Laura Finzi

Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping

The overall topology of DNA profoundly influences the regulation of transcription and is determined by DNA flexibility as well as the binding of proteins that induce DNA torsion, distortion, and/or looping. Gal repressor (GalR) is thought to repress transcription from the two promoters of the gal operon of Escherichia coli by forming a DNA loop of ≈40 nm of DNA that encompasses the promoters. Associated evidence of a topological regulatory mechanism of the transcription repression is the requirement for a supercoiled DNA template and the histone-like heat unstable nucleoid protein (HU). By using single-molecule manipulations to generate and finely tune tension in DNA molecules, we directly detected GalR/HU-mediated DNA looping and characterized its kinetics, thermodynamics, and supercoiling dependence. The factors required for gal DNA looping in single-molecule experiments (HU, GalR and DNA supercoiling) correspond exactly to those necessary for gal repression observed both in vitro and in vivo. Our single-molecule experiments revealed that negatively supercoiled DNA, under slight tension, denatured to facilitate GalR/HU-mediated DNA loop formation. Such topological intermediates may operate similarly in other multiprotein complexes of transcription, replication, and recombination.

Calibration of optical tweezers with differential interference contrast signals

A comparison of different calibration methods for optical tweezers with the differential interference contrast (DIC) technique was performed to establish the uses and the advantages of each method. A detailed experimental and theoretical analysis of each method was performed with emphasis on the anisotropy involved in the DIC technique and the noise components in the detection. Finally, a time of flight method that permits the reconstruction of the optical potential well was demonstrated.

BASIC PENTACYSTEINE1, a GA Binding Protein That Induces Conformational Changes in the Regulatory Region of the Homeotic Arabidopsis Gene SEEDSTICK

The mechanisms for the regulation of homeotic genes are poorly understood in most organisms, including plants. We identified BASIC PENTACYSTEINE1 (BPC1) as a regulator of the homeotic Arabidopsis thaliana gene SEEDSTICK (STK), which controls ovule identity, and characterized its mechanism of action. A combination of tethered particle motion analysis and electromobility shift assays revealed that BPC1 is able to induce conformational changes by cooperative binding to purine-rich elements present in the STK regulatory sequence. Analysis of STK expression in the bpc1 mutant showed that STK is upregulated. Our results give insight into the regulation of gene expression in plants and provide the basis for further studies to understand the mechanisms that control ovule identity in Arabidopsis.

Design and application of a computer‐controlled confocal scanning differential polarization microscope

Based on the confocal scanning and differential polarization imaging technique, a computer‐controlled confocal scanning differential polarization microscope has been built. This system possesses extensive image processing capability that provides digitized regular and/or differential polarization images. This microscope combines the advantages of the confocal design and the extended electronic sensitivity of polarization modulated instrumentation to achieve the measurement of an anisotropy ratio as small as 10−5. In this paper, the basic theory and the instrument are described. In addition, some samples are used to test the actual performance of the system, and it is found that the system provides high resolution (0.3 μm at wavelength 546 nm), reduced depth of field, and high signal‐to‐noise ratio (83 dB at 10‐ms integration time) images. Finally, some biological applications are shown.

Direct demonstration and quantification of long-range DNA looping by the λ bacteriophage repressor

Recently, it was proposed that DNA looping by the λ repressor (CI protein) strengthens repression of lytic genes during lysogeny and simultaneously ensures efficient switching to lysis. To investigate this hypothesis, tethered particle motion experiments were performed and dynamic CI-mediated looping of single DNA molecules containing the λ repressor binding sites separated by 2317 bp (the wild-type distance) was quantitatively analyzed. DNA containing all three intact operators or with mutated o3 operators were compared. Modeling the thermodynamic data established the free energy of CI octamer-mediated loop formation as 1.7 kcal/mol, which decreased to –0.7 kcal/mol when supplemented by a tetramer (octamer+tetramer-mediated loop). These results support the idea that loops secured by an octamer of CI bound at oL1, oL2, oR1 and oR2 operators must be augmented by a tetramer of CI bound at the oL3 and oR3 to be spontaneous and stable. Thus the o3 sites are critical for loops secured by the CI protein that attenuate cI expression.

Diffusion of light-harvesting complex II in the thylakoid membranes

The light‐harvesting complex II (LHCII) is the main energy absorber for photosynthesis in green plants, and its translocation between photosystems I and II is the primary means of energy redistribution between them. Using single‐particle tracking, we performed the first measurement of the mobility of LHCII in the photosynthetic membranes in both the nonphosphorylated and the phosphorylated (P‐LHCII) conformations. These are part of an important, reversible, energy re‐equilibration process called the state transition. We found that the population of P‐LHCII in unappressed membranes is more mobile than the population of non‐P‐LHCII from the same regions.

MADS Domain Transcription Factors Mediate Short-Range DNA Looping That Is Essential for Target Gene Expression in Arabidopsis

The MADS domain factors STK and SEP3 directly regulate VDD expression. STK-SEP3 dimers induce loop formation in the VDD promoter by binding to two nearby CArG boxes, and this loop is essential for VDD expression. In vivo data suggest that the size and/or position of this loop determine the spatial expression profile of VDD. This study provides in vivo evidence for the floral quartet model. MADS domain transcription factors are key regulators of eukaryotic development. In plants, the homeotic MIKC MADS factors that regulate floral organ identity have been studied in great detail. Based on genetic and protein–protein interaction studies, a floral quartet model was proposed that describes how these MADS domain proteins assemble into higher order complexes to regulate their target genes. However, despite the attractiveness of this model and its general acceptance in the literature, solid in vivo proof has never been provided. To gain deeper insight into the mechanisms of transcriptional regulation by MADS domain factors, we studied how SEEDSTICK (STK) and SEPALLATA3 (SEP3) directly regulate the expression of the reproductive meristem gene family transcription factor–encoding gene VERDANDI (VDD). Our data show that STK-SEP3 dimers can induce loop formation in the VDD promoter by binding to two nearby CC(A/T)6GG (CArG) boxes and that this is essential for promoter activity. Our in vivo data show that the size and position of this loop, determined by the choice of CArG element usage, is essential for correct expression. Our studies provide solid in vivo evidence for the floral quartet model.

Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro

The prophage state of bacteriophage λ is extremely stable and is maintained by a highly regulated level of λ repressor protein, CI, which represses lytic functions. CI regulates its own synthesis in a lysogen by activating and repressing its promoter, PRM. CI participates in long-range interactions involving two regions of widely separated operator sites by generating a loop in the intervening DNA. We investigated the roles of each individual site under conditions that permitted DNA loop formation by using in vitro transcription assays for the first time on supercoiled DNA that mimics in vivo situation. We confirmed that DNA loops generated by oligomerization of CI bound to its operators influence the autoactivation and autorepression of PRM regulation. We additionally report that different configurations of DNA loops are central to this regulation—one configuration further enhances autoactivation and another is essential for autorepression of PRM.

Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage lambda

The tethered particle motion (TPM) technique has attracted great interest because of its simplicity and the wealth of information that it can provide on protein-induced conformational changes in nucleic acids. Here we present an approach to TPM methodology and analysis that increases the efficiency of data acquisition and facilitates interpretation of TPM assays. In particular, the statistical analysis that we propose allows fast data processing, minimal data selection and visual display of the distribution of molecular behaviour. The methodology proved useful in verifying CI protein-mediated DNA looping in bacteriophage λ and in differentiating between two different types of loops, stable and dynamic, whose relative occurrence seems to be a function of the distance between the operators as well as their relative angular orientation. Furthermore, the statistical analysis indicates that CI binding per se slightly shortens the DNA.

Alignment of biological microparticles by a polarized laser beam

The optical alignment of biological samples is of great relevance to microspectrometry and to the micromanipulation of single particles. Recently, Bayoudh et al. (J. Mod. Opt. 50:1581–1590, 2003) have shown that isolated, disk-shaped chloroplasts can be aligned in a controlled manner using an in-plane-polarized Gaussian beam trap, and suggested that this is due to their nonspherical shape. Here we demonstrate that the orientation of various micrometer-sized isolated biological particles, trapped by optical tweezers, can be altered in a controlled way by changing the plane of linear polarization of the tweezers. In addition to chloroplasts, we show that subchloroplast particles of small size and irregular overall shape, aggregated photosynthetic light-harvesting protein complexes as well as chromosomes can be oriented with the linearly polarized beam of the tweezers. By using a laser scanning confocal microscope equipped with a differential polarization attachment, we also measured the birefringence of magnetically oriented granal chloroplasts, and found that they exhibit strong birefringence with large local variations, which appears to originate from stacked membranes. The size and sign of the birefringence are such that the resulting anisotropic interaction with the linearly polarized laser beam significantly contributes to the torque orienting the chloroplasts.