World of small RNAs: from ribozymes to siRNA and miRNA

RNAs, besides bridging genetic information to proteins, the major determinants of bio-structures and functions, serve as active regulators of gene expression. Initiated nearly 20 years ago with ribozymes (the small RNAs with catalytic activity providing fine tuning of gene expression and function, used as molecular scissors and tools for gene discovery), an era of more complex and coordinated gene regulation by small RNAs, siRNA, and miRNA has recently started. Simple nucleotide complementarity results in highly ordered and regulated events, such as assembly of RNA and proteins, resulting in gene silencing either by mRNA degradation or suppression of translation. This article reviews our contributions to the understanding of structure, the function of small RNAs, their use in biotechnology, and the understanding of phenotypes such as apoptosis, metastasis, and differentiation.     

Genetics of durable resistance to leaf rust and stripe rust of an Indian wheat cultivar HD2009

The Indian bread wheat cultivar HD2009 has maintained its partial resistance to leaf rust and stripe rust in India since its release in 1976. To examine the nature, number and mode of inheritance of its genes for partial leaf rust and stripe rust resistance, this cultivar was crossed with cultivar WL711, which is susceptible to leaf rust and stripe rust. The F1, F2, F3 and F5 generations from this cross were assessed separately for adult plant disease severity under artificial epidemic of race 77-5 of leaf rust and race 46S119 of stripe rust. Segregation for rust reaction in the F2, F3 and F5 generations indicated that resistance to each of these rust diseases is based on 2 genes, each with additive effects. Although the leaf rust resistance of HD2009 is similar in expression to that conferred by the gene Lr34, but unlike the wheats carrying this gene, cultivar HD2009 did not show leaf tip necrosis, a morphological marker believed to be tightly linked to the leaf rust resistance gene Lr34. Thus, the non-hypersensitive resistance of HD2009 was ascribed to genes other than Lr34.     

Menkes Copper ATPase (Atp7a) is a novel metal-responsive gene in rat duodenum, and immunoreactive protein is present on brush-border and basolateral membrane domains

We previously noted strong induction of genes related to intestinal copper homeostasis (Menkes Copper ATPase (Atp7a) and metallothionein) in the duodenal epithelium of iron-deficient rats across several stages of postnatal development (Collins, J. F., Franck, C. A., Kowdley, K. V., and Ghishan, F. K. (2005) Am. J. Physiol., 288, G964-G971). We now report significant copper loading in the livers and intestines of iron-deficient rats. These findings are consistent with the hypothesis that there is increased intestinal copper transport during iron deficiency. We additionally found that hepatic Atp7b gene expression does not change with iron deficiency, suggesting that liver copper excretion is not altered. We have developed polyclonal antibodies against rat ATP7A, and we demonstrate the specificity of the immunogenic reaction. We show that the ATP7A protein is present on apical domains of duodenal enterocytes in control rats and on brush-border and basolateral membrane domains in iron-deprived rats. This localization is surprising, as previous in vitro studies have suggested that ATP7A traffics between the trans-Golgi network and the basolateral membrane. We further demonstrate that ATP7A protein levels are dramatically increased in brush-border and basolateral membrane vesicles isolated from iron-deficient rats. Other experiments show that iron refeeding partially corrects the hematological abnormalities seen in iron-deficient rats but that it does not ameliorate ATP7A protein induction, suggesting that Atp7a does not respond to intracellular iron levels. We conclude that ATP7A is involved in copper loading observed during iron deficiency and that increased intestinal copper transport is of physiological relevance, as copper plays important roles in overall body iron homeostasis.     

Proteome analysis of membrane and cell wall associated proteins from Staphylococcus aureus

Pathogenesis of Staphylococcus aureus, an opportunistic human pathogen, is complex and involves many virulence factors including an array of surface proteins (adhesins) that promote bacterial interactions with extracellular matrix components. A better understanding of these interactions can be achieved by studying the expression of membrane and cell wall associated proteins using a proteome analysis approach. To accomplish this, our goal here was to construct a reference map of membrane and cell wall associated proteins for S. aureus. Various lytic and solubilization methods have been tested to identify a suitable methodology for detection of these proteins in two-dimensional electrophoresis (2DE). Results demonstrate that cell lysis with lysostaphin, which lyses staphylococcal peptidoglycan, followed by solubilization with urea, thiourea, amidosulfobetaine 14 (ASB 14) and dithiothreitol (DTT) is an effective method, yielding a sample comprising proteins of wide molecular ranges and isoelectric points with minimum contamination from cytosolic proteins. Mass spectrometric analysis was employed to identify the membrane and cell surface proteins present in the sample and consequently an initial proteomic map of membrane and cell wall associated proteins for S. aureus is presented.     

A major functional difference between the mouse and human ARF tumor suppressor proteins

Suppression of tumorigenesis is considerably more stringent in the human than in the much shorter lived mouse species, and the reasons for this difference are poorly understood. We investigated functional differences in the control of the ARF (alternative reading frame) protein that acts upstream of p53 and is encoded along with p16(INK4a) at a major tumor suppressor locus in both the human and mouse genomes. The mouse and human ARF proteins are substantially divergent at their carboxyl termini. We have shown that the mouse ARF protein (p19ARF) interacts with Pex19p in the cell cytoplasm leading to its nuclear exclusion and repression of its p53 activation function. The human ARF protein (p14ARF) is substantially smaller than its mouse counterpart and is not subject to this functional inactivation by Pex19p. In an identical cellular background, ribozymes directed against Pex19p enhanced p19ARF- but not p14ARF-activated p53 function. This is the first demonstration of a functional difference between the mouse and human ARF proteins. In view of the major role of ARF in tumor suppression, this distinction may contribute to the different levels of tumor proneness of these species.     

Flavour profile of idli batter prepared from defined microbial starter cultures

Idli is a traditional cereal/legume-based naturally fermented steamed product with a soft and spongy texture which is highly popular and widely consumed as a snack food item in India. The predominant fermentation microflora comprises lactic acid bacteria and yeasts and causes an improvement in the nutritional, textural and flavour characteristics of the final product. The flavour profile of idli batter prepared with initial levels of 2 × 10⁴ c.f.u. g⁻¹ of Candida versatilis CFR 505 and 2 × 10¹ c.f.u. g⁻¹ of Pediococcus pentosaceus CFR 2123 in 500 g idli batter, packed in polyester polylaminate pouches and stored at 30 ± 2 °C was periodically analysed by GC-MS. The desirable flavour compounds such as ketones, diols and acids were found to be present upto 8 days of storage, whereas undesirable flavours like sulphurous and oxazolidone compounds, ethanone and thiazole appeared in the batter subsequent to 6 days of storage. The sensory attributes of idlis (final product) prepared from the stored batter related well to the determined flavour profile. The present study appeared to indicate that the flavour profile of traditional fermented foods can be a reliable qualitative and quantitative parameter for objective assessment. This revised version was published online in July 2006 with corrections to the Cover Date.