Sequence Analysis of a 25-kb Segment in the 17{degrees}-19{degrees} Region of the Bacillus subtilis Chromosome Containing ada Locus

As a part of the Bacillus subtilis genome sequencing project,we have determined a 25-kb sequence covering the 17°–19°region. This region contains 26 complete open reading frames(ORFs) including the alkA and adaA/B operon, which encode genesfor adaptive response to DNA alkylation. A homology search forthe newly identified 21 ORFs revealed that 4 of them exhibita significant similarity to known proteins, e.g., methicillin-resistantStaphylococcus aureus (MRSA) protein homolog, proteins involvedin chloramphenicol resistance, glucosamine synthase and an ABCtransporter protein. The remaining 17 ORFs did not show anysignificant sequence similarities to known gene products inthe database.     

Cloning and Sequencing of a 27.8-kb Nucleotide Sequence of the 79{degrees}-81{degrees}. Region of the Bacillus subtilis Genome Containing the sspE Locus

The nucleotide sequence of a 27830-bp DNA segment in the 79°–81°.region of the Bacillus subtilis genome has been determined.This region contains 29 complete ORFs including the sspE gene,which encodes a small acid-soluble spore protein gamma and locateson the one side terminal of our assigned region. A homologysearch for the products deduced from the 29 ORFs revealed thatnine of them exhibit significant similarity to known proteins,e.g. proteins involved in an iron uptake system, a multidrugresistance protein, a chloramphenicol resistance protein, epoxidehydrolase, adenine glycosylase, and a glucose-1-dehydrogenasehomolog.     

An 8 kb Nucleotide Sequence at the 3' Flanking Region of the sspC Gene (184{degrees}) on the Bacillus subtilis 168 Chromosome Containing an Intein and an Intron

As part of the Bacillus subtilis genome sequencing project,we determined the complete nucleotide sequence of an 8000-bpfragment downstream of the sspC gene (184°) of the B. subtilis168 chromosome. The sequence analysis shows that the sspC geneis located inside of the SPß region, which differsfrom the current genetic map of B. subtilis 168. This regioncontains 12 putative ORFs (yojQ through yojZ and sspC). A homologysearch for the deduced products of the ORFs shows signi.cantsimilarities to enzymes involved in deoxyribonucleotide metabolism:ribonucleotide reductase (Nrd) E, NrdF, thioredoxinand dUTPase.Interestingly, this DNA fragment includes two split genes, yojPcontaining conserved motifs of an intein and yojQ and yojS withan 808-bp intervening sequence for a putative intron structure.In addition, the yojR gene includes a putative new DNA replicationterminator.     

Sequence Analysis of the groESL-cotA Region of the Bacillus subtilis Genome, Containing the Restriction/Modification System Genes

We have determined a 35-kb sequence of the groESL-gutR-cotA(45°–52°) region of the Bacillus subtilis genome.In addition to the groESL, gutRB and cotA genes reported previously,we have newly identified 24 ORFs including gutA and fruC genes,encoding glucitol permease and fructokinase, respectively. Theinherent restriction/modification system genes, hsdMR and hsdMM,were mapped between groESL and gutRB, and we have identifiedtwo open reading frames (ORFs) encoding 5-methylcytosine formingDNA methyl transferase and an operon probably encoding a restrictionenzyme complex. The unusual genome structure of few ORFs andlower GC content around the restriction/modification genes stronglysuggests that the region originated from a bacteriophage integratedduring evolution.     

Nucleotide Sequence and Genetic Analysis of the Region Essential for Functional Expression of the Gene for Ferredoxin I, fdxN, in Rhodobacter capsulatus: Sharing of One Upstream Activator Sequence in Opposite Directions by Two Operons Related to Nitrogen Fixation

Nucleotide sequencing of the region upstream of two ferredoxingenes, fdxC and fdxN, of Rhodobacter capsulatus revealed theexistence of one open reading frame (ORF), ORFU1,in the sameorientation as these genes and two other ORFs, ORFU2 and ORFU3,in the opposite orientation. Two potential –24/–12promoters were found in front of ORFU1 and ORFU2, respectively,and there was a putative upstream activator sequence (UAS) orNifA-binding site between them. The ORFs corresponded to noknown nif genes. However, analysis of their putative productsshowed that the product of ORFU1 (M_r 47,912) and that of ORFU3(M_r 19,090) flavodoxin-like domain and a 2[4Fe-4S] ferredoxin-likedomain, respectively, and that the product of ORFU2 (M_r 20,424)was a hydrophobic protein with six potential membrane-spanningportions. Results of interposon mutagenesis and complementationexperiments indicated ORFU2 but not ORFU1 is essential for nitrogenfixation and that additional gene(s) essential nitrogen fixationmust be present in the unsequenced region adjacent to ORFU3.Translational fusion analysis involving lacZYA and fdxN or ORFU3provided evidence that the putative UAS responsible for regulationof both ORFUl-fdxC-fdxNand ORFU2-ORFU3 operons in opposite orientations,and that the control of the latter is stricter than that ofthe former. (Received August 19, 1992; Accepted November 16, 1992)     

Construction of a Contiguous 874-kb Sequence of the Escherichia coli-K12 Genome Corresponding to 50.0-68.8 min on the Linkage Map and Analysis of Its Sequence Features

The contiguous 874.423 base pair sequence corresponding to the50.0–68.8 min region on the genetic map of the Escherichiacoli K-12 (W3110) was constructed by the determination of DNAsequences in the 50.0–57.9 min region (360 kb) and twolarge (100 kb in all) and five short gaps in the 57.9–68.8min region whose sequences had been registered in the DNA databases.We analyzed its sequence features and found that this regioncontained at least 894 potential open reading frames (ORFs),of which 346 (38.7%) were previously reported, 158 (17.7%) werehomologous to other known genes, 232 (26.0%) were identicalor similar to hypothetical genes registered in databases, andthe remaining 158 (17.7%) showed no significant similarity toany other genes. A homology search of the ORFs also identifiedseveral new gene clusters. Those include two clusters of fimbrialgenes, a gene cluster of three genes encoding homologues ofthe human long chain fatty acid degradation enzyme complex inthe mitochondrial membrane, a cluster of at least nine genesinvolved in the utilization of ethanolamine, a cluster of thesecondary set of 11 hyc genes participating in the formate hydrogenlyasereaction and a cluster of five genes coding for the homologuesof degradation enzymes for aromatic hydrocarbons in Pseudomonasputida. We also noted a variety of novel genes, including twoORFs, which were homologous to the putative genes encoding xanthinedehydrogenase in the fly and a protein responsible for axonalguidance and outgrowth of the rat, mouse and nematode. An isoleucinetRNA gene, designated ileY , was also newly identified at 60.0min.     

Control of heat-shock response of young gametophytes of the sensitive fern is at the translational level

Young gametophytes of the sensitive fern, Onoclea sensibilis,respond to heat-shock by synthesizing in excess certain proteinsthat are made at normal growth temperature. Enhanced proteinsynthesis occurred during a 2 h heat-shock at a range of temperaturesbetween 38 °C and 50 °C. Although a temperature of 50°C proved lethal, a 5 min pulse at 50 °C resulted inenhanced synthesis of heat-shock proteins which continued forseveral hours at 25 °C. After heat-shock at 50 °C for10 or 15 min, the gametophytes temporarily lost their capacityfor protein synthesis but normal protein synthesis was resumedwithin 24 h of heat-shock. A heat-shock at 38 °C precedingone at 50 °C did not have any protecting effect on the gametophytes.In vitro translation of poly(A)+ RNA isolated from heat-shockedgametophytes yielded several proteins including heat-shock proteins.The results suggest that, rather than activating genes encodingnew messages for the synthesis of stress proteins, heat-shockof gametophytes of O. sensibilis triggers a controlling systemwhich enhances the translation of certain messages that aresynthesized at normal growth temperature. Key words: Onoclea sensibilis, heat-shock response, protein synthesis, sensitive fern, in vitro translation     

Sequencing of three lambda clones from the genome of alkaliphilic Bacillus sp. strain C-125

The nucleotide sequences of three independent fragments (designated no. 3, 4, and 9; each 15–20 kb in size) of the genome of alkaliphilic Bacillus sp. C-125 cloned in a λ phage vector have been determined. Thirteen putative open reading frames (ORFs) were identified in sequenced fragment no. 3 and 11 ORFs were identified in no. 4. Twenty ORFs were also identified in fragment no. 9. All putative ORFs were analyzed in comparison with the BSORF database and non-redundant protein databases. The functions of 5 ORFs in fragment no. 3 and 3 ORFs in fragment no. 4 were suggested by their significant similarities to known proteins in the database. Among the 20 ORFs in fragment no. 9, the functions of 11 ORFs were similarly suggested. Most of the annotated ORFs in the DNA fragments of the genome of alkaliphilic Bacillus sp. C-125 were conserved in the Bacillus subtilis genome. The organization of ORFs in the genome of strain C-125 was found to differ from the order of genes in the chromosome of B. subtilis, although some gene clusters (ydh, yqi, yer, and yts) were conserved as operon units the same as in B. subtilis. Received: April 17, 1998 / Accepted: June 23, 1998     

Sequence Analysis of the 36-kb Region Between gntZ and trnY Genes of Bacillus Subtilis Genome*

Within the framework of an international Bacillus subtilis genomesequencing project, we have determined a 36-kb sequence coveringthe region between the gntZ and trnY genes. In addition to fivegenes sequenced and characterized previously, 27 putative proteincoding sequences (open reading frame; ORF) were identified.A homology search for the newly identified ORFs revealed thatsix of them had similarities to known proteins. It is notablethat new ORFs belonging to response-regulator aspartate phosphatase(Rap) and its regulator (Phr) families, and response regulatorand sensory kinase families of two-component signal transductionsystems have been identified. Furthermore, we found that some180-bp non-coding sequence, that might be an remnant of an ancientIS element, is preserved in at least five loci of the B. subtilisgenome.     

Size-fractionated mesozooplankton biomass, metabolism and grazing along a 50{degrees}N-30{degrees}S transect of the Atlantic Ocean

Size-fractionated mesozooplankton grazing and metabolism wereinvestigated along the wide latitudinal range (50°N–30°S)covered during the Atlantic Meridional Transect (AMT) 11 cruise.Five different oceanic provinces were traversed in this cruise:North Atlantic Drift (NADR), North Atlantic Subtropical Gyral(NAST), Canary Coastal (CNRY), Eastern Tropical Atlantic (ETRA),and South Atlantic Gyral (SATL). CNRY and ETRA were affectedby the upwelling Mauritanian and equatorial respectively andprimary production in these provinces was higher than in theoligotrophic subtropical gyres (NAST and SATL). Both mesozooplanktonand phytoplankton biomass were highest around the equator. Theamount of chlorophyll a ingested daily by copepods was noticeablyhigher in mesotrophic than in oligotrophic provinces as shownby the spatial distribution of gut content values and the highabundances of copepods recorded at the equator. Grazing impactalong the transect ranged from 0.2 to 5.6% of the phytoplanktonstanding stock and from 1.6 to 14.5% of primary production.If only phytoplankton >2 µm are considered, the rangesare 1.0–19.4% (stock) and 3.4–44.7% (primary production).Grazing impact upon both phytoplankton biomass and primary productionfollowed a spatial distribution similar to that of chlorophylla ingestion, with higher values in upwelling zones than in thegyres. Weight-specific rates of respiration and NH₄⁺ and PO₄^3–excretion showed large variability both along the transect andwithin provinces, but did not differ between provinces. Therefore,zooplankton assemblages inhabiting the different provinces visitedin the AMT 11 seem to be adapted to the prevailing thermal conditions.Given the substantial proportion of nitrogen and phosphorusthat are supplied to primary producers through the excretoryactivity of mesozooplankton (the percentage of nitrogen andphosphorus requirements of phytoplankton accounted for by mesozooplanktonexcretion was >30% in all the provinces) it follows thatthey may play a crucial role as nutrient regenerators, especiallyin the oligotrophic gyres where regenerated production dominates.     

Complete Genome Sequence of an Aerobic Hyper-thermophilic Crenarchaeon, Aeropyrum pernix K1

The complete sequence of the genome of an aerobic hyper-thermophiliccrenarchaeon, Aeropyrum pernix K1, which optimally grows at95°C, has been determined by the whole genome shotgun methodwith some modifications. The entire length of the genome was1,669,695 bp. The authenticity of the entire sequence was supportedby restriction analysis of long PCR products, which were directlyamplified from the genomic DNA. As the potential protein-codingregions, a total of 2,694 open reading frames (ORFs) were assigned.By similarity search against public databases, 633 (23.5%) ofthe ORFs were related to genes with putative function and 523(19.4%) to the sequences registered but with unknown function.All the genes in the TCA cycle except for that of alpha-ketoglutaratedehydrogenase were included, and instead of the alpha-ketoglutaratedehydrogenase gene, the genes coding for the two subunits of2-oxoacid:ferredoxin oxidoreductase were identified. The remaining1,538 ORFs (57.1%) did not show any significant similarity tothe sequences in the databases. Sequence comparison among theassigned ORFs suggested that a considerable member of ORFs weregenerated by sequence duplication. The RNA genes identifiedwere a single 16S–23S rRNA operon, two 5S rRNA genes and47 tRNA genes including 14 genes with intron structures. Allthe assigned ORFs and RNA coding regions occupied 89.12% ofthe whole genome. The data presented in this paper are availableon the internet homepage (http://www.mild.nite.go.jp).     

A Comparative Study of the Influence of Salt Type and Concentration on 14CO2 Fixation in Potato Slices at 25{degrees} C and 0{degrees} C

Dark fixation of ¹⁴CO₂ was followed in potato disks under varyingsalt treatments at 0° C and 25° C. It is shown thatthe specific activity of the ¹⁴CO₂ supplied is heavily dilutedby endogenously produced CO₂ and that the apparently greaterfixation of ¹⁴CO₂, at 0° C as compared with that at 25 °C is due to the lower respiration rate at 0° C, with consequentlyless dilution of the ¹⁴CO₂. supplied. At 25° C organic acidformation in response to different salt treatments fulfils thecommon expectation, ¹⁴CO₂ fixation increasing in the presenceof K₂SO₄ and decreasing in CaCl₂ relative to that in KCl. Therole of organic acids in maintaining ionic balance within thecell at 25° C is thereby indicated but at 0° C organicacid adjustments did not follow the normal pattern. At 25°C but not at o° C increasing external concentration of KCIresulted in an increased level of ¹⁴CO₂ fixation.     

Translocation at 0{degrees} C in Helianthus annuus

Potassium uptake by Helianthus annuus plants growing in waterculture was found to be closely dependent upon the translocationof sugar to the roots. This relationship was used to determinethe effect of cooling on the rate of translocation. A Q₁₀ ofapproximately 3 over the range 0–25° C was obtainedbut tracer experiments showed that translocation was not stoppedat 0° C. A complete recovery in translocation rate appeared to occurin some experiments after prolonged cooling. It is concludedthat this can only be satisfactorily explained on the assumptionthat carbohydrates move in the sieve tubes by mass flow. Thedriving force of such a mass flow is considered to be locatedin each sieve element.     

Development of Ethylene Biosynthesis in Pear Fruits at --1 {degrees}C

Knee, M. 1987. Development of ethylene biosynthesis in pearfruits at — 1 °C.—J. exp. Bot. 38: 1724–1733. The regulation of ethylene synthesis in pear fruits was investigated.During storage for 60 d at — 1 °C the rate of ethylenesynthesis increased 100-fold but the concentration of 1-aminocyclopropane-l-carboxylicacid (ACC) increased only 2-fold and ACC synthase activity waslow. On transfer to 15 °C after storage at — 1 °Cethylene synthesis increased 10-fold within 10 h but ACC synthaseactivity only increased rapidly after 24 h; the decline in ACClevels during the first 16 h at 15 °C was insufficient tosustain ethylene synthesis. Ethylene synthesis was further investigatedusing discs cut from the mid cortex of pear fruits. Synthesiswas inhibited by aminoethoxyvinylglycine (AVG) and amino-oxyaceticacid at all stages of ripening. The rate of synthesis and ACCsynthase activity increased rapidly after slicing of pears heldat — 1 °C but more slowly in discs cut from pearsimmediately after harvest. Cycloheximide (CHI) inhibited theseincreases and reversed increases resulting from pre-incubationof discs. A combination of CHI and AVG abolished the capacityof discs to synthesize ACC and ethylene production was curtailed.Cordycepin and actinomycin-D were less effective as inhibitorsof the development of ethylene synthesis and ACC synthase activitythan as inhibitors of incorporation of 5-[³H] uridine into totalRNA or poly A rich RNA. The ability of discs to develop ethylenesynthesis and ACC synthase activity in the presence and absenceof cordycepin increased concurrently during storage of wholefruits at — 1 °C. This suggested that mRNA for ACCsynthase was formed at — 1 °C. Key words: 1-Aminocyclopropane-l-carboxylic acid, ethylene, fruit ripening, Pyrus communis L. (fruit ripening)     

Heat Shock Proteins of Cyanobacterium Anacystis nidulans

Cells of Anacystis nidulans grown at 30°C were incubatedwith ¹⁴C-Chlorella protein hydrolysate at the elevated temperatures(30–55°C) and the effect of heat shock treatment onprotein synthesis was studied. Incubation temperatures higherthan 45°C caused a significant decrease in the incorporationof amino acids into proteins. Further, the heat shock treatmentinduced significant changes in the fluorographic profile ofthe newly synthesized proteins. (Received October 25, 1985; Accepted December 4, 1985)     

Microzooplankton grazing in a coastal embayment off Concepcion, Chile, (~36{degrees} S) during non-upwelling conditions

The impact of grazing by natural assemblages of microzooplanktonwas estimated in an upwelling area (Concepción, Chile)during the non-upwelling season in 2003 and 2004. Seawater dilutionexperiments using chlorophyll a (Chl a) as a tracer were usedto estimate daily rates of phytoplankton growth and microzooplanktongrazing. Initial Chl a concentrations ranged from 0.4 to 1.4mg Chl a m^–3 and phytoplankton prey biomass and abundancewere numerically dominated by components <20 µm. Phytoplanktongrowth and microzooplankton grazing rates were 0.19–0.25day^–1 and 0.26–0.52 day ^–1, respectively.These results suggest that microzooplankton exert a significantremoval of primary production (>100%) during the non-upwellingperiod.     

A novel {beta}-galactosidase gene isolated from the bacterium Xanthomonas manihotis exhibits strong homology to several eukaryotic {beta}-galactosidases

The gene encoding a ß-galactosidase from Xanthomonasmanihotis was cloned into Escherichia coli. The gene resideson a 2.4 kb DNA fragment which was isolated from a partial Sau3Alibrary in the cloning vector pUC19 using 5-bromo-4-chloro-3-indolyl-ß-D-galactopyranoside(X-gal) as the selection. The enzyme produced by the clone hasa specificity for ß1-3->ß1-4-linked galactose.The nucleotide sequence of the gene was determined. The deducedprotein sequence contained 597 amino acids yielding a monomericmolecular mass of 66 kDa. The cloned ß-galactosidaseshowed no similarity to any known prokaryotic ß-galactosidase.However, extensive similarity was observed with eukaryotic ß-galactosidasesfrom animals, plants and fungi. The strongest similarity waswith the ß-galactosidases found hi the human and mouselysosomes (42 and 41% identity, respectively). Alignment ofthe X.manihotis and eukaryotic ß-galactosidase sequencesrevealed seven highly conserved domains common to each protein.Additionally, Domain 1 in X.manihotis showed similarity to regionswithin catalytic domains from seven xylanases and cellulasesbelonging to family 10 of glucosyl hydrolases. A region spanningDomain 2 showed similarity to the catalytic domain of endo ß1-3glucanases from tobacco and barley. cellulase ß-galactosidase G_M$$$gangliosidosis Morquio B syndrome Xanthomonas     

Relationship between biomass and enzymatic activity of a bloom-forming dinoflagellate (Dinophyceae) in southern Chile (41{degrees} S): a field approach

In a coastal area of southern Chile (41° S), the major ammoniumassimilating enzyme glutamine synthetase (GS) was detected ina green dinoflagellate bloom during April 2003. High chlorophylla concentrations (1000 µg L^–1) attributable to Gymnodiniumcf. chlorophorum in surface waters were associated with highand very low nitrate reductase activities. Coincident with thebloom, dissolved inorganic nitrogen concentrations were nearthe detection limit (NO₃^– + NH₄⁺ <0.5 µM). SinceGS correlates with the use of ammonium as an external nitrogensource, we suggest that GS activity seems to be a good indicatorof ammonium utilization in a period dominated by a single dinoflagellatespecies.