A single spacer nucleotide determines the specificities of two mRNA regulatory proteins.

Regulation of messenger RNA is crucial in many contexts, including development, memory and cell growth. The 3' untranslated region is a rich repository of regulatory elements that bind proteins and microRNAs. Here we focus on PUF proteins, an important family of mRNA regulatory proteins crucial in stem-cell proliferation, pattern formation and synaptic plasticity. We show that two Caenorhabditis elegans PUF proteins, FBF and PUF-8, differ in RNA-binding specificity. FBF requires the presence of a single 'extra' nucleotide in the middle of an eight-nucleotide site, whereas PUF-8 requires its absence. A discrete protein segment is responsible for the difference. We propose that a structural distortion in the central region of FBF imposes the requirement for the additional nucleotide and that this mode of PUF specificity may be common. We suggest that new specificities can be designed and selected using the PUF scaffold.

Dose-dependent control of proliferation and sperm specification by FOG-1/CPEB.

RNA-binding proteins control germline development in metazoans. This work focuses on control of the C. elegans germline by two RNA-binding proteins: FOG-1, a CPEB homolog; and FBF, a PUF family member. Previous studies have shown that FOG-1 specifies the sperm fate and that FBF promotes proliferation. Here, we report that FOG-1 also promotes proliferation. Whereas fbf-1 fbf-2 double mutants make approximately 120 germ cells, fog-1; fbf-1 fbf-2 triple mutants make only approximately 10 germ cells. The triple mutant germline divides normally until early L2, when germ cells prematurely enter meiosis and begin oogenesis. Importantly, fog-1/+; fbf-1 fbf-2 animals make more germ cells than fbf-1 fbf-2 double mutants, demonstrating that one dose of wild-type fog-1 promotes proliferation more effectively than two doses - at least in the absence of FBF. FOG-1 protein is barely detectable in proliferating germ cells, but abundant in germ cells destined for spermatogenesis. Based on fog-1 dose effects, together with the gradient of FOG-1 protein abundance, we suggest that low FOG-1 promotes proliferation and high FOG-1 specifies spermatogenesis. FBF binds specifically to regulatory elements in the fog-1 3'UTR, and FOG-1 increases in animals lacking FBF. Therefore, FBF represses fog-1 expression. We suggest that FBF promotes continued proliferation, at least in part, by maintaining FOG-1 at a low level appropriate for proliferation. The dose-dependent control of proliferation and cell fate by FOG-1 has striking parallels with Xenopus CPEB, suggesting a conserved mechanism in animal development.

Cytokine genotype polymorphisms in breast carcinoma: associations of TGF-beta1 with relapse.

Markers of angiogenesis, cell proliferation, and cytokine regulation are associated with the development and course of autoimmune and malignant diseases. We investigated associations between cytokine production genotypes in breast cancer patients compared with controls and explored associations with known prognostic indices and relapse status. Eighty-eight females with breast carcinoma (BC) were studied in this case-control study comparing the cytokine genotypes of TNF-alpha TGF-beta1, IL-10, IL-6, and IFN-gamma with controls. Cytokine polymorphisms were identified by sequence-specific primers for codons, introns, or promoters regulating cytokine production. Patient characteristics, such as estrogen and progesterone receptor status, DNA ploidy, Her-2 neu expression, lymph node involvement, tumor size, and relapse status were evaluated. Cytokine genotypes were not associated with breast cancer compared with controls. Correlations between TGF-beta1 high-production genotypes and greater than four positive lymph nodes (OR=2.3; p=ns) and TNF-alpha high-production genotype and the mean level of estrogen receptor expression (66 +/- 24 vs. 34 +/- 36, p=0.016) were identified. The median patient follow-up interval from diagnosis to evaluation was 50.1 months (range 13-387 months). Relapse status was known for 84 of the patients. The odds of relapse in TGF-beta1 codon 10 CC genotypes was 2.81 times that in TGF-beta1 high-production genotypes (OR=2.81; 95% CI for OR: 1.0, 7.8; p=0.04). Mean progesterone receptor expression was decreased in relapsed patients (40.9 +/- 29.9% vs. 23.1 +/- 24.5, p=0.05). The other cytokine genotypes studied (IL-10, IL-6, IFN-gamma, and TNF-alpha production were not associated with breast cancer overall or relapse status. In this study, TGF-beta1 low-production genotypes (TGF-beta1 10 CC) were associated with an increased odds of disease relapse. This finding should be confirmed in a longitudinal study to further investigate the regulatory function of cytokine production as a prognostic indicator of relapse.

Regulation of the mitosis/meiosis decision in the Caenorhabditis elegans germline.

During the development of multicellular organisms, the processes of growth and differentiation are kept in balance to generate and maintain tissues and organs of the correct size, shape and cellular composition. We have investigated the molecular controls of growth and differentiation in the Caenorhabditis elegans germline. A single somatic cell, called the distal tip cell, promotes mitotic proliferation in the adjacent germline by GLP-1/Notch signalling. Within the germline, the decisions between mitosis and meiosis and between spermatogenesis and oogenesis are controlled by a group of conserved RNA regulators. FBF, a member of the PUF (for Pumilio and FBF) family of RNA-binding proteins, promotes mitosis by repressing gld-1 mRNA activity; the GLD-1, GLD-2, GLD-3 and NOS-3 proteins promote entry into meiosis by regulating mRNAs that remain unknown. The regulatory balance between opposing FBF and GLD activities is crucial for controlling the extent of germline proliferation. PUF proteins regulate germline stem cells in both Drosophila and C. elegans and are localized to germline stem cells of the mammalian testis. Therefore, this post-transcriptional regulatory switch may be an ancient mechanism for controlling maintenance of stem cells versus differentiation.

A conserved RNA-binding protein controls germline stem cells in Caenorhabditis elegans.

Germline stem cells are defined by their unique ability to generate more of themselves as well as differentiated gametes. The molecular mechanisms controlling the decision between self-renewal and differentiation are central unsolved problems in developmental biology with potentially broad medical implications. In Caenorhabditis elegans, germline stem cells are controlled by the somatic distal tip cell. FBF-1 and FBF-2, two nearly identical proteins, which together are called FBF ('fem-3 mRNA binding factor'), were originally discovered as regulators of germline sex determination. Here we report that FBF also controls germline stem cells: in an fbf-1 fbf-2 double mutant, germline proliferation is initially normal, but stem cells are not maintained. We suggest that FBF controls germline stem cells, at least in part, by repressing gld-1, which itself promotes commitment to the meiotic cell cycle. FBF belongs to the PUF family ('Pumilio and FBF') of RNA-binding proteins. Pumilio controls germline stem cells in Drosophila females, and, in lower eukaryotes, PUF proteins promote continued mitoses. We suggest that regulation by PUF proteins may be an ancient and widespread mechanism for control of stem cells.

Analyzing mRNA-protein complexes using a yeast three-hybrid system.

RNA-protein interactions are essential for the proper execution and regulation of every step in the life of a eukaryotic mRNA. Here we describe a three-hybrid system in which RNA-protein interactions can be analyzed using simple phenotypic or enzymatic assays in Saccharomyces cerevisiae. The system can be used to detect or confirm an RNA-protein interaction, to analyze RNA-protein interactions genetically, and to discover new protein or RNA partners when only one is known. Multicomponent complexes containing more than one protein can be detected, identified, and analyzed. We describe the method and how to use it, and discuss applications that bear particularly on eukaryotic mRNAs.

A PUF family portrait: 3'UTR regulation as a way of life.

In eukaryotic cells, mRNAs are exquisitely controlled, often through regulatory elements in their 3' untranslated regions (3'UTRs). Proteins that bind to those sites are key players in controlling mRNA stability, translation and localization. One family of regulatory proteins--the PUF proteins--are not only structurally related, but also bind to 3'UTRs and modulate mRNA expression in a wide variety of eukaryotic species. They do so either by enhancing turnover or repressing translation, and act combinatorially with other regulatory proteins. Here, we discuss the evolution, biological function and mechanisms of action of the PUF protein family, and suggest that a primordial function of PUF proteins is to sustain mitotic proliferation of stem cells.