Genes Encoding the Group I Intron-containing tRNALeu and Subunit L of NADH Dehydrogenase from the Cyanobacterium Synechococcus PCC 6301

A part of the tRNA^Leu (UAA) gene containing a 240-nucleotidegroup I intron was amplified by PCR from cyanobacterium SynechococcusPCC 6301 genomic DNA. The pre-tRNA synthesized from the clonedPCR product was efficiently self-spliced in vitro under physiologicalconditions. The gene encoding the tRNA^Leu (UAA), trnL-UAA, wasisolated from a Synechococcus PCC 6301 genomic library and thenucleotide sequence of a 2,167-bp portion was determined. ThetrnL-UAA consists of a 34-bp 5' exon, a 240-bp group I intronand a 50-bp 3' exon. In addition, three open reading frames(ORF1, ORF2 and ORF3) were found in the 5' and 3' flanking regionsof trnL-UAA. The predicted protein sequence of ORF3, which islocated 74-bp upstream from trnL-UAA on the opposite strand,shows 66.2% amino acid identity to that of the SynechocystisPCC 6803 gene encoding subunit L of NADH dehydrogenase (ndhL).     

Cloning and Sequencing of the Gene Encoding the Soluble Fumarate Reductase from Saccharomyces cerevisiae

A gene of the soluble fumarate reductase (FRDS) that binds FADnon-covalently was cloned by polymerase chain reaction (PCR)using degenerate oligonucleotides designed from partial aminoacid sequences of highly purified enzyme. The nucleotide sequenceof a 0.99-kb amplified product was found to be nearly identicalto a partial sequence of an open reading frame (ORF) previouslyreported (EMBL database accession number S-30830). Accordingto the sequence in the EMBL database, we cloned 1.7-kb fragmentcontaining entire sequence of this ORF by PCR and found thatthis fragment contained a perfect match to the 0.99-kb sequenceamplified with the degenerate primers. From these results, weconcluded that this ORF is the FRDS gene. The amino acid sequencesof the regions involved in the non-covalent binding of FAD andthe active site, which are conserved among the flavoproteinsubunits of membrane-bound fumarate reductase and succinatedehydrogenase, were found in FRDS. However, unlike the membrane-boundenzymes, FRDS did not contain the histidine residue that covalentlybinds the isoalloxazine ring of FAD at or near the correspondingposition. FRDS showed high homology to the product of S. cerevisiaeOSM1 gene which was reported to be required for growth in hypertonicmedia.     

Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research

Based on the genomic sequence data of Escherichia coli K-12strain, we have constructed a complete set of cloned individualgenes encoding Histidine-tagged proteins with or without GFPfused for functional genomic analysis. Each clone encodes aprotein of predicted ORF attached by Histidines and seven spaceramino acids at the N-terminal end, and five spacer amino acidsand GFP at the C-terminal end. SfiI restriction sites are generatedat both the N- and C-terminal boundaries of ORF upon cloning,which enables easy transfer of ORF to other vector systems bycutting with SfiI. Expression of cloned ORF is under the controlof an IPTG-inducible promoter, which is strictly repressed bylacI^q repressor gene product. The set of cloned ORFs describedhere should provide unique resources for systematic functionalgenomic approaches including (i) construction of DNA microarray,(ii) production and purification of proteins, (iii) analysisof protein localization by monitoring GFP fluorescence and (iv)analysis of protein–protein interaction.     

Identification of the chlB Gene and the Gene Product Essential for the Light-Independent Chlorophyll Biosynthesis in the Cyanobacterium Plectonema boryanum

We cloned a 6.0-kb HindIII fragment from the cyanobacteriumPlectonema boryanum using the chloroplast chlB (ORF513) geneof the liverwort (Marchantia polymorpha) as a probe. An openreading frame (ORF508) encoding a polypeptide of 508 amino acidresidues was found within the nucleotide sequence of the 4,437-bpHindIII-EcoRV subfragment. The deduced amino acid sequence ofORF508 shows very high similarity to that encoded by the liverwortchlB gene (72.7%). A mutant, YFB14, in which ORF508 was inactivatedby the insertion of a kanamycin-resistance cartridge, was unableto synthesize chlorophyll, accumulating protochlorophyllidein darkness while synthesizing chlorophyll normally in the light.Thus, the chlB gene is the third gene that is essential forthe light-independent reduction of protochlorophyllide. Theother two genes are chlL and chlN, and the results suggest thatthe light-independent protochlorophyllide reductase consistsof at least three subunits, which are encoded by chlL, chlNand chlB. Using an antiserum prepared against a ChlB-6xHis fusionprotein expressed in Escherichia coli, we detected a proteinwith an apparent molecular weight of 58,000 in the membranefraction of the cyanobacterium. These results indicate thateither the cytoplasmic or thylakoid membranes could be the siteof the light-independent reduction of protochlorophyllide. (Received November 16, 1995; Accepted February 7, 1996)     

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.     

Systematic Sequencing of the 180 Kilobase Region of the Bacillus Subtilis Chromosome Containing the Replication Origin

We have determined a 180 kb contiguous sequence in the replicationorigin region of the Bacillus subtilis chromosome. Open readingframes (ORF) in this region were unambiguously identified fromthe determined sequence, using criteria characteristic for theB. subtilis gene structure, i.e., starting with an ATG, GTGor TTG codon preceded by sequences complementary to the 3' endof the 16S rRNA. Four rRNA gene sets, 7 individual tRNA genesand 1 scRNA gene were identified, occupying 20 kb in total.In the remaining 160 kb region, 158 ORFs were identified, suggestingthat 1 ORF is coded on average by 1 kb of DNA of the B. subtilisgenome. Among the 158 ORFs, the functions of 48 ORFs were assignedand those of 11 ORFs are suggested through significant similaritiesto known proteins present in data banks. However, the functionsof more than half of the ORFs (63%) remain to be determined.     

r{beta}Carotene Hydroxylase Gene from the Cyanobacterium Synechocystis sp. PCC6803

The ORF sll1468 of Synechocystis sp. PCC6803 was identifiedas a gene for rß-carotene hydroxylase by functionalcomplementation in a rß-carotene-producing Escherichiacoll. The gene product of ORF sll11468 added hydroxyl groupsto the rß-ionone rings of rß-carotene (rß,rß-carotene)to form zeaxanthin (rß,rß-carotene-3,3'-diol).This newly identified rß-carotene hydroxylase doesnot show overall amino acid sequence similarity to the knownrß-carotene hydroxylases. However, it showed significantsequence similarity to rß-carotene ketolases of marinebacteria and a green alga. (Received November 29, 1997; Accepted March 6, 1998)     

Identification of a nifDK-Like Gene (ORF467) Involved in the Biosynthesis of Chlorophyll in the Cyanobacterium Plectonema boryanum

The frxC gene, which is found in chloroplast DNA (ctDNA) andin cyanobacteria, encodes a protein that is required for thelight-independent reduction of protochlorophyllide (Pchlide)to chlorophyllide a (Chlide). A DNA fragment downstream of frxCin the filamentous cyanobacterium Plectonema boryanum was clonedand analyzed. Sequencing of the DNA fragment revealed an openreading frame (ORF) that encoded a protein of 467 amino acidresidues (designated ORF467), which showed extensive homologyto the proteins encoded by genes on ctDNAs (ORF465 in liverwort,gidA in pine and chlN in Chlamydomonas reinhardtii) and to ORF469protein of the cyanobacterium Synechocystis sp. strain PCC 6803.We isolated a targeted mutant YFM6D-3 in which ORF467 was inactivatedby the insertion of a kanamycin-resistance gene into the codingregion. YFM6D-3 exhibited a phenotype similar to that of YFC1004,an frxC-disrupted mutant, which did not synthesize chlorophyll(Chl) and accumulated Pchlide, a precursor to Chl, in the dark.These phenotypic characteristics of YFM6D-3 indicate that thelight-independent reduction of Pchlide requires not only theFrxC protein but also the ORF467 protein. The amino acid sequencesof the homologues of ORF467 exhibit low but significant similarityto those of the and ß subunits of nitrogenase MoFe-protein,suggesting a phylogenetic relationship between the light-independentPchlide reductase and nitrogenase, as is observed between theFrxC protein and the Fe-protein of nitrogenase. ¹Institute for Protein Research, Osaka University, Suita, Osaka,565 Japan     

Cloning and analysis of the MNN4 gene required for phosphorylation of N-linked oligosaccharides in Saccharomyces cerevisiae

The Saccharomyces cerevisiae MNN4 gene, which is involved inmannosylphosphate transfer from GDP-mannose to N-linked oligosaccharide,has been cloned from a lambda phage containing a yeast chromosomeXI DNA fragment The MNN4 ORF encodes a protein of 1178 aminoacids. The deduced amino acid sequence shows a topology of typeII membrane proteins and has a unique repeated sequence of lysineand glutamic acid at the C-terminus. Disruption and overexpressionof MNN4 led to a decrease and increase, respectively, of themannosylphosphate content in cell wall mannans prepared fromboth mnn4 and wild type strains. A dramatic decrease of mannosylphosphateoccurs in     

Synergistic Function of rolB, rolC, ORF13 and ORF14 of TL-DNA of Agrobacterium rhizogenes in Hairy Root Induction in Nicotiana tabacum

Comparison of the frequency of rooting in the tobacco leaf segmentsinoculated with Agrobacterium tumefaciens harboring variouscombinations of rolB, rolC, ORF13 and ORF14 of TL-DNA of Riplasmid (pRiHRI) revealed that the genes differ in their functionto stimulate adventitious root induction. A single gene rolBinduced roots, while rolC, ORF13 and ORF14 independently promotedthe root induction by the rolB gene. The effects of these geneson the rolB-mediated rooting were in the order of ORF13>rolCORF14. Present address: Laboratory of Phylogenetic Botany, Departmentof Biology, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba,263-8522 Japan. ² Present address: Department of Chemical and Biological Sciences,Faculty of Science, Japan Women's University, 2-8-1 Mejirodai,Bunkyo-ku, Tokyo, 112-8681 Japan.     

Cloning of the Gene Encoding a Protochlorophyllide Reductase: the Physiological Significance of the Co-Existence of Light-Dependent and -Independent Protochlorophyllide Reduction Systems in the Cyanobacterium Plectonema boryanum

Cyanobacteria have two protochlorophyllide (Pchlide) reductasescatalyzing the conversion of Pchlide to chloro-phyllide, a keystep in the biosynthetic pathway of chlorophylls (Chls); a light-dependent(LPOR) and a light-independent (DPOR) reductase. We found anopen reading frame (ORF322) in a 2,131-bp EcoRI fragment fromthe genomic DNA of the cyanobacterium Plectonema boryanum. Becausethe deduced amino acid sequence showed a high similarity tothose of various plant LPORs and the LPOR activity was detectedin the soluble fraction of Esche-richia coli cells over-expressingthe ORF322 protein, ORF322 was defined as the por gene encodingLPOR in P. boryanum. A por-disrupted mutant, YFP12, was isolatedby targeted mutagenesiss to investigate the physiological importanceof LPOR. YFP12 grew as well as wild type under low light conditions(10-25 µE m^–2 S^–1). However, its growth wassignificantly retarded as a result of a significant decreasein its Chl content under higher light conditions (85-130 µEm^–2 s^–1). Furthermore, YFP12 stopped growing andsuffered from photobleaching under the highest light intensity(170 µE m^–2 s^–1). In contrast, a chlL-dis-rupted(DPOR-less) mutant YFC2 grew as well as wild type irrespectiveof light intensity. From these phenotypic characteristics, weconcluded that, although both LPOR and DPOR contribute to Chlsynthesis in the cells growing in the light, the extent of thecontribution by LPOR increases with increasing light intensity;without it, the cells are unable to grow under light intensitiesof more than 130 µ Em^–2s-^–. (Received September 26, 1997; Accepted November 21, 1997)     

东亚飞蝗中肠几丁质酶基因的克隆、序列分析及组织定位

通过RACE方法,克隆了东亚飞蝗Locusta migratoria manilensis (Meyen)几丁质酶基因 (LmChi)cDNA全序列 (GenBank 登录号：EF092841)。获得的cDNA全长1 604 bp,其中可读框1 452 bp, 编码483个氨基酸。推测其氨基酸序列与18家族昆虫几丁质酶有较高的相似性。与其他几丁质酶一样,东亚飞蝗几丁质酶序列也包含一个信号肽、一个几丁质酶活性位点、一个碳端丝氨酸富集区和一个几丁质结合域。半定量RT-PCR研究表明,LmChi基因只在东亚飞蝗不同发育阶段的中肠组织中表达,而在东亚飞蝗体壁、前肠和后肠均没有发现LmChi基因的转录。     

Isolation of a Gene for a Metallothionein-Like Protein from Soybean

Using a synthetic oligonucleotide that corresponded to the consensusnucleotide sequence of the N-terminal region of mammalian metallothioneinas probe, we isolated a cDNA clone from a soybean library. Theclone had an ORF that encode a protein of 79 amino acids whichshowed significant homology to both N- and C-terminal regionsof mammalian and Neurospora crassa metallothioneins ⁴Present address: Department of Biosciences, Teikyo University,Toyosatodai, Utsunomiya, Tochigi, 320 Japan (Received March 13, 1991; Accepted June 17, 1991)     

Nucleotide Sequence and Features of the Bacillus licheniformis gnt Operon

Bacillus licheniformis was able to utilize gluconate as thesole carbon source as efficiently as Bacillus subtilis did.Southern analysis indicated that B. licheniformis likely possessesonly one gnt determinant. The nucleotide sequence (6278 bp)of the B. licheniformis DNA containing the gnt operon was determined,revealing the five complete open reading frames (ORF; genes).The putative product of the first gene, oug, did not show anysignificant homology to known proteins, but those of the secondto fifth genes exhibited striking homology to the gntRKPZ genesof B. subtilis, respectively, indicating that they are the correspondinggnt genes of B. licheniformis. Not only is the organizationof the gnt genes of these two Bacilli highly conserved, butso are the cis regulatory elements of their gnt operon. Sequenceanalysis of the upstream regions of these two gnt operons impliedthat a chromosome rearrangement in B. subtilis might have occurredimmediately upstream of the gnt operon during evolution, causingit to diverge from a common ancestor into B. licheniformis andB. subtilis.     

家蝇细胞凋亡起始酶Caspase-1基因的克隆及在不同虫态的表达

为了研究Caspases家族在昆虫发育变态中的作用,通过RT-PCR扩增并结合RACE技术,克隆得到家蝇Musca domestica Caspase-1基因1条,命名为Mdom-Caspase-1（GenBank中cDNA序列号为EU854472, 氨基酸序列号为ACF71490）。该基因全长1 295 bp,阅读框序列870 bp,共编码289个氨基酸,理论分子量32.83 kDa,等电点8.67。 Mdom-Caspase-1蛋白有5个保守的半胱氨酸位点QACQG, 具有Caspase的典型特征; 整个分子呈现亲水性, 有8个区域共89个氨基酸为亲酯性, 蛋白质二级结构主要由11个α螺旋区、7个β-折叠区、17个β-转角区组成。昆虫间Caspase-1分子具有明显的保守性, Mdom-Caspase-1与黑腹果蝇Drosophila melanogaster、埃及伊蚊Aedes aegypti和致倦库蚊Culex quinquefasciatus的Caspase-1氨基酸序列相似性为65%~77%。RT-PCR半定量分析结果表明, Mdom-Caspase-1基因在家蝇各个虫态中均有表达, 但在卵期、3龄幼虫、预蛹、蛹和羽化5 d的雌虫中的表达量明显高于其他虫态。这些结果提示Caspase-1可能与昆虫发育变态关系密切, 为进一步研究昆虫Caspase-1功能、设计Caspase-1抑制剂提供了分子基础。     

小菜蛾烟碱型乙酰胆碱受体α亚基cDNA的克隆、序列分析与不同发育阶段表达分析

烟碱型乙酰胆碱受体(nAChR)介导昆虫中枢神经系统中胆碱能突触兴奋性神经递质的快速传递,也是新烟碱类杀虫剂和多杀菌素的作用靶标。本研究利用RT-PCR和RACE技术,克隆了小菜蛾Plutella xylostella nAChR α亚基的一个新基因(Pxα8)的全长cDNA(GenBank登录号为EU914853)。Pxα8的cDNA序列全长1 744 bp,开放阅读框为1 602 bp,编码534个氨基酸,具有nAChR α亚基的典型特征,与其他昆虫nAChR α8亚基具有77%～96%的相似性,与果蝇nAChR β2亚基具有76%的相似性。Pxα8的开放阅读框存在单核苷酸多态性位点,导致多个位点氨基酸的替换。雌性4龄幼虫的多态性位点多于雄性4龄幼虫,而且雌、雄4龄幼虫的多态性位点均不相同。半定量RT-PCR研究结果表明,Pxα8 mRNA在成虫期表达量高于蛹期和4龄幼虫期。本研究结果为进一步研究小菜蛾nAChR 亚基的多样性和对多杀菌素的靶标抗性机制提供重要基础。     

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)