Genome-Wide Survey of Pseudogenes in 80 Fully Re-sequenced Arabidopsis thaliana Accessions

Pseudogenes (Ψs), including processed and non-processed Ψs, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed Ψs utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of Ψs within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing ∼28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these Ψs on chromosomes showed a significantly negative correlation between Ψs/ORFs and their local gene densities, suggesting a higher proportion of Ψs in gene desert regions, e.g. near centromeres. On the other hand, compared with the non-Ψ loci, even the intact coding sequences (CDSs) in the Ψ loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the Ψs mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations.     

Loss-Function of EGY1 Results in Photosynthesis Damage through Reducing Stability of Photosystem II in Arabidopsis thaliana

Russian Journal of Plant Physiology - In egy1 (ethylene-dependent gravitropism-deficient and yellow-green 1) mutants of Arabidopsis thaliana (L.) Heynh., there is reduced granal thylakoids, smaller...     

Photosystem II Regulation and Dynamics of the Chloroplast D1 Protein in Arabidopsis Leaves during Photosynthesis and Photoinhibition

Arabidopsis thaliana leaves were examined in short-term (1 h) and long-term (10 h) irradiance experiments involving growth, saturating and excess light. Changes in photosynthetic and chlorophyll fluorescence parameters and in populations of functional photosystem II (PSII) centers were independently measured. Xanthophyll pigments, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU)-binding sites, the amounts of D1 protein, and the rates of D1 protein synthesis were determined. These comprehensive studies revealed that under growth or light-saturating conditions, photosynthetic parameters remained largely unaltered. Photoprotection occurred at light saturation indicated by a dark-reversible increase in non-photochemical quenching accompanied by a 5-fold increase in antheraxanthin and zeaxanthin. No consistent change in the concentrations of functional PSII centers, DCMU-binding sites, or D1 protein pool size occurred. D1 protein synthesis was rapid. In excess irradiance, quantum yield of O2 evolution and the efficiency of PSII were reduced, associated with a 15- to 20-fold increase in antheraxanthin and zeaxanthin and a sustained increase in nonphotochemical quenching. A decrease in functional PSII center concentration occurred, followed by a decline in the concentration of D1 protein; the latter, however, was not matched by a decrease in DCMU-binding sites. In the most extreme treatments, DCMU-binding site concentration remained 2 times greater than the concentration of D1 protein recognized by antibodies. D1 protein synthesis rates remained unaltered at excess irradiances.     

Arabidopsis thaliana type I and II chaperonins

An examination of the Arabidopsis thaliana genome sequence led to the identification of 29 predicted genes with the potential to encode members of the chaperonin family of chaperones (CPN60 and CCT), their associated cochaperonins, and the cytoplasmic chaperonin cofactor prefoldin. These comprise the first complete set of plant chaperonin protein sequences and indicate that the CPN family is more diverse than previously described. In addition to surprising sequence diversity within CPN subclasses, the genomic data also suggest the existence of previously undescribed family members, including a 10-kDa chloroplast cochaperonin. Consideration of the sequence data described in this review prompts questions about the complexities of plant CPN systems and the evolutionary relationships and functions of the component proteins, most of which have not been studied experimentally.     

Kinetics of excitation trapping in intact Photosystem I of Chlamydomonas reinhardtii and Arabidopsis thaliana

We measured picosecond time-resolved fluorescence of intact Photosystem I complexes from Chlamydomonas reinhardtii and Arabidopsis thaliana. The antenna system of C. reinhardtii contains about 30-60 chlorophylls more than that of A. thaliana, but lacks the so-called red chlorophylls, chlorophylls that absorb at longer wavelength than the primary electron donor. In C. reinhardtii, the main lifetimes of excitation trapping are about 27 and 68 ps. The overall lifetime of C. reinhardtii is considerably shorter than in A. thaliana. We conclude that the amount and energies of the red chlorophylls have a larger effect on excitation trapping time in Photosystem I than the antenna size.     

The Photosystem II Light-Harvesting Protein Lhcb3 Affects the Macrostructure of Photosystem II and the Rate of State Transitions in Arabidopsis

The main trimeric light-harvesting complex of higher plants (LHCII) consists of three different Lhcb proteins (Lhcb1-3). We show that Arabidopsis thaliana T-DNA knockout plants lacking Lhcb3 (koLhcb3) compensate for the lack of Lhcb3 by producing increased amounts of Lhcb1 and Lhcb2. As in wild-type plants, LHCII-photosystem II (PSII) supercomplexes were present in Lhcb3 knockout plants (koLhcb3), and preservation of the LHCII trimers (M trimers) indicates that the Lhcb3 in M trimers has been replaced by Lhcb1 and/or Lhcb2. However, the rotational position of the M LHCII trimer was altered, suggesting that the Lhcb3 subunit affects the macrostructural arrangement of the LHCII antenna. The absence of Lhcb3 did not result in any significant alteration in PSII efficiency or qE type of nonphotochemical quenching, but the rate of transition from State 1 to State 2 was increased in koLhcb3, although the final extent of state transition was unchanged. The level of phosphorylation of LHCII was increased in the koLhcb3 plants compared with wild-type plants in both State 1 and State 2. The relative increase in phosphorylation upon transition from State 1 to State 2 was also significantly higher in koLhcb3. It is suggested that the main function of Lhcb3 is to modulate the rate of state transitions.     

Photosystem II and Pigment Dynamics among Ecotypes of the Green Alga Ostreococcus

We investigated the photophysiological responses of three ecotypes of the picophytoplankter Ostreococcus and a larger prasinophyte Pyramimonas obovata to a sudden increase in light irradiance. The deepwater Ostreococcus sp. RCC809 showed very high susceptibility to primary photoinactivation, likely a consequence of high oxidative stress, which may relate to the recently noted plastid terminal oxidase activity in this strain. The three Ostreococcus ecotypes were all capable of deploying modulation of the photosystem II repair cycle in order to cope with the light increase, but the effective clearance of photoinactivated D1 protein appeared to be slower in the deepwater Ostreococcus sp. RCC809, suggesting that this step is rate limiting in the photosystem II repair cycle in this strain. Moreover, the deepwater Ostreococcus accumulated lutein and showed substantial use of the xanthophyll cycle under light stress, demonstrating its high sensitivity to light fluctuations. The sustained component of the nonphotochemical quenching of fluorescence correlated well with the xanthophyll deepoxidation activity. Comparisons with the larger prasinophyte P. obovata suggest that the photophysiology of Ostreococcus ecotypes requires high photosystem II repair rates to counter a high susceptibility to photoinactivation, consistent with low pigment package effects in their minute-sized cells.The prasinophytes are marine planktonic green algae with a phylogenetic position branching near the base of the green lineage (Baldauf, 2003; Turmel et al., 2009). They are widespread in temperate (Diez et al., 2001; Zhu et al., 2005) and polar (Lovejoy et al., 2007) marine habitats, in which they are often significant contributors to primary production (Not et al., 2004). The prasinophytes include the smallest known eukaryotic photoautotroph, Ostreococcus tauri (Courties et al., 1994; Chrétiennot-Dinet et al., 1995), whose particularly simple structure makes it an attractive model minimal chlorophyte, and indeed, minimal eukaryote (Derelle et al., 2006). Recently, genomic sequences for three Ostreococcus strains, isolated from different ecological niches, have become available (Derelle et al., 2006; Palenik et al., 2007), thus increasing the interest of these models for understanding acclimation processes in this deep-branching group of chlorophytes.Photoacclimation strategies differ in two Ostreococcus strains (Cardol et al., 2008; Six et al., 2008), which, although belonging to different phylogenetic clades, are nonetheless morphologically indistinguishable (Rodríguez et al., 2005). O. tauri, a eutrophilic lagoon species, modulates PSII content to enable acclimation and growth over a wide range of irradiances. In marked contrast, Ostreococcus sp. (O. sp.) RCC809, isolated at 105 m depth in the tropical Atlantic Ocean, modulates the size of its large PSII antenna in a strategy that accommodates a narrower range of light levels but that incurs lower nutrient costs compared with photoacclimation in O. tauri (Six et al., 2008). The evidence for different light acclimation strategies between these two Ostreococcus ecotypes raises the question of the underlying physiological processes for niche adaptation in these closely related organisms. Cardol et al. (2008) recently analyzed the coastal O. tauri and the deepwater O. sp. RCC809 grown under low to moderate light and found exciting evidence for a plastid terminal oxidase electron flow path in O. sp. RCC809 from PSII back to oxygen, short-circuiting the usual Z scheme in a mechanism to generate a transthylakoidal pH gradient without net generation of reductant. Like all oxygenic photoautotrophs, the prasinophytes suffer photoinactivation of PSII (Aro et al., 1993; Tyystjarvi, 2008; Guskov et al., 2009) at a rate approximately proportional to the incident irradiance (Nagy et al., 1995; Hakala et al., 2005). To counter this photoinactivation, a PSII repair cycle proteolytically removes the photoinactivated D1 protein (Silva et al., 2003) and replaces it through de novo synthesis and reassembly with the remaining subunits (Aro et al., 1993). If photoinactivation outruns the rate of repair, the PSII pool suffers net photoinhibition (Aro et al., 2005; Nishiyama et al., 2005, 2006; Murata et al., 2007), leading to a decrease in photosynthetic capacity and potentially to a decrease in growth. To limit photoinhibition, photosynthetic cells use physiological processes that dissipate excess light energy into heat, thereby preempting the generation of toxic reactive oxygen species (Baroli et al., 2004; Holt et al., 2004) that can inhibit metabolism, notably including the PSII repair processes (Nishiyama et al., 2006; Murata et al., 2007). These excitation dissipation mechanisms manifest as a drop in PSII fluorescence yield termed nonphotochemical quenching of fluorescence (NPQ). In land plants and characterized chlorophytes, NPQ is notably associated with changes in light-harvesting complex conformation along with pigmentation changes (Demmig-Adams and Adams, 1992; Baroli et al., 2004; Holt et al., 2004; Li et al., 2004).The specialization of Ostreococcus ecotypes to contrasting environments suggests that they may have evolved distinct capacities to cope with rapid fluctuations in light. Here, we investigate this question by subjecting three different Ostreococcus ecotypes to short-term increases in light irradiance to uncover their capacities for PSII repair and susceptibilities to photoinactivation. We use a target theory approach (Nagy et al., 1995; Sinclair et al., 1996) to parameterize their susceptibility to primary photoinactivation in a form useful for predicting and modeling responses to changes in irradiance. We moreover compare the Ostreococcus strains to a much larger prasinophyte derived from temperate surface waters, Pyramimonas obovata, to explore how cell size can influence photophysiology in the prasinophytes.     

Arabidopsis thaliana Genes Encoding Defense Signaling and Recognition Proteins Exhibit Contrasting Evolutionary Dynamics

The interplay between pathogen effectors, their host targets, and cognate recognition proteins provides various opportunities for antagonistic cycles of selection acting on plant and pathogen to achieve or abrogate resistance, respectively. Selection has previously been shown to maintain diversity in plant proteins involved in pathogen recognition and some of their cognate pathogen effectors. We analyzed the signatures of selection on 10 Arabidopsis thaliana genes encoding defense signal transduction proteins in plants, which are potential targets of pathogen effectors. There was insufficient evidence to reject neutral evolution for 6 genes encoding signaling components consistent with these proteins not being targets of effectors and/or indicative of constraints on their ability to coevolve with pathogen effectors. Functional constraints on effector targets may have provided the driving selective force for the evolution of guard proteins. PBS1, a known target of an effector, showed little variation but is known to be monitored by a variable guard protein. Evidence of selection maintaining diversity was present at NPR1, PAD4, and EDS1. Differences in the signatures of selection observed may reflect the numbers of effectors that target a particular protein, the presence or absence of a cognate guard protein, as well as functional constraints imposed by biochemical activities or interactions with plant proteins.     

拟南芥RPS14基因的克隆表达及功能初步研究

拟南芥RPS14(Ribosomal protein S14)是从拟南芥中分离出的一种核糖体蛋白,是核糖体40S亚基的组成成分,属于S11P核糖体蛋白家族,主要负责RNA转录后加工。提取拟南芥总RNA,用RT-PCR技术得到RPS14全长基因,经T-A克隆插入到pEASY-T3载体上。利用亚克隆法成功构建pGEX-6P-1-RPS14原核表达质粒。GST-RPS14融合蛋白在大肠杆菌BL21(DE3)中表达,分子量约为43 kD。运用同样方法构建pET-28a-AK6原核表达质粒,获得大小约为26 kD的HIS-AK6融合蛋白。运用体外pull-down技术,并用SDS-PAGE和Western blot进行验证,证明拟南芥RPS14蛋白与AK6蛋白之间存在相互作用。因此,推测拟南芥的AK6与RPS14蛋白共同参与核酸代谢过程,影响RNA转录后加工,进而抑制拟南芥茎细胞的生长,使植株表现矮小特征。     

Three divergent approaches identified the same RGF1 receptors in Arabidopsis thaliana

正During adaptation to terrestrial environment,plants evolved an important vegetative organ,root,to achieve immobilization,absorption of water and nutrients,biosynthesis,transportation and other physiological functions.Stem cell niche in root apical meristem,including quiescent center(QC)cells and their surrounding stem cells(Figure 1),is critical for normal root growth and development.Positions of stem cells within the stem cell niche determine their cell fates.QC     

拟南芥叶绿体中DEG蛋白酶功能的研究进展

DEGP家族蛋白酶广泛分布于原核生物和真核生物细胞中。在拟南芥中有16个DEGP类似的蛋白酶,根据蛋白质组学数据,其中有4个定位于叶绿体中,分别命名为DEG1、DEG2、DEG5和DEG8。结合生物化学和分子生物学等研究手段对拟南芥叶绿体中的DEGP蛋白酶进行了分析,现有的研究初步证明了这些蛋白酶参与光系统II（PSII）复合物反应中心D1蛋白的降解,从而在PSII复合物的修复循环和功能维护中起重要作用。该文概述了拟南芥叶绿体中DEG蛋白酶的结构和功能的最新研究进展。     

Three oxidative metabolites of indole-3-acetic acid from Arabidopsis thaliana

Three metabolites of indole-3-acetic acid (IAA), N-(6-hydroxyindol-3-ylacetyl)-phenylalanine (6-OH-IAA-Phe), N-(6-hydroxyindol-3-ylacetyl)-valine (6-OH-IAA-Val), and 1-O-(2-oxoindol-3-ylacetyl)-beta-d-glucopyranose (OxIAA-Glc), were found by a liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS)-based search for oxidative IAA metabolites during the vegetative growth of Arabidopsis. Their structures were confirmed by making a comparison of chromatographic characteristics and mass spectra between naturally occurring compounds and synthetic standards. An incorporation study using deuterium-labeled compounds showed that 6-OH-IAA-Phe and 6-OH-IAA-Val were biosynthesized from IAA-Phe and IAA-Val, respectively, which strongly suggested the formation of these amino acid conjugates of IAA in plants. Both 6-OH-IAA-Phe and 6-OH-IAA-Val were inactive as auxins, as indicated by no significant root growth inhibition in Arabidopsis. Quantitative analysis demonstrated that OxIAA-Glc was present in the largest amount among the metabolites of IAA in Arabidopsis, suggesting that the conversion into OxIAA-Glc represents the main metabolic process regarding IAA in Arabidopsis.     

Phosphorylation of Photosystem II Controls Functional Macroscopic Folding of Photosynthetic Membranes in Arabidopsis

Photosynthetic thylakoid membranes in plants contain highly folded membrane layers enriched in photosystem II, which uses light energy to oxidize water and produce oxygen. The sunlight also causes quantitative phosphorylation of major photosystem II proteins. Analysis of the Arabidopsis thaliana stn7xstn8 double mutant deficient in thylakoid protein kinases STN7 and STN8 revealed light-independent phosphorylation of PsbH protein and greatly reduced N-terminal phosphorylation of D2 protein. The stn7xstn8 and stn8 mutants deficient in light-induced phosphorylation of photosystem II had increased thylakoid membrane folding compared with wild-type and stn7 plants. Significant enhancement in the size of stacked thylakoid membranes in stn7xstn8 and stn8 accelerated gravity-driven sedimentation of isolated thylakoids and was observed directly in plant leaves by transmission electron microscopy. Increased membrane folding, caused by the loss of light-induced protein phosphorylation, obstructed lateral migration of the photosystem II reaction center protein D1 and of processing protease FtsH between the stacked and unstacked membrane domains, suppressing turnover of damaged D1 in the leaves exposed to high light. These findings show that the high level of photosystem II phosphorylation in plants is required for adjustment of macroscopic folding of large photosynthetic membranes modulating lateral mobility of membrane proteins and sustained photosynthetic activity.The use of captured sunlight energy to split water and drive oxygenic photosynthesis by photosystem II (PSII) (Barber, 2006) inevitably generates reactive oxygen species and causes oxidative damage to the PSII protein pigment complex. The light-induced damage to PSII, in particular to the D1 reaction center protein, requires PSII repair to sustain its photosynthetic function (Takahashi and Murata, 2008). Impairment and degradation of D1 increase with rising light intensities, and this protein has the fastest turnover rate among the photosynthetic proteins of plants, algae, and cyanobacteria (Yokthongwattana and Melis, 2006). However, in plants, the PSII is segregated in highly stacked membrane layers of very large thylakoid membranes (Andersson and Anderson, 1980; Kirchhoff et al., 2008), which are densely folded to fit inside chloroplasts (Mullineaux, 2005; Shimoni et al., 2005). As a consequence, the PSII repair cycle in plants is slower than in cyanobacteria (Yokthongwattana and Melis, 2006), and it includes migration of the PSII complex from the stacked membrane domains (grana) to the unstacked membranes (stroma lamellae), where proteolysis and insertion of a newly synthesized D1 protein occurs (Baena-Gonzalez and Aro, 2002; Yokthongwattana and Melis, 2006). High light also causes quantitative phosphorylation of the membrane surface–exposed regions of D1, D2, CP43, and PsbH proteins of PSII in plants (Rintamäki et al., 1997; Vener et al., 2001), but the function of this phosphorylation is largely unknown and reports on its importance for the D1 protein turnover are conflicting (Bonardi et al., 2005; Tikkanen et al., 2008).Phosphorylation of the PSII proteins in Arabidopsis thaliana depends mostly on the light-activated protein kinase STN8 (Vainonen et al., 2005), while the STN7 kinase is essential for phosphorylation of the light-harvesting proteins of PSII (Bellafiore et al., 2005; Bonardi et al., 2005; Tikkanen et al., 2006). An earlier study on Arabidopsis mutants lacking both STN7 and STN8 (stn7xstn8), as well as only STN8, concluded that protein phosphorylation was not essential for PSII repair (Bonardi et al., 2005), while more recent work revealed a dramatic retardation in D1 degradation under high light in the stn8 and stn7xstn8 mutants (Tikkanen et al., 2008). Moreover, it was shown that the lack of PSII phosphorylation resulted in accumulation of photodamaged PSII complexes and in general oxidative damage of photosynthetic proteins in the thylakoid membranes under high light (Tikkanen et al., 2008). The other study revealed that the stn7xstn8 double mutant grown under natural field conditions produced 41% less seeds than wild-type plants (Frenkel et al., 2007), which also indicated physiological importance of thylakoid protein phosphorylation in maintenance of plant fitness.To uncover the function of light-dependent protein phosphorylation in plant photosynthetic membranes, we performed a detailed analysis of the Arabidopsis mutants deficient in the protein kinases STN7 and STN8. The earlier published results on protein phosphorylation analyses in the stn7xstn8 mutant of Arabidopsis were restricted to antiphosphothreonine antibody-based immunodetection and did not reveal any phosphorylation of PSII core proteins (Bonardi et al., 2005; Tikkanen et al., 2008). Using a mass spectrometry (MS) approach and immunoblot analyses with two complementary antiphosphothreonine antibodies, we find remaining light-independent phosphorylation of PsbH and D2 proteins of PSII in stn7xstn8. We demonstrate that degradation and aggregation patterns of the D1 protein in stn7xstn8 differ from those in wild-type, stn7, and stn8 plants. We also observe a reproducible delay in the degradation of D1 in high light–treated leaves of stn7xstn8 and stn8 compared with the wild-type and stn7 plants. Finally, we show that phosphorylation of PSII proteins modulates macroscopic rearrangements of the entire membrane network of plant thylakoids, which facilitates lateral mobility of membrane proteins, required for repair and sustained activity of PSII.