TY - JOUR TI - Primary Structures of Arabidopsis Calmodulin Isoforms Deduced from the Sequences of cDNA Clones AU - Ling, Vincent AU - Perera, Imara AU - Zielinski, Raymond E. T2 - Plant Physiology AB - Complementary DNA (cDNA) clones encoding calmodulin isoforms were isolated from an Arabidopsis leaf lambdagt10 library by screening with cloned barley calmodulin cDNA probes. Two cDNAs, one a 626-base pair partial-length clone (ACaM-1) and one a 1400-base pair full-length clone (ACaM-2), encode calmodulin polypeptides that differ by four conservative amino acid substitutions. None of the amino acid sequence differences occur within the four Ca(2+)-binding domains of the proteins. Whereas the deduced amino acid sequences of the two Arabidopsis calmodulin isoforms share 97% identity, the nucleotide sequences encoding the two isoforms share 87% sequence identity. Most of these nucleotide sequence differences (80%) occur in codon wobble positions. ACaM-1 and ACaM-2 both hybridize with a distinct set of restriction fragments of Arabidopsis total DNA, indicating that they were derived from transcripts of separate genes; these genes are single- or very low-copy in the Arabidopsis genome. Both cDNAs hybridize to messenger RNA (mRNA) species of 0.8 kilobases that are expressed to a greater extent in developing siliques compared with leaves, flowers, and stems. Northern blot and polymerase chain reaction assays both indicate that ACaM-1 mRNA is more highly expressed than ACaM-2 mRNA in developing siliques. The steady-state levels of both isoform mRNAs increase as a result of touch stimulation; the kinetics and extent of increase are comparable for the two mRNAs. DA - 1991/8/1/ PY - 1991/8/1/ DO - 10.1104/pp.96.4.1196 VL - 96 IS - 4 SP - 1196-1202 J2 - Plant Physiol. LA - en OP - SN - 0032-0889 1532-2548 UR - http://dx.doi.org/10.1104/pp.96.4.1196 DB - Crossref ER - TY - JOUR TI - Kinetic analysis of the interaction of nitric oxide with the membrane-associated, nickel and iron-sulfur-containing hydrogenase from Azotobacter vinelandii. T2 - Biochimica et biophysica acta AB - The effects of nitric oxide (NO) on the membrane-associated form of the nickel and iron-sulfur-containing hydrogenase from Azotobacter vinelandii have been investigated. In the presence of H2 and an electron acceptor (turnover conditions), NO acts as a noncompetitive inhibitor vs. methylene blue (Ki = 12 microM). There is no element of competition between NO and H2, implying that the site of NO action is not the H2-activating site of the hydrogenase. When the membrane-associated hydrogenase is incubated under non-turnover conditions, the enzyme is irreversibly inactivated by NO in a time-dependent process. The inactivation is a non-saturable, pseudo-first-order process which is consistent with a direct chemical reaction between NO and the hydrogenase. Kinetic evidence is presented which is compatible with an interaction between NO and a redox-active component other than the H2-activating site on the enzyme. The complex inhibition pattern of NO has been interpreted in terms of two distinct interactions of NO with iron-sulfur centers of the hydrogenase. DA - 1991/1/1/ PY - 1991/1/1/ DO - 10.1016/0167-4838(91)90261-w UR - https://doi.org/10.1016/0167-4838(91)90261-w KW - HYDROGENASE KW - NITRIC OXIDE INHIBITION KW - (AZOTOBACTER-VINELANDII) ER - TY - JOUR TI - Factors Limiting Aliphatic Chlorocarbon Degradation by Nitrosomonas europaea: Cometabolic Inactivation of Ammonia Monooxygenase and Substrate Specificity. T2 - Applied and environmental microbiology DA - 1991/10/1/ PY - 1991/10/1/ UR - https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/16348568/?tool=EBI ER - TY - JOUR TI - Description of the Erythromycin-Producing Bacterium Arthrobacter sp. Strain NRRL B-3381 as Aeromicrobium erythreum gen. nov., sp. nov. AU - Miller, E. S. AU - Woese, C. R. AU - Brenner, S. T2 - International Journal of Systematic Bacteriology AB - Arthrobacter sp. strain NRRL B-3381T (T = type strain) is a nonmycelial, nonsporulating actinomycete that produces the macrolide antibiotic erythromycin. This bacterium differs in many ways from the type species of the genus Arthrobacter (Arthrobacter globiformis), suggesting that a taxonomic revision is appropriate. The G + C content of strain NRRL B-3381T DNA is 71 to 73 mol%, and the peptidoglycan of this organism contains LL-diaminopimelic acid. Evolutionary distance data obtained from 16S rRNA sequences identified NRRL B-3381T as the deepest branching member of the Nocardioides group of actinomycetes. The principal long-chain fatty acids which we identified that distinguished strain NRRL B-3381T from related G + C-rich bacteria were 10-methyloctadecanoic (tuberculosteric), octadecenoic, and hexadecanoic acids. These characteristics, together with phage typing and biochemical characteristics, form the basis for our recommendation that strain NRRL B-3381 should be the type strain of a new taxon, for which we propose the name Aeromicrobium erythreum. DA - 1991/7/1/ PY - 1991/7/1/ DO - 10.1099/00207713-41-3-363 VL - 41 IS - 3 SP - 363-368 J2 - International Journal of Systematic Bacteriology LA - en OP - SN - 0020-7713 1465-2102 UR - http://dx.doi.org/10.1099/00207713-41-3-363 DB - Crossref ER - TY - JOUR TI - Cloning vectors, mutagenesis, and gene disruption (ermR) for the erythromycin-producing bacterium Aeromicrobium erythreum. AU - Miller, E S T2 - Applied and Environmental Microbiology AB - Genetic systems for study of Aeromicrobium erythreum, a gram-positive, G + C-rich (72%) bacterium with the capacity for erythromycin biosynthesis, are described. High-copy-number plasmids suitable as gene cloning vectors include derivatives of the Streptomyces plasmids pIJ101, pVE1, and pJV1. pIJ101 derivatives with missense substitutions at the rep gene BamHI site do not replicate in A. erythreum. Ethyl methanesulfonate treatment generated several amino acid auxotrophs and non-erythromycin-producing (Ery-) strains. Using the Ery- strain AR1807 as a recipient for plasmid-directed integrative recombination, the chromosomal ermR gene (encoding 23S rRNA methyltransferase) was disrupted. Phenotypic characterizations demonstrated that ermR is the sole determinant of macrolide antibiotic resistance in A. erythreum. DA - 1991/// PY - 1991/// DO - 10.1128/aem.57.9.2758-2761.1991 VL - 57 IS - 9 SP - 2758-2761 LA - en OP - SN - 0099-2240 1098-5336 UR - http://dx.doi.org/10.1128/aem.57.9.2758-2761.1991 DB - Crossref ER - TY - JOUR TI - Identification of phospholipase activities in the exotoxin of Edwardsiella tarda AU - Chung, Y.W. AU - Hsieh, T.-F. AU - Wang, C.T. T2 - Reports On Fish Disease Research DA - 1991/// PY - 1991/// VL - 29 SP - 39–46 ER - TY - JOUR TI - Nuclear scaffold and scaffold attachment regions (SARs) in higher plants AU - Hall, G. AU - Allen, G.C. AU - Loer, D.S. AU - Thompson, W.F. AU - Spiker, S. T2 - Proceedings of the National Academy of Sciences of United States of America AB - DNA in the nuclei of eukaryotic organisms undergoes a hierarchy of folding to be packaged into interphase and metaphase chromosomes. The first level of packaging is the 11-nm nucleosome fiber, which is further coiled into a 30-nm fiber. Evidence from fungal and animal systems reveals the existence of higher order packaging consisting of loops of the 30-nm fibers attached to a proteinaceous nuclear scaffold by an interaction between the scaffold and specific DNA sequences called scaffold-attachment regions (SARs). Support for the ubiquitous nature of such higher order packaging of DNA is presented here by our work with plants. We have isolated scaffolds from tobacco nuclei using buffers containing lithium diiodosalicylate to remove histones and then using restriction enzymes to remove the DNA not closely associated with the scaffold. We have used Southern hybridization to show that the DNA remaining bound to the scaffolds after nuclease digestion includes SARs flanking three root-specific tobacco genes. This assay for SARs is termed the endogenous assay because it identifies genomic sequences as SARs by their endogenous association with the scaffold. Another assay, the exogenous assay, depends upon the ability of scaffolds to specifically bind exogenously added DNA fragments containing SARs. The tobacco scaffolds specifically bind a well-characterized yeast SAR, and cloned DNA fragments derived from the 3'-flanking regions of the root-specific genes are confirmed to contain SARs by this exogenous assay. DA - 1991/// PY - 1991/// DO - 10.1073/pnas.88.20.9320 VL - 88 IS - 20 SP - 9320–9324 KW - CHROMATIN KW - CHROMOSOMES KW - NUCLEI KW - TOBACCO ER - TY - JOUR TI - Identification of the mitochondrial genome in the chrysophyte alga Ochromonas danica AU - Coleman, A.W. AU - Thompson, W.F. AU - Goff, L.J. T2 - Journal of Protozoology AB - ABSTRACT. Analysis of total DNA isolated from the Chrysophyte alga Ochromonas danica revealed, in addition to nuclear DNA, two genomes present as numerous copies per cell. The larger genome (˜120 kilobase pairs or kbp) is the plastid DNA, which is identified by its hybridization to plasmids containing sequences for the photosynthesis genes rbcL, psbA, and psbC. The smaller genome (40 kbp) is the mitochondrial genome as identified by its hybridization with plasmids containing gene sequences of plant cytochrome oxidase subunits I and II. Both the 120‐ and 40‐kbp genomes contain genes for the small and large subunits of rDNA. The mitochondrial genome is linear with terminal inverted repeats of about 1.6 kbp. Two other morphologically similar species were examined, Ochromonas minuta and Poteriochromonas malhamensis. All three species have linear mitochondrial DNA of 40 kbp. Comparisons of endonuclease restriction‐fragment patterns of the mitochondrial and chloroplast DNAs as well as those of their nuclear rDNA repeats failed to reveal any fragment shared by any two of the species. Likewise, no common fragment size was detected by hybridization with plasmids containing heterologous DNA or with total mitochondrial DNA of O. danica; these observations support the taxonomic assignment of these three organisms to different species. The Ochromonas mitochondrial genomes are the first identified in the chlorophyll a/c group of algae. Combining these results with electron microscopic observations of putative mitochondrial genomes reported for other chromophytes and published molecular studies of other algal groups suggests that all classes of eukaryote algae may have mitochondrial genomes < 100 kbp in size, more like other protistans than land plants. DA - 1991/3// PY - 1991/3// DO - 10.1111/j.1550-7408.1991.tb06032.x VL - 38 IS - 2 SP - 129–135 KW - DNA KW - OCHROMONAS-MINUTA KW - PLASTID DNA KW - POTERIOCHROMONAS-MALHAMENSIS KW - RDNA KW - SPECIATION ER - TY - CHAP TI - Unusual Features of the Light Response System Regulating Ferredoxin Gene Expression AU - Thompson, W. F. AU - Elliott, R. C. AU - Dickey, L. F. AU - Gallo, M. AU - Pedersen, T. J. AU - Sowinski, D. A. T2 - Phytochrome Properties and Biological Action PY - 1991/// DO - 10.1007/978-3-642-75130-1_14 SP - 201-216 OP - PB - Springer Berlin Heidelberg SN - 9783642751325 9783642751301 UR - http://dx.doi.org/10.1007/978-3-642-75130-1_14 DB - Crossref ER - TY - JOUR TI - Concatemer chain reaction: A taq DNA polymerase-mediated mechanism for generating long tandemly repetitive DNA sequences AU - White, Michael J. AU - Fristensky, Brian W. AU - Thompson, William F. T2 - Analytical Biochemistry AB - The concatemer chain reaction (CCR) uses Taq DNA polymerase to synthesize double- or single-stranded DNA concatemers whose length and yield can be controlled by varying the number of thermal cycling steps. Although the reactions which occur in CCR are slower and more complex than in polymerase chain reaction (PCR), the practical application of the CCR technique is simple. The CCR technique is less expensive, faster, and easier than conventional methods for producing concatemers and gives greatly improved yields. The templates used in CCR may be: (i) double-stranded concatemer templates produced by ligation, (ii) double-stranded concatemers from previous CCRs, or (iii) single-stranded oligonucleotides consisting of one copy of the sense strand repeat and a complementary but overlapping repeat for the antisense strand. Different molar ratios and lengths (masses) of the two strands of the helix may be obtained. We have used both single-stranded and double-stranded concatemers as targets for RNA hybridization. Applications of this concatemer technology are discussed, including the use of concatemers as hybridization probes or targets in applications such as run-on transcription or analysis of repetitive DNA sequences. DA - 1991/12// PY - 1991/12// DO - 10.1016/0003-2697(91)90087-a VL - 199 IS - 2 SP - 184-190 J2 - Analytical Biochemistry LA - en OP - SN - 0003-2697 UR - http://dx.doi.org/10.1016/0003-2697(91)90087-a DB - Crossref ER - TY - JOUR TI - The Inheritance and Linkage Mapping of Ferredoxin-1 in Pea AU - Polans, N. O. AU - Folta, K. M. AU - Elliott, R. C. AU - Thompson, W. F. T2 - Journal of Heredity AB - The Inheritance and Linkage Mapping of Ferredoxin-1 in Pea Get access N. O. Polans, N. O. Polans Search for other works by this author on: Oxford Academic PubMed Google Scholar K. M. Folta, K. M. Folta Search for other works by this author on: Oxford Academic PubMed Google Scholar R. C. Elliott, R. C. Elliott Search for other works by this author on: Oxford Academic PubMed Google Scholar W. F. Thompson W. F. Thompson Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 82, Issue 3, May/June 1991, Pages 259–261, https://doi.org/10.1093/oxfordjournals.jhered.a111080 Published: 01 May 1991 DA - 1991/5/1/ PY - 1991/5/1/ DO - 10.1093/oxfordjournals.jhered.a111080 VL - 82 IS - 3 SP - 259-261 LA - en OP - SN - 1465-7333 0022-1503 UR - http://dx.doi.org/10.1093/oxfordjournals.jhered.a111080 DB - Crossref ER - TY - JOUR TI - High mobility group chromosomal proteins bind to AT-rich tracts flanking plant genes AU - Pedersen, Thomas J. AU - Arwood, Laura J. AU - Spiker, Steven AU - Guiltinan, Mark J. AU - Thompson, William F. T2 - Plant Molecular Biology DA - 1991/1// PY - 1991/1// DO - 10.1007/bf00017920 VL - 16 IS - 1 SP - 95-104 J2 - Plant Mol Biol LA - en OP - SN - 0167-4412 1573-5028 UR - http://dx.doi.org/10.1007/bf00017920 DB - Crossref KW - AT-RICH SEQUENCES KW - DNA-BINDING PROTEINS KW - FERREDOXIN-I KW - HMG KW - HIGH MOBILITY GROUP PROTEINS ER - TY - JOUR TI - Nucleotide sequence ofCab-215, a Type II gene encoding a photosystem II chlorophylla/b-binding protein inPisum AU - Falconet, Denis AU - White, Michael J. AU - Fristensky, Brian W. AU - Dobres, Michael S. AU - Thompson, William F. T2 - Plant Molecular Biology DA - 1991/7// PY - 1991/7// DO - 10.1007/bf00036815 VL - 17 IS - 1 SP - 135-139 J2 - Plant Mol Biol LA - en OP - SN - 0167-4412 1573-5028 UR - http://dx.doi.org/10.1007/bf00036815 DB - Crossref KW - CAB GENES KW - CHLOROPHYLL A/B-BINDING PROTEIN KW - PISUM-SATIVUM KW - NUCLEOTIDE SEQUENCE ER - TY - JOUR TI - Nucleotide sequence ofCab-8, a new type I gene encoding a chlorophylla/b-binding protein of LHC II inPisum AU - Alexander, Laura AU - Falconet, Denis AU - Fristensky, Brian W. AU - White, Michael J. AU - Watson, John C. AU - Roe, Bruce A. AU - Thompson, William F. T2 - Plant Molecular Biology DA - 1991/9// PY - 1991/9// DO - 10.1007/bf00040649 VL - 17 IS - 3 SP - 523-526 J2 - Plant Mol Biol LA - en OP - SN - 0167-4412 1573-5028 UR - http://dx.doi.org/10.1007/bf00040649 DB - Crossref KW - CAB GENES KW - CHLOROPHYLL-A/B-BINDING PROTEIN KW - PISUM-SATIVUM KW - NUCLEOTIDE SEQUENCE ER - TY - JOUR TI - Kinetic analysis of the interaction of nitric oxide with the nickel and iron-sulfur-containing membrane-bound hydrogenase from Azotobacter vinelandii AU - Hyman, M.R. AU - Arp, D. J. T2 - Biochimica Biophysica Acta DA - 1991/// PY - 1991/// VL - 1076 SP - 167–174 ER - TY - JOUR TI - Factors Limiting Aliphatic Chlorocarbon Degradation by Nitrosomonas europaea: Cometabolic Inactivation of Ammonia Monooxygenase and Substrate Specificity AU - Rasche, M. E. AU - Hyman, M. R. AU - Arp, D. J. T2 - Applied and Environmental Microbiology C2 - PMC183909 DA - 1991/10// PY - 1991/10// VL - 57 IS - 10 SP - 2986-2994 J2 - J. Bacteriol. LA - eng SN - 0099-2240 ST - Factors Limiting Aliphatic Chlorocarbon Degradation by Nitrosomonas europaea DB - PubMed ER - TY - JOUR TI - SHOOT MERISTEM ACTIVITY DURING FLORAL TRANSITION IN GLYCINE-MAX (L) MERR AU - THOMAS, JF AU - KANCHANAPOOM, ML T2 - BOTANICAL GAZETTE AB - The soybean (Glycine max [L.] Merr.) is a quantitative short-day (SD) plant requiring two inductive cycles for floral initiation, which occurs first in the most undifferentiated meristem in an axil of a main stem leaf. Floral initiation at the main stem apex, however, requires additional SD inductive cycles. Under continuous SD the transition to flowering in the main stem apex is completed after 8 SD cycles. Differentiation and organogenesis of the first flower in the terminal raceme is apparent after 10 SD cycles. The changes in apical size and geometry, nuclear DNA, and rate of leaf initiation were followed daily during this 10-d period and compared with apices from plants kept under noninductive long days (LD). At emergence all plants had initiated three trifoliolate leaf primordia and during the vegetative stage of development maintained a plastochron of 2.0 d/leaf. The plastochron was shortened to 1.0 d/leaf in SD plants on day 7, just prior to the end of the transition. Apical size and geometry remained unchanged until after 6 SD cycles when height of the dome decreased and there was less elongation of the rib meristem. Earlier events included significantly lower amounts of nuclear DNA in cells of SD apices after 1 and 3 SD cycles. Later, the amount of nuclear DNA increased in cells of SD apices beginning after 5 SD and peaking after 6 SD before decreasing back to control levels. Shifts in increasing proportions of the population of nuclei from the 4C to 2C condition occurred after 1 SD and 3 SD. As in other species, both of these shifts are apparently essential components for the floral transition at the shoot apex in soybean. The first shift, or "mitotic" stimulus, signals that the process of the floral transition has begun, while the second shift, or "floral" stimulus, is required for completion of the process. DA - 1991/6// PY - 1991/6// DO - 10.1086/337873 VL - 152 IS - 2 SP - 139-147 SN - 0006-8071 ER - TY - JOUR TI - PHYSIOLOGICAL AND MOLECULAR STUDIES OF LIGHT-REGULATED NUCLEAR GENES IN HIGHER-PLANTS AU - THOMPSON, WF AU - WHITE, MJ T2 - ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY AB - INTRODUCTION .. . . . . . . . . ..... . . .. .... .... .. .. .. . . ......... ... . . . . . ....... .. .. . . ....... 424 Photoreceptors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 424 Light Responses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428 D IVERSITY OF RESPONSES... . .. . . . . . . . . . . . . . . . . . . . . ....... . . . ...... 429 Etiolated Seedlings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429 Green Plants . .... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433 TRANSC RIPTIONAL CONTROLS 433 In Vitro Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433 Transgenic Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435 POSTIRANSCRIPTIONAL CONTROLS . . . . . . . .. . . ... . . . . 437 Comparison of Transcription and mRNA Abundance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 438 The Ferredoxin System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439 DA - 1991/// PY - 1991/// DO - 10.1146/annurev.pp.42.060191.002231 VL - 42 SP - 423-466 SN - 1040-2519 KW - GENE EXPRESSION KW - PHOTOBIOLOGY KW - TRANSCRIPTION KW - POSTTRANSCRIPTIONAL CONTROL KW - TRANSLATIONAL CONTROL KW - POSTTRANSLATIONAL CONTROL ER -