Efficiency of feedback selection for recombination in Drosophila

A number of theoretical models have been developed in population genetics to explain the evolution of recombination system under natural selection for adaptive traits. Using Drosophila cage populations of large size the effect of selection for resistance to daily temperature fluctuations on the rec-system was studied in this work. It is established that selection for population adaptability to extreme conditions leads during several tens of generations to significant increase in crossing-over rate within various parts of the genome (especially in b-cn and ru-h of chromosomes 2 and 3), as well as to relaxation of exchange interference for adjacent and non-adjacent segments. The Fisher's theoretical prognosis about tightening of linkage in optimal constant conditions was experimentally confirmed for the first time.     

A paradoxical role for inhibition in initiation

Subliminal stimuli, of which subjects are unaware, affect movements made to subsequent visible cues. Sumner and colleagues in this issue of Neuron show that restricted supplementary motor and eye field lesions compromise voluntary control of action because they disrupt the normal unconscious and automatic inhibition of alternative movements partially activated by subliminal stimuli.     

A role for homologous recombination proteins in cell cycle regulation

Eukaryotic cells respond to DNA breaks, especially double-stranded breaks (DSBs), by activating the DNA damage response (DDR), which encompasses DNA repair and cell cycle checkpoint signaling. The DNA damage signal is transmitted to the checkpoint machinery by a network of specialized DNA damage-recognizing and signal-transducing molecules. However, recent evidence suggests that DNA repair proteins themselves may also directly contribute to the checkpoint control. Here, we investigated the role of homologous recombination (HR) proteins in normal cell cycle regulation in the absence of exogenous DNA damage. For this purpose, we used Chinese Hamster Ovary (CHO) cells expressing the Fluorescent ubiquitination-based cell cycle indicators (Fucci). Systematic siRNA-mediated knockdown of HR genes in these cells demonstrated that the lack of several of these factors alters cell cycle distribution, albeit differentially. The knock-down of MDC1, Rad51 and Brca1 caused the cells to arrest in the G2 phase, suggesting that they may be required for the G2/M transition. In contrast, inhibition of the other HR factors, including several Rad51 paralogs and Rad50, led to the arrest in the G1/G0 phase. Moreover, reduced expression of Rad51B, Rad51C, CtIP and Rad50 induced entry into a quiescent G0-like phase. In conclusion, the lack of many HR factors may lead to cell cycle checkpoint activation, even in the absence of exogenous DNA damage, indicating that these proteins may play an essential role both in DNA repair and checkpoint signaling.     

A role for single-strand breaks in bacteriophage phi-X174 genetic recombination

Formation of genetic recombinants in bacteriophage φX174 is stimulated up to 50-fold in host cells carrying the recA⁺ allele by subjecting the virus particles to ultraviolet irradiation before infection, or by starving the host cell for thymine during infection; in recA host strains no such increases are observed.φX174 replicative form DNA molecules formed in vivo from ultraviolet-irradiated bacteriophage consist of an intact, circular full-length viral (+) strand and a partially complete complementary (?) strand extending from the point of origin of complementary strand DNA synthesis to an ultraviolet lesion. φX174 replicative form DNA molecules formed in thymine-deficient host strains during thymine starvation have nearly complete circular viral (+) and complementary (?) strands, which contain random single-strand nicks or gaps.Correlation of these structures with the observed increases in recombination suggests that single-strand “breaks” are aggressive intermediate structures in the formation of φX174 genetic recombinants mediated by the host recA⁺ gene product.     

A possible coordinating role for presynaptic inhibition

Conditioning stimuli were applied to the common peroneal or superficial peroneal nerve in acute experiments on anesthetized cats. Changes in the N₁-component of the dorsal cord potential evoked by stimulation of one of these nerves or of other nerves (tibial, deep peroneal) and changes in the amplitude of antidromic action potentials in the afferent fibers of these nerves were investigated. The degree of reinforcement of antidromic action potentials, reflecting the degree of depolarization of the afferent terminals, was found to be greater for the passive nerve than for the active to which the conditioning stimulus was applied. Inhibition of the N₁-component of the dorsal cord potential was deeper when a pair of stimuli was applied to two different nerves (under these conditions only the mechanism of presynaptic inhibition was activated) than when they were applied to the same nerve. It is concluded that presynaptic inhibition, by selectively controlling afferent volleys, can evidently play a coordinating role.     

Proteasome-dependent proteolysis has a critical role in fine-tuning the feedback inhibition of cytokinin signaling

The ubiquitin/26S proteasome-dependent proteolysis of response regulators is a critical element of many plant hormone signaling pathways. We have recently shown that cytokinin signaling requires the AXR1 component of the related to ubiquitin (RUB) protein modification pathway to promote the proteasome-dependent degradation of the cytokinin response inhibitor ARR5. Here, we show that ARR5 also accumulates in the 26S proteasome mutant rpn12a-1, and leads to a marked resistance to cytokinins. Collectively, these results suggest that proteasome-dependent proteolysis of feedback inhibitors such as ARR5 is essential for the maintenance of optimal responsivity and plasticity in cytokinin signaling.     

Optimizing interneuron circuits for compartment-specific feedback inhibition

Cortical circuits process information by rich recurrent interactions between excitatory neurons and inhibitory interneurons. One of the prime functions of interneurons is to stabilize the circuit by feedback inhibition, but the level of specificity on which inhibitory feedback operates is not fully resolved. We hypothesized that inhibitory circuits could enable separate feedback control loops for different synaptic input streams, by means of specific feedback inhibition to different neuronal compartments. To investigate this hypothesis, we adopted an optimization approach. Leveraging recent advances in training spiking network models, we optimized the connectivity and short-term plasticity of interneuron circuits for compartment-specific feedback inhibition onto pyramidal neurons. Over the course of the optimization, the interneurons diversified into two classes that resembled parvalbumin (PV) and somatostatin (SST) expressing interneurons. Using simulations and mathematical analyses, we show that the resulting circuit can be understood as a neural decoder that inverts the nonlinear biophysical computations performed within the pyramidal cells. Our model provides a proof of concept for studying structure-function relations in cortical circuits by a combination of gradient-based optimization and biologically plausible phenomenological models.     

A role for topoisomerase III in a recombination pathway alternative to RuvABC

The physiological role of topoisomerase III is unclear for any organism. We show here that the removal of topoisomerase III in temperature sensitive topoisomerase IV mutants in Escherichia coli results in inviability at the permissive temperature. The removal of topoisomerase III has no effect on the accumulation of catenated intermediates of DNA replication, even when topoisomerase IV activity is removed. Either recQ or recA null mutations, but not helD null or lexA3, partially rescued the synthetic lethality of the double topoisomerase III/IV mutant, indicating a role for topoisomerase III in recombination. We find a bias against deleting the gene encoding topoisomerase III in ruvC53 or DeltaruvABC backgrounds compared with the isogenic wild-type strains. The topoisomerase III RuvC double mutants that can be constructed are five- to 10-fold more sensitive to UV irradiation and mitomycin C treatment and are twofold less efficient in transduction efficiency than ruvC53 mutants. The overexpression of ruvABC allows the construction of the topoisomerase III/IV double mutant. These data are consistent with a role for topoisomerase III in disentangling recombination intermediates as an alternative to RuvABC to maintain the stability of the genome.     

A role for RAD54B in homologous recombination in human cells.

In human somatic cells, homologous recombination is a rare event. To facilitate the targeted modification of the genome for research and gene therapy applications, efforts should be directed toward understanding the molecular mechanisms of homologous recombination in human cells. Although human genes homologous to members of the RAD52 epistasis group in yeast have been identified, no genes have been demonstrated to play a role in homologous recombination in human cells. Here, we report that RAD54B plays a critical role in targeted integration in human cells. Inactivation of RAD54B in a colon cancer cell line resulted in severe reduction of targeted integration frequency. Sensitivity to DNA-damaging agents and sister-chromatid exchange were not affected in RAD54B-deficient cells. Parts of these phenotypes were similar to those of Saccharomyces cerevisiae tid1/rdh54 mutants, suggesting that RAD54B may be a human homolog of TID1/RDH54. In yeast, TID1/RDH54 acts in the recombinational repair pathway via roles partially overlapping those of RAD54. Our findings provide the first genetic evidence that the mitotic recombination pathway is functionally conserved from yeast to humans.     

A role for XLF in DNA repair and recombination in human somatic cells

Classic non-homologous end-joining (C-NHEJ) is required for the repair of radiation-induced DNA double-strand breaks (DSBs) in mammalian cells and plays a critical role in lymphoid V(D)J recombination. A core C-NHEJ component is the DNA ligase IV co-factor, Cernunnos/XLF (hereafter XLF). In patients, mutations in XLF cause predicted increases in radiosensitivity and deficits in immune function, but also cause other less well-understood pathologies including neural disorders. To characterize XLF function(s) in a defined genetic system, we used a recombinant adeno-associated virus-mediated gene targeting strategy to inactivate both copies of the XLF locus in the human HCT116 cell line. Analyses of XLF-null cells (which were viable) showed that they were highly sensitive to ionizing radiation and a radiomimetic DNA damaging agent, etoposide. XLF-null cells had profound DNA DSB repair defects as measured by in vivo plasmid end-joining assays and were also dramatically impaired in their ability to form either V(D)J coding or signal joints on extrachromosomal substrates. Thus, our somatic XLF-null cell line recapitulates many of the phenotypes expected from XLF patient cell lines. Subsequent structure:function experiments utilizing the expression of wild-type and mutant XLF cDNAs demonstrated that all of the phenotypes of an XLF deficiency could be rescued by the overexpression of a wild-type XLF cDNA. Unexpectedly, mutant forms of XLF bearing point mutations at amino acid positions L115 and L179, also completely complemented the null phenotype suggesting, in contrast to predictions to the contrary, that these mutations do not abrogate XLF function. Finally, we demonstrate that the absence of XLF causes a small, but significant, increase in homologous recombination, implicating XLF in DSB pathway choice regulation. We conclude that human XLF is a non-essential, but critical, C-NHEJ-repair factor.     

细菌苏氨酸脱水酶受L-异亮氨酸反馈抑制的关键在于其调控结构域

苏氨酸脱水酶是细菌L-异亮氨酸合成途径中的关键酶,酶活力受终产物L-异亮氨酸的反馈抑制。苏氨酸脱水酶包含催化结构域及调控结构域,其中调控结构域所起的作用有待进一步研究。本文在大肠杆菌中分别克隆表达了四种不同的苏氨酸脱水酶:来自谷氨酸棒杆菌的苏氨酸脱水酶CgIlvA及其不合调控结构域的突变体CgIlvA~M和来自大肠杆菌的苏氨酸脱水酶EcIlvA及其不合调控结构域的突变体EcIlvA~M。通过蛋白纯化和酶活分析发现,CgIlvA~M和EcIlvA~M的酶活力比CgIlvA和EcIlvA的酶活力有所降低,但它们不再受L-异亮氨酸的反馈抑制,说明L-异亮氨酸对苏氨酸脱水酶的反馈抑制是通过其调控结构域来实现的。     

A role for p38 MAPK in the regulation of ciliary motion in a eukaryote

Background  

Motile cilia are essential to the survival and reproduction of many eukaryotes; they are responsible for powering swimming of protists and small multicellular organisms and drive fluids across respiratory and reproductive surfaces in mammals. Although tremendous progress has been made to comprehend the biochemical basis of these complex evolutionarily-conserved organelles, few protein kinases have been reported to co-ordinate ciliary beat. Here we present evidence for p38 mitogen-activated protein kinase (p38 MAPK) playing a role in the ciliary beat of a multicellular eukaryote, the free-living miracidium stage of the platyhelminth parasite Schistosoma mansoni.     

A critical role for the ubiquitin-conjugating enzyme Ubc13 in initiating homologous recombination

The ubiquitin (Ub)-conjugating enzyme Ubc13 is implicated in Rad6/Rad18-dependent postreplication repair (PRR) in budding yeast, but its function in vertebrates is not known. We show here that disruption or siRNA depletion of UBC13 in chicken DT40 or human cells confers severe growth defects due to chromosome instability, and hypersensitivity to both UV and ionizing radiation, consistent with a conserved role for Ubc13 in PRR. Remarkably, Ubc13-deficient cells are also compromised for DNA double-strand break (DSB) repair by homologous recombination (HR). Recruitment and activation of the E3 Ub ligase function of BRCA1 and the subsequent formation of the Rad51 nucleoprotein filament at DSBs are abolished in Ubc13-deficient cells. Furthermore, generation of ssDNA/RPA complexes at DSBs is severely attenuated in the absence of Ubc13. These data reveal a critical and unexpected role for vertebrate Ubc13 in the initiation of HR at the level of DSB processing.     

A role for recombination in the production of "free-loader" lambda bacteriophage particles

Density-labeled crosses were performed with bacteriophage lambda under conditions which diminish DNA duplication. The production of viable phage containing fully conserved parental DNA was found to be dependent upon the action of the genetic recombination systems. The production of phage containing DNA with one newly synthesized chain was less dependent upon recombination. The production of phage with chromosomes both of whose chains were synthesized following infection show little, if any, dependence on recombination. One can speculate that some step in the maturation process of bacteriophage lambda is inseparable from the reduction of lambda DNA to the monomeric rods characteristic of lambda virions.     

Temperature-dependent feedback inhibition of photosynthesis in peanut

Arachis hypogaea L. is a tropical crop that is slow-growing at temperatures below 25°C. Unadapted CO₂-assimilation rate (A) showed insufficient variation between 15 and 30°C in the short term (hours) to explain this marked reduction in growth. However, at longer periods (12 d), A was depressed as were growth rate and leafproduction rate. To examine the possible relationship between growth, A and sink demand plants were transferred from 30°C, which is near the optimum for growth, to a suboptimal temperature (19°C). In the first 2 d of cooling, A decreased by 50–70%, the stomata stayed open, and the intercellular CO₂ concentration (c_i) rose, i.e. the decrease in A of the cooled plants was the result of non-stomatal factors. Changes in dark respiration did not account for the decline in A.Clear evidence was obtained of sink control of A by independently manipulating the temperature of different leaves on the plant. Cooling (to 19°C) most of the plant (the sink) led to a 70% decline in A of the remaining leaves at 30°C after 3 d, whereas the converse treatments (30°C sink, 19°C source) resulted in small changes (17%). In plants at 19°C which were exposed to low CO₂ concentration to prevent photosynthesis, A was not reduced when measured at normal CO₂ concentrations, indicating that carbohydrate accumulation was responsible for the decline in A. Dry-matter build-up at suboptimal temperature was also consistent with end-product inhibition of photosynthesis.Abbreviations and symbols A (mol·m^-2·s^-1) rate of net CO₂ assimilation - C_i (l·l^-1) substomatal CO₂ concentration - DW (g) dry weight - g (mol·m^-2·s^-1) stomatal conductance to diffusion of water vapour - PFD (mol·m^-2·s^-1) photon flux density     

A central role for p38 MAPK in the early transcriptional response to stress

A study using phylogenetic hypothesis testing, published in BMC Evolutionary Biology, suggests that non-mimetic forms of the North American white admiral butterfly evolved from a mimetic ancestor. This case might provide one of the first examples in which mimicry was gained and then lost again, emphasizing the evolutionary lability of Batesian mimicry. See research article http://www.biomedcentral.com/1471-2148/10/239