Mutant tRNA<Superscript>His</Superscript> Ineffective in Repression and Lacking Two Pseudouridine Modifications

TRANSFER RNA has been implicated in the regulation of a number of amino-acid biosynthetic operons^1–4. Histidyl-tRNA^His has been shown to be involved in regulation of the histidine operon by analysis of six genes (hisO, hisR, hisS, hisT, hisU, hisW), mutation of which causes derepression of the enzymes of the histidine biosynthetic pathway in Salmonella typhimurium^5–7. A class of derepressed mutants (hisR) has only about 55% as much tRNA^His as the wild type⁴ and in the one example sequenced, contains tRNA^HIS with a structure identical to that of the wild type⁸. Studies of mutants of the gene for histidyl-tRNA synthetase (hisS) indicated that the derepressed phenotype was associated with defects in the charging of tRNA^HISin vitro². The amounts of charged and uncharged tRNA^His present in vivo during physiological derepression of the wild type and in the six classes of regulatory mutants, have been determined⁹. This work has shown that repression of the histidine operon is correlated directly with the concentration of charged histidyl-tRNA^Hisin vivo and not with the ratio of charged to uncharged or the absolute amount of uncharged tRNA^His. The derepression observed in mutants, of hisS (the gene for histidyl-tRNA synthetase), hisR (the presumed structural gene for the single species of tRNA^His) and hisU and hisW (genes presumably involved in tRNA modification) may be explained by the lower cellular concentration of charged tRNA^His which these mutants contain.     

<Emphasis Type="Italic">Nonomuraea insulae</Emphasis> sp. nov., isolated from forest soil

Strain H2R21^T, a novel actinobacterium, isolated from a forest soil sample collected from Heybeliada, Istanbul, Turkey, and a polyphasic approach was used for characterisation of the strain. Chemotaxonomic and morphological characterisation of strain H2R21^T indicated that it belongs to the genus Nonomuraea. 16S rRNA gene sequence similarity showed that the strain is closely related to Nonomuraea purpurea 1SM4-01^T (99.1%) and Nonomuraea solani CGMCC 4.7037^T (98.4%). DNA–DNA relatedness values were found to be lower than 70% between the isolate and its phylogenetic neighbours N. purpurea 1SM4-01^T, N. solani CGMCC 4.7037^T and Nonomuraea rhizophila YIM 67092^T. The whole cell hydrolysates of strain H2R21^T were found to contain meso-diaminopimelic acid as the diagnostic diamino acid and glucose, madurose, mannose and ribose as the cell sugars. The polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, dihydroxy-phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, two glycophospholipids and two unidentified lipids. The predominant menaquinones were identified as MK-9(H₄) and MK-9(H₆). The major fatty acids were found to be iso-C_16:0, iso-C_16:0 2OH and C_17:0 10-methyl. On the basis of DNA–DNA relatedness data and some phenotypic characteristics, it is evident that strain H2R21^T can be distinguished from the closely related species in the genus Nonomuraea. Thus, it is concluded that strain H2R21^T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea insulae sp. nov. is proposed. The type strain is H2R21^T (= DSM 102915^T = CGMCC 4.7338^T = KCTC 39769^T).     

<Emphasis Type="Italic">Nibribacter flagellatus</Emphasis> sp. nov., isolated from rhizosphere of <Emphasis Type="Italic">Hibiscus syriacus</Emphasis> and emended description of the genus <Emphasis Type="Italic">Nibribacter</Emphasis>

A Gram-stain negative, aerobic, motile by flagella, rod-shaped strain (THG-T16^T) was isolated from rhizosphere of Hibiscus syriacus. Growth occurred at 10–40 °C (optimum 28–30 °C), at pH 6.0–8.0 (optimum 7.0) and at 0–1.0% NaCl (optimum 0%). Based on 16S rRNA gene sequence analysis, the near phylogenetic neighbours of strain THG-T16^T were identified as Nibribacter koreensis KACC 16450^T (98.6%), Rufibacter roseus KCTC 42217^T (94.7%), Rufibacter immobilis CCTCC AB 2013351^T (94.5%) and Rufibacter tibetensis CCTCC AB 208084^T (94.4%). The DNA G+C content of strain THG-T16^T was determined to be 46.7 mol%. DNA–DNA hybridization values between strain THG-T16^T and N. koreensis KACC 16450^T, R. roseus KCTC 42217^T, R. immobilis CCTCC AB 2013351^T, R.tibetensis CCTCC AB 208084^T were 33.5?±?0.5% (31.7?±?0.7% reciprocal analysis), 28.1?±?0.2% (25.2?±?0.2%), 17.1?±?0.9% (10.2?±?0.6%) and 8.1?±?0.3% (5.2?±?0.1%). The polar lipids were identified as phosphatidylethanolamine, two unidentified aminophospholipids, an unidentified aminolipid and three unidentified lipids. The quinone was identified as MK-7 and the polyamine as sym-homospermidine. The major fatty acids were identified as C_16:1 ω5c, C_17:1 ω6c, iso-C_15:0, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and summed feature 4 (iso-C_17:1 I and/or anteiso-C_17:1 B). On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics, and DNA–DNA hybridization data, strain THG-T16^T represents a novel species of the genus Nibribacter, for which the name Nibribacter flagellatus sp. nov. is proposed. The type strain is THG-T16^T(=?KACC 19188^T?=?CCTCC AB 2016246^T).     

<Emphasis Type="Italic">Phenylobacterium terrae</Emphasis> sp. nov., isolated from a soil sample of Khyber-Pakhtun-Khwa,Pakistan

A Gram-stain negative, aerobic, motile, non-spore-forming and rod-shaped bacterial strain, designated YIM 730227^T, was isolated from a soil sample, collected from Karak district, Khyber-Pakhtun-Khwa, Pakistan. The bacterium was characterized using a polyphasic taxonomic approach. Pairwise comparison of the 16S rRNA gene sequences showed that strain YIM 730227^T is closely related to Phenylobacterium lituiforme FaiI3^T (97.5% sequence similarity), Phenylobacterium muchangponense A8^T (97.4%), Phenylobacterium panacis DCY109^T (97.1%), Phenylobacterium immobile E^T (97.1%) and Phenylobacterium composti 4T-6^T (97.0%), while also sharing 98.0% sequence similarity with Phenylobacterium hankyongense HKS-05^T after NCBI blast, showing it represents a member of the family Caulobacteraceae. The major respiratory quinone was Q-10 and the major fatty acids were C_16:0, summed feature 8 (comprising C_18:1ω7c and/or C_18:1ω6c), C_18:1ω7c 11-methyl and C_17:0. The polar lipids were phosphatidylglycerol, unidentified glycolipids, phospholipid and unidentified lipid. The G?+?C content of the genomic DNA was 68.2 mol%. The DNA–DNA relatedness values of strain YIM 730227^T with P. hankyongense HKS-05^T, P. lituiforme FaiI3^T, P. muchangponense A8^T, P. panacis DCY109^T, P. immobile E^T and P. composti 4T-6^T were 31.3?±?0.6, 26.1?±?0.2, 24.3?±?0.1, 21.8?±?0.9, 19.8?±?0.6 and 18.2?±?1.1%, respectively, values lower than 70%. Besides the morphological and chemotaxonomic characteristics, phylogenetic analyses of 16S rRNA gene sequences and the biochemical characteristics indicated that the strain YIM 730227^T represents a novel member of the genus Phenylobacterium, for which the name Phenylobacterium terrae sp. nov. (type strain YIM 730227^T =?KCTC62324^T?=?CGMCC 1.16326^T) is proposed.     

On the Mechanism of Action of <Emphasis Type="Italic">lac</Emphasis> Repressor

Chen et al. have proved conclusively that lac repressor and RNA polymerase bind independently to wild type lac DNA in vitro. To explain the lacp ^s mutation, which causes competitive binding between repressor and polymerase, they suggest that a new promoter site has been created near the lac operator.     

Effect of Rifampicin on the Development of Tumours induced by Adenovirus in Male Hamsters

INITIAL in vitro studies established that rifampicin, one of a group of rifamycin SV derivatives^1,2, prohibits bacterial growth and phage replication by binding to a polypeptide component of the microbial DNA-dependent RNA polymerase^3–7. The trachoma agent and related psittacosis-lymphogranuloma agents are also inhibited in vitro and in embryonated eggs by this drug⁸. Further studies have shown that rifampicin is active against a number of bacteria in vivo, both after parenteral and oral administration^1,9,10. It also inhibits malaria in mice¹¹ and trachoma in monkeys^12,13 and is of special value in the treatment of human tuberculosis^14–16. The low toxicity of the rifamycins in mammals¹⁷ has been attributed to the observed relative insensitivity of mammalian RNA polymerase to the rifamycins in vitro^3,18.     

<Emphasis Type="Italic">Cellulomonas macrotermitis</Emphasis> sp. nov., a chitinolytic and cellulolytic bacterium isolated from the hindgut of a fungus-growing termite

To investigate the symbiotic roles of the gut microbiota in the fungus-growing termite Macrotermes barneyi, a novel strain with chitinolytic and cellulolytic activity, designated strain an-chi-1^T, was isolated from the hindgut of M. barneyi. Strain an-chi-1^T grows optimally at 28–30 °C, pH 8.0 in PYG medium. On the basis of 16S rRNA gene sequence analysis, this isolate belongs to the genus Cellulomonas with high sequence similarity to Cellulomonas iranensis (99.4%), followed by Cellulomonas flavigena (98.4%), Cellulomonas phragmiteti (97.4%), Cellulomonas oligotrophica (97.2%) and Cellulomonas terrae (97.0%). The DNA–DNA relatedness between an-chi-1^T and the type strains of C. iranensis and C. flavigena DSM20109^T are 35.4% and 23.7%, respectively. The major cellular fatty acids are anteiso-C_15:0 and C_14:0. The polar lipid profile consists of diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylinositol dimannosides and one unidentified phospholipid. The cell-wall sugar is ribose. The peptidoglycan contains glutamic acid, aspartic acid and alanine. The DNA G+C content is 67.3 mol%. Based on its distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, an-chi-1^T represents a novel species of the genus Cellulomonas, for which the name Cellulomonas macrotermitis sp. nov. is proposed. The type strain is an-chi-1^T (= JCM 31923^T = CICC 24195^T).     

Check of Gene Number during the Process of rDNA Magnification

THE multiple sequences of rDNA (DNA complementary to ribosomal RNA) of the Drosophila genome are localized at the bobbed locus, located in the X chromosome, position 66 and in the short arm of the Y chromosome^1,2. Wild bobbed (bb⁺) is that locus which, without a partner, gives rise to a normal phenotype. That locus which in similar conditions is incapable of giving rise to a normal phenotype is called a bobbed mutation (bb) and contains fewer genes for rRNA. The number of genes for rRNA in different individuals can vary considerably. One mechanism for rDNA variation is unequal crossing over³. Another mechanism, described by Tartof⁴, becomes apparent when individual flies, carrying only one bobbed locus, are constructed and only if such a locus is on the X chromosome; that is, if one constructs Xbb⁺/O males (and also Xbb/O males) or Xbb⁺/X_NO- females. Such individuals show a higher rDNA content than expected from the analysis of the same locus in Xbb⁺/Xbb⁺ females or in Xbb⁺/Ybb⁺ males. The increase of rDNA in this case is not inheritable⁴.     

Defective DNA Synthesis in Permeabilized Yeast Mutants

THE simple eukaryote, Saccharomyces cerevisiae, is suitable for combined genetic and biochemical analysis of the cell division cycle. More than forty temperature-sensitive mutants of S. cerevisiae defective in fifteen genes that control various steps of the yeast cell cycle have been detected by screening a collection of mutants with time-lapse photomicroscopy¹. Mutations in two genes, cdc4 and cdc8, result in defective DNA synthesis at the restrictive temperature². The product of cdc8 is apparently required throughout the period of DNA synthesis, because if a strain defective in this gene is shifted to 36° C within the S period, DNA replication ceases. In contrast, the product of cdc4 is apparently required only at the initiation of DNA synthesis because when a strain carrying a defect in this gene is shifted to 36° C, DNA replication already in progress is not impaired. Cells defective in cdc4, however, fail to initiate new rounds of DNA synthesis at the restrictive temperature. Based on these observations the DNA mutants have been tentatively classified as defective in DNA replication (cdc8) and in the initiation of DNA synthesis (cdc4).     

<Emphasis Type="Italic">Limnobacter humi</Emphasis> sp. nov., a thiosulfate-oxidizing,heterotrophic bacterium isolated from humus soil,and emended description of the genus <Emphasis Type="Italic">Limnobacter</Emphasis> Spring <Emphasis Type="Italic">et al.</Emphasis> 2001

Three Gram-negative, strictly aerobic, chemolithoheterotrophic bacterial strains, designated UCM-30, UCM-33, and UCM-39^T, were isolated in South Korea. Based on their 16S rRNA gene sequences, the three isolated strains were found to be similar to Limnobacter thiooxidans CS-K2^T (97.41–97.68%), Limnobacter litoralis KP1-19^T (95.55–95.76%), and various genera belonging to the class Betaproteobacteria (90.34–93.34%). DNA-DNA hybridization showed 79.3–83.9% similarity between the genomic DNA of UCM-39^T, UCM-30, and UCM-33, while the sequence similarity between UCM-39^T and L. thiooxidans KACC 13837T or L. litoralis LMG 24869T was 23.7% and 18.6%, respectively. The DNA G+C content of UCM 39T was 59.7 mol%, the major ubiquinone was Q-8, and the optimal oxidation rate was observed at 10 mM thiosulfate. The major fatty acids (≥ 10%) were summed features 3 (C_16:1 ω7c and/or C_16:1 ω6c) and 8 (C_18:1 ω7c and/or C_18:1 ω6c), and C_16:0. The major polar lipids (diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol) were found in all members of genus Limnobacter. Based on phenotypic, physiological, and phylogenetic analyses, the UCM-39T strain was found to be significantly distinct to represent a novel species affiliated to the genus Limnobacter. We propose to name it Limnobacter humi sp. nov. with the type strain UCM-39^T (=KACC 18574^T =NBRC 111650^T).     

Mutant Ribosomal Protein with Defective RNA Binding Site

THE 30S ribosomal subunits of Escherichia coli contain twenty-one different proteins^1–4, which together with 16S RNA can reassemble in vitro to form functional 30S particles⁵. Five proteins can individually bind to specific sites on the 16S RNA^6–8 and these are S4, S7, S8, S15 and S20 (in the nomenclature recently adopted by several laboratories to report results with the E. coli system⁹). We report here the first identification of a mutation that affects a ribosomal protein-nucleic acid interaction.     

Inhibition of Bacterial DNA Replication by 6-(<Emphasis Type="Italic">p</Emphasis>-Hydroxyphenylazo)-uracil

THE semi-conservative replication of DNA of Gram-positive bacteria is specifically inhibited by 6-(p-hydroxyphenyIazo)-uracil (HPUra; obtained from ICI) in an apparently novel mechanism^1–4. We have attempted to characterize the HPUra-sensitive site in replication using in vitro preparations of drug-sensitive bacteria. In particulate and soluble preparations of sensitive bacteria, however, HPUra at high concentration does not significantly inhibit polymerization of deoxyribonucleotides^2,4. Since these systems may not accurately represent the process of DNA replication as it occurs in vivo, we have examined the effect of HPUra on a more suitable, toluene-treated preparation of Bacillus subtilis described by Matsushita et al.⁵. In this preparation, DNA replication is ATP-dependent, utilizes deoxyribonucleotides to give biologically active DNA, semi-conservatively and sequentially in the proper gene order. HPUra can inhibit DNA replication by this system. We describe here the characteristics of HPUra inhibition and the conditions necessary for it to occur.     

<Emphasis Type="Italic">Streptomyces xiangluensis</Emphasis> sp. nov., a novel actinomycete isolated from soil

A novel actinomycete, designated strain NEAU-LA29^T, was isolated from soil collected from Xianglu Mountain and subjected to a polyphasic taxonomic study. Based on a polyphasic taxonomic approach comprising chemotaxonomic, phylogenetic, morphological and physiological characterisation, the isolate has been affiliated to the genus Streptomyces. 16S rRNA gene sequence analysis showed that the isolate is closely related to Streptomyces vastus JCM4524^T (98.8% identity) and Streptomyces cinereus DSM43033^T (97.9%). However, multilocus sequence analysis based on five other house-keeping genes (atpD, gyrB, rpoB, recA and trpB) and low DNA–DNA relatedness values enabled the strain to be differentiated from these closely related species of the genus Streptomyces. Thus, strain NEAU-LA29^T is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces xiangluensis sp. nov. is proposed. The type strain is NEAU-LA29^T (=?CGMCC 4.7466^T?=?DSM 105786^T).     

<Emphasis Type="Italic">Novosphingobium profundi</Emphasis> sp. nov. isolated from a deep-sea seamount

A marine bacterial strain, F72^T, was isolated from a solitary scleractinian coral, collected in Yap seamounts in the Pacific Ocean. Strain F72^T is a Gram-negative, light-yellow-pigmented, motile, rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F72^T is related to the genus Novosphingobium and has high 16S rRNA gene sequence similarities with the type strains of Novosphingobium pentaromativorans US6-1^T (97.7 %), Novosphingobium panipatense SM16^T (97.6 %), Novosphingobium mathurense SM117^T (97.2 %) and Novosphingobium barchaimii LL02^T (97.1 %). Ubiquinone Q-10 was detected as the dominant quinone. The predominant cellular fatty acids were C_18:1ω7c and C_17:1ω6c. The genomic DNA G+C content of strain F72^T was 63.4 mol %. The polar lipids profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, sphingoglycolipid and one uncharacterized lipid. Strain F72^T shared DNA relatedness of 25 % with N. pentaromativorans JCM 12182^T, 31 % with N. panipatense DSM 22890^T, 21 % with N. mathurense DSM 23374^T and 26 % with N. barchaimii DSM 25411^T. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that the strain F72^T is a representative of a novel species of the genus Novosphingobium, for which we propose the name Novosphingobium profundi sp. nov. (type strain F72^T = KACC 18566^T = CGMCC 1.15390^T).     

<Emphasis Type="Italic">Streptomyces gamaensis</Emphasis> sp. nov., a novel actinomycete with antifungal activity isolated from soil in Gama,Chad

During an investigation exploring potential sources of novel species and natural products, a novel actinomycete with antifungal activity, designated strain NEAU-Gz11^T, was isolated from a soil sample, which was collected from Gama, Chad. The isolate was found to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. 16S rRNA gene sequence similarity studies showed that strain NEAU-Gz11^T belongs to the genus Streptomyces with high sequence similarity to Streptomyces hiroshimensis JCM 4098^T (98.0 %). Similarities to other type strains of the genus Streptomyces were lower than 98.0 %. However, the physiological and biochemical characteristics and low levels of DNA–DNA relatedness could differentiate the isolate genotypically and phenotypically from S. hiroshimensis JCM 4098^T. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces gamaensis sp. nov. is proposed. The type strain is NEAU-Gz11^T (=CGMCC 4.7304^T=DSM 101531^T).     

Poly U Tracts absent from Viral RNA

Polyadenylic acid (poly A) is covalently attached to the RNA molecules in which it occurs^1–4, but its exact location is not definitely established. It was at first thought to exist only at the 3′OH terminus of RNA molecules^5–6 but recently Ryskov et al. claimed to have found it at the 5′ terminus of light nuclear RNA7 and it is possible that it also exists internally.