The Nature of the Nucleotide at the 5' Side of the tRNA Su9 Anticodon Affects UGA Suppression in Escherichia coli

In Escherichia coli a UGA codon can be efficiently suppressedby a suppressor tRNA^Trp called Su9. Here, we show that the levelof UGA suppression is determined by the nature of the nucleotideat the 5' side of the anticodon of the suppressor (position33). UGA suppression occurs when a pyrimidine residue is locatedin position 33 of the tRNA, and suppression is more efficientwith a U than with a C in this position. On the other hand,when a purine residue is located at this position UGA suppressionis extremely low. These results show that in the case of tRNASu9, the UGA codon context effect does not require base pairingbetween the nucleotide at the 3' side of the codon and the 5'side of the anticodon.     

Isolation and Characterization of cDNA Clones with Enhanced Expression in Tobacco Plants Expressing the Rice Homeobox Gene, OSH1

We have used subtractive hybridization to isolate cDNA cloneswhose expression were up-regulated in transgenic tobacco ectopicallyexpressing the rice homeobox gene, OSH1. Thirty-nine distinctcDNA clones, which we term HRGs (Homeobox Regulated Genes),were identified. Some of them were specifically expressed intransformants, indicating that their expression was possiblyregulated by transgene. (Received January 9, 1997; Accepted March 8, 1997)     

Intergenic transcripts containing a novel human cytochrome P450 2C exon 1 spliced to sequences from the CYP2C9 gene

The cytochrome P450 2C (CYP2C) gene locus was found to includea novel exon 1 sequence with high similarity to the canonicalexon 1 of CYP2C18. Rapid amplification of cDNA ends (RACE) andPCR amplifications of human liver cDNA revealed the presenceof several intergenic species containing the CYP2C18 exon 1–likesequence spliced to different combinations of exonic and intronicsequences from the CYP2C9 gene. One splice variant was foundto have an open reading frame starting at the canonical translationinitiation codon of the CYP2C18 exon 1–like sequence.Another variant consisted of the nine typical CYP2C9 exons splicedafter the CYP2C18 exon 1–like sequence through a segmentof CYP2C9 5' flanking sequences. Moreover, analysis of bacterialartificial chromosome (BAC) clones revealed that the CYP2C18exon 1–like sequence was located in the intergenic regionbetween the CYP2C19 and CYP2C9 genes. The finding that a solitaryexon is spliced with sequences from a neighboring gene may beinterpreted as representing a general evolutionary mechanismaimed at using the full expression potential of a cell's genomicinformational content.     

Isolation of the ALG6 locus of Saccharomyces cerevisiae required for glucosylation in the N-linked glycosylation pathway

N-Linked protein glycosylation in most eukaryotic cells initiateswith the transfer of the oligosaccharide Glc₃Man₉GlcNAc₂ fromthe lipid carrier dolichyl pyrophosphate to selected asparagineresidues. In the yeast Saccharomyces cerevisiae, alg mutationswhich affect the assembly of the lipid-linked oligosaccharideat the membrane of the endoplasmic reticulum result in the accumulationof lipid-linked oligosaccharide intermediates and a hypoglycosylationof proteins. Exploiting the synthetic growth defect of alg mutationsin combination with mutations affecting oligosaccharyl transferaseactivity (Stagljar et al., 1994), we have isolated the ALG6locus. alg6 mutants accumulate lipid-linked Man₉GlcNAc₂, suggestingthat this locus encodes an endoplasmic glucosyltransferase.Alg6p has sequence similarity to Alg8p, a protein required forglucosylation of Glc₁Man⁹GlcNAc². Saccharomyces cerevisiae endoplasmic reticulum glycosyltransferase dolichol     

Isolation of Genes for Low-Temperature-Induced Proteins in Rice by a Simple Subtractive Method

We have isolated cDNAs that correspond to three distinct low-temperature-inducedmRNAs from rice cells using an effective, simple subtractionmethod. The corresponding genes were designated lip (gene encodinglow-temperature-induced protein) –5,–9 and –19.The expression of these genes was slightly stimulated lip5 andlip19) or unaffected (lip9) by abscisic acid, unlike the expressionof the rabl6A-D genes which are readily induced by either abscisicacid or high osmotic stress. Time-course analysis revealed thatwhile the lip5 gene was induced 3 h after temperature down-shift,and the lip9 and lipl9 genes were induced 6 h after such a shift. ¹Present address: Division of Molecular Medicine, Clinical ResearchCentre, Northwick Park Hospital, Harrow, Middlesex HA1 3UJ,U.K. (Received June 29, 1991; Accepted October 7, 1991)     

Distribution of Calanus species in Kongsfjorden, a glacial fjord in Svalbard

The distribution of Calanus species was investigated in Kongsfjordenin summer of 1996 and 1997. In both years Calanus finmarchicusand Calanus glacialis dominated, although the boreal C. finmarchicuswas more abundant than the Arctic C. glacialis in 1997. Thiscoincided with a 2°C higher water temperature at 50 m in1997, indicating stronger influence of Atlantic origin waterthat year. Advected Calanus finmarchicus occurred in deep andsubsurface layers of the outer fjord in 1996 (200 ind. m^-3,mainly CIII). A less abundant local population aggregated insurface layers of the inner fjord (100 ind. m^-3). Similarly,advected C. finmarchicus occurred in subsurface layers in 1997(446 ind. m^-3, mainly CIII and CIV) and a local population insurface layers (183 ind. m^-3, mainly CI). Calanus glacialisin 1996 aggregated as CII and CIII in the deep layers of theouter fjord (272 ind. m^-3), whereas CIII–CV were abundant(216 ind. m^-3) in cold surface waters of the inner fjord. In1997 C. glacialis (mostly CIII–CV) was more abundant inthe outer than in the inner part of the fjord (40 and 192 ind.m^-3, respectively). Within Kongsfjorden, Calanus finmarchicusneeds one year to complete its life cycle, whereas Calanus glacialisneeds two. Calanus hyperboreus seems to be an expatriate inthe fjord system.     

MROS1, a Male Stamen-Specific Gene in the Dioecious Campion Silene latifolia Is Expressed in Mature Pollen

The MROS1 gene, one of the genes that are expressed specificallyin male reproductive organs of a dioecious campion Silene latifolia,was predicted to encode only 36 amino acids but have an intron.In situ hybridization revealed that MROS1 mRNA was localizedin mature pollen grains. (Received January 30, 1997; Accepted February 24, 1997)     

云斑车蝗线粒体基因组全序列测定与分析

采用长距 PCR 扩增及保守引物步移法并结合克隆测序测定并注释了云斑车蝗 Gastrimargus marmoratus （Thunberg）的线粒体基因组全序列。结果表明：云斑车蝗线粒体基因组全序列为15 904 bp（GenBank登录号为EU527334）,A+T含量略高于非洲飞蝗Locusta migratoria,为76.04%,包括13个蛋白质编码基因,22个tRNA 基因,2个rRNA基因和一段1 057 bp的A+T富集区。蛋白质基因的起始密码子中,除COⅠ和ND5为TTG以外,均为昆虫典型的起始密码子ATN。ND5基因使用了不完全终止密码子T,其余基因均为典型的TAA或TAG。预测了22个tRNA基因的二级结构,发现tRNA^Ser（AGN）缺少DHU臂, tRNA^Ser（UGY）的反密码子环上有9个碱基。预测了云斑车蝗12S和16S rRNA二级结构,分别包括3个结构域30个茎环和6个结构域44个茎环。A+T富集区含有3个串联重复序列。     

Nucleotide Sequences of Genes Coding for Photosynthetic Reaction Centers and Light-Harvesting Proteins of Acidiphilium rubrum and Related Aerobic Acidophilic Bacteria

The nucleotide sequences of the puf operons of the Zn-bacteriochlorophylla(Zn-BChl a)-containing photosynthetic aerobic bacteria, Acidiphiliumrubrum and Acidiphilium angustum, were determined. The nucleotidesequences of the pufL and –M of Acidiphilium cryptum,Acidiphilium multivorum, and Acidiphilium organovorum were alsodetermined. The puf operons of A. rubrum and A. angustum containedpufB, –A,–L, –M, and –C as seen in otherpurple bacteria with an unknown gene directly upstream of pufB.Comparing the deduced amino acid sequences of the puf genesof the Acidiphilium species with those of other purple bacteriashowed that His L168, which is highly conserved in other bacteria,is replaced by a glu-tamic acid in the Acidiphilium species.The three-dimensional structures of the reaction centers ofBlastochloris (Rhodopseudomonas) viridis and Rhodobacter sphaeroidessuggest that this residue locates closely to a special pairof bacteriochlorophylls and may be involved in the stabilizationand function of "Zn-BChl a". The relative content of chargedamino acid residues in the L and M subunit is a little lowerin A. rubrum (10%of total) than in B. viridis (12%), and thetendency is more pronounced in the cyto-chrome subunit: 12.5%in A. rubrum and 18.8% in B. viridis. (Received July 24, 1997; Accepted September 9, 1997)     

Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to Escherichia coli Genome

We present an expression measure of a gene, devised to predictthe level of gene expression from relative codon bias (RCB).There are a number of measures currently in use that quantifycodon usage in genes. Based on the hypothesis that gene expressivityand codon composition is strongly correlated, RCB has been definedto provide an intuitively meaningful measure of an extent ofthe codon preference in a gene. We outline a simple approachto assess the strength of RCB (RCBS) in genes as a guide totheir likely expression levels and illustrate this with an analysisof Escherichia coli (E. coli) genome. Our efforts to quantitativelypredict gene expression levels in E. coli met with a high levelof success. Surprisingly, we observe a strong correlation betweenRCBS and protein length indicating natural selection in favourof the shorter genes to be expressed at higher level. The agreementof our result with high protein abundances, microarray dataand radioactive data demonstrates that the genomic expressionprofile available in our method can be applied in a meaningfulway to the study of cell physiology and also for more detailedstudies of particular genes of interest.     

果蝇Drosophila saltans种亚组(双翅目:果蝇科)系统发育关系:形态学能否解决分子冲突?(英文)

正确的系统发生重建对于理解进化事件至关重要。尽管分子系统学对于解决此类问题取得了极大的成功,由于一些诸如密码子使用偏性等的内在约束,来源于DNA的信息可能仍然存在着局限。因为发生在祖先的替代性转换,果蝇Drosophila saltans 5个种亚组由不同基因构建的分子系统树之间存在着冲突（在以往发表的分子系统学研究中,这些种组的每一个种亚组至少有一个代表）。本文用40个形态学特征重新分析了这些种组。不同于以前发表的大多数假说,本研究支序分类学的结果表明,果蝇sturtevanti种亚组是一个较早的分支, 而剩下的4个亚组形成一个支持度较高的类群;后者又可以再分为两个姐妹群：一个包含cordata 和elliptica 亚组,另一个包含parasaltans和saltans亚组。本研究结果修正了果蝇saltans种组的分子进化（密码子使用偏性）,并强调形态学对于系统发生重建和理解分子进化现象的重要作用。     

Identification of phytochrome B amino acid residues mutated in three new phyB mutants of Arabidopsis thaliana

The growth and development of plants is regulated by light viathe action of photoreceptors which are responsive to the red/far-red,blue and UV regions of the spectrum. Phytochrome B (the apoproteinof which is encoded by the PHYB gene) is one of the red/far-redabsorbing photoreceptors active in this process. In this paper,the isolation and characterization of three new EMS-inducedmutations of Arabidopsis which confer phytochrome B deficiencyare described. Complementation analysis showed that these mutations(phyB-101, phyB-102 and phyB-104) were allelic with PHYB. DNAsequence analysis showed that all three mutants contain nucleotidesubstitutions in the PHYB-101 gene sequence. phyB-101 carriesa nucleotide substitution within the second exon of the PHYBgene. This G-to-A substitution is a missense mutation that convertsa glutamate residue at position 812 of the phytochrome B apoproteinto a lysine residue. phyB-102, another missense mutant, carriesa C-to-T substitution which converts a serine residue at position349 of the phytochrome B apoprotein to a phenylalanine residue.phyB-104 carries a premature stop codon as a result of a G-to-Amutation 1190 bp down-stream of the ATG start codon of the PHYBsequence. The missense mutations in phyB-101 and phyB-102 causesignificant alterations in the predicted second ary structureof their respective mutant polypeptides, and identify aminoacid residues playing crucial roles in phytochrome B function,assembly or stability. Key words: Arabidopsis thaliana, phytochromet, phyB mutants, missense mutations     

Interannual variability in a predator-prey interaction: climate, chaetognaths and copepods in the southeastern Bering Sea

The interaction of the chaetognath Sagitta elegans with thecopepod community of the southeast Bering Sea middle shelf wasexamined in relation to environmental conditions during 1995–1999.Predation impact was estimated for 2 years, 1995 and 1997, usinggut content analysis, experimentally derived digestion time(DT) and abundances of chaetognaths and prey. Pseudocalanusconcentrations correlated with water temperature and Calanusmarshallae with sea ice extent. Sagitta elegans were less abundantbut individuals were larger in 1995, when C. marshallae predominated,compared to 1997, when Pseudocalanus and Acartia were the primaryprey. Predation by S. elegans removed <1% standing stockday^–1 of Pseudocalanus or C. marshallae in 1995 and 1.7to 2.3% of Pseudocalanus in 1997. The percent of the copepodcommunity biomass required by chaetognaths was estimated tobe <1% in 1995 compared with 8–12% in 1997. Calanusmarshallae may be more vulnerable than Pseudocalanus to cumulativepredation effects because of its reproductive strategy. Theeffect of chaetognath predation on the copepod community dependson which copepod species is predominant and its susceptibilityto cumulative predation effects, as well as on daily predationimpact, both of which varied between years with different climaticconditions.     

Adaptive evolution of sperm bindin tracks egg incompatibility in neotropical sea urchins of the genus Echinometra

Bindin is a gamete recognition protein known to control species-specificsperm-egg adhesion and membrane fusion in sea urchins. Previousanalyses have shown that diversifying selection on bindin aminoacid sequence is found when gametically incompatible speciesare compared, but not when species are compatible. The presentstudy analyzes bindin polymorphism and divergence in the threeclosely related species of Echinometra in Central America: E.lucunter and E. viridis from the Caribbean, and E. vanbruntifrom the eastern Pacific. The eggs of E. lucunter have evolveda strong block to fertilization by sperm of its neotropicalcongeners, whereas those of the other two species have not.As in the Indo-West Pacific (IWP) Echinometra, the neotropicalspecies show high intraspecific bindin polymorphism in the samegene regions as in the IWP species. Maximum likelihood analysisshows that many of the polymorphic codon sites are under mildpositive selection. Of the fixed amino acid replacements, mosthave accumulated along the bindin lineage of E. lucunter. Weanalyzed the data with maximum likelihood models of variationin positive selection across lineages and codon sites, and withmodels that consider sites and lineages simultaneously. Ourresults show that positive selection is concentrated along theE. lucunter bindin lineage, and that codon sites with aminoacid replacements fixed in this species show by far the highestsignal of positive selection. Lineage-specific positive selectionparalleling egg incompatibility provides support that adaptiveevolution of sperm proteins acts to maintain recognition ofbindin by changing egg receptors. Because both egg incompatibilityand bindin divergence are greater between allopatric speciesthan between sympatric species, the hypothesis of selectionagainst hybridization (reinforcement) cannot explain why adaptiveevolution has been confined to a single lineage in the AmericanEchinometra. Instead, processes acting to varying degrees withinspecies (e.g., sperm competition, sexual selection, and sexualconflict) are more promising explanations for lineage-specificpositive selection on bindin.     

The Expression of an Abscisic Acid-Responsive Glycine-Rich Protein Coincides with the Level of Seed Dormancy in Fagus sylvatica

By differential screening of a cDNA library constructed frompoly (A⁺) RNA of ABA-treated seeds of Fagus sylvatica L., wehave isolated an ABA-responsive clone that is present in dormantseeds and under conditions that maintain dormancy, but it tendsto disappear under conditions breaking seed dormancy. A searchof the sequence data bases showed that the clone codes for aGlycine-Rich Protein and has sequence similarity to RNA-bindingproteins. The clone, which exibits the characteristics of lea-genes,is up-regulated by ABA and down-regulated by GA3. Paclobutrazolabolishes the effect of GA³, which is restored upon additionof GA3. The possible relationship of this Glycine-Rich Proteinto seed dormancy in F. sylvatica is discussed. (Received May 23, 1997; Accepted September 22, 1997)     

dad-1, A Putative Programmed Cell Death Suppressor Gene in Rice

The human dad-1 cDNA homolog was isolated from rice plants.The amino acid sequence of the predicted protein product iswell conserved in both animals and plants. This rice dad-1 homologcan rescue the temperature-sensitive dad-1 mutants of hamstercells from apoptotic death, suggesting that the rice dad-1 homologalso functions as a suppressor for programmed cell death. (Received December 24, 1997; Accepted January 27, 1997)     

Regulation of Stoichiometry between PSI and PSII in Response to Light Regime for Photosynthesis Observed with Synechocystis PCC 6714: Relationship between Redox State of Cyt b6-f Complex and Regulation of PSI Formation

The effect of the Cyt b₆-f redox state on the PSI formationwas examined with the cyanophyte Synechocystis PCC 6714 by usinga Q-cycle inhibitor, HQNO (2-n-heptyl-4-hydroxyquinoline N-oxide).HQNO inhibited the rapid reduction of flash-oxidized Cyt f,the reaction correlating with the stimulation of PSI formation,on one hand, and accumulated reduced Cyt b₆, on the other, indicatingthat the electron flow in the Q-cycle correlates with regulationof PSI synthesis. HQNO also inhibited the stimulation of PSIformation under PSII light, resulting in a low PSI/PSII ratioeven under PSII light, while the PSI formation under PSI lightwas not suppressed by HQNO. Simultaneous inhibition of Cyt b₆oxidation through the Q-cycle and the stimulated PSI formationby HQNO suggests that an HQNO-sensitive Cyt b₆ oxidation isinvolved in the mechanism of monitoring the state of electrontransport system for regulation of PSI formation. (Received March 3, 1993; Accepted August 9, 1993)