Identification and characterization of the mitochondrial RNA polymerase and transcription factor in the fission yeast Schizosaccharomyces pombe

We have characterized the mitochondrial transcription factor (Mtf1) and RNA polymerase (Rpo41) of Schizosaccharomyces pombe. Deletion mutants show Mtf1 or Rpo41 to be essential for cell growth, cell morphology and mitochondrial membrane potential. Overexpression of Mtf1 and Rpo41 can induce mitochondrial transcription. Mtf1 and Rpo41 can bind and transcribe mitochondrial promoters in vitro and the initiating nucleotides were the same in vivo and in vitro. Mtf1 is required for efficient transcription. We discuss the functional differences between Mtf1 and Rpo41 of S. pombe with Saccharomyces cerevisiae and higher organisms. In contrast to S. cerevisiae, the established model for mitochondrial transcription, S. pombe, a petite-negative yeast, resembles higher organisms that cannot tolerate the loss of mitochondrial function. The S. pombe and human mitochondrial genomes are similar in size and much smaller than that of S. cerevisiae. This is an important first step in the development of S. pombe as an alternative and complementary model system for molecular genetic and biochemical studies of mitochondrial transcription and mitochondrial–nuclear interactions. This is the first systematic study of the cellular function and biochemistry of Rpo41 and Mtf1 in S. pombe

Sedimentology and accumulation rates of ODP Site 184-1143 in the South China Sea (Appendix B)

128 samples from Ocean Drilling Program (ODP) Site 1143 in the southern South China Sea were analyzed for grain size, clay minerals, biogenic opal content and quartz in order to reconstruct changes in East Asian monsoon climate since 8.5 Ma. An abrupt change of terrigenous mass accumulation rate (MAR), clay mineral assemblage, median grain size and biogenic opal MAR about 5.2 Ma suggests that between 8.5-5.2 Ma the source of terrigenous sediment was mainly in the region of surface uplift and basaltic volcanism in southern Vietnam. A simple model of East Asian summer monsoon evolution was based on the clay/feldspar ratio, kaolinite/chlorite ratio and biogenic opal MAR. The summer monsoon has two periods of maximum strength at 8.5-7.6 Ma and 7.1-6.2 Ma. Subsequently, there was a relatively stable period at 6.2-3.5 Ma, continued intensification about 3.5-2.5 Ma, and gradually weakening after 2.5 Ma. Since 1 Ma the monsoon has intensified, with remarkable high-frequency and amplitude variability. Simultaneous increase in sedimentation rates at ODP Sites 1143, 1146 and 1148, as well as in MAR of terrigenous materials, quartz, feldspar and clay minerals at ODP Site 1143 at 3.5-2.5 Ma, may be the erosional response to both global climatic deterioration and the strengthening of the East Asian summer monsoon after about 3-4 Ma

Development of the East Asian summer monsoon: Evidence from the sediment record in the South China Sea since 8.5 Ma

128 samples from Ocean Drilling Program (ODP) Site 1143 in the southern South China Sea were analyzed for grain size, clay minerals, biogenic opal content and quartz in order to reconstruct changes in East Asian monsoon climate since 8.5 Ma. An abrupt change of terrigenous mass accumulation rate (MAR), clay mineral assemblage, median grain size and biogenic opal MAR about 5.2 Ma suggests that between 8.5-5.2 Ma the source of terrigenous sediment was mainly in the region of surface uplift and basaltic volcanism in southern Vietnam. A simple model of East Asian summer monsoon evolution was based on the clay/feldspar ratio, kaolinite/chlorite ratio and biogenic opal MAR. The summer monsoon has two periods of maximum strength at 8.5-7.6 Ma and 7.1-6.2 Ma. Subsequently, there was a relatively stable period at 6.2-3.5 Ma, continued intensification about 3.5-2.5 Ma, and gradually weakening after 2.5 Ma. Since 1 Ma the monsoon has intensified, with remarkable high-frequency and amplitude variability. Simultaneous increase in sedimentation rates at ODP Sites 1143, 1146 and 1148, as well as in MAR of terrigenous materials, quartz, feldspar and clay minerals at ODP Site 1143 at 3.5-2.5 Ma, may be the erosional response to both global climatic deterioration and the strengthening of the East Asian summer monsoon after about 3-4 Ma. © 2006 Elsevier B.V. All rights reserved

Exploiting the Symmetry of Zn\mathbb{Z}^n: Randomization and the Automorphism Problem

$\mathbb{Z}^n$ is one of the simplest types of lattices, but the computational problems on its rotations, such as $\mathbb{Z}$SVP and $\mathbb{Z}$LIP, have been of great interest in cryptography. Recent advances have been made in building cryptographic primitives based on these problems, as well as in developing new algorithms for solving them. However, the theoretical complexity of $\mathbb{Z}$SVP and $\mathbb{Z}$LIP are still not well understood. In this work, we study the problems on rotations of $\mathbb{Z}^n$ by exploiting the symmetry property. We introduce a randomization framework that can be roughly viewed as `applying random automorphisms’ to the output of an oracle, without accessing the automorphism group. Using this framework, we obtain new reduction results for rotations of $\mathbb{Z}^n$. First, we present a reduction from $\mathbb{Z}$LIP to $\mathbb{Z}$SCVP. Here $\mathbb{Z}$SCVP is the problem of finding the shortest characteristic vectors, which is a special case of CVP where the target vector is a deep hole of the lattice. Moreover, we prove a reduction from $\mathbb{Z}$SVP to $\gamma$-$\mathbb{Z}$SVP for any constant $\gamma = O(1)$ in the same dimension, which implies that $\mathbb{Z}$SVP is as hard as its approximate version for any constant approximation factor. Second, we investigate the problem of finding a nontrivial automorphism for a given lattice, which is called LAP. Specifically, we use the randomization framework to show that $\mathbb{Z}$LAP is as hard as $\mathbb{Z}$LIP. We note that our result can be viewed as a $\mathbb{Z}^n$-analogue of Lenstra and Silverberg\u27s result in [JoC2017], but with a different assumption: they assume the $G$-lattice structure, while we assume the access to an oracle that outputs a nontrivial automorphism

Substrate Recognition and Modification by the Nosiheptide Resistance Methyltransferase

<div><p>Background</p><p>The proliferation of antibiotic resistant pathogens is an increasing threat to the general public. Resistance may be conferred by a number of mechanisms including covalent or mutational modification of the antibiotic binding site, covalent modification of the drug, or the over-expression of efflux pumps. The nosiheptide resistance methyltransferase (NHR) confers resistance to the thiazole antibiotic nosiheptide in the nosiheptide producer organism Streptomyces actuosus through 2ʹO-methylation of 23S rRNA at the nucleotide A1067. Although the crystal structures of NHR and the closely related thiostrepton-resistance methyltransferase (TSR) in complex with the cofactor S-Adenosyl-L-methionine (SAM) are available, the principles behind NHR substrate recognition and catalysis remain unclear.</p><p>Methodology/Principal Findings</p><p>We have analyzed the binding interactions between NHR and model 58 and 29 nucleotide substrate RNAs by gel electrophoresis mobility shift assays (EMSA) and fluorescence anisotropy. We show that the enzyme binds to RNA as a dimer. By constructing a hetero-dimer complex composed of one wild-type subunit and one inactive mutant NHR-R135A subunit, we show that only one functional subunit of the NHR homodimer is required for its enzymatic activity. Mutational analysis suggests that the interactions between neighbouring bases (G1068 and U1066) and A1067 have an important role in methyltransfer activity, such that the substitution of a deoxy sugar spacer (5ʹ) to the target nucleotide achieved near wild-type levels of methylation. A series of atomic substitutions at specific positions on the substrate adenine show that local base-base interactions between neighbouring bases are important for methylation.</p><p>Conclusion/Significance</p><p>Taken together these data suggest that local base-base interactions play an important role in aligning the substrate 2’ hydroxyl group of A1067 for methyl group transfer. Methylation of nucleic acids is playing an increasingly important role in fundamental biological processes and we anticipate that the approach outlined in this manuscript may be useful for investigating other classes of nucleic acid methyltransferases.</p></div

Comparison of binding and methylation activity on model RNA substrates by NHR.

<p>Comparison of binding (Kd) and methylation activity (Km) on model 29 nt and 58 nt RNA substrates by NHR.</p><p>Comparison of binding and methylation activity on model RNA substrates by NHR.</p

Investigation of neighbouring group influence on methylation of 29 nt substrate RNA.

<p><b>A.</b> The 29 nt hairpin substrate, with A1067 and positions in the loop marked. <b>B.</b> The relative specificity for methylation of mutated nucleotides positioned 3′ to A1067. <b>C.</b> The relative specificity for methylation of mutated nucleotides located 5′ to A1067. <b>D.</b> Structure of the abasic deoxy (ds-linker) linker, that was used to replace U1066 (1066ds) and G1068 (1068ds). <b>E.</b> The relative specificity for methylation of linker modified 1066ds and 1068ds RNA.</p