Biotransformation of dicarboxylic acid by immobilized Cryptococcus cells

Altering the cell permeability by treating Cryptococcus neoformans with 1% (v/v) hexane stimulated the yield of transformation of n-pentadecane to the corresponding dioic acid, tridecane 1,13-dicarboxylic acid (DC-15); however, the biotransformation process was inhibited by the elevated levels of DC-15. To avoid product inhibition, a continuous process with immobilized cells was performed, and the result showed that the yield of DC-15 production was increased up to fivefold as compared with the batch type of DC-15 production. To integrate the product recovery process with the biotransformation, Amberlite XAD-2 resin was used for adsorbing DC-15 and configured as an external in situ product recovery system. The continuous process described in this study is adaptable for large-scale production of DC-15.     

Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content

Background  

Introns comprise a large fraction of eukaryotic genomes, yet little is known about their functional significance. Regulatory elements have been mapped to some introns, though these are believed to account for only a small fraction of genome wide intronic DNA. No consistent patterns have emerged from studies that have investigated general levels of evolutionary constraint in introns.     

Module-intron correlation and intron sliding in family F/10 xylanase genes

Xylanases are classified into two families, numbered F/10 and G/11 according to the similarity of amino acid sequences of their catalytic domain (Henrissat, B., Bairoch, A., 1993. New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 293, 781-788). Three-dimensional structure of the catalytic domain of the family F/10 xylanase was reported (White, A., Withers, S.G., Gilkes, N.R., Rose, D.R., 1994. Crystal structure of the catalytic domain of the beta-1,4-glycanase Cex from Cellulomonas fimi. Biochemistry 33, 12546-12552). The domain was decomposed into 22 modules by centripetal profiles (Go, M., Nosaka, M., 1987. Protein architecture and the origin of introns. Cold Spring Harbor Symp. Quant. Biol. 52, 915-924; Noguti, T., Sakakibara, H., Go, M., 1993. Localization of hydrogen-bonds within modules in barnase. Proteins 16, 357-363). A module is a contiguous polypeptide segment of amino acid residues having a compact conformation within a globular domain. Collected 31 intron sites of the family F/10 xylanase genes from fungus were found to be correlated to module boundaries with considerable statistical force (p values <0.001). The relationship between the intron locations and protein structures provides supporting evidence for the ancient origin of introns, because such a relationship cannot be expected by random insertion of introns into eukaryotic genes, but it rather suggests pre-existence of introns in the ancestral genes of prokaryotes and eukaryotes. A phylogenetic tree of the fungal and bacterial xylanase sequences made two clusters; one includes both the bacterial and fungal genes, but the other consists of only fungal genes. The mixed cluster of bacterial genes without introns and the fungal genes with introns further supports the ancient origin of introns. Comparison of the conserved base sequences of introns indicates that sliding of a splice site occurred in Aspergillus kawachii gene by one base from the ancestral position. Substrate-binding sites of xylanase are localized on eight modules, and introns are found at both termini of six out of these functional modules. This result suggests that introns might play a functional role in shuffling the exons encoding the substrate-binding modules.     

A novel group I intron in Candida dubliniensis is homologous to a Candida albicans intron

In the present study, we determined the sequence of group I self-splicing introns found in the large ribosomal RNA subunit of Candida albicans, Candida stellatoidea and the recently-described species Candida dubliniensis. It was found that both the intron and ribosomal RNA nucleotide sequences are almost perfectly identical between different C. albicans strains as well as between C. albicans and C. stellatoidea strains. Comparisons of ribosomal RNA sequences suggest that local isolates of atypical C. albicans from individuals infected with human immunodeficiency virus can be assigned to the C. dubliniensis species. C. dubliniensis strains also harbor a group I intron in their ribosomal RNA, as observed in about 40% of C. albicans strains and all C. stellatoidea strains. This novel C. dubliniensis group I intron is identical to the C. albicans and C. stellatoidea intron, except for two widely divergent stem-loop regions. Despite these differences, the C. dubliniensis intron possesses self-splicing ability in an in vitro assay. Taken together, these data support the idea that C. albicans and C. stellatoidea should be joined together as variants of the same species while C. dubliniensis is a distinct but closely related microorganism. To our knowledge, the C. albicans and C. dubliniensis introns are the first example of a pair of homologous group I introns differing only by the presence of apparently facultative sequences in some stem-loops suspected to be involved in stabilization of tertiary structure.     

In Bradyrhizobium japonicum the common nodulation genes, nodABC, are linked to nifA and fixA

Summary Using cloned Rhizobium phaseoli nodulation (nod) genes as hybridization probes homologous restriction fragments were detected in the genome of the slow-growing soybean symbiont, Bradyrhizobium japonicum strain 110. These fragments were isolated from a cosmid library, and were shown to lie 10 kilobasepairs (kb) upstream from the nifA and fixA genes. Specific nod probes from Rhizobium leguminosarum were used to identify nodA-, nodB-, and nodC-like sequences clustered within a 4.5 kb PstI fragment. A mutant was constructed in which the kanamycin resistance gene from Tn5 was inserted into the nodA homologous B. japonicum region. This insertion was precisely located, by DNA sequencing, to near the middle of the nodA gene. B. japonicum mutants carrying this insertion were completely nodulation deficient (Nod^-).     

A rare case of Plasmodium (Haemamoeba) relictum infection in a free-living Red Knot (Calidris canutus rufa, Scolopacidae)

The Red Knot (Calidris canutus rufa) is a Nearctic migrant shorebird that breeds in the Canadian Arctic and spends the winter season in coastal sites in South America. A rare case of a blood protozoan was found by molecular analyses from an adult bird captured during spring migration at the last refuelling stopover in Delaware Bay USA in 2006. The parasite was identified as Plasmodium relictum belonging to subgenus Haemamoeba based on the shape of meronts, roundish gametocytes, and its position in the erythrocytes from the blood smears examination. A partial cytochrome b sequence was a 100% match to a sequence of Plasmodium relictum, sequence Genbank accession number: id DQ659543.1 (lineage code haplotype P5). This is the first report of avian malaria in a wild individual of C. c. rufa.     

recB recJ mutants ofSalmonella typhimurium are deficient in transductional recombination, DNA repair and plasmid maintenance

recB recJ mutants ofSalmonella typhimurium are deficient in transduction of chromosomal markers and ColE1-derived plasmids, and also in the maintenance of ColE1 and F plasmids. Plasmid instability is less severe inrecD recJ strains; ColE1 plasmid DNA preparations from these strains show an increased yield of high molecular weight (HMW) linear multimers and a concomitant reduction in plasmid monomers compared to the wild type. Plasmids remain unstable inrecA recD recJ mutants; since these do not produce HMW linear concatemers, we propose that a decrease in monomer production leads to plasmid instability.recB recJ strains also display decreased viability, a component of which may be related to their deficiency in DNA repair. In contrast to their severe defects in recombination, DNA repair and plasmid maintenance,recB recJ mutants ofS. typhimurium behave similarly to the wild type in the segregation of chromosome duplications. The latter observation suggests that neither RecBCD nor RecJ functions are required for chromosomal recombination events that do not involve the use of free ends as recombination substrates.     

Genetic diversity in Isoetes yunguiensis, a rare and endangered endemic fern in China

Isoetes yunguiensis is an endangered and endemic fern in China. Field survey indicated that only one population and no more than 50 individuals occur in the wild. The genetic variation of 46 individuals from the population remaining at Pingba (Guizhou Province, China) was assessed by Random Amplified Polymorphic DNA (RAPD) finger-printing. Twelve primers were screened from sixty ten-bp arbitrary primers, and a total of 95 DNA fragments were scored. Of these, 62.1% were polymorphic loci, which indicated that high level genetic variation existed in the natural population. The accumulation of genetic variation in the history of the taxon and the apparent minimal reduction effect on genetic diversity following destruction of habitat might be responsible for the high level genetic diversity presently remaining in the I. yunguiensis population. However, with the continuing decrease of population size, the genetic diversity will gradually be lost. We suggest that the materials from the extant population should be used for re-establishment of the populations. Translated from Journal of Wuhan University (Natural Sciences Edition), 2005, 51(6): 767–770 [译自: 武汉大学学报 (理学版)]     

江西武夷山珍稀濒危植物南方铁杉种群动态与空间分布

明晰江西武夷山国家级自然保护区内180年生的珍稀濒危植物南方铁杉(Tsuga chinensis var.tchekiangensis)的种群特征,并提出针对性的保护策略,对南方铁杉种群的就地保护具有现实意义。通过分析保护区内6.4 hm~2动态监测固定样地的南方铁杉种群数据,编制了静态生命表,绘制了存活曲线、死亡率和消失率曲线、生存函数曲线,采用了时间序列模型对种群数量特征进行未来预测;同时,运用点格局分析Ripley′s K函数中的成对相关函数g(r)判断不同生长阶段的南方铁杉种群在不同尺度下的空间分布格局。结果表明：(1)南方铁杉种群的年龄结构呈“金字塔”型,属于衰退型种群;各龄级间的数量变化动态关系显示该种群在当前阶段呈增长型,但是种群的天然更新能力较差;(2)南方铁杉种群的存活曲线表现为Deevey-I型,种群个体在进入生理死亡阶段后产生一定的波动;(3)南方铁杉种群的生存率随龄级增加而逐渐下降,累积死亡率逐渐递增;死亡密度整体偏低,在第1—2龄级较高,总体波动幅度较小;危险率曲线总体呈现上升的趋势;(4)在经过不同龄级的时间后,南方铁杉幼龄树数量降低,中龄树和老龄树数量持平...     

The nifU, nifS and nifV gene products are required for activity of all three nitrogenases of Azotobacter vinelandii

Summary Strains with mutations in 23 of the 30 genes and open reading frames in the major nif gene cluster of A. vinelandii were tested for ability to grow on N-free medium with molybdenum (Nif phenotype), with vanadium (Vnf phenotype), or with neither metal present (Anf phenotype). As reported previously, nifE, nifty, nifU, nifS and nifV mutants were Nif^– (failed to grow on molybdenum) while nifM mutants were Nif^–, Vnf^– and Anf^–. nifV, nifS, and nifU mutants were found to be unable to grow on medium with or without vanadium, i.e. were Vnf^– Anf–. Therefore neither vnf nor anf analogoues of nifU, nifS, nifV or nifM are expected to be present in A. vinelandii.     

Miniribozymes, small derivatives of the sunY intron, are catalytically active.

The self-splicing sunY intron from bacteriophage T4 has the smallest conserved core secondary structure of any of the active group I introns. Here we show that several nonconserved regions can be deleted from this intron without complete loss of catalytic activity. The 3' stems P9, P9.1, and P9.2 can be deleted while retaining 5' cleaving activity. Two base-paired stems (P7.1 and P7.2) that are peculiar to the group IA introns can also be deleted; however, the activities of the resulting derivatives depend greatly on the choice of replacement sequences and their lengths. The smallest active derivative is less than 180 nucleotides long. These experiments help to define the minimum structural requirements for catalysis.     

Retrotransposons IDEFIX and ZAM are responsible for transposition in Drosophila melanogaster MS strain mutant for the flamenco gene

Transposition activity of Drosophila melanogaster gypsy retrotransposon is controlled by the flamenco locus. Transposition activity of the gypsy, ZAM, Idefix, springer, nomad, rover, Quasimodo, 17.6, 297, and Tirant retrotransposons was investigated in isogenic SS and MS strains of D. melanogaster mutant for the flamenco gene. It has been shown that gypsy, ZAM, and Idefix have different genomic surrounding in the studied strains that evidences to their transposition in these strains.     

Cloning and expression of the Apa LI, Nsp I, Nsp HI, Sac I, Sca I, and Sap I restriction-modification systems in Escherichia coli

The genes encoding the ApaLI (5′-G^TGCAC-3′), NspI (5′-RCATG^Y-3′), NspHI (5′-RCATG^Y-3′), SacI (5′-GAGCT^C-3′), SapI (5′-GCTCTTCN1^-3′, 5′-^N4GAAGAGC-3′) and ScaI (5′-AGT^ACT-3′) restriction-modification systems have been cloned in E.␣coli. Amino acid sequence comparison of M.ApaLI, M.NspI, M.NspHI, and M.SacI with known methylases indicated that they contain the ten conserved motifs characteristic of C5 cytosine methylases. NspI and NspHI restriction-modification systems are highly homologous in amino acid sequence. The C-termini of the NspI and NlaIII (5′-CATG-3′) restriction endonucleases share significant similarity. 5mC modification of the internal C in a SacI site renders it resistant to SacI digestion. External 5mC modification of a SacI site has no effect on SacI digestion. N4mC modification of the second base in the sequence 5′-GCTCTTC-3′ blocks SapI digestion. N4mC modification of the other cytosines in the SapI site does not affect SapI digestion. N4mC modification of ScaI site blocks ScaI digetion. A DNA invertase homolog was found adjacent to the ApaLI restriction-modification system. A DNA transposase subunit homolog was found upstream of the SapI restriction endonuclease gene. Received: 15 April 1998 / Accepted: 3 August 1998     

Rearrangements at a hobo element inserted into the first intron of the singed gene in the unstable sn 49 system of Drosophila melanogaster

The cytological structure of the X chromosome and the DNA organisation of the singed locus were examined in five singed bristle mutants of Drosophila melanogaster. These mutants are all derived from the unstable mutant singed-49, isolated from a wild population in the Russian Far East in 1975. Rearrangements were found at a site within the first intron of the singed gene, where a hobo element is inserted in these mutants. One rearrangement, which is associated with a strong bristle phenotype, has an inversion between 2D and the location of singed at 7D, which separates the singed promoter from the singed coding region. Two phenotypically wild-type derivatives have smaller rearrangements within the first intron which do not appear to interfere with singed expression. Two derivatives with bristle phenotypes have more complex rearrangements, and one of them shows a dominant or antimorphic phenotype. DNA blotting and in situ hybridisation experiments show that, in addition to these rearrangements at a hobo element inserted at singed, other hobo elements in these strains have been mobilised. This system is therefore similar to others in which functional hobo elements continue to transpose, resulting in elevated rates of mutation and chromosome rearrangement. Received: 19 February 1997 / Accepted: 8 October 1997     

The chloroplastchIL gene of the green algaChlorella vulgaris C-27 contains a self-splicing group I intron

ThechiL gene product is involved in the light-independent synthesis of chlorophyll in photosynthetic bacteria, green algae and non-flowering plants. The chloroplast genome ofChlorella vulgaris strain C-27 contains the first example of a splitchiL gene, which is interrupted by a 951 bp group I intron in the coding region. In vitro synthesized pre-mRNA containing the entire intron and parts of the flanking exon sequences is able to efficiently self-splice in vitro in the presence of a divalent and a monovalent cation and GTP, to yield the ligated exons and other splicing intermediates characteristic of self-splicing group I introns. The 5 and 3 splice sites were confirmed by cDNA sequencing and the products of the splicing reaction were characterized by primer extension analysis. The absence of a significant ORF in the long P9 region (522 nt), separating the catalytic core from the 3 splice site, makes this intron different from the other known examples of group I introns. Guanosine-mediated attack at the 3 splice site and the presence of G-exchange reaction sites internal to the intron are some other properties demonstrated for the first time by an intron of a protein-coding plastid gene.