Bacteriophage lysis: mechanism and regulation.

A large fraction, sometimes the largest fraction, of a eukaryotic genome consists of repeated DNA sequences. Copy numbers range from several thousand to millions per diploid genome. All classes of repetitive DNA sequences examined to date exhibit apparently general, but little studied, patterns of "concerted evolution." Historically, concerted evolution has been defined as the nonindependent evolution of repetitive DNA sequences, resulting in a sequence similarity of repeating units that is greater within than among species. This intraspecific homogenization of repetitive sequence arrays is said to take place via the poorly understood mechanisms of "molecular drive." The evolutionary population dynamics of molecular drive remains largely unstudied in natural populations, and thus the potential significance of these evolutionary dynamics for population differentiation is unknown. This review attempts to demonstrate the potential importance of the mechanisms responsible for concerted evolution in the differentiation of populations. It contends that any natural grouping that is characterized by reproductive isolation and limited gene flow is capable of exhibiting concerted evolution of repetitive DNA arrays. Such effects are known to occur in protein and RNA-coding repetitive sequences, as well as in so-called "junk DNA," and thus have important implications for the differentiation and discrimination of natural populations.

Concerted evolution of repetitive dna sequences in eukaryotes

The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing

Ribosomal DNA variation was used to study evolutionary relationships among five fungal-like protoctistan Phytophthora species. On the basis of morphological and ecological characteristics, four of these species--P. palmivora, P. megakarya, P. capsici, and P. citrophthora--were once thought to be related. Variation within a species was extensively studied in a fifth, outgroup species--P. cinnamomi--known, on the basis of ecological, isozyme, and mitochondrial DNA studies, to be variable. Internal transcribed spacer regions (ITS I, between the 18S and 5.8S rDNAs; and ITS II, between the 5.8S and 25S rDNAs) from 27 isolates of these five species were analyzed by polymerase chain reaction amplification and direct sequencing. Intraspecific variability was undetected or low. Interspecific nucleotide difference was 0.3%-14.6%, and comparisons of variable regions permitted the evaluation of phylogenetic relationships among species. Both neighbor-joining and parsimony analysis of ITS variability support a close relationship between cacao isolates of P. capsici and P. citrophthora and a common lineage for P. palmivora and P. megakarya. Large distance values were estimated between P. cinnamomi and the other species. Inferred relationships based on ITS variability were compared with those based on other characters. The catalog of sequences provides the information necessary to design taxon-specific probes potentially useful in taxonomic, ecological, and population-level studies.

Phylogeny of five fungus-like protoctistan Phytophthora species, inferred from the internal transcribed spacers of ribosomal DNA.

Acetyl-coenzyme A carboxylase (ACCase) occurs in at least two forms in rapeseed (Brassica napus): a homomeric (HO) and presumably cytosolic isozyme and a heteromeric, plastidial isozyme. We investigated whether the HO-ACCase of Arabidopsis can be targeted to plastids of B. napus seeds. A chloroplast transit peptide and the napin promoter were fused to the Arabidopsis ACC1 gene and transformed into B. napus, with the following results. (a) The small subunit transit peptide was sufficient to provide import of this very large protein into developing seed plastids. (b) HO-ACCase in isolated plastids was found to be biotinylated at a level comparable to extraplastidial HO-ACCase. (c) In vitro assays of HO-ACCase in isolated plastids from developing seeds indicate that it occurs as an enzymatically active form in the plastidial compartment. (d) ACCase activity in mature B. napus seeds is normally very low; however, plants expressing the SSU/ACC1 gene had 10- to 20-fold higher ACCase activity in mature seeds, suggesting that plastid localization prevents the turnover of HO-ACCase. (e) ACCase over-expression altered seed fatty acid composition, with the largest effect being an increase in oleic acid. (f) The total oil content of seeds was increased approximately 5% by the expression of HO-ACCase in plastids.

/pdf/targeting-of-the-arabidopsis-homomeric-acetyl-coenzyme-a-yyherpbi2g.pdf

Targeting of the Arabidopsis homomeric acetyl-coenzyme A carboxylase to plastids of rapeseeds.

Seed storage proteins of grain crops meet the major dietary protein requirement of over half of the world population. However, seed proteins in general are deficient in some essential amino acids and hence are of poor nutritional quality. Therefore, intensive research is going on to isolate and characterize these proteins and their genes, and to produce transgenic crop plants with modified seed protein genes, with a view to improving their nutritive value as human food and animal feed. Many seed storage protein genes from cereals, legumes and oil seeds have been isolated, sequenced and their regulation has been studied by promoter deletion assay in transgenic plants. The amino acid composition of seed proteins of some transgenic crops has been marginally improved by modifying these genes for more methionine and lysine codons by sitedirected mutagenesis or by introducing heterologous genes. The synthesis, processing and targeting of the introduced gene products and their stable expression in successive generations of transgenic plants have also been studied. The potentiality of such genetic engineering approaches has been amply demonstrated. But problems of control over copy number and site of integration of the foreign gene and the position effect of the changes in the amino acid in the polypeptide chain on the final level of expression and deposition of the correctly processed storage protein remains unsolved. More basic research is needed before large-scale application of this approach for improvement of nutritional quality of seed proteins becomes possible.

Seed storage proteins and approaches for improvement of their nutritional quality by genetic engineering.

Publisher Summary This chapter discusses the organization and transcription of the rRNA genes of eukaryotes with an emphasis on the nucleotide sequences in relation to function. The rRNA genes (rDNAs) are organized in repeating pre-rRNA transcription units separated by nontranscribed spacers (NTS). The pre-rRNAs transcription unit consists of coding sequences corresponding to mature 18-S, 28-SY, and 5.8-S rRNA, or their equivalents, and both external and internal transcribed spacer (ETS and ITS) sequences, which are transcribed as parts of the pre-rRNA molecule, but are lost during maturation. One transcription unit and the adjoining NTS constitute one rDNA repeating unit. The tandem head-to-tail arrangement of the repeated units is the basic feature in the organization of rRNA genes in most eukaryotes. The determination of nucleotide sequences at the transcription initiation and termination sites and at the gene-spacer boundaries has revealed some general features regarding sequence conservation and divergence in rDNAs. In general, the structural and functional domains of rRNA have been conserved in evolution in spite of wide divergence in the transcribed and nontranscribed spacers.

The organization and transcription of eukaryotic ribosomal RNA genes

Precursor of the Inactive 2S Seed Storage Protein from the Indian Mustard Brassica juncea Is a Novel Trypsin Inhibitor CHARACTERIZATION, POST-TRANSLATIONAL PROCESSING STUDIES, AND TRANSGENIC EXPRESSION TO DEVELOP INSECT-RESISTANT PLANTS

This paper describes the isolation and purification of two RNA polymerases (CI and CII) and several protein fractions (A, B and C) from the chromosomal acidic proteins of coconut endosperm nuclei. The method involves disruption of isolated nuclei in dilute salt medium, centrifugation to sediment the crude chromatin, solubilization of chromatin in concentrated salt, dialysis of soluble chromatin to dilute salt to precipitate DNA-histone complex and centrifugation to get the acidic proteins in the supernatant. Further purification involves ammonium sulphate fractionation and chromatography on DEAE-cellulose and QAE-Sephadex.



RNA polymerase CI purified through the QAE-Sephadex step gives a single band on polyacrylamide gel electrophoresis. In gels containing dodecylsulfate, this enzyme shows multiple bands indicating its subunit nature. The pH optima for both RNA polymerases is 8.0. RNA polymerase CI is maximally activated by Mn2+; while CII, by Mg2+. The activities of both the enzymes are stimulated by fraction B. All the fractions except A are substantially free from nucleases. Both RNA polymerases require the addition of DNA for activity. Fraction B is ineffective either with denatured coconut DNA or native λ DNA.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1972.tb01716.x

RNA polymerase from eukaryotic cells. Isolation and purification of enzymes and factors from chromatin of coconut nuclei.

THE stimulation of RNA synthesis in plant cells by auxins1,2 may be due, in part, to gene derepression, since chromatin isolated from hormone-treated cells is a better template. Mathysse and Phillips3 demonstrated that an acceptor protein for auxin can interact with the chromatin to derepress the genome. In their system the hormone and protein do not affect the rate of RNA synthesis if pure DNA. is used as a template. However, the actual mechanism of auxin on RNA synthesis by isolated RNA polymerase system has yet to be elucidated.

R. K. Mandal

Papers

Seed storage proteins and approaches for improvement of their nutritional quality by genetic engineering.

The organization and transcription of eukaryotic ribosomal RNA genes

Precursor of the Inactive 2S Seed Storage Protein from the Indian Mustard Brassica juncea Is a Novel Trypsin Inhibitor CHARACTERIZATION, POST-TRANSLATIONAL PROCESSING STUDIES, AND TRANSGENIC EXPRESSION TO DEVELOP INSECT-RESISTANT PLANTS

RNA polymerase from eukaryotic cells. Isolation and purification of enzymes and factors from chromatin of coconut nuclei.

RNA Stimulated by Indole Acetic Acid