Stability of the ‘L12 stalk’ in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria

The ribosomal stalk complex, consisting of one molecule of L10 and four or six molecules of L12, is attached to 23S rRNA via protein L10. This complex forms the so-called ‘L12 stalk’ on the 50S ribosomal subunit. Ribosomal protein L11 binds to the same region of 23S rRNA and is located at the base of the ‘L12 stalk’. The ‘L12 stalk’ plays a key role in the interaction of the ribosome with translation factors. In this study stalk complexes from mesophilic and (hyper)thermophilic species of the archaeal genus Methanococcus and from the Archaeon Sulfolobus solfataricus, as well as from the Bacteria Escherichia coli, Geobacillus stearothermophilus and Thermus thermophilus, were overproduced in E.coli and purified under non-denaturing conditions. Using filter-binding assays the affinities of the archaeal and bacterial complexes to their specific 23S rRNA target site were analyzed at different pH, ionic strength and temperature. Affinities of both archaeal and bacterial complexes for 23S rRNA vary by more than two orders of magnitude, correlating very well with the growth temperatures of the organisms. A cooperative effect of binding to 23S rRNA of protein L11 and the L10/L12(4) complex from mesophilic and thermophilic Archaea was shown to be temperature-dependent

A SUMO-regulated activation function controls synergy of c-Myb through a repressor–activator switch leading to differential p300 recruitment

Synergy between transcription factors operating together on complex promoters is a key aspect of gene activation. The ability of specific factors to synergize is restricted by sumoylation (synergy control, SC). Focusing on the haematopoietic transcription factor c-Myb, we found evidence for a strong SC linked to SUMO-conjugation in its negative regulatory domain (NRD), while AMV v-Myb has escaped this control. Mechanistic studies revealed a SUMO-dependent switch in the function of NRD. When NRD is sumoylated, the activity of c-Myb is reduced. When sumoylation is abolished, NRD switches into being activating, providing the factor with a second activation function (AF). Thus, c-Myb harbours two AFs, one that is constitutively active and one in the NRD being SUMO-regulated (SRAF). This double AF augments c-Myb synergy at compound natural promoters. A similar SUMO-dependent switch was observed in the regulatory domains of Sp3 and p53. We show that the change in synergy behaviour correlates with a SUMO-dependent differential recruitment of p300 and a corresponding local change in histone H3 and H4 acetylation. We therefore propose a general model for SUMO-mediated SC, where SUMO controls synergy by determining the number and strength of AFs associated with a promoter leading to differential chromatin signatures

A functional SUMO-interacting motif in the transactivation domain of c-Myb regulates its myeloid transforming ability

c-Myb is an essential hematopoietic transcription factor that controls proliferation and differentiation of progenitors during blood cell development. Whereas sumoylation of the C-terminal regulatory domain (CRD) is known to have a major impact on the activity of c-Myb, no role for noncovalent binding of small ubiquitin-like modifier (SUMO) to c-Myb has been described. Based on the consensus SUMO-interacting motif (SIM), we identified and examined putative SIMs in human c-Myb. Interaction and reporter assays showed that the SIM in the in the transactivation domain of c-Myb (V 267 NIV) is functional. This motif is necessary for c-Myb to be able to interact noncovalently with SUMO, preferentially SUMO2/3. Destroying the SUMO-binding properties by mutation resulted in a large increase in the transactivation potential of c-Myb. Mutational analysis and overexpression of conjugation-defective SUMO argued against intramolecular repression caused by sumoylated CRD and in favor of SUMO-dependent repression in trans. Using both a myeloid cell line-based assay and a primary hematopoietic cell assay, we addressed the transforming abilities of SUMO binding and conjugation mutants. Interestingly, only loss of SUMO binding, and not SUMO conjugation, enhanced the myeloid transformational potential of c-Myb. c-Myb with the SIM mutated conferred a higher proliferative ability than the wild-type and caused an effective differentiation block. This establishes SUMO binding as a mechanism involved in modulating the transactivation activity of c-Myb, and responsible for keeping the transforming potential of the oncoprotein in check

Anatomy of Escherichia coli σ(70) promoters

Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base −7, rather than −11, of the −10 may be flipping to initiate transcription. We found that the sequence conservation of σ(70) binding sites is 6.5 ± 0.1 bits. Some promoters lack a −35 region, but have a 6.7 ± 0.2 bit extended −10, almost the same information as the bipartite promoter. These results and similarities between the contacts in the extended −10 binding and the −35 suggest that the flexible bipartite σ factor evolved from a simpler polymerase. Binding predicted by the bipartite model is enriched around 35 bases upstream of the translational start. This distance is the smallest 5′ mRNA leader necessary for ribosome binding, suggesting that selective pressure minimizes transcript length. The promoter model was combined with models of the transcription factors Fur and Lrp to locate new promoters, to quantify promoter strengths, and to predict activation and repression. Finally, the DNA-bending proteins Fis, H-NS and IHF frequently have sites within one DNA persistence length from the −35, so bending allows distal activators to reach the polymerase

Changes in seismic velocity and apparent attenuation due to isotropic and anisotropic scattering : results from physical modeling

Much work is presently being done concerning small scale heterogeneities in the earth's crust. These heterogeneities range from pores in sedimentary rocks up to fluctuations in the density and seismic constants of the earth's crust with scale lengths of kilometers. The ability to study and quantify these heterogeneities using seismic methods would be a major advance in the earth sciences. Physical modeling has been shown to be a useful technique for investigating various aspects of wave propagation. In this thesis, two physical modeling experiments (one three-dimensional and one two-dimensional) are used to investigate the scattering of seismic waves from small scale heterogeneities and the changes in seismic velocity and apparent attenuation resulting from this scattering. The effects of both isotropic and anisotropic scattering on velocity and apparent attenuation are calculated. These experimental results are compared to theoretical results. The theory used for isotropic scattering for the three-dimensional experiment is a modified version of Wu's single scattering theory, where instead of calculating the scattering for a single scatterer using the Born approximation, the exact results for scattering from a cylindrical shape are used. While the results for compressional waves and both components of shear waves compare reasonably well for small scatterer volume fractions, at larger scatterer volume fractions, where the need for multiple scattering is more likely, the results for all waves do not compare as well. Many theories used to test anisotropic scattering predict changes in velocity rather than changes in apparent attenuation. The velocity changes are used primarily in this work due to geometrical focusing by a seismic lens that biases the amplitudes (and hence the estimates of apparent attenuation) at low frequencies where most theories predict apparent attenuation. Velocities are calculated from the data using travel times and low frequency phase shifts for the compressional waves and for one component of the shear waves measured in this two-dimensional experiment. Theories that are used to predict compressional and shear wave velocities for both isotropic and anisotropic scatterers are based on a fractional volume method (isotropic), two crack methods (isotropic and anisotropic), and a finely layered method (anisotropic). The isotropic experimental results have much larger, non-linear changes in the velocities than do the isotropic theoretical results. The anisotropic experimental results have similar shapes to both theoretical anisotropic methods for compressional waves and to the theoretical anisotropic crack method for shear waves. Attenuation is computed using log spectral ratios and compares as well with the theoretical results as can be expected within the limits set. A method using anisotropic apparent attenuation to help quantify the scatterers is developed for use with field data