TY - JOUR TI - Characterization of a chloroplast sequence-specific DNA binding factor AU - Lam, E. AU - Hanley Bowdoin, L. AU - Chua, N. H. T2 - Journal of Biological Chemistry DA - 1988/// PY - 1988/// VL - 263 SP - 8288–8293 ER - TY - JOUR TI - Role of hydrogen in the activation and regulation of hydrogen oxidation by the soluble hydrogenase from Alcaligenes eutrophus H16. T2 - The Biochemical journal AB - The activation kinetics of the H2-oxidizing activity of the soluble hydrogenase from Alcaligenes eutrophus H16 were investigated. Activation with Na2S2O4 plus 101 kPa H2 resulted in a rapid increase in activity over 1 h and constant activity after 3 h incubation. Less-stable activations were achieved if enzyme was incubated with Na2S2O4 under 1 kPa H2 or 101 kPa N2. The enzyme could also be partly activated either with NADH alone or with H2 alone. The level of activity obtained with both 101 kPa H2 and NADH present was greater than that obtained with either 101 kPa H2 or NADH alone. Activation with H2 plus NADH was virtually independent of NADH concentration but highly dependent on H2 concentration. The effects of various concentrations of H2 and constant concentration of NADH on the level of activation were the same whether H2 oxidation was assayed by H2-dependent Methylene Blue or NAD+ reduction. Diaphorase activity did not require activation and was little affected by the treatments that activated H2-oxidizing activity. The results suggest that H2 plays an important role in regulating the level of H2-oxidizing activity in this soluble hydrogenase. DA - 1988/9/1/ PY - 1988/9/1/ DO - 10.1042/bj2540463 UR - https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/3052435/?tool=EBI ER - TY - JOUR TI - Acetylene inhibition of metalloenzymes T2 - Analytical Biochemistry DA - 1988/9// PY - 1988/9// DO - 10.1016/0003-2697(88)90181-9 UR - http://dx.doi.org/10.1016/0003-2697(88)90181-9 ER - TY - JOUR TI - Interaction of Ammonia Monooxygenase from Nitrosomonas europaea with Alkanes, Alkenes, and Alkynes. T2 - Applied and environmental microbiology DA - 1988/12/1/ PY - 1988/12/1/ UR - https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/16347810/?tool=EBI ER - TY - JOUR TI - Aerobic, inactive forms of Azotobacter vinelandii hydrogenase: activation kinetics and insensitivity to C2H2 inhibition. T2 - Biochimica et biophysica acta AB - Azotobacter vinelandii hydrogenase (EC class 1.12), either purified or membrane-associated, was obtained aerobically in an inactive state. The kinetics of activation by treatment with a reductant (H2 or dithionite) were determined. Three distinct phases of the activation were observed. Aerobically prepared, inactive hydrogenase was insensitive to acetylene inhibition, but could be rendered acetylene-sensitive by reduction with dithionite. These findings indicate that acetylene inhibition of hydrogenase requires catalytically active enzyme. DA - 1988/11/1/ PY - 1988/11/1/ DO - 10.1016/0167-4838(88)90160-4 UR - https://doi.org/10.1016/0167-4838(88)90160-4 ER - TY - JOUR TI - Transcription of the wheat chloroplast gene that encodes the 32 kd polypeptide AU - Hanley-Bowdoin, Linda AU - Chua, Nam-Hai T2 - Plant Molecular Biology DA - 1988/// PY - 1988/// DO - 10.1007/bf00029880 VL - 10 IS - 4 SP - 303-310 J2 - Plant Mol Biol LA - en OP - SN - 0167-4412 1573-5028 UR - http://dx.doi.org/10.1007/bf00029880 DB - Crossref ER - TY - JOUR TI - Transient expression of heterologous RNAs using tomato golden mosaic virus AU - Hanley-Bowdoin, L. AU - Elmer, J. S. AU - Rogers, S. G. T2 - Nucleic Acids Research AB - The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules designated as components A and B. The A component contains the only virally-encoded function required for autonomous replication in infected plant cells. We used agroinoculation of petunia leaf discs with the A component to develop a transient expression system which permits direct examination of viral transcripts by S1 nuclease protection. The AR1 gene, which encodes the TGMV coat protein, was transcribed transiently in leaf discs after agroinoculation of TGMV A DNA. Synthesis of AR1 RNA was dependent on T-DNA transfer and TGMV DNA replication, demonstrating that it is a plant transcription product. The AL open reading frames of TGMV A were also expressed transiently in leaf discs. The ratio between AR1 RNA and the major leftward RNA was constant and was used to normalize AR1 transcription for viral DNA copy number. The bacterial genes encoding chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS) were transiently expressed in leaf discs from the AR1 promoter in TGMV A. The levels of AR1 and GUS RNAs were similar in leaf discs after adjusting for viral DNA copy number, while CAT RNA was less abundant. The geminivirus transient expression system allows rapid analysis of RNAs transcribed from foreign genes and can serve as a preliminary screen in the construction of transgenic plants. DA - 1988/11/25/ PY - 1988/11/25/ DO - 10.1093/nar/16.22.10511 VL - 16 IS - 22 SP - 10511-10528 J2 - Nucleic Acids Research LA - en OP - SN - 0305-1048 1362-4962 UR - http://dx.doi.org/10.1093/nar/16.22.10511 DB - Crossref ER - TY - JOUR TI - Cytosine methylation in ribosomal DNA and nucleolus organiser expression in wheat AU - Flavell, R.B. AU - O'Dell, M. AU - Thompson, W.F. T2 - Journal of Molecular Biology AB - Cytosine methylation has been studied in wheat rRNA genes at nucleolar organizers displaying different activities. The methylation pattern within a specific multigene locus is influenced by the number and type of rRNA genes in other rDNA loci in the cell. One CCGG site 164 base-pairs upstream from the start of transcription is preferentially unmethylated in some genes. Dominant, very active loci have a higher proportion of rRNA genes with unmethylated cytosine residues in comparison with recessive and inactive loci. It is concluded that cytosine methylation in rDNA is regulated and that the methylation pattern correlates with the transcription potential of an rRNA gene. DA - 1988/// PY - 1988/// DO - 10.1016/0022-2836(88)90352-X VL - 204 SP - 500–534 ER - TY - CHAP TI - Chromatin structure and expression of plant ribosomal RNA genes AU - Thompson, W.F. AU - Flavell, R.B. AU - Watson, J.C. AU - Kaufman, L.S. T2 - Architecture of Eukaryotic Genes A2 - Kahl, G. PY - 1988/// SP - 385–396 PB - VCH Verlagsgesellschaft ER - TY - CHAP TI - Purification and restriction endonuclease analysis of plant nuclear DNA AU - Watson, J.C. AU - Thompson, W.F. T2 - Methods for Plant Molecular Biology A2 - Weissbach, A. A2 - Weissbach, H. PY - 1988/// PB - Academic Press ER - TY - BOOK TI - Molecular Plant Development AU - Murphy, T.M. AU - Thompson, W.F. DA - 1988/// PY - 1988/// PB - Prentice Hall ER - TY - JOUR TI - Inversions in legume chloroplast DNAs AU - Palmer, J.D. AU - Osorio, B.O. AU - Thompson, W.F. T2 - Current Genetics DA - 1988/// PY - 1988/// VL - 14 SP - 65–74 ER - TY - CHAP TI - Patterns of phytochrome-induced gene expression in etiolated pea buds AU - Thompson, W. F. AU - Kaufman, L. S. AU - Horwitz, B. A. AU - Sagar, A. D. AU - Watson, J. C. AU - Briggs, W. R. T2 - Biomechanisms Regulating Growth and Development PY - 1988/// DO - 10.1007/978-94-009-1395-0_18 SP - 269-284 OP - PB - Springer Netherlands SN - 9789401071239 9789400913950 UR - http://dx.doi.org/10.1007/978-94-009-1395-0_18 DB - Crossref ER - TY - JOUR TI - A transcription map of the pea chloroplast genome AU - Woodbury, Neal W. AU - Roberts, Linda L. AU - Palmer, Jeffrey D. AU - Thompson, William F. T2 - Current Genetics AB - A set of 53 cloned pea chloroplast DNA fragments representing approximately 90% of the chloroplast genome was used to probe Northern blots of total pea RNA, resulting in a nearly complete chloroplast transcription map. Similar analyses were performed for RNAs extracted from pea seedlings grown under several different light regimes. We have found that at least 85 kb of the 120 by pea chloroplast genome is represented as detectable transcripts. For many regions of the genome, we have detected multiple overlapping transcripts including both small, gene-sized RNAs and large transcripts covering entire gene clusters. All transcripts detected were more abundant (as a fraction of total cellular RNA) in light grown plants than in plants entirely in the dark. However, larger transcripts were generally more abundant in plants that had been exposed to only 24 h of white light (after germination in the dark) than in plants grown in continuous light. This study indicates that chloroplast genes are often grouped into multigene transcriptional units which can be cotranscribed, and that light-stimulated plastid development involves changes in the relative abundance of the overlapping RNAs of different length that result from transcription of these genes or gene clusters. DA - 1988/7// PY - 1988/7// DO - 10.1007/bf00405857 VL - 14 IS - 1 SP - 75-89 J2 - Curr Genet LA - en OP - SN - 0172-8083 1432-0983 UR - http://dx.doi.org/10.1007/bf00405857 DB - Crossref ER - TY - JOUR TI - Photoregulation: diverse gene responses in greening seedlings AU - Thompson, W. F. T2 - Plant, Cell and Environment AB - Abstract. Light effects on the expression of nuclear genes for plastid proteins and for the 18S, 5.8S and 25S ribosomal RNAs are discussed, together with some recent information concerning the expression of chloroplast genes in developing plastids. Emphasis is given to the diversity of different responses observed with different genes and evidence for light effects at both transcriptional and post‐transcriptional levels. DA - 1988/7// PY - 1988/7// DO - 10.1111/j.1365-3040.1988.tb01355.x VL - 11 IS - 5 SP - 319-328 J2 - Plant Cell Environ LA - en OP - SN - 0140-7791 1365-3040 UR - http://dx.doi.org/10.1111/j.1365-3040.1988.tb01355.x DB - Crossref ER - TY - JOUR TI - DNase I sensitivity of ribosomal RNA Genes in chromatin and nucleolar dominance in wheat AU - Thompson, W.F. AU - Flavell, R.B. T2 - Journal of Molecular Biology AB - Ribosomal RNA genes at different nucleolar organizer (NOR) loci in hexaploid wheat are expressed at different levels. The degree of expression of a particular organizer depends on the genetic background, especially on the presence of other NOR loci. For example, when chromosome 1U of Aegilops umbellulata is introduced into the hexaploid wheat cultivar “Chinese Spring” the A. umbellulata NOR accounts for most of the nucleolar activity and seems to suppress the activity of the wheat NOR loci. Even in wild-type “Chinese Spring”, the NOR on chromosome 1B is partially dominant to that on chromosome 6B, since the 1B locus is more active in spite of having fewer genes. We have previously shown that these and other examples of nucleolar dominance in wheat are associated with undermethylation of cytosine residues in certain regions of the dominant rDNA. Here, we show that rRNA genes at dominant loci are organized in a chromatin conformation that renders them more sensitive to DNase I digestion than other rRNA genes. In addition, we have mapped several DNase I-hypersensitive sites in the intergenic spacer region of the rDNA repeating unit. Some of these sites are located near the initiation region for the 45 S rRNA precursor, while others are associated with a series of short direct repeats 5′ to the 45 S rRNA initiation site. The results are discussed in terms of a model in which repeated sequences in the wheat intergenic DNA are presumed to function as upstream promoters and transcriptional enhancers similar to those in Xenopus. DA - 1988/12// PY - 1988/12// DO - 10.1016/0022-2836(88)90353-1 VL - 204 IS - 3 SP - 535-548 J2 - Journal of Molecular Biology LA - en OP - SN - 0022-2836 UR - http://dx.doi.org/10.1016/0022-2836(88)90353-1 DB - Crossref ER - TY - JOUR TI - Nuclear-Cytoplasmic Partitioning of Phytochrome-Regulated Transcripts in Pisum sativum AU - Sagar, A. D. AU - Briggs, W. R. AU - Thompson, W. F. T2 - PLANT PHYSIOLOGY AB - Nuclear and cytoplasmic mRNAs for several phytochrome-regulated genes were examined in Pisum seedlings in order to investigate possible light effects on mRNA partitioning between the nucleus and cytoplasm. Transcripts from each of five light-regulated genes exhibited different responses to a variety of light treatments, but for each transcript we observed a characteristic linear relationship between nuclear and cytoplasmic levels over a wide range of total transcript abundance. Different mRNAs are characterized by different nuclear-cytoplasmic `partitioning coefficients', indicating that post-transcriptional events play a significant role in regulating the accumulation of these mRNAs during light induction. DA - 1988/12/1/ PY - 1988/12/1/ DO - 10.1104/pp.88.4.1397 VL - 88 IS - 4 SP - 1397-1402 J2 - PLANT PHYSIOLOGY LA - en OP - SN - 0032-0889 1532-2548 UR - http://dx.doi.org/10.1104/pp.88.4.1397 DB - Crossref ER - TY - JOUR TI - Light Effects on Several Chloroplast Components in Norflurazon-Treated Pea Seedlings AU - Sagar, A. D. AU - Horwitz, B. A. AU - Elliott, R. C. AU - Thompson, W. F. AU - Briggs, W. R. T2 - PLANT PHYSIOLOGY AB - Changes occurring in several chloroplast components during Norflurazon-induced photobleaching of Pisum sativum seedlings were investigated. mRNA steady state levels of the chlorophyll a/b-binding protein of photosystem II, ferredoxin I, the small and large subunits of ribulose 1,5-bisphosphate carboxylase, and pEA214 and pEA207, two other light-responsive genes, were determined during chlorophyll photooxidation. Relative transcription rates were assayed in isolated nuclei. The results illustrate a complex set of interactions regulating expression of the nuclear and chloroplast genomes. Photobleaching was found to affect the expression of the various genes in different ways. While transcript levels of the chlorophyll a/b-binding protein decreased by more than 80% under photooxidative light conditions in carotenoid-deficient peas, levels of ferredoxin, the small and large subunits of ribulose 1,5-bisphosphate carboxylase, and pEA214 mRNAs were reduced by less than 50%. pEA207 mRNA levels, on the other hand, were resistant to the effects of photobleaching. Analyses of chlorophylls a and b and the chlorophyll a/b-binding protein suggest that accumulation of the protein and its mRNA are coordinated with chlorophyll abundance at several steps. In addition to post-transcriptional regulation at the level of mRNA and protein stability, there may exist coordination at the transcriptional stage. DA - 1988/10/1/ PY - 1988/10/1/ DO - 10.1104/pp.88.2.340 VL - 88 IS - 2 SP - 340-347 J2 - PLANT PHYSIOLOGY LA - en OP - SN - 0032-0889 1532-2548 UR - http://dx.doi.org/10.1104/pp.88.2.340 DB - Crossref ER - TY - JOUR TI - Phytochrome Regulation of Greening in Pisum: Chlorophyll Accumulation and Abundance of mRNA for the Light-Harvesting Chlorophyll a/b Binding Proteins AU - Horwitz, B. A. AU - Thompson, W. F. AU - Briggs, W. R. T2 - PLANT PHYSIOLOGY AB - A brief pulse of red light eliminates or reduces the lag in chlorophyll accumulation that occurs when dark-grown pea seedlings are transferred to continuous white light. The red light pulse also induces the accumulation of specific mRNAs. We compared time courses, escape from reversal by far-red light, and fluence-response behavior for induction of mRNA for the light-harvesting chlorophyll a/b binding proteins (Cab mRNA) with those for induction of rapid chlorophyll accumulation in seedlings of Pisum sativum cv Alaska. In both cases the time courses of low fluence and very low fluence responses diverged from each other in a similar fashion: the low fluence responses continued to increase for at least 24 hours, while the very low fluence responses reached saturation by 8 to 16 hours. Both responses escaped from reversibility by far-red slowly, approaching the red control level after 16 hours. The fluence-response curve for the Cab mRNA increase, on the other hand, showed threshold and saturation at fluences 10-fold lower than threshold and saturation values for the greening response. Therefore, the level of Cab mRNA, as measured by the presence of sequences hybridizing to a cDNA probe, does not limit the rate of chlorophyll accumulation after transfer of pea seedlings to white light. The Cab mRNA level in the buds of seedlings grown under continuous red light remained high even when the red fluence rate was too low to allow significant greening. In this case also, abundance of Cab mRNA cannot be what limits chlorophyll accumulation. DA - 1988/1/1/ PY - 1988/1/1/ DO - 10.1104/pp.86.1.299 VL - 86 IS - 1 SP - 299-305 J2 - PLANT PHYSIOLOGY LA - en OP - SN - 0032-0889 1532-2548 UR - http://dx.doi.org/10.1104/pp.86.1.299 DB - Crossref ER - TY - JOUR TI - Interaction of Ammonia Monooxygenase from Nitrosomonas europaea with Alkanes, Alkenes, and Alkynes AU - Hyman, Michael R. AU - Murton, Ian B. AU - Arp, Daniel J. T2 - Applied and Environmental Microbiology C2 - PMC204451 DA - 1988/12// PY - 1988/12// VL - 54 IS - 12 SP - 3187-3190 J2 - Appl Environ Microbiol SN - 0099-2240 UR - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC204451/ DB - PubMed Central Y2 - 2019/2/1/ ER - TY - JOUR TI - Reversible and irreversible effects of nitric oxide on the soluble hydrogenase from Alcaligenes eutrophus H16 AU - Hyman, M. R. AU - Arp, D. J. T2 - Biochemical Journal AB - The effects of NO on the H2-oxidizing and diaphorase activities of the soluble hydrogenase from Alcaligenes eutrophus H16 were investigated. With fully activated enzyme, NO (8-150 nM in solution) inhibited H2 oxidation in a time- and NO-concentration-dependent process. Neither H2 nor NAD+ appeared to protect the enzyme against the inhibition. Loss of activity in the absence of an electron acceptor was about 10 times slower than under turnover conditions. The inhibition was partially reversible; approx. 50% of full activity was recoverable after removal of the NO. Recovery was slower in the absence of an electron acceptor than in the presence of H2 plus an electron acceptor. The diaphorase activity of the unactivated hydrogenase was not affected by NO concentrations of up to 200 microM in solution. Exposure of the unactivated hydrogenase to NO irreversibly inhibited the ability of the enzyme to be fully activated for H2-oxidizing activity. The enzyme also lost its ability to respond to H2 during activation in the presence of NADH. The results are interpreted in terms of a complex inhibition that displays elements of (1) a reversible slow-binding inhibition of H2-oxidizing activity, (2) an irreversible effect on H2-oxidizing activity and (30 an irreversible inhibition of a regulatory component of the enzyme. Possible sites of action for NO are discussed. DA - 1988/9/1/ PY - 1988/9/1/ DO - 10.1042/bj2540469 VL - 254 IS - 2 SP - 469-475 LA - en SN - 0264-6021, 1470-8728 UR - http://www.biochemj.org/content/254/2/469 DB - www.biochemj.org Y2 - 2019/2/1/ ER - TY - JOUR TI - Role of hydrogen in the activation and regulation of hydrogen oxidation by the soluble hydrogenase from Alcaligenes eutrophus H16 AU - Hyman, M R AU - Fox, C A AU - Arp, D J T2 - Biochemical Journal C2 - PMC1135100 DA - 1988/9/1/ PY - 1988/9/1/ VL - 254 IS - 2 SP - 463-468 J2 - Biochem J SN - 0264-6021 UR - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1135100/ DB - PubMed Central Y2 - 2019/2/1/ ER - TY - JOUR TI - Acetylene inhibition of metalloenzymes AU - Hyman, M. R. AU - Arp, D. J. T2 - Analytical Biochemistry DA - 1988/9// PY - 1988/9// VL - 173 IS - 2 SP - 207-220 J2 - Analy Biochem LA - eng SN - 0003-2697 DB - PubMed ER - TY - JOUR TI - Aerobic, inactive forms of Azotobacter vinelandii hydrogenase: activation kinetics and insensitivity to C2H2 inhibition AU - Hyman, M. R. AU - Seefeldt, L. C. AU - Arp, D. J. T2 - Biochimica Et Biophysica Acta DA - 1988/11/2/ PY - 1988/11/2/ VL - 957 IS - 1 SP - 91-96 J2 - Biochim. Biophys. Acta LA - eng SN - 0006-3002 ST - Aerobic, inactive forms of Azotobacter vinelandii hydrogenase DB - PubMed ER -