Functional constraints of nuclear-mitochondrial DNA interactions in xenomitochondrial rodent cell lines

The co-evolution of nuclear and mitochondrial genomes in vertebrates led to more than 100 specific interactions that are crucial for an optimized ATP generation. These interactions have been examined by introducing rat mtDNA into mouse cells devoid of mitochondrial DNA (mtDNA). When mtDNA-less cells derived from the common mouse (Mus musculus domesticus) were fused to cytoplasts prepared from Mus musculus, Mus spretus, or rat (Rattus norvegicus), a comparable number of respiring clones could be obtained. Mouse xenomitochondrial cybrids harboring rat mtDNA had a slower growth rate in medium containing galactose as the carbon source, suggesting a defect in oxidative phosphorylation. These clones respired approximately 50% less than the parental mouse cells or xenomitochondrial cybrids harboring Mus spretus mtDNA. The activities of respiratory complexes I and IV were approximately 50% lower, but mitochondrial protein synthesis was unaffected. The defects in complexes I and IV were associated with decreased steady-state levels of respective subunits suggesting problems in assembly. We also showed that the presence of 10% mouse mtDNA co-existing with rat mtDNA was sufficient to restore respiration to normal levels. Our results suggest that evolutionary distance alone is not a precise predictor of nuclear-mitochondrial interactions as previously suggested for primates.     

Diversity in protein-protein interactions of connexins: emerging roles

Gap junctions, specialised membrane structures that mediate cell-to-cell communication in almost all tissues, are composed of channel-forming integral membrane proteins termed connexins. The activity of these intercellular channels is closely regulated, particularly by intramolecular modifications as phosphorylations of proteins by protein kinases, which appear to regulate the gap junction at several levels, including assembly of channels in the plasma membrane, connexin turnover as well as directly affecting the opening and closure ("gating") of channels. The regulation of membrane channels by protein phosphorylation/dephosphorylation processes commonly requires the formation of a multiprotein complex, where pore-forming subunits bind to auxiliary proteins (e.g. scaffolding proteins, catalytic and regulatory subunits), that play essential roles in channel localisation and activity, linking signalling enzymes, substrates and effectors into a structure frequently anchored to the cytoskeleton. The present review summarises the up-to-date progress regarding the proteins capable of interacting or at least of co-localising with connexins and their functional importance.     

Bladder tumours among rodent operatives handling ANTU.

The rodenticide ANTU (alpha-naphthylthiourea) was used in the United Kingdom mainly in the late 1940s and early 1950s. The product then contained up to 0.2% of beta-naphthylamine as an impurity, and it was finally withdrawn in 1967 as a suspected carcinogen. Fourteen cases of urothelial tumours among rodent operatives exposed to ANTU are reported: in one district four out of 27 staff were affected, and in another area two out of 10. These cases strongly suggest that the early ANTU manufactured in the United Kingdom posed a cancer hazard to users. ANTU is still made or used in various countries, though the current product may be relatively pure and no longer contaminated by beta-naphthylamine. Recent laboratory evidence shows that even pure ANTU is mutagenic in the Ames test, and the safety of this rodenticide may need review.     

Cellular interactions determine neuronal phenotypes in rodent retinal cultures.

Progenitor cells isolated from early rat embryo retinas differentiate into phenotypes normally generated early in retinal development (e.g., ganglion cells), whereas progenitors isolated from postnatal retinas differentiate into later-generated retinal cell types (e.g., rod photoreceptors; Reh and Kljavin, J. Neurosci. 9:4179-4189; 1989; Adler and Hatlee, 1989; Science 243:391-393; Sparrow, Hicks, and Barnstable, 1990, Dev. Brain Res. 51:69-84). To determine whether this change in committment is intrinsic to the progenitor cells, or alternatively can be modified by interactions with their developing environment, I co-cultured mouse and rat retinal cells, from different developmental stages, and identified the resulting phenotypes with species-specific and cell class-specific antibodies. I found that the phenotypes into which mouse neuroepithelial cells differentiate depends on the phenotypes of the rat cells that surround them. Retinal precursor cells from embryonic day (E) 10-12 will adopt the rod photoreceptor phenotype only when close to cells expressing this phenotype. By contrast, when the E10-12 retinal progenitor cells are cultured with cells from the cerebral cortex, they differentiate primarily into large multipolar neurons, similar in their morphology and antigen expression to retinal ganglion cells. These results indicate that interactions among the cells of the developing retina are important in the determination of cell fate.     

Host-parasite interactions in rodent nematode infections

In rodents, Trichinella spiralis and Nippostrongylus brasiliensis infect the small intestine and Trichuris muris resides in the colon. The intestinal host response in these animals is characterized by changes in mucosal architecture and inflammation and is associated with worm expulsion. The requirement of T cell-mediated host response in worm expulsion has been demonstrated over many years. Subsequent studies have shown that Th2-type, but not Th1-type, responses mediate resistance to the nematodes. Investigations using neutralizing antibodies and genetically manipulated mice have characterized the contribution of individual Th2-type cytokines in not only worm expulsion, but also specific cellular changes that occur in the mucosa, such as alterations in epithelial phenotype and smooth muscle. There is also increasing appreciation of the contribution of non-bone marrow-derived cells in innate and adaptive host responses in these models.     

Kinetics of protein-protein interactions of connexins: use of enzyme linked sorbent assays

Determination of the protein-protein interactions of connexins has become a rapidly expanding field of research. While there are multiple methods of determining the identity of binding partners, determination of the strengths of interactions is not as simple. Here we describe the use of the in vitro method Enzyme Linked Sorbent Assay (ELSA) to compare binding affinities of known protein partners for Connexin43. We used the binding of Cx43 Carboxyl Terminal domain to the PDZ-2 domain of Zonula Occludens-1 and to the SH3 domain of c-Src. In the ELSA assay we found that while the binding of the SH3 domain of c-Src is pH-dependent, the interaction of the PDZ domain of ZO-1 is not. These data confirm findings using Surface Plasmon Resonance (1) and indicate that ELSA can be a useful tool in determining the kinetics of protein-protein interactions.     

Functional asymmetries in the rodent barrel cortex

Neurophysiological and 2-deoxyglucose (2DG) studies of the rodent whisker barrel cortex have demonstrated asymmetries in its functional organization. To examine the possibility that the activity gradients observed in metabolic studies can be attributed to subtle rostral-caudal and dorsal-ventral asymmetries in electrophysiologically measured surround or cross-whisker inhibition, we compared 2DG results with predictions generated from quantitative single-cell receptive field data. Despite differences in the two experimental approaches, there is remarkable agreement between the findings. (1) The distribution of 2DG activity declines across the barrel cortex of the behaving animal from anteromedial barrels to posterolateral barrels, and is qualitatively and quantitatively similar to the values predicted from neurophysiology. (2) The strength of surround inhibition in barrel neurons predicts the twofold increase in activation of the C3 barrel following acute clipping of adjacent whiskers. And (3) within a cortical column, the decrease in metabolic activity associated with adjacent whisker stimulation is greatest in layer IV and least in the infragranular layers; this corresponds to the laminar distribution of inhibitory interactions observed electrophysiologically.     

Identification of synergistic interactions among microorganisms in biofilms by digital image analysis.

Digital image analysis showed that reductions in biofilm plating efficiency were due to the loss of protection provided by two benzoate-degrading strains of Pseudomonas fluorescens. This loss in protection was due to the spatial separation of the protective organisms from benzoate-sensitive organisms during the dilution process. Communities were cultivated in flow cells irrigated with trypticase soy broth. When the effluent from these flow cells was plated on 0.15% benzoic acid, satellite colonies formed only in the vicinity of primary colonies. A digital image analysis procedure was developed to measure the size and spatial distribution of these satellites as a function of distance from the primary colony. The size of satellites served as a measure of growth, and the number per unit area served as a measure of survival. At the three dilutions tested, the size and concentration of satellite colonies varied inversely with distance from the primary colonies. When these measurements were plotted, the slopes were used to quantify the effect of bacterial association on the growth and survivability of the satellites. In the absence of the primary colonies, satellites grew in axenic culture only at low benzoate concentrations. Thus benzoate-degrading organisms are capable of creating a protective microenvironment for other members of biofilm communities.     

Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water.

The light-driven proton pump, bacteriorhodopsin (bR) contains a retinal molecule with a Schiff base moiety that can participate in hydrogen-bonding interactions in an internal, water-containing channel. Here we combine quantum chemistry and molecular mechanics techniques to determine the geometries and energetics of retinal Schiff base-water interactions. Ab initio molecular orbital calculations are used to determine potential surfaces for water-Schiff base hydrogen-bonding and to characterize the energetics of rotation of the C-C single bond distal and adjacent to the Schiff base NH group. The ab initio results are combined with semiempirical quantum chemistry calculations to produce a data set used for the parameterization of a molecular mechanics energy function for retinal. Using the molecular mechanics force field the hydrated retinal and associated bR protein environment are energy-minimized and the resulting geometries examined. Two distinct sites are found in which water molecules can have hydrogen-bonding interactions with the Schiff base: one near the NH group of the Schiff base in a polar region directed towards the extracellular side, and the other near a retinal CH group in a relatively nonpolar region, directed towards the cytoplasmic side.     

Conservation of RNA-protein interactions among picornaviruses.

Picornavirus genomes encode unique 5' noncoding regions (5' NCRs) which are approximately 600 to 1,300 nucleotides in length, contain multiple upstream AUG codons, and display the ability to form extensive secondary structures. A number of recent reports have shown that picornavirus 5' NCRs are able to facilitate cap-independent internal initiation of translation. This mechanism of translation occurs in the absence of viral gene products, suggesting that the host cell contains the necessary components for the cap-independent internal initiation of translation of picornavirus RNAs as well as cellular mRNAs. In an attempt to identify some of the perhaps novel cellular proteins involved in this newly discovered mechanism of translation, we utilized RNA mobility shifts assays to identify and characterize interactions that occur between the 5'NCR of poliovirus type 1 (PV1) and cellular proteins. In this report, we describe two separate interactions between RNA structures from the 5' NCR of PV1 and proteins present in extracts from HeLa cells as well as other cell types. We describe the interaction between nucleotides 186 to 220 (stem-loop D) and a cellular protein(s) present in HeLa cell extracts. Mutational analysis of this stem-loop structure suggests that maintenance of a base-paired structure in the lower stem is necessary to present the sequences which directly interact with the protein(s). We also describe the interaction between nucleotides 220 to 460 (stem-loop E) and a cellular protein present in HeLa cell extracts. This RNA binding activity fractionates to a specific ammonium sulfate fraction (A cut) of a ribosomal salt wash. Mutational analysis of the stem-loop E structure suggests that the preservation of an extensive RNA structure is necessary for a strong interaction with the cellular protein(s), although smaller RNAs derived from this region of the 5' NCR can interact to lesser extents. Finally, we show that both of these RNA-protein interactions are conserved among the closely related enteroviruses PV1 and coxsackievirus type B3, human rhinovirus type 14, and the more distantly related cardiovirus Theiler's murine encephalomyelitis virus, suggesting that such RNA-protein interactions serve basic functions which are conserved and utilized by each of these picornaviruses.     

Genome analysis for nucleotide interactions in fully sequenced genomes of selective prokaryotes

Fully sequenced prokaryotic genomes ofEscherichia coli, Haemophilus influenzae andMethanococcus janaschii were subjected .to genome analysis for nucleotide interactions. The analysis was restricted to inter-nucleotide relations like two nucleotides in a dinucleotide, three nucleotides in a codon and two codons in a dicon. This relational analysis was carried out in C language and was compiled on a C++ compiler. The relational analysis showed a preferential dinucleotide frequency (the observed frequencies of AA and TT were higher than the expected frequency and the observed frequencies of CC and GG). From codon frequency distribution analysis, sub-codonic elements have been noticed, exerting that the first one or first two nucleotide may reasonably determine the next nucleotide(s) in a codon. The analysis further reveals the existence of short-range randomness or chaotic behaviour in prokaryotic genomes, which might be a forerunner for the origin of introns in eukaryotes, besides being involved in a regulatory role.     

Functional interactions of an Escherichia coli ribosomal ATPase.

The gene encoding ribosome-bound ATPase (RbbA), which occurs bound to 70S ribosomes and 30S subunits, has been identified. The amino-acid sequence of RbbA reveals the presence of two ATP-binding domains in the N-terminal half of the protein. RbbA harbors an intrinsic ATPase activity that is stimulated by both 70S ribosomes and 30S subunits. Here we show that purified recombinant RbbA markedly stimulates polyphenylalanine synthesis in the presence of the elongation factors Tu and G (EF-Tu and EF-G) and that the hydrolysis of ATP by RbbA is required to stimulate synthesis. RbbA is reported to have affinity for EF-Tu but not for EF-G. Additionally, RbbA copurifies with 30S ribosomal subunits and can be crosslinked to the ribosomal protein S1. Studies using a spectrum of antibiotics, including some of similar function, revealed that hygromycin, which binds to the 30S subunit, has a significant effect on the ATPase activity and on the affinity of RbbA for ribosomes. A possible role for RbbA in protein-chain elongation is proposed.     

Antagonistic interactions among marine pelagic bacteria.

Recent studies suggest that bacterial abundance and species diversity in the ocean's water column are variable at the millimeter scale, apparently in response to the small-scale heterogeneity in the distribution of organic matter. We hypothesized that bacterium-bacterium antagonistic interactions may contribute to variations in community structure at the microscale. We examined each of the 86 isolates for their inhibition of growth of the remaining 85 isolates by the Burkholder agar diffusion assay. More than one-half of the isolates expressed antagonistic activity, and this trait was more common with particle-associated bacteria than with free-living bacteria. This was exemplified by members of the alpha subclass of the class Proteobacteria (alpha-proteobacteria), in which production of antagonistic molecules was dominated by attached bacteria. We found that gamma-proteobacteria (members of the orders Alteromonadales and Vibrionales) are the most prolific producers of inhibitory materials and also the most resilient to them, while members of the Bacteriodetes were the organisms that were least productive and most sensitive to antagonistic interactions. Widespread interspecies growth inhibition is consistent with the role of this phenomenon in structuring bacterial communities at the microscale. Furthermore, our results suggest that bacteria from pelagic marine particles may be an underutilized source of novel antibiotics.     

苔藓植物相互作用的研究进展

综述了苔藓植物种内和种间正相互作用、种内和种间竞争、生态位与共存等的研究现状及其进展.苔藓植物常为严酷环境中的优势植物,并在保持水分和获取光及养分资源两方面存在权衡.因严酷环境中竞争的重要性相对较低,苔藓植物的正相互作用较为多见.然而,在苔藓植物种内、种间及其与维管植物之间,均不乏竞争的实例.在严酷性较低的环境如过湿的泥炭地中,竞争的重要性增加.多种苔藓植物间可存在竞争等级,该等级往往随环境的变化而变化.随机过程、物种的殖民本质以及更新策略的差异可导致苔藓植物生态位的重叠与共存,但竞争导致生态位分化也是苔藓植物共存的机理之一.苔藓植物不应简单地归类于耐压-杂草型生活史策略者,竞争仍是构建某些苔藓植物群落及其与维管植物共存群落的重要因子之一.     

Genetic interactions among late-flowering mutants of Arabidopsis.

Flowering time in Arabidopsis is controlled by a large number of genes, identified by induced mutations. Forty-two double mutants involving 10 of these loci were obtained and analyzed for their flowering behavior under long-day conditions, with and without vernalization, and under short-day conditions. The genetic interactions between the various mutants proved to be complex, although a major epistatic group (called group A) could be identified corresponding to the mutants, which are relatively insensitive to vernalization and daylength. In contrast, the genetic behavior of the mutants much more responsive to these environmental factors (group B) is more complex. The vernalization responsiveness of the group B mutants did not compensate for the lateness of the group A mutants. This indicated that these genes do not control vernalization sensitivity as such, but provide a factor that becomes limiting in short days. The classification of these mutants in different physiological groups is discussed in relation to the detected genetic interactions, and based on these interactions a more detailed model of their role in flowering initiation is proposed.     

Selective interactions among the multiple connexin proteins expressed in the vertebrate lens: the second extracellular domain is a determinant of compatibility between connexins

Gap junctions are collections of intercellular channels composed of structural proteins called connexins (Cx). We have examined the functional interactions of the three rodent connexins present in the lens, Cx43, Cx46, and Cx50, by expressing them in paired Xenopus oocytes. Homotypic channels containing Cx43, Cx46, or Cx50 all developed high conductance. heterotypic channels composed of Cx46 paired with either Cx43 or Cx50 were also well coupled, whereas Cx50 did not form functional channels with Cx43. We also examined the functional response of homotypic and heterotypic channels to transjunctional voltage and cytoplasmic acidification. We show that all lens connexins exhibited sensitivity to cytoplasmic acidification as well as to voltage, and that voltage-dependent closure of heterotypic channels for a given connexin was dramatically influenced by its partner connexins in the adjacent cell. Based on the observation that Cx43 can discriminate between Cx46 and Cx50, we investigated the molecular determinants that specify compatibility by constructing chimeric connexins from portions of Cx46 and Cx50 and testing them for their ability to form channels with Cx43. When the second extracellular (E2) domain in Cx46 was replaced with the E2 of Cx50, the resulting chimera could no longer form heterotypic channels with Cx43. A reciprocal chimera, where the E2 of Cx46 was inserted into Cx50, acquired the ability to functionally interact with Cx43. Together, these results demonstrate that formation of intercellular channels is a selective process dependent on the identity of the connexins expressed in adjacent cells, and that the second extracellular domain is a determinant of heterotypic compatibility between connexins.