An examination of 51 mRNA sequences in GenBank has revealed that calculated mRNA folding is more stable than expected by chance. Free energy minimization calculations of native mRNA sequences are more negative than randomized mRNA sequences with the same base composition and length. Randomization of the coding region of genes yields folding free energies of less negative magnitude than the original native mRNA sequence. Randomization of codon choice, while still preserving original base composition, also results in less stable mRNAs. This suggests that a bias in the selection of codons favors the potential formation of mRNA structures which contribute to folding stability.

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We used degenerate oligodeoxyribonucleotides derived from the N-terminal sequence of the s-triazine hydrolase from Rhodococcus corallinus NRRL B-15444R in an amplification reaction to isolate a DNA segment containing a 57-bp fragment from the trzA gene. By using the nucleotide sequence of this fragment, a nondegenerate oligodeoxyribonucleotide was synthesized and used to screen a genomic library of R. corallinus DNA for fragments containing trzA. A 5.3-kb PstI fragment containing trzA was cloned, and the nucleotide sequence of a 2,450-bp region containing trzA was determined. No trzA expression was detected in Escherichia coli or several other gram-negative bacteria. The trzA gene was subcloned into a Rhodococcus-E. coli shuttle vector, pBS305, and transformed into several Rhodococcus strains. Expression of trzA was demonstrated in all Rhodococcus transformants. Rhodococcus sp. strain TE1, which possesses the catabolic gene (atrA) for the N-dealkylation of the herbicides atrazine and simazine, was able to dechlorinate the dealkylated metabolites of atrazine and simazine when carrying the trzA gene on a plasmid. A plasmid carrying both atrA and trzA was constructed and transformed into three atrA-and trzA-deficient Rhodococcus strains. Both genes were expressed in the transformants. The s-triazine hydrolase activity of the recombinant strains carrying the trzA plasmid were compared with that of the R. corallinus strain from which it was derived.The s-triazine herbicides have been used in a variety of weed control programs with major crops. Atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) is one of the most heavily used herbicides in North America (21). The detection of atrazine in groundwater and surface water has prompted some environmental concerns (1, 14). There has been considerable interest in finding microbial activities that might be used to degrade atrazine and other s-triazine compounds in herbicide wastes and contaminated soils (6,7,12,16,24). Several microorganisms that can metabolize atrazine have been isolated during the last few years (2,3,17,18,25,33). We recently reported that Rhodococcus sp. strain TE1 can degrade atrazine efficiently to produce the dealkylated metabolites deisopropylatrazine (2-chloro-4-ethylamino-6-amino-s-triazine [CEAT]) and deethylatrazine (2-chloro-4-amino-6-isopropylamino-s-triazine [CIAT]) and that this catabolic function was associated with an indigenous 77-kb plasmid in this bacterium (4, 28). Two recently reported Pseudomonas isolates (18, 33) degrade atrazine efficiently but by different pathways.Cook and Hutter (5, 8) isolated and characterized an isolate of Rhodococcus corallinus that dechlorinates and deaminates the dealkylated s-triazine compounds CEAT and CIAT but not atrazine. The enzyme, named s-triazine hydrolase and encoded by the trzA gene, has been purified (23). The combination of the catabolic activities of both Rhodococcus sp. strain TE1 and R. corallinus would result in dealkylation and dechlorination of atrazine.We have been involved in...

Extensive studies of gene expression programs in carrot somatic embryos identified a gene, designated Dc3, that serves as a reliable molecular marker for the acquisition of embryogenic potential by carrot cells in culture. The complete sequence of a carrot genomic region, DcG3, encoding a Dc3-like mRNA, was determined. The DcG3 transcription unit contains a single intron and encodes mRNA that is expressed at high levels in embryonic tissue but is undetectable in somatic tissue of carrot. The predicted protein sequence of DcG3 is 163 amino acids and includes two approximately 50 amino acid direct repeats which in turn include additional repetitive elements with an unusual distribution of charged amino acids. Dc3 and Dc3-like mRNAs are encoded by a small divergent gene family. Furthermore, similarities of the Dc3 gene family with genes from other plant species that are expressed in response to environmental and developmental cues suggest a possible role in seed desiccation and possibly in more general water-stress responses in plants. Analysis of transgenic tobacco containing a beta-glucuronidase (GUS) reporter gene fused to a 1.7 kb 5' upstream element of DcG3 defined a promoter/enhancer complex that confers developmentally and environmentally regulated expression of GUS activity. Thus, DcG3 is phylogenetically conserved together with the trans-acting factors required for its regulated expression in transgenic tobacco.

Serous subtype of ovarian cancer is considered to originate from fallopian epithelium mucosa that has been exposed to physiological changes resulting from ovulation. Ovulation influences an increased in inflammation of epithelial ovarian cells as results of constant exposure of cells to ROS. The imbalance between ROS and antioxidant capacities, as well as a disruption of redox signaling, causes a wide range of damage to DNA, proteins, and lipids. This study applied spectrophotometric, dinitrophenylhydrazone (DNPH) assay, two-dimensional gel electrophoresis, and Western blot analyses to assess the levels of oxidatively modified proteins in 100 primary serous epithelial ovarian carcinoma and normal/surrounding tissues. These samples were obtained from 56 Caucasian and 44 African-American patients within the age range of 61 ± 10 years. Analyses showed that the levels of reactive protein carbonyl groups increased as stages progressed to malignancy. Additionally, the levels of protein carbonyls in serous ovarian carcinoma among African Americans are 40% (P < 0.05) higher relative to Caucasian at similar advanced stages. Results suggest that oxidative stress is involved in the modification of carbonyl protein groups, leading to increased aggressiveness of epithelial ovarian tumors and may contribute to the disease's invasiveness among African Americans.