Conservation and divergence on plant seed 11S globulins based on crystal structures

The crystal structures of two pro-11S globulins namely: rapeseed procruciferin and pea prolegumin are presented here. We have extensively compared them with the other known structures of plant seed 11S and 7S globulins. In general, the disordered regions in the crystal structures among the 11S globulins correspond to their five variable regions. Variable region III of procruciferin is relatively short and is in a loop conformation. This region is highly disordered in other pro-11S globulin crystals. Local helical and strand variations also occur across the group despite general structure conservation. We showed how these variations may alter specific physicochemical, functional and physiological properties. Aliphatic hydrophobic residues on the molecular surface correlate well with T_m values of the globulins. We also considered other structural features that were reported to influence thermal stability but no definite conclusion was drawn since each factor has additive or subtractive effect. Comparison between proA3B4 and mature A3B4 revealed an increase in r.m.s.d. values near variable regions II and IV. Both regions are on the IE face. Secondary structure based alignment of 11S and 7S globulins revealed 16 identical residues. Based on proA3B4 sequence, Pro60, Gly128, Phe163, Phe208, Leu213, Leu227, Ile237, Pro382, Val404, Pro425 and Val 466 are involved in trimer formation and stabilization. Gly28, Gly74, Asp135, Gly349 and Gly397 are involved in correct globular folding.     

Secondary structure of globulins from plant seeds: a re-evaluation from circular dichroism measurements

The secondary structure parameters of plant seed globulins (11S from Brassica napus L, 11S from Helianthus annuus L, IIS from Vicia faba, 7S from Phaseolus vulgaris L) have been determined from their circular dichroism spectra by the method of Provencher and Glöckner. According to this method, the proteins contain 40–50% β-sheet structure and only about 10% helical structure. We conclude, therefore, that the plant seed globulins belong to the class of β-sheet proteins. Their overall secondary structure is homologous. It is shown that the method of Provencher and Glöckner provides reasonable secondary structure parameters for proteins which are rich in β-sheet structure even if the spectral range utilized for analysis is restricted to 210–240 nm.     

苦荞全基因组11S种子储藏蛋白基因的鉴定及表达分析

以苦荞（Fagopyrum tataricum（L.）Gaertn）全基因组数据为平台,采用生物信息学方法,挖掘出9个11S种子储藏蛋白基因,并对其定位、蛋白结构、系统发育及表达模式进行了分析。结果表明,苦荞9个11S种子储藏蛋白基因编码的蛋白长度为189~914 aa,等电点位于5.18~9.82之间,分子量为21.27~103.33 kD;定位分析结果显示,这些成员位于苦荞基因组的6条连锁群上（Megascaffold2/5以及scaffold77/344/395/861）;序列比对分析发现,除了1个11S种子储藏蛋白sample1_00009513-RA具有1个cupin保守结构域外,其余8个都含有2个cupin结构域,并且在cupin保守结构域中,苦荞和拟南芥（Arabidopsis thaliana（L.）Heynh）共有14个保守的氨基酸残基;蛋白结构预测表明,苦荞11S种子储藏蛋白的结构具有2种类型;苦荞与其它6个物种[拟南芥、花生（Arachis hypogaea Linn.）、大豆（Glycine max（Linn.）Merr.）、杏仁（Armeniaca vulgaris Lam.）、胡桃（Juglans regia L.）和芝麻（Sesamum indicum Linn.）]11S种子储藏蛋白以及苦荞过敏蛋白（TBb和TBt）系统发育分析结果表明,这些蛋白可以分为3类,共具有4对旁系同源蛋白和3对直系同源蛋白;与已报道的苦荞过敏性储藏蛋白以及其它5个物种（花生、大豆、杏仁、胡桃和芝麻）的11S过敏蛋白比较发现,5个11S种子储藏蛋白（sample1_00013128-RA、sample1_00013130-RA、sample1_00021677-RA、sample1_00021668-RA和sample1_00021674-RA）与苦荞2个过敏蛋白的同源性较高,同时它们与胡桃11S过敏蛋白的同源性最高,但尚需进一步实验来确定这5个成员是否为食物过敏原;RNA-Seq转录组数据显示,4个基因（sample1_00018411-RA、sample1_00026786-RA、sample1_00021674-RA、sample1_00022718-RA）在2种荞麦属植物的灌浆期种子中表达水平较高,且在‘大苦1号’中的表达水平要高于‘大甜1号’。     

Expression and characterization of the Arabidopsis thaliana 11S globulin family

The 11S globulins are the principal seed storage proteins in a variety of major crop species, including members of the legume and mustard families. They are targets for protein engineering studies attempting to alter the physicochemical properties of seed protein extracts (e.g. soybean) and to improve the nutritional quality of important agricultural crops. A key factor that has limited the success of this approach to date is insufficient accumulation of the engineered protein variants in vivo due to their improper folding and/or reduced stability, compared to the native protein. We have developed the Arabidopsis thaliana 11S proglobulins as a model system to enable studies exploring the factors underlying structural stability in this family of proteins. Yields of 1.5–4 mg/L were achieved for the three A. thaliana 11S proglobulins expressed in the Origami Escherichia coli cell line in super broth media at 20 °C for 16 h and purified via immobilized-metal affinity chromatography. We also demonstrate that differential scanning fluorimetry is an effective and accessible technique to facilitate the screening of variants to enable the successful engineering of 11S seed storage proteins. The relative in vitro stability of the A. thaliana 11S proglobulins (proAtCRU1 > proAtCRU3 > proAtCRU2) is consistent between chemical and thermal denaturation studies.     

Degradation of storage proteins in germinating seeds

The criteria for the participation of proteases in the mobilization of storage proteins during seed germination are formulated. The proteases that satisfy these criteria, namely the acid cysteine endopeptidases, serine carboxypeptidases and neutral aminopeptidases, are reviewed. The possibility of other seed proteases participating in storage protein degradation is discussed. The course of 11S and 7S storage protein degradation through the action of endogenous and exogenous proteases is described. The 11S and 7S proteins are modified during the early stages of proteolysis and the effects of these modifications on the regulation of breakdown are examined. A scheme for 11S protein degradation in germinating seeds is presented.     

OCCURRENCE OF LOW MOLECULAR WEIGHT AND HIGH CYSTEINE CONTAINING ALBUMIN STORAGE PROTEINS IN OILSEEDS OF DIVERSE SPECIES

The proteins in the oilseeds of species from 11 families, including sunflower, mustard, linseed, almond, lupin, peanut, cucumber, Brazil nut, hazelnut, yucca, castor bean, and cottonseed were studied. Sucrose gradient centrifugation showed that a substantial proportion of the total seed protein from each species migrated with a 2S sedimentation coefficient. The 2S proteins, being water-soluble and thus termed albumins, comprised 20–60% of the total seed proteins, while faster migrating globulins comprised the rest. The amino acid compositions of the 2S proteins were characterisitic of storage proteins by having a high amide content. However, the 2S proteins are different from the classical globulin storage proteins in having a high content of cysteine. It is proposed that 2S albumins are seed storage proteins with a wide distribution and with chemical properties distinct from those of the globulin storage proteins. They play an additional and unique role of providing sulfur reserve for germination.     

The structure of S100A11 fragment explains a local structural change induced by phosphorylation

S100A11 protein is a member of the S100 family containing two EF‐hand motifs. It undergoes phophorylation on residue T10 after cell stimulation such as an increase in Ca²⁺ concentration. Phosphorylated S100A11 can be recognized by its target protein, nucleolin. Although S100A11 is initially expressed in the cytoplasm, it is transported to the nucleus by the action of nucleolin. In the nucleus, S100A11 suppresses the growth of keratinocytes through p21^CIP1/WAF1 activation and induces cell differentiation. Interestingly, the N‐terminal fragment of S100A11 has the same activity as the full‐length protein; i.e. it is phosphorylated in vivo and binds to nucleolin. In addition, this fragment leads to the arrest of cultured keratinocyte growth. We examined the solution structure of this fragment peptide and explored its structural properties before and after phosphorylation. In a trifluoroethanol solution, the peptide adopts the α‐helical structure just as the corresponding region of the full‐length S100A11. Phosphorylation induces a disruption of the N‐capping conformation of the α‐helix, and has a tendency to perturb its surrounding structure. Therefore, the phosphorylated threonine lies in the N‐terminal edge of the α‐helix. This local structural change can reasonably explain why the phosphorylation of a residue that is initially buried in the interior of protein allows it to be recognized by the binding partner. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.     

Subunit Structure of Legumin-like Globulins of Fagus sylvatica Seeds

The 11S (legumin-like) globulins, which are the major seed proteinsof Fagus sylvatica L., have been isolated and characterized.The subunit structure of the 280 kD oligomers was investigatedusing different two-dimensional electrophoretic methods. Sucha structure is within the accepted model for this type of protein.However, an acidic polypeptide with 20 kD was found not to becovalently linked to any other component of the oligomers.     

Comparison of the fine-scale genetic structure of three dipterocarp species

We investigated the fine-scale genetic structure of three tropical-rainforest trees, Hopea dryobalanoides, Shorea parvifolia and S. acuminata (Dipterocarpaceae), in Peninsular Malaysia, all of which cooccurred within a 6-ha plot in Pasoh Forest Reserve. A significant genetic structure was found in H. dryobalanoides, weaker (but still significant) genetic structure in S. parvifolia and nonsignificant structure in S. acuminata. Seeds of all three species are wind dispersed, and their flowers are thought to be insect pollinated. The most obvious difference among these species is their height: S. parvifolia and S. acuminata are canopy species, whereas H. dryobalanoides is a subcanopy species. Clear differences were also found among these species in their range of seed dispersal, which depends on the height of the release point; so taller trees disperse their seed more extensively. The estimates of seed dispersal area were consistent with the degree of genetic structure found in the three species. Therefore, tree height probably had a strong influence on the fine-scale genetic structure of the three species.     

The role of copper and quaternary structure on the conformational properties of Octopus vulgaris hemocyanin

Some structural properties of Octopus vulgaris hemocyanin have been investigated by fluorescence spectroscopy. The three-dimensional structure of Octopus hemocyanin is remarkably tight, resulting in a deep burial of almost all the tryptophyl residues of the protein. The hemocyanin conformation has been studied in the two main aggregation states (11 S, 50 S) of the protein, and with respect to the presence or absence of copper in the active site. Upon changing the pH of the solution, Octopus hemocyanin in the 50 S aggregation state can assume at least three different conformations. During the transition between each conformation the fluorescence quantum yield changes, but the environment of tryptophans does not change. Dissociation of the protein from 50 S to 11 S strongly enhances its susceptibility toward denaturating agents such as pH or temperature, and modifies the effects of fluorescence quenchers such as acrylamide. Moreover, these effects are more pronounced when copper is removed from the active site. A comparative analysis of the results shows that the subunit-subunit interactions exerted within the 50 S species are more important in the maintenance of the conformational stability than the copper ions present in the active sites. This behavior can be accounted for by the large amount of Ca(II) ions linked to 50 S hemocyanin.     

Solution structure of pardaxin P-2

Pardaxin is a mucosal secretion of the Pacific sole Pardachirus pavoninus that exhibits unusual shark repellent and surfactant properties [Thompson, S. A., Tachibana, K., Nakanishi, K., & Kubota, I. (1986) Science 233, 341-343]. This 33 amino acid polypeptide folds into ordered structures in trifluoroethanol-water solution and in micelles but adopts a random-coiled structure in water solution. The complete proton NMR spectrum of pardaxin P-2 has been assigned in CF3CD2OD/H2O (1:1) solution, and the three-dimensional structure has been elucidated with distance restrained molecular dynamics calculations. It is demonstrated that peptide segments within the 7-11 and 14-26 residue stretches are helical while residues at the C- and N-terminus exist predominantly in extended conformations in solution. The dipeptide 12-13 segment connecting the two helices exists as a bend or a hinge allowing the two helices to be oriented in a L-shaped configuration. These studies establish that pardaxin P-2 adopts a novel amphiphilic helix (7-11)-bend (12-13)-helix (14-26) motif with Pro-13 forming the focal point of the turn or bend between the two helices.     

Structural properties of caleosin: a MS and CD study

We have investigated the covalent and secondary solution structure of caleosin, a 27-kDa protein also called ATS1 or AtClo1 (At4g26740) found within Arabidopsis thaliana seed lipid bodies. The native protein was partly phosphorylated at S225. Purified bacterially expressed caleosin (recClo) was not phosphorylated; cysteine residues C221 and C230 were connected by a disulfide bridge. In solution it exists as a mixture of predominant monomers and covalent dimers. We have used recClo as a model for the study of AtClo1 secondary structure. recClo is folded in aqueous solution (16% alpha-helix, 29% beta-sheet), its secondary structure being dramatically influenced by the polarity of media, as deduced from CD spectra measured in the presence of increasing concentrations of various aliphatic alcohols.     

Seed dispersal in a patchy environment with global age dependence

A model of seed population dynamics proposed by S. A. Levin, A. Hastings, and D. Cohen is presented and analyzed. With the environment considered as a mosaic of patches, patch age is used along with time as an independent variable. Local dynamics depend not only on the local state, but also on the global environment via dispersal modelled by an integral over all patch ages. Basic technical properties of the time varying solutions are examined; necessary and sufficient conditions for nontrivial steady states are given; and general sufficient conditions for global asymptotic stability of these steady states are established. Primary tools of analysis include a hybrid Picard iteration, fixed point methods, monotonicity of solution structure, and upper and lower solutions for differential equations.This work was supported in part by National Science Foundation Grants MCS-7903497 and MCS-790349701     

The solution structure of ribosomal protein S4 delta41 reveals two subdomains and a positively charged surface that may interact with RNA.

S4 is one of the first proteins to bind to 16S RNA during assembly of the prokaryotic ribosome. Residues 43-200 of S4 from Bacillus stearothermophilus (S4 Delta41) bind specifically to both 16S rRNA and to a pseudoknot within the alpha operon mRNA. As a first step toward understanding how S4 recognizes and organizes RNA, we have solved the structure of S4 Delta41 in solution by multidimensional heteronuclear nuclear magnetic resonance spectroscopy. The fold consists of two globular subdomains, one comprised of four helices and the other comprised of a five-stranded antiparallel beta-sheet and three helices. Although cross-linking studies suggest that residues between helices alpha2 and alpha3 are close to RNA, the concentration of positive charge along the crevice between the two subdomains suggests that this could be an RNA-binding site. In contrast to the L11 RNA-binding domain studied previously, S4 Delta41 shows no fast local motions, suggesting that it has less capacity for refolding to fit RNA. The independently determined crystal structure of S4 Delta41 shows similar features, although there is small rotation of the subdomains compared with the solution structure. The relative orientation of the subdomains in solution will be verified with further study.     

Genetic control of Endosperm Balance Number (EBN): three additive loci in a threshold-like system

Summary The genetic control of Endosperm Balance Number (EBN) was investigated by a complete diallel of four exceptional diploid Solanum commersonii-S. chacoense hybrids (1 1/2 EBN) and backcrosses to their species parents, S. commersonii (1 EBN) and S. chacoense (2 EBN). Crosses in which the female parent had a higher EBN value than the male, S. chacoense (2 EBN)XF₁ (11/2 EBN) and F₁ (11/2 EBN)X S. commersonii (1 EBN), produced viable seed to aborted seed ratios of 11.1 and 11.3, respectively, and had average to small sized viable seed. Crosses in which the female parent had a lower EBN value than the male, S. commersonii (1 EBN)XF₁ (11/2 EBN) and F₁ (11/2 EBN)XS. chacoense (2 EBN), produced viable seed to aborted seed ratios of 1 7.9 and 1 6.7, respectively, and had average to large sized viable seeds. The results of these crosses appear to be consistent with the relative EBN values of the male and female parent. A model is proposed for the system regulating endosperm development. The assumptions of this model are: (1) three unlinked loci control the system; (2) the loci are homozygous within a species; (3) the genes have additive effects and are of equal strength within a species; (4) the genes within S. chacoense have twice the effect with respect to endosperm regulation as those within S. commersonii; and (5) a slight excess maternal dosage will produce the qualitative effect of small but viable seed. This model, in which quantitative genes operate in a dosage dependent system bears many similarities to classical, threshold-type genetic models.     

Comparative effects of limited tryptic hydrolysis on physicochemical and structural features of seed 11S globulins

The effect of the limited proteolysis by trypsin on selected seed storage 11S globulins (broad bean and pea legumins, glycinin and helianthinin) was studied by high-sensitive differential scanning calorimetry, fluorescence spectroscopy and analysis of proteolysis kinetics. Different behaviour of glycinin and helianthinin, on one hand, and broad bean and pea legumins, on the other, were observed: in the first group changes in the physicochemical characteristics of the proteins due to their limited proteolysis are more pronounced in comparison with the second one, in relation with the extent of primary structure modifications. The differences observed have been evaluated in relation with the amino acid sequence features of the four 11S globulin studied and agree with the literature data concerning the protein structural changes in the course of the limited proteolysis.     

Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. II. NMR solution structure

The solution structure of the conserved 690 hairpin from Escherichia coli 16 S rRNA was determined by NMR spectroscopy. The 690 loop is located at the surface of the 30 S subunit in the platform region and has been implicated in interactions with P-site bound tRNA, E-site mRNA, S11 binding, IF3 binding, and in RNA-RNA interactions with the 790 loop of 16 S rRNA and domain IV of 23 S rRNA. The structure reveals a novel sheared type G690.U697 base-pair with a single hydrogen bond from the G690 amino to U697-04. G691 and A696 also form a sheared pair and U692 forms a U-turn with an H-bond to the A695 non-bridging phosphate oxygen. The sheared pairs and U-turn result in the continuous single-stranded stacking of five residues from 6693 to U697 with their Watson-Crick functional groups exposed in the minor groove. The overall fold of the 690 hairpin is similar to the anticodon loop of tRNA. The structure provides an explanation for chemical protection patterns in the loop upon interaction with tRNA, the 50 S subunit, and S11. In vivo genetic studies demonstrate the functional importance of the motifs observed in the solution structure of the 690 hairpin.     

玉兰肉质外种皮挥发性成分与功能的初步研究

以玉兰(Magnolia denudata Desr.)发育成熟的种子为材料,采用水蒸气蒸馏法和GC-MS技术对其肉质外种皮化学成分的种类和含量进行了分析研究,并就玉兰肉质外种皮对其种子吸水和失水的影响以及化感作用进行比较研究,以探讨其相应的生态学和生物学功能。结果表明:(1)玉兰肉质外种皮占整个完整种子重量的48.25%,有无肉质外种皮对其种子自身吸水没有明显影响,但在失水过程中有肉质外种皮的种子失水较慢,具有一定的保水作用。(2)玉兰种子肉质外种皮中萜烯类和醇类的种类较多,分别有12种和11种;但酮类和酯类的相对含量较高,分别为32.84%和18.03%,其中含量较多的成分依次是甲基庚烯酮(31.95%)、乙酸丁酯(17.69%)、对伞花烃(13.64%)和芳樟醇(6.61%)。(3)玉兰肉质外种皮浸提液对豌豆、白菜种子萌发具有明显的抑制作用,且随着浸提液浓度增加,豌豆种子发芽率由86.7%下降为6.0%,白菜种子发芽率由28.0%下降为0。研究推测,玉兰种子的肉质外种皮在功能上可能是一种类似肉质果果肉的结构,具有丰富的化学成分,不仅可以吸引鸟类传播其种子,也具有一定的化感作用。     

Electron microscopy of seed-storage globulins

The quaternary structures of a range of seed globulins, including examples of both the so-called 7 S and 11 S types, have been examined by electron microscopy. The legume 7 S proteins, phaseolin (bean), beta-conglycinin (soybean), and vicilin (pea), appear as flat discs of diameter ca. 8.5 nm and thickness ca. 3.5 nm formed by association of three subunit domains. Phaseolin converts to an 18 S tetramer at acid pH, and images recorded under these conditions suggest that four of the 7 S protomer discs associate to form the faces of a regular tetrahedron. The classical 11 S seed globulins, cucurbitin (pumpkin) and legumin (pea), are approximately spherical molecules of diameter ca. 8.8 nm composed of six subunits. In contrast, the hexameric 10 S storage protein from lupin seed, conglutin gamma, appears toroidal in shape with outer diameter ca. 10.3 nm and thickness ca. 2.2 nm. These results indicate that constraints imposed on seed proteins by their role in sustaining the germinating plant may have allowed a variety of different globulin structures to accumulate in the protein-storage bodies of seeds.