Riboregulation stands for RNA-based control of gene expression. In bacteria, small non-coding RNAs (sRNAs) are a major class of riboregulatory elements, most of which act at the post-transcriptional level by base-pairing target mRNA genes. The RNA chaperone Hfq facilitates antisense interactions between target mRNAs and regulatory sRNAs, thus influencing mRNA stability and/or translation rate. In the α-proteobacterium Sinorhizobium meliloti strain 2011, the identification and detection of multiple sRNAs genes and the broadly pleitropic phenotype associated to the absence of a functional Hfq protein both support the existence of riboregulatory circuits controlling gene expression to ensure the fitness of this bacterium in both free living and symbiotic conditions. In order to identify target mRNAs subject to Hfq-dependent riboregulation, we have compared the proteome of an hfq mutant and the wild type S. meliloti by quantitative proteomics following protein labelling with 15N. Among 2139 univocally identified proteins, a total of 195 proteins showed a differential abundance between the Hfq mutant and the wild type strain; 65 proteins accumulated ≥2-fold whereas 130 were downregulated (≤0.5-fold) in the absence of Hfq. This profound proteomic impact implies a major role for Hfq on regulation of diverse physiological processes in S. meliloti, from transport of small molecules to homeostasis of iron and nitrogen. Changes in the cellular levels of proteins involved in transport of nucleotides, peptides and amino acids, and in iron homeostasis, were confirmed with phenotypic assays. These results represent the first quantitative proteomic analysis in S. meliloti. The comparative analysis of the hfq mutant proteome allowed identification of novel strongly Hfq-regulated genes in S. meliloti.
The isolation of the Popeye gene family was based on its preferential expression in striated muscle tissue. Recently, a monoclonal antibody against chick Popdc1 (also known as Bves) became available and was used in this study to comparatively analyze the expression pattern of Popdc1 at both the protein and mRNA level during early chick embryogenesis. Using whole-mount immunohistochemistry, expression in the heart was first observed at Hamburger and Hamilton (HH) stage 10 in the presumptive left ventricular segment. Cardiac expression was confined to differentiated cardiac myocytes, and undifferentiated myocytes at the anterior and posterior pole showed little expression. After looping, the outer curvature myocardium showed prominent Popdc1 staining, whereas the inner curvature was unlabeled. Despite previous reports, Popdc1 protein was not detectable at any time point in the proepicardium, epicardium, or the smooth muscle layer of the coronary vessels. Whole-mount in situ hybridization using a full-length Popdc1 probe detected novel expression domains, which have not been described previously. Popdc1 mRNA was found in Hensen's node at HH stage 4, and by HH stage 5؉, expression became asymmetric. In addition, Popdc1 mRNA was found in pharyngeal endoderm and in the notochordal plate. Subsequently, beginning at HH stage 9, Popdc1 mRNA expression was found in the cardiac mesoderm and expression was maintained in the heart in a pattern very similar to the one observed by antibody staining. Developmental Dynamics 235: 691-700, 2006.
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