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.     

A 460-kb DNA Sequence of the Escherichia coli K-12 Genome Corresponding to the 40.1-50.0 min Region on the Linkage Map

The 465,813 base pair sequence corresponding to the 40.1–50.0min region on the genetic map of Escherichia coli K-12 (W3110)was determined. Analysis of the sequence revealed that thisregion contained at least 466 potential open reading frames,of which 187 (40%) were previously reported, 105 (23%) werehomologous to other known genes, 103 (22%) were identical orsimilar to hypothetical genes registered in databases, and theremaining 71 (15%) did not show a significant similarity toany other gene. At the 45.2–46.0 min region, we founda very large cluster of about 30 genes, whose functions areinvolved in the biosynthesis of polysaccharides as the componentsof outer membranes. In addition, we identified anew asn-tRNAgene, designated asnW, between the asnT and asnU genes and anew lysogenic phage attachment site as the cis-element.     

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.     

Sequence Analysis of the Bacillus subtilis 168 Chromosome Region between the sspC and odhA Loci (184{degrees}-180{degrees})

The nucleotide sequence of 45,389 bp in the 184°-;180°region of the Bacillus subtilis chromosome, containing the cgecluster, which is controlled by the sporulation regulatory proteinGerE, was determined. Fifty-four putative ORFs with putativeribosome-binding sites were recognized. Seven of them correspondto previously characterized genes: cgeB, cgeA, cgeC, cgeD, cgeE,ctpA, and odhA. The deduced products of 25 ORFs were found todisplay significant similarities to proteins in the data banks.We have identified genes involved in detoxification, cell walls,and in the metabolism of biotins, purines, fatty acids, carbohydratesand amino acids. The remaining 22 ORFs showed no similarityto known proteins. Both an attachment site of the SPßprophage and 2 new putative DNA replication terminators wereidentified in this region.     

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.     

Cell Cycle Timing of Replication of the Nuclear Gene Encoding Chloroplastic NADP-Specific Glutamate Dehydrogenase Isoenzymes in Chlorella sorokiniana

In synchronized Chlorella sorokiniana cells, the NH₄⁺ inducibleNADP-specific glutamate dehydrogenase enzyme (NADP-GDH) accumulatedin a linear manner throughout the first cell cycle. Early inthe following second cell cycle, an increase in its rate ofaccumulation occurred that was proportional to the increasein total cellular DNA in the previous cell cycle. In synchronizedbacterial cells, increases in rate of linear accumulation ofinducible enzymes coincide with the time of replication of theirstructural genes. To determine whether the rate change in NADPGDHaccumulation resulted from a delay in replication of its nuclearstructural gene (gdhN) in fully induced C. sorokiniana cells,the cell cycle timing of replication of this gene was comparedto that of another nuclear gene, nitrate reductase (nia), andof a chloroplast gene, ribulose bisphosphate carboxylase large-subunit(rbcL), in synchronized cells cultured in NH₄⁺ or NO₃^–(uninduced) medium. The gdhN and nia genes replicated withinthe period of nDNA synthesis and rbcL within the period of ctDNAsynthesis in cells growing in either nitrogen source. Therefore,the delayed rate change in enzyme accumulation results froma process that regulates expression of the gdhN gene after itsreplication. (Received July 16, 1994; Accepted November 28, 1994)     

Novel Immune-type Receptor Genes and the Origins of Adaptive and Innate Immune Recognition

The prototypic forms of teleost novel immune-type receptors(NITRs) consist of a variable (V) region, a unique V-like C2(V/C2) domain, a transmembrane region and a cytoplasmic tailcontaining immunoreceptor tyrosine-based inhibition motifs (ITIMs).NITRs encode diversified V regions in large multigene familiesbut do not undergo somatic rearrangement. Studies in four differentbony fish model systems have identified a number of differentorganizational forms of NITRs. Specifically, NITR genes encodeN-terminal ectodomains of the V-type but otherwise vary in the:total number of extracellular immunoglobulin domains, numberand location of joining (J) region-like motifs, presence oftransmembrane regions, presence of charged residues within transmembraneregions, presence of cytoplasmic tails, and/or distributionof ITIM(s) within the cytoplasmic tails. V region-containingNITRs constitute a far more complex family than recognized originallyand currently include individual members that potentially functionthrough inhibitory as well as activating mechanisms. The genomicorganization of the NITR gene cluster as well as the structuraldiversity and overall architecture of the NITR proteins is reminiscentof genes encoded at the mammalian leukocyte receptor cluster(LRC); however, there presently is no functional evidence tosupport an orthologous relationship between NITR and LRC geneproducts. Comparisons of the predicted structures of the NITRshave identified several short regions of sequence identity anda novel cloning strategy has been devised that selects for secretoryand transmembrane proteins that encode these short motifs. Usingthis approach, related genes termed immune-type receptors (ITRs)have been identified in cartilaginous fish. Taken together,these studies indicate that leukocyte regulatory receptors,including those that mediate natural killer function, mighthave emerged early in vertebrate evolution and that the NITR/ITRgenes represent a new and potentially highly significant linkbetween innate and adaptive immune responses.     

Molecular diversity of bacterial production of the climate-changing gas, dimethyl sulphide, a molecule that impinges on local and global symbioses

This paper describes the ddd genes that are involved in theproduction of the gas dimethyl sulphide from the substrate dimethylsulphoniopropionate(DMSP), an abundant molecule that is a stress protectant inmany marine algae and a few genera of angiosperms. What is knownof the arrangement of the ddd genes in different bacteria thatcan undertake this reaction is reviewed here, stressing thefact that these genes are probably subject to horizontal genetransfer and that the same functions (e.g. DMSP transport) maybe accomplished by very different mechanisms. A surprising numberof DMS-emitting bacteria are associated with the roots of higherplants, these including strains of Rhizobium and some rhizospherebacteria in the genus Burkholderia. One newly identified strainthat is predicted to make DMS is B. phymatum which is a highlyunusual β-proteobacterium that forms N₂-fixing noduleson some tropical legumes, in this case, the tree Machaeriumlunatum, which inhabits mangroves. The importance of DMSP catabolismand DMS production is discussed, not only in terms of nutritionalacquisition by the bacteria but also in a speculative scheme(the ‘messy eater’ model) in which the bacteriamay make DMS as an info-chemical to attract other organisms,including invertebrates and other plankton. Key words: Acyl CoA transferase, Burkholderia, CLAW hypothesis, dimethyl sulphide, dimethylsulphoniopropionate, Marinomonas, nitrogen fixation, Rhizobium, rhizosphere, root nodules, Spartina Received 30 May 2007; Revised 27 September 2007 Accepted 1 October 2007     

Expression of Vernalization Genes in Near-lsogenic Wheat Lines: Duration of Vernalization Period

Vernalization periods ranging from 0 to 11 weeks at 4 °Cwere used to study the reproductive development of four near-isogeniclines of wheat (Triticum aestivum L. em. Thell). From the resultsfor days to anthesis two types of gene action were identified,a threshold (all-or-nothing) response (vrn3 and/or vrn4) anda cumulative (graded) response (vrn1). The action of anothergene (vrn2) intensified these two responses. Based on the actionof genes, a model relating days to anthesis to genotype wasderived. Final leaf number and days to anthesis were shown tobe closely related after adjusting for differences due to theduration of vernalization treatment. No relationship betweendays to anthesis and spikelet number was observed. This studyemphasises the need to understand vernalization at the levelof the gene in terms of responses and interactions. Such knowledgeshould enable the plant breeder to predict and more preciselycontrol reproductive development. Triticum aestivum L., wheat, vernalization, gene action, isogenic lines     

Influence of temperature on growth, reproduction and longevity of Moina salina Daday, 1888 (Cladocera, Moinidae)

This paper presents the results of a study of the effects oftemperature on the growth, reproduction and longevity of thecladoceran Moina salina, a species of potential use as livefood in marine aquaculture. The growth rate of M.salina increasedwith increasing temperature. Some parameters of development,such as length at death and the number of adult instars, werealso positively related to temperature. Other parameters (durationof juvenile and adult instars) decreased with increasing temperature,while the number of juvenile instars was unaffected. An increasein temperature resulted in a reduction in age at maturity anda decrease in the number of days between broods. The numberof young per female, the number of broods per female, the numberof youngper day of reproductive life, and the number of youngper brood, increased up to a temperature of 25°C. At 15and 20°C. substantial degeneration of eggs and/or embryosoccurred. Likewise, temperature affected the type of reproductioncarried out by sexual females. Temperature and longevity wereinversely correlated. It was concluded that temperature actsas a very important factor regulating the life cycle of M.salina.Temperature >30°C may correspond to sublethal levels,while a temperature of 15°C is considered to impose stress.The range 20–25°C is optimal for the development andreproduction of this species.     

A 718-kb DNA Sequence of the Escherichia coli K-12 Genome Corresponding to the 12.7-28.0 min Region on the Linkage Map

The 718,122 base pair (bp) sequence of the Escherichia coliK-12 genome corresponding to the region from 12.7 to 28.0 minuteson the genetic map is described. This region contains at least682 potential open reading frames, of which 278 (41%) have beenpreviously identified, 147 (22%) were homologous to other knowngenes, 138 (20%) are identical or similar to the hypotheticalgenes registered in databases, and the remaining 119 (17%) didnot show a significant similarity to any other gene. In thisregion, we assigned a cluster of cit genes encoding multienzymecitrate lyase, two clusters of fimbrial genes and a set of lysogenicphage genes encoding integrase, excisionase and repressor inthe e14 genetic element. In addition, a new valine tRNA gene,designated valZ, and a family of long directly repeated sequences,LDR-A, -B and -C, were found.     

Predation of cockles (Cerastoderma edule) by the whelk (Buccinum undatum) under laboratory conditions

The feeding rate and behaviour of whelks (Buccinum undatum)offered cockles (Cerastoderma edule) in laboratory experimentswere examined. When presented with cockles in a range of sizes(10–40 mm), 14 B. undatum (34.6–88.3 mm),held individually in aquaria, consumed a wide size range ofcockles. Small whelks (<40 mm) consumed cockles (<23 mm),whereas large whelks, (>60 mm) ate a greater numberof larger cockles (>30 mm) and a wider size range ofcockles (12–40 mm) than smaller whelks. The majority(90%) of the shells of the predated cockles were undamaged andthe few (<10%) that were damaged showed only slight abrasionsto the anterior and posterior shell margin. Filmed observationsof B. undatum feeding on C. edule showed a method of attackthat has not previously been reported and involved the use ofthe whelk's foot to asphyxiate the cockle or to pull the shellvalves apart. No filmed evidence was found for the previouslyreported shell ‘wedging’ technique for prising openthe closed shell valves of C. edule, although 10% of the shellsof consumed cockles in feeding experiments had damaged shellmargins. (Received 4 April 2007; accepted 30 June 2007)