Novel DNA–peptide interaction networks

Allostery in the binding of peptides to DNA has been studied by quantitative DNase I footprinting using four newly designed peptides containing the XP(Hyp)RK motif and N-methylpyrrole (Py) moieties. Apparent binding constants in the micromolar range as well as Hill coefficients were determined for each peptide. The results, together with previous studies on five other peptides support the proposal that interaction network cooperativity is highly preferred in DNA–peptide interactions that involve multiple recognition sites. It is envisaged that interstrand bidentate interactions participate in the relay of conformational changes between recognition sites on the complementary strands. Models for interpreting DNA allostery based upon interaction networks are outlined. Circular dichroism experiments involving the titration of peptides against a short oligonucleotide duplex indicate that some of these peptides bind in a dimeric manner to DNA via the minor groove, inducing characteristic conformational changes. These insights should prompt the design of new DNA-binding peptides for investigating allosteric interactions between peptides and DNA, as well as novel interaction networks, and ultimately may shed light upon the fundamental chemical rules that govern allostery in more complex biological process such as DNA–protein interaction networks.     

Detection of multiple network-based allosteric interactions between peptides and arrays of DNA binding sites

Quantitative DNase I footprinting shows that three designed peptides containing N-methylpyrrole (Py) moieties display different types of network-based allosteric communication in binding to DNA: circuit type, incomplete-circuit type, and non-circuit type characterized by interstrand bidentate interactions. Positive cooperative binding of all three peptides to individual DNA binding sites is commonly observed. CD spectral characterization of the interaction between peptides and model undecanucleotide duplexes is consistent with the footprinting results and supports the allosteric model. This study provides insights relating to the interaction network nature of allostery in complex DNA–small molecule interactions.     

Design, synthesis, and testing of potential antisickling agents. 9. Cyclic tetrapeptide homologs as mimics of the mutation site of hemoglobin S

As part of our continuing search for new agents which might be useful for the treatment of sickle-cell anemia, we have synthesized two cyclic tetrapeptide homologs, cyclo(-Val-Glu[-Thr-Pro-]-OH) (1a) and cyclo(-Phe-Glu[-Thr-Pro-]-OH (1b), and a tetrapeptide lactone homolog cyclo(H-Thr-Pro-Val-Glu-OH) (2). The intent was that these peptides would mimic a tetrapeptide region around the mutation site of HbS and thus be able to bind at the acceptor site of HbS and thereby inhibit polymerization. The synthesis of the linear peptides was accomplished in solution using both the polymeric reagent (PHBT) and DCC/HOBT methods; cyclization was accomplished by an improved method. 13C-n.m.r. studies were performed which allowed us to assign the conformation about the Thr-Pro bond in 1a and 2 as trans. The cyclic peptides were tested for their ability to increase the solubility of HbS under deoxygenating conditions, but only 1a had any antigelling activity, albeit low.     

Reovirus outer capsid protein micro1 induces apoptosis and associates with lipid droplets, endoplasmic reticulum, and mitochondria

The mechanisms by which reoviruses induce apoptosis have not been fully elucidated. Earlier studies identified the mammalian reovirus S1 and M2 genes as determinants of apoptosis induction. However, no published results have demonstrated the capacities of the proteins encoded by these genes to induce apoptosis, either independently or in combination, in the absence of reovirus infection. Here we report that the mammalian reovirus micro1 protein, encoded by the M2 gene, was sufficient to induce apoptosis in transfected cells. We also found that micro1 localized to lipid droplets, endoplasmic reticulum, and mitochondria in both transfected cells and infected cells. Two small regions encompassing amphipathic alpha-helices within a carboxyl-terminal portion of micro1 were necessary for efficient induction of apoptosis and association with lipid droplets, endoplasmic reticulum, and mitochondria in transfected cells. Induction of apoptosis by micro1 and its association with lipid droplets and intracellular membranes in transfected cells were abrogated when micro1 was coexpressed with sigma3, with which it is known to coassemble. We propose that micro1 plays a direct role in the induction of apoptosis in infected cells and that this property may relate to the capacity of micro1 to associate with intracellular membranes. Moreover, during reovirus infection, association with sigma3 may regulate apoptosis induction by micro1.     

Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild‐to‐weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed‐shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.     

中国伞形科两新种

本文记载了产于我国云南的亮蛇床属植物新种长萼亮蛇床和四川前胡属新种木里前胡。     

High-resolution proton nuclear magnetic resonance studies of the glucocerebrosidase activator protein from Gaucher spleen

A heat-stable protein factor (HSF) obtained from the spleen of a patient with Gaucher's disease that activates glucocerebrosidase was studied by 600-MHz proton NMR spectroscopy. Assignments for a number of aromatic and aliphatic resonances were made on the basis of spin-decoupling, pH-titration, and resolution-enhancement experiments. The upfield ring current shifted aliphatic region and the downfield aromatic region were examined by nuclear Overhauser effect (NOE) methods using both pulsed Fourier-transform spectroscopy and correlation spectroscopy. It was found that a number of upfield-shifted methyl groups and certain methylene groups of specific aliphatic amino acid residues are in proximity relationships with several aromatic residues, forming a compact hydrophobic clustering site. Of special interest, tyrosine A, phenylalanine A, tryptophan B1, and tryptophan B2 were found to be located close to a cluster of aliphatic residues, indicating that the hydrophobic site of the HSF is conformationally rigid and its tertiary structure very compact. A two-dimensional structural model of the hydrophobic site of HSF is proposed.     

LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers

Plant genetic resources often constitute the foundation of successful breeding programs. Pepper (Capsicum annuum L.) is one of the most economically important and diversely utilized Solanaceous crop species worldwide, but less studied compared to tomato and potato. We developed and used molecular markers based on two copia-type retrotransposons, Tnt1 and T135, in a set of Capsicum species and wild relatives from diverse geographical origins. Results showed that Tnt1 and T135 insertion polymorphisms are very useful for studying genetic diversity and relationships within and among pepper species. Clusters of accessions correspond to cultivar types based on fruit shape, pungency, geographic origin and pedigree. Genetic diversity values, normally reflective of past transposition activity and population dynamics, showed positive correlation with the average number of insertions per accession. Similar evolutionary relationships are observed to that inferred by previous karyosystematics studies. These observations support the possibility that retrotransposons have contributed to genome inflation during Capsicum evolution.     

Cytotaxonomy of Ferula L. in China

The karyotypes of somatic cells of three species in Ferula L. (Umbelliferae) from China are reported for the first time in this paper. F. licentiana Hand. -Mazz., endemic to China, has the karyotype formula of 2n= 22= 14m+ 2sm+ 6st( 2SAT), which consists of nine pairs of L chromosomes (the relative length > 8.0) and two pairs of M chromosomes (the relative length, 8.0- 6.0). The index of the karyotypic asymmetry (AS. K%) is 36.36%, and the karyotype belongs to 2A (Stebbins 1971). F. licentiana var. tunshanica (Su) Shan et Q. X. Liu has the karyotypic formula of 2n=22= 14m+ 8st(2SAT), and the other characters of karyotype are very similar to those of F. licentiana. The karyotypic formula of F. bungeana Kitag. is 2n=22= 12m+ 6sm+ 2st. There are 8 pairs of L chromosomes and 3 pairs of M chromosomes in this karyotype. The AS.K% is 45.45% and thus the karyotype is rather symmetrical (2A). Based on above data, F.licentiana var. tunshanica may be treated as a variety of F.licentiana and F.bungeana be separated from Subgen. Peucedanoides. According to our study and available data, we consider that the basic chromosome number of Ferula is x= 11. The karyotypic evolution of 11 species in the genus from China is analysed. All species are grouped into 5 groups based on the cluster analysis of chromosome data: I.F. akitschensis B. Fedtsch. ex K.-Pol.; II. F. lapidosa Korov., III. F. bungeana. The above-mentioned three species belong to Subgen. Peucedanoides in classification. IV. This group is divided into two subgroups: (1) F. syreitschikowii K.-Pol. and F. ovina (Boiss.) Boiss.; (2) F. lehmannii Boiss., F. licentiana, F. licentiana var. tunshanica, F. Kirialovii Pimen. and F. sumbul (Kauffm.)Hook. f., in which F.lehmannii belongs to Subgen. Merwia, F. syteritschikowii to Subgen. Narthex and the rest five species to Subgen.Peucedanoides. V. F.caspica M. Bieb. of Subgen. Doromatoides.     

Cyclorhiza and Chuanminshen—Two newly proposed genera in Umbelliferae (Apiaceae)

Cyclorhiza, a new genus based upon Ligusticum waltonii Wolff, is here proposed. From the ample materials now in our herbarium, we found that the genus differs from the species of Ligusticum. As the result of our study, the systematic position of this new genus should be considered as a member of the tribe Smyrnieae Koch. Chuanminshen, another new monotypic genus, is here also proposed. It was often considered as not different from Changium Wolff, but it is a cleary deliminated natural genus being quite remote from Changium Wolff. This new genus is quite reasonably to be placed in the tribePeucedaneae.