further, some of the tertiary interactions (hydrogen bonds) found in the crystal structure are also probably present before the synthesis is completed. These findings are generalized to consider the precursor of the tRNA as well as other tRNAs.     

Responses of root length/leaf area ratio and specific root length of an understory herb, Pteridophyllum racemosum, to increases in irradiance

The understory evergreen perennial Pteridophyllum racemosum Sieb. et Zucc. (Papaveraceae) has the ability to increase root mass per unit transpiring leaf area (RMA) if irradiance increases gradually over several years. In this study, we examined how P. racemosum changes its root length/leaf area ratio and specific root length when the species encounters abrupt increases in irradiance, such as sudden and unexpected canopy openings. Plants were transplanted from a low light condition in a subalpine wave-regenerating forest (photon flux density on the forest floor relative to the full sun (RPFD) was 2.7%) to a high light condition in a glasshouse (30% RPFD) (LH treatment). Transplantation from the low light condition in the forest to a low light condition in the glasshouse (LL) and transplantation from a high light condition in the forest (33% RPFD) to a high light condition in the glasshouse (HH) were also conducted as controls. Compared to the LL plants, the LH plants exhibited significant increases in RMA and root length/leaf area ratio from 30 to 70 days after transplantation. On the other hand, the effect of increased irradiance on specific root length (SRL) was weak, and both the LL and LH plants showed increased SRL from 30 to 70 days after transplantation. Increased SRL results from longer root length per unit construction cost. We concluded that increased root length/leaf area ratio of P. racemosum in response to abrupt increases in irradiance was caused by a combination of enhanced carbon allocation to roots with increased SRL.     

Non‐native plants have greater impacts because of differing per‐capita effects and nonlinear abundance–impact curves

Invasive, non‐native species can have tremendous impacts on biotic communities, where they reduce the abundance and diversity of local species. However, it remains unclear whether impacts of non‐native species arise from their high abundance or whether each non‐native individual has a disproportionate impact – that is, a higher per‐capita effect – on co‐occurring species compared to impacts by native species. Using a long‐term study of wetlands, we asked how temporal variation in dominant native and non‐native plants impacted the abundance and richness of other plants in the recipient community. Non‐native plants reached higher abundances than natives and had greater per‐capita effects. The abundance–impact relationship between plant abundance and richness was nonlinear. Compared with increasing native abundance, increasing non‐native abundance was associated with steeper declines in richness because of greater per‐capita effects and nonlinearities in the abundance–impact relationship. Our study supports eco‐evolutionary novelty of non‐natives as a driver of their outsized impacts on communities.     

Chromogenic detection of antigen in bacteriophage plaques: a microplaque method applicable to large-scale screening

We have developed a simple and rapid (24 h) enzyme-linked immuno-detection method to screen for rare antigen-positive phage among large numbers of antigen-negative ones. Horse-radish peroxidase-antibody conjugate, incorporated into the soft agar layer of a plaque assay system, is precipitated locally by antigen produced during plaque formation, and is detected by standard chromogenic methods. The method has been used to screen plaques of bacteriophage beta tox+ for the presence of diphtheria toxin and related cross-reacting material. When phage were plated on very dense bacterial lawns, they formed minute plaques (microplaques). Because of the high local concentration of antigen generated by lysis of the dense lawn, the microplaques gave more intense chromogenic signals than larger plaques formed on less dense Corynebacterium diphtheriae lawns. Thus, antigen-positive microplaques could be easily recognized even in the presence of very large numbers of antigen-negatives. In a reconstruction experiment, small numbers of antigen-positive phage were detected with high efficiency (greater than 75%) against a background of 3.8 X 10(4) antigen-negatives/cm2 of agar surface (equivalent to 2.4 X 10(6) plaques/9 cm petri plate). This screening method should facilitate isolation of phage mutants affecting production of given antigens and may be of particular value in detecting specific genes cloned into phage vectors.     

Participation of chlorobiumquinone in the transplasma membrane electron transport system of Leishmania donovani promastigote: Effect of near-ultraviolet light on the redox reaction of plasma membrane

The respiratory quinone composition of the parasitic protozoa Leishmania donovani promastigote was investigated. 1′-oxomenaquinone-7, a chlorobiumquinone was found to be the major isoprenoid quinone. Substantial level of ubiquinone-9 was also present. Isolation and identification of the quinone from the purified plasma membrane yielded mainly 1′-oxomenaquinone-7 and ubiquinone-9; menaquinone was not detected. Membrane bound 1′-oxomenaquinone-7 could be destroyed by near-ultraviolet irradiation, with a concomitant loss or stimulation of plasma membrane electron transport activities. The abilities of different quinones to restore α-lipoic acid and ferricyanide reductase activity in near UV-irradiated cell preparations were compared. The order was; conjugate of chlorobiumquinone and sphingosine base ? conjugate of 2-methyl-3-(1′-oxooctadecyl)-1,4-napthoquinone and octadecylamine >> chlorobiumquinone ? 2-methyl-3-(1′-oxooctadecyl)-1,4-napthoquinone > menaquinone-4 ? ubiquinone-10. After irradiation with near-UV light, transmembrane α-lipoic acid reduction was inhibited, while transmembrane ferricyanide reduction was stimulated. The result obtained indicates that chlorobiumquinone mediates the plasma membrane electron transport between cytosolic reductant and oxygen as well as α-lipoic acid. UV-inactivation of chlorobiumquinone shuts down the plasma membrane oxygen uptake and diverts the electron flux towards ferricyanide reduction via ubiquinone-9. Chlorobiumquinone is the only example of a polyisoprenoid quinone containing a side chain carbonyl group from photosynthetic green-sulphur bacteria. Recent work has revealed numerous genes of trypanosomatid sharing common ancestry with plants and/or bacteria. These observations pose some fascinating questions about the evolutionary biology of this important group of parasitic protozoa.     

Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8

The ATP-binding cassette (ABC) sterol transporters are responsible for maintaining cholesterol homeostasis in mammals by participating in reverse cholesterol transport (RCT) or transintestinal cholesterol efflux (TICE). The heterodimeric ABCG5/G8 carries out selective sterol excretion, preventing the abnormal accumulation of plant sterols in human bodies, while homodimeric ABCG1 contributes to the biogenesis and metabolism of high-density lipoproteins. A sterol-binding site on ABCG5/G8 was proposed at the interface of the transmembrane domain and the core of lipid bilayers. In this study, we have determined the crystal structure of ABCG5/G8 in a cholesterol-bound state. The structure combined with amino acid sequence analysis shows that in the proximity of the sterol-binding site, a highly conserved phenylalanine array supports functional implications for ABCG cholesterol/sterol transporters. Lastly, in silico docking analysis of cholesterol and stigmasterol (a plant sterol) suggests sterol-binding selectivity on ABCG5/G8, but not ABCG1. Together, our results provide a structural basis for cholesterol binding on ABCG5/G8 and the sterol selectivity by ABCG transporters.     

Smash ridge tillage strongly influence soil functionality,physiology and rice yield

The practice of smash-ridging on dry land crop cultivation has shown much promise. However, the mechanism how does soil functionality and root traits can affect rice yield under smash ridge tillage with reduced nitrogen fertilization have not yet been explored. To fill this knowledge gap, we used three tillage methods—smash-ridging 40 cm (S40), smash-ridging 20 cm (S20), and traditional turn-over plowing 20 cm (T)—and two rice varieties (hybrid rice and conventional rice) and measured soil quality, root traits, rice yield and their correlation analysis at different growth stages. Soil physical and chemical properties were significantly improved by smash-ridging, including improvements in root morphological and physiological traits during three growth stages compared with T. S40 had the highest leaf area index (LAI), plant height (PH), and biomass accumulation (BA). Increment in biomass and panicle number (PN) resulted in higher grain yield (GY) of 6.9–9.4% compared with T. Correlation analysis revealed that root total absorption area (RTAA), root active absorption area (RAA), and root area ratio (RAR) were strongly correlated with soil quality. Root injury flow (RIF) and root biomass accumulation (RBA) were strongly correlated with LAI and above-ground plant biomass accumulation (AGBA). Conclusively, S40 is a promising option for improving soil quality, root traits, and consequently GY.     

On the rigidity of RNA in tomato bushy stunt virus

The motional state of RNA in tomato bushy stunt virus, both in the crystalline state and in solution, has been investigated using ³¹P nuclear magnetic resonance methods. It has been found that the RNA is highly immobile in the native virus and it is suggested that the lack of a high-resolution X-ray diffraction pattern for either the RNA or the N-terminal regions of the protein coat molecules (Harrison et al., 1978) is due to static disorder in the crystals. Dynamic disorder has been detected in the virus after treatment with EDTA, which causes a structural change and an increase in particle size.