Reverse engineering: the architecture of biological networks

We adopt a control theory approach to reverse engineer the complexity of a known system--the bacterial heat shock response. Using a computational dynamic model, we explore the organization of the heat shock system and elucidate its various regulation strategies. We show that these strategies are behind much of the complexity of the network. We propose that complexity is a necessary outcome of robustness and performance requirements that are achieved by the heat shock system's exquisite regulation modules. The techniques we use rely on dynamic computational models and principles from the field of control theory.     

Innate immunity: has poplar made its BED?

The perennial plant model species Populus trichocarpa has received considerable attention in the last 5 yr because of its potential use as a bioenergy crop. The completion of its genome sequence revealed extensive homologies with the herbaceous annual species Arabidopsis thaliana. This review highlights the similarities and differences at the qualitative defence response components level, notably in putative NBS-LRR protein content and downstream defence regulators. With almost a twofold NBS-LRR gene complement compared with A. thaliana, P. trichocarpa also encodes some putative R-proteins with unusual architectures and possible DNA-binding capacity. P. trichocarpa also possesses all the known main components characteristic of TIR-NB-LRR and CC-NB-LRR signalling. However, very little has been done with regard to the components involved in the poplar qualitative response to pathogens. In addition, the relationship between plant-biotroph perception/signalling and the role of salicylic acid, an important defence compound, remains uncertain. This review aims to identify the genomic components present in poplar that could potentially participate in the qualitative response and highlights where efforts should be devoted to obtain a better understanding of the poplar qualitative defence response.     

高山植物圆锥南芥的光合系统耐热性及其修复机制(英文)

高温胁迫包括极端高温和中高温,严重影响了植物的一系列生理活动,尤其是光合作用,而植物应对极端高温和中高温胁迫具有不同的策略。高山植物因长期生长于相对寒冷的环境中,相比而言应缺少对高温胁迫的适应机制。本文以圆锥南芥作为一种高山模式植物来探索其在中高温下是否表现出耐热能力,如果具有耐热能力,那么在光合方面与拟南芥存在怎样的差异。研究发现,圆锥南芥在中高温处理后具有更高的光化学效率及快速可逆的恢复过程,表现出了较强的耐热能力。两物种的F0没有明显的差异,而圆锥南芥在热处理后及恢复过程中具有更高的Fm,促进其快速光合修复。在热处理后,非光化学能量耗散快速瞬时上升,及时保护光系统II免受光损伤和热伤害,另外,HSP101蛋白迅速诱导可能启动了光化学修复。最后,圆锥南芥在严重高温处理后具有更高的存活率再次验证了它在中高温下的耐热能力。结果表明,圆锥南芥具有更耐热的光合系统以及有效的光合修复机制来耐受中高温胁迫。     

Visual pigments and optical habitats of surfperch (Embiotocidae) in the California kelp forest

We studied the optical microhabitat use and visual pigment variation among a group of closely related teleosts (surfperch: Embiotocidae) living along the nearshore central California coast. We employed a diver-operated spectroradiometer to record the optical microhabitat use of eight surfperch species in Monterey Bay. and microspectrophotometry to measure visual pigment absorbance for nine surfperch species. Species were dichromatic with mixtures of A1- and A2-based visual pigments exhibiting extensive maximum absorbance (lambda(max)) variation across species: 455-482 nm for SWS cones and 527-546 nm for LWS cones. Interspecific variation in sidewelling irradiance measurements (mean lambdaFmaxs) significantly accounted for 63% of the variation in surfperch LWS visual pigments and 83% of the interspecific variation in SWS visual pigments using a phylogenetically-corrected regression technique. Optimality models for maximizing relative photon capture of background radiance demonstrate that the LWS cone lambda(max) values are tuned for maximizing photon capture of the species-specific horizontal visual field, while the SWS cone lambda(max), are well offset from the dominant background radiance. This study is one of the first to demonstrate species-specific differences in habitat usage at microhabitat scales accounting for differences in photoreceptor peak absorbance among closely related, sympatric species.     

Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana.

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.     

Cis-regulatory evolution of chalcone-synthase expression in the genus Arabidopsis

The contribution of cis-regulation to adaptive evolutionary change is believed to be essential, yet little is known about the evolutionary rules that govern regulatory sequences. Here, we characterize the short-term evolutionary dynamics of a cis-regulatory region within and among two closely related species, A. lyrata and A. halleri, and compare our findings to A. thaliana. We focused on the cis-regulatory region of chalcone synthase (CHS), a key enzyme involved in the synthesis of plant secondary metabolites. We observed patterns of nucleotide diversity that differ among species but do not depart from neutral expectations. Using intra- and interspecific F1 progeny, we have evaluated functional cis-regulatory variation in response to light and herbivory, environmental cues, which are known to induce CHS expression. We find that substantial cis-regulatory variation segregates within and among populations as well as between species, some of which results from interspecific genetic introgression. We further demonstrate that, in A. thaliana, CHS cis-regulation in response to herbivory is greater than in A. lyrata or A. halleri. Our work indicates that the evolutionary dynamics of a cis-regulatory region is characterized by pervasive functional variation, achieved mostly by modification of response modules to one but not all environmental cues. Our study did not detect the footprint of selection on this variation.     

Saccharomyces cerevisiae mRNA populations of different intrinsic stability in unstressed and heat shocked cells display almost constant m7GpppA:m7GpppG 5'-cap structure ratios

The half-lives of mRNAs in yeast vary from about 1 to over 100 min. While mRNA stabilities must strongly influence overall gene expression in this organism, very little is known about how they are determined. Labellings of yeast cells were conducted to investigate whether the 5'-cap structures of yeast mRNAs might influence their stability. Variation of the pulse-labelling period from 7.5 min to 120 min did not have any major influence on the relative labelling of m7GpppA (A cap) and m7GpppG (G cap) in total polyadenylated RNA. Whether an mRNA has the A cap or the G cap does not therefore have a marked effect on its stability. During the heat shock response the relative labelling of A caps to G caps in total polyadenylated RNA also does not fluctuate appreciably. This indicates that cap structure alone does not determine the destabilisation of non-heat shock mRNAs and stabilisation of heat shock mRNAs during this stress response.     

拟南芥RPP1A参与幼苗生长的蛋白质组学分析

核糖体蛋白不仅参与蛋白质合成,而且参与植物生长发育的调控.利用拟南芥核糖体磷酸蛋白P1(ribosomal phosphoprotein P1,RPP1)家族基因RPP1A缺失突变体rpp1a研究RPP1A缺失对幼苗蛋白质表达水平的影响,揭示其参与调控幼苗生长的作用机制.表型分析发现,与野生型WT相比,RPP1A缺失导...     

Differential regulation of small heat-shock genes in plants: analysis of a water-stress-inducible and developmentally activated sunflower promoter

We have isolated two sunflower genes, Ha hsp 18.6 G2 and Ha hsp 17.7 G4, that encode small heat shock proteins (sHSPs). RNAse A protection experiments, carried out with RNA probes transcribed from each gene and hybridized to sunflower total RNA, allowed us to distinguish their mRNA accumulation patterns. In sunflower, Ha hsp 17.7 G4 mRNAs accumulated during zygotic embryogenesis at 25°C. In vegetative tissues, these mRNAs accumulated in response to either heat shock (42°C), abscisic acid (ABA), or mild water stress treatments. In all cases, the mRNAs were transcribed from the same initiation site. In contrast, Ha hsp 18.6 G2 mRNAs accumulated only in response to heat-shock. This result demonstrates differential regulation of these two sHSP genes. The complex regulation depicted by the Ha hsp 17.7 G4 promoter has been further analyzed in transgenic tobacco, using G4::GUS translational fusions. Developmental induction of Ha hsp 17.7 G4 during zygotic embryogenesis was faithfully reproduced in the transgenic plants. 5-distal sequences (between -1132 and -395) were required to confer a preferential spatial expression of GUS activity in the cotyledons. More proximal sequences (from -83 to +163) conferred to the chimeric genes most of the developmental regulation, and the responses to ABA and heat shock characteristic of the Ha hsp 17.7 G4 promoter. The water stress response of this gene was not reproduced in transgenic tobacco and, thus, could be uncoupled from its regulation during embryogenesis.     

Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis

MicroRNAs (miRNAs) are small, noncoding RNAs that can play crucial regulatory roles in eukaryotes by targeting mRNAs for silencing. To test whether miRNAs play roles in the regulation of wood development in tree species, we isolated small RNAs from the developing xylem of Populus trichocarpa stems and cloned 22 miRNAs. They are the founding members of 21 miRNA gene families for 48 miRNA sequences, represented by 98 loci in the Populus genome. A majority of these miRNAs were predicted to target developmental- and stress/defense-related genes and possible functions associated with the biosynthesis of cell wall metabolites. Of the 21 P. trichocarpa miRNA families, 11 have sequence conservation in Arabidopsis thaliana but exhibited species-specific developmental expression patterns, suggesting that even conserved miRNAs may have different regulatory roles in different species. Most unexpectedly, the remaining 10 miRNAs, for which 17 predicted targets were experimentally validated in vivo, are absent from the Arabidopsis genome, suggesting possible roles in tree-specific processes. In fact, the expression of a majority of the cloned miRNAs was upregulated or downregulated in woody stems in a manner consistent with tree-specific corrective growth against tension and compression stresses, two constant mechanical loads in trees. Our results show that plant miRNAs can be induced by mechanical stress and may function in one of the most critical defense systems for structural and mechanical fitness.