Interaction of human and bacterial AlkB proteins with DNA as probed through chemical cross-linking studies

The Escherichia coli AlkB protein was recently found to repair cytotoxic DNA lesions 1-methyladenine and 3-methylcytosine by using a novel iron-catalyzed oxidative demethylation mechanism. Three human homologs, ABH1, ABH2 and ABH3, have been identified, and two of them, ABH2 and ABH3, were shown to have similar repair activities to E.coli AlkB. However, ABH1 did not show any repair activity. It was suggested that ABH3 prefers single-stranded DNA and RNA substrates, whereas AlkB and ABH2 can repair damage in both single- and double-stranded DNA. We employed a chemical cross-linking approach to probe the structure and substrate preferences of AlkB and its three human homologs. The putative active site iron ligands in these proteins were mutated to cysteine residues. These mutant proteins were used to cross-link to different DNA probes bearing thiol-tethered bases. Disulfide-linked protein–DNA complexes can be trapped and analyzed by SDS–PAGE. Our results show that ABH2 and ABH3 have structural and functional similarities to E.coli AlkB. ABH3 shows preference for the single-stranded DNA probe. ABH1 failed to cross-link to the probes tested. This protein, unlike other AlkB proteins, does not seem to interact with DNA in its E.coli expressed form.     

Novel Fusicoccins R and S, and the fusicoccin S aglycon (phomopsiol) from Phomopsis amygdali niigata 2-A, and their seed germination-stimulating activity in the presence of abscisic acid

Our search for new 3-hydroxyfusicoccins structurally related to cotylenin A from a culture of Phomopsis amygdali Niigata 2-A resulted in the isolation of novel 3-hydroxy fusicoccins, called fusicoccins R and S, and the fusicoccin S aglycon, called phomopsiol, together with known 3alpha-hydroxyfusicoccin J. The structure of phomopsiol was identified as that of O-demethyl-3-epicotylenol based on spectroscopic evidence. The structures of fusicoccins R and S were also determined to be those of 3'-deacetyl-3alpha-hydroxyfusicoccin A and 3beta-hydroxy-3-epifusicoccin H. The lettuce seed germination-stimulating activity of fusicoccins R and S, phomopsiol and 3alpha-hydroxyfusicoccin J was examined in the presence of ABA; fusicoccin R and 3alpha-hydroxyfusicoccin J were highly active, while fusicoccin S and phomopsiol were inactive. The possible biosynthetic relationships among these novel fusicoccins having a 3alpha- or 3beta-hydroxy group in their diterpene moiety are briefly discussed.     

Fusicocca-3(16),10(14)-diene, and beta- and delta-araneosenes, new fusicoccin biosynthesis-related diterpene hydrocarbons from Phomopsis amygdali

Further isolation and examination of fusicoccane hydrocarbons biosynthetically related to fusicoccin from Phomopsis amygdali allowed us to identify new fungal diterpene hydrocarbons of fusicoccadiene and araneosene. These were assigned as (+)-fusicocca-3(16),10(14)-diene, and (+)-beta- and (+)-delta-araneosenes. These findings led to the experimental clarification of the structures of the biosynthetic hydrocarbon intermediates presumed earlier.     

Absolute stereochemistry of acremolactone A, a novel herbicidal epoxydihydropyranyl gamma-lactone from Acremonium roseum I4267

Acremolactone A was chemically degraded to the bicyclic hemiacetal gamma-lactone and an epoxycyclohexenol, and their stereochemistry was determined by spectroscopic methods. These observations and data from NOE experiments on acremolactone A led to the configurational assignment of all asymmetric carbons in acremolactone A, enabling its stereostructure to be established.     

Temporal and spatial variation of forest biomass in relation to stand dynamics in a mature,lowland tropical rainforest,Malaysia

To clarify consistency in the size of carbon pool of a lowland tropical rainforest, we calculated changes in above-ground biomass in the Pasoh Forest Reserve, Peninsular Malaysia. We estimated the total above-ground biomass of a mature stand using tree census data obtained in a 6-ha plot every 2years from 1994 to 1998. The total above-ground biomass decreased consistently from 1994 (431Mgha^–1) to 1998 (403Mgha^–1) (1Mg=10³ kg). These are much lower than that in 1973 for a 0.2ha portion of the same area, suggesting that the the total above-ground biomass reduction might have been consistent in recent decades. This trend contrasted with a major trend for neotropical forests. During 1994–1998, the forest gained 23.0 and 0.88Mgha^–1 of the total above-ground biomass by tree growth and recruitment, respectively, and lost 51.9Mgha^–1 by mortality. Overall, the biomass decreased by 28.4Mgha^–1 (i.e. 7.10Mgha^–1·year^–1), which is almost equivalent to losing a 76-cm-diameter living tree per hectare per year. Analysis of positive and negative components of biomass change revealed that deaths of large trees dominated the total above-ground biomass decrease. The forest biomass also varied spatially, with the total above-ground biomass density ranging 212–655Mgha^–1 on a 0.2-ha basis (n= 30 subplots, 1998) and 365–440Mgha^–1 on a 1ha basis. A large decrease of the total above-ground biomass density (>50Mg per ha per 2years) in several 0.2-ha subplots contributed to the overall decrease in the 6-ha total above-ground biomass. In the present study, we discuss the association between forest dynamics and biomass fluctuation, and the implication for carbon cycling in mature forests with emphasis on forest monitoring and assessments of soil and decomposition systems.     

Monitoring ovarian cycle and conception by fecal progesterone analysis in sika deer

The ovarian cycle and conception of sika deer were studied to reveal factors responsible for delayed conception. Concentration of progesterone in feces from 12 female Hokkaido sika deer (Cervus nippon yesoensis Heude, 1884) was measured during the mating season in 2000. The cyclic pattern of fecal progesterone synchronized with estrous symptoms, which could hence be interpreted as indicating ovarian cycle. All observed females ovulated by 14 October. However, during the early mating season, females did not permit copulation at ovulation, and the length of luteal phase following ovulation without estrus was 9.8±4.6 days (5–24days). Most females conceived at the first copulation, which were confirmed by progesterone profiles that was sustained at a high level after the copulation. This indicates the presence of a functional corpus luteum, a state of pregnancy. Thus, some females had repeated ovulation without copulation several times, creating a 3–4week variation in the timing of conception. But some females conceived very late in the mating season after the repetition of ovulation and copulation.     

Plant acetyl-CoA carboxylase: structure, biosynthesis, regulation, and gene manipulation for plant breeding

Acetyl-CoA carboxylase (ACCase) catalyzes the first committed step of fatty acid synthesis, the carboxylation of acetyl-CoA to malonyl-CoA. Two physically distinct types of enzymes are found in nature. Heteromeric ACCase composed of four subunits is usually found in prokaryotes, and homomeric ACCase composed of a single large polypeptide is found in eukaryotes. Most plants have both forms, the heteromeric form in plastids, in which de novo fatty acids are synthesized, and the homomeric form in cytosol. This review focuses on the structure and regulation of plant heteromeric ACCase and its manipulation for plant breeding.