作用于cip-cel mRNA的核糖核酸内切酶的鉴定

【目的】本研究以革兰氏阳性细菌解纤维素梭菌(Ruminiclostridium cellulolyticum)为研究对象,筛选作用于纤维小体编码基因簇cip-cel mRNA的核糖核酸内切酶。【方法】通过对预测的4个假定编码核糖核酸内切酶基因进行基因敲除、体内过表达、体外过表达和活性分析等方法,分析它们对cip-cel mRNA剪切位点的剪切能力。【结果】敲除rnc和rnj基因,对cip-cel mRNA剪切没有任何影响;体内过表达RNase时能够加速cip-cel mRNA的降解,而过表达RNase G时,则结果与野生型对照菌株无异;RNase G基因rng和RNase Y基因rny的体外活性鉴定分析,发现RNase G对体外转录的包含cip-cel mRNA剪切位点的RNA没有作用,而RNase Y能够对其进行剪切和降解。【结论】RNase Y是能够作用于cip-cel mRNA的核酸内切酶。该研究结果对理解革兰氏阳性细菌核糖核酸内切酶的作用机制,及其在转录后水平的调控基因差异表达等方面具有重大意义。     

The xylA promoter of Bacillus megaterium mediates constitutive gene expression in Escherichia coli

In the present study, we demonstrate that the Escherichia coli–Bacillus megaterium shuttle vector pHIS1522 can be used as a versatile expression vector. Recombinant genes under the control of the xylA promoter are constitutively expressed at a high level in E. coli strains, whereas their expression is strongly induced by the addition of xylose in B. megaterium. The utilization of D ‐xylose is known to be dependent on the xylAB genes in a number of bacteria. For B. megaterium a XylA‐based expression system was established that allows tightly regulated and highly efficient heterologous gene expression. The open reading frame (ORF) of the fluorescent protein turboRFP was cloned under the control of the xylA promoter of B. megaterium in the shuttle vector pHIS1522. Unexpectedly, tRFP expression was not only observed in B. megaterium, but also in E. coli. Based on fluorescence measurements and Western blot analysis, expression was comparable or slightly higher compared with the commonly used pET vectors. Therefore, pHIS1522 can be used as a versatile expression vector in both, B. megaterium and E. coli.     

Molecular characterization of phytoplasmas in lilies with fasciation in the Czech Republic

Lilium spp. with symptoms of severe fasciation were observed in Southern and central Bohemia during the period 1999-2003. Nucleic acids extracted from symptomatic and asymptomatic plants were used in nested-PCR assays with primers amplifying 16S-23S rRNA sequences specific for phytoplasmas. The subsequent nested-PCR with phytoplasma group-specific primers followed by RFLP analyses and the 16S ribosomal gene sequencing, allowed classification of the detected phytoplasmas in the aster yellows group, subgroups 16SrI-B and 16SrI-C alone, and in mixed infection. Samples infected by 16SrI-C phytoplasmas showed different overlapping RFLP profiles after TruI digestion of R16F2/R2 amplicons. Two of these amplicons were sequenced, one of them directly and the other after cloning; sequence analyses and blast alignment confirmed the presence of two different overlapping patterns in samples studied. The sequences obtained were closely related, respectively, to operon A and operon B ribosomal sequences of the clover phyllody phytoplasma. Direct PCR followed by RFLP analyses of the tuf gene with two restriction enzymes showed no differences from reference strain of subgroup 16SrI-C. Infection with aster yellows phytoplasmas of 16SrI-B subgroup in asymptomatic lilies cv. Sunray was also detected.     

Crystal structure of atypical cytoplasmic ABC-ATPase SufC from Thermus thermophilus HB8

SufC, a cytoplasmic ABC-ATPase, is one of the most conserved Suf proteins. SufC forms a stable complex with SufB and SufD, and the SufBCD complex interacts with other Suf proteins in the Fe-S cluster assembly. We have determined the crystal structure of SufC from Thermus thermophilus HB8 in nucleotide-free and ADP-Mg-bound states at 1.7A and 1.9A resolution, respectively. The overall architecture of the SufC structure is similar to other ABC ATPases structures, but there are several specific motifs in SufC. Three residues following the end of the Walker B motif form a novel 3(10) helix which is not observed in other ABC ATPases. Due to the novel 3(10) helix, a conserved glutamate residue involved in ATP hydrolysis is flipped out. Although this unusual conformation is unfavorable for ATP hydrolysis, salt-bridges formed by conserved residues and a strong hydrogen-bonding network around the novel 3(10) helix suggest that the novel 3(10) helix of SufC is a rigid conserved motif. Compared to other ABC-ATPase structures, a significant displacement occurs at a linker region between the ABC alpha/beta domain and the alpha-helical domain. The linker conformation is stabilized by a hydrophobic interaction between conserved residues around the Q loop. The molecular surfaces of SufC and the C-terminal helices of SufD (PDB code: 1VH4) suggest that the unusual linker conformation conserved among SufC proteins is probably suitable for interacting with SufB and SufD.     

Xylem transport and shoot accumulation of lumichrome, a newly recognized rhizobial signal, alters root respiration, stomatal conductance, leaf transpiration and photosynthetic rates in legumes and cereals

* Root respiration, stomatal conductance, leaf transpiration and photosynthetic rates were measured in phytotron and field-grown plants following the application of 5 or 10 nM lumichrome, 10 nM ABA (abscisic acid) and 10 ml of 0.2 OD600 infective rhizobial cells. * Providing soybean and cowpea roots with their respective homologous rhizobia and/or purified lumichrome increased the concentration of this molecule in xylem sap and leaf extracts. Relative to control, rhizobial inoculation and lumichrome application significantly increased root respiration in maize, decreased it in lupin, but had no effect on the other test species. * Applying either lumichrome (10 nM), infective rhizobial cells or ABA to roots of plants for 44 h in growth chambers altered leaf stomatal conductance and transpiration in cowpea, lupin, soybean, Bambara groundnut and maize, but not in pea or sorghum. Where stomatal conductance was increased by lumichrome application or rhizobial inoculation, it resulted in increased leaf transpiration relative to control plants. Treating roots of field plants of cowpea with this metabolite up to 63 d after planting showed decreased stomatal conductance, which affected CO2 intake and reduction by Rubisco. * The effect of rhizobial inoculation closely mirrored that of lumichrome application to roots, indicating that rhizobial effects on these physiological activities were most likely due to lumichrome released into the rhizosphere.     

Contribution of dppA to urease activity in Helicobacter pylori 26695

BACKGROUND: The gastric pathogen Helicobacter pylori produces urease in amounts up to 10% of its cell protein. This enzyme, which catalyzes the hydrolysis of urea to ammonia and carbon dioxide, protects the bacterium from gastric acid. Urease, a nickel metalloenzyme, requires active uptake of nickel ions from the environment to maintain its activity. NixA is a nickel transport protein that resides in the cytoplasmic membrane. Mutation of nixA significantly reduces but does not abolish urease activity, strongly suggesting the presence of a second transporter. We postulated that the dipeptide permease (dpp) genes that are homologous to the nik operon of Escherichia coli could be a second nickel transporter. The predicted Dpp polypeptides DppA, DppC, and DppD of H. pylori share approximately 40%, 53%, and 56% amino acid sequence identity with their respective E. coli homologs. METHODS: A mutation in dppA, constructed by insertional inactivation with a chloramphenicol resistance cassette, was introduced by allelic exchange into H. pylori strain 26695. RESULTS: When compared to the parental strain, urease activity was not decreased in a dppA mutant. CONCLUSIONS: DppA does not contribute to the synthesis of catalytically active urease in H. pylori 26695 and is likely not a nickel importer in H. pylori.     

Isolation and characterization of phenanthrene-degrading <Emphasis Type="Italic">Sphingomonas paucimobilis</Emphasis> strain ZX4

Phenanthrene-degrading bacterium strain ZX4 was isolated from an oil-contaminated soil, and identified as Sphingomonas paucimobilis based on 16S rDNA sequence, cellular fatty acid composition, mol% G + C and Biolog-GN tests. Besides phenanthrene, strain ZX4 could also utilize naphthalene, fluorene and other aromatic compounds. The growth on salicylic acid and catechol showed that the strain degraded phenanthrene via salicylate pathway, while the assay of catechol 2, 3-dioxygenase revealed catechol could be metabolized through meta-cleavage pathway. Three genes, including two of meta-cleavage operon genes and one of GST encoding gene were obtained. The order of genes arrangement was similar to S-type meta-pathway operons. The phylogenetic trees based on 16S rDNA sequence and meta-pathway gene both revealed that strain ZX4 is clustered with strains from genus Sphingomonas.     

Esrom, an ortholog of PAM (protein associated with c-myc), regulates pteridine synthesis in the zebrafish

Zebrafish esrom mutants have an unusual combination of phenotypes: in addition to a defect in the projection of retinal axons, they have reduced yellow pigmentation. Here, we investigate the pigment phenotype and, from this, provide evidence for an unexpected defect in retinal neurons. Esrom is not required for the differentiation of neural crest precursors into pigment cells, nor is it essential for cell migration, pigment granule biogenesis, or translocation. Instead, loss of yellow color is caused by a deficiency of sepiapterin, a yellow pteridine. The level of several other pteridines is also affected in mutants. Importantly, the cofactor tetrahydrobiopterin (BH4) is drastically reduced in esrom mutants. Mutant retinal neurons also appear deficient in this pteridine. BH4-synthesizing enzymes are active in mutants, indicating a defect in the regulation rather than production of enzymes. Esrom has recently been identified as an ortholog of PAM (protein associated with c-myc), a very large protein involved in synaptogenesis in Drosophila and C. elegans. These data thus introduce a new regulator of pteridine synthesis in a vertebrate and establish a function for the Esrom protein family outside synaptogenesis. They also raise the possibility that neuronal defects are due in part to an abnormality in pteridine synthesis.     

Hemolysis of Human Red Blood Cells by Riboflavin-Cu(II) System: Enhancement by Azide

Photoactivated riboflavin in the presence of Cu(II) generates reactive oxygen species (ROS) which can hemolyze human red blood cells (RBC). In the present work we examined the effect of sodium azide (NaN3) on RBC in the presence of riboflavin and Cu(II). The addition of NaN3 to the riboflavin-Cu(II) system enhanced K+ loss and hemolysis. The extent of K+ loss and hemolysis were time and concentration dependent. Bathocuproine, a Cu(I)-sequestering agent, inhibited the hemolysis completely. Among various free radical scavengers used to identify the major ROS involved in the reaction, thiourea was found to be the most effective scavenger. Thiourea caused almost 85% inhibition of hemolysis suggesting that *OH is the major ROS involved in the reaction. Using spectral studies and other observations, we propose that when NaN3 is added to the riboflavin-Cu(II) system, it inhibits the photodegradation of riboflavin resulting in increased *OH generation. Also, the possibility of azide radical formation and its involvement in the reaction could not be ruled out.