稀土元素生物效应的蛋白质组学研究

蛋白质组学是研究细胞内全部蛋白的动态表达及其相互关系的新兴学科，是功能基因组学研究的重要组成部分和战略制高点，广泛应用于生命科学的各个领域，研究对象涵盖微生物、动物和植物等。 　　稀土元素（rare earth elements），亦称镧系元素（lanthanides），是性质相似的15种金属元素。随着稀土元素在工业、农牧业和医疗等领域的应用日益深入，它们对生物体的作用机制亟待研究。生物固氮作用为生命世界提供75%的绿色氮源，根瘤菌是重要的固氮微生物，具有基因组结构简单、培养周期短等特点。酿酒酵母是与人类关系最密切的一种酵母，不仅因为传统上其用于制作食品及酿酒，而且是现代分子生物学和细胞生物学中的真核模式生物。为了全面地了解稀土元素对细胞的作用，我们运用高分辨率的蛋白质双向电泳分离技术和高通量的蛋白质质谱分析手段以及生物信息学等方法，分析了稀土元素钆（Gadolinium，Gd）在原核生物费氏中华根瘤菌（Sinorhizobium fredii）USDA205和真核生物酿酒酵母（Saccharomyces cerevisiae）YM4271的生物效应。 　　结果表明，经1mM Gd(NO3)3处理12小时后，费氏中华根瘤菌USDA205中 22个蛋白质表达有差异。这些蛋白质可根据功能分为8类，包括转运蛋白、胁迫相关蛋白、代谢相关蛋白等。其中13个蛋白质表达量增加，9个蛋白质表达量下降。膜蛋白在差异蛋白中占有很大比重。另外，我们分析了不同浓度的钆处理后蛋白质表达的变化情况，发现蛋白质组的变化是与处理浓度密切相关的。研究中还发现同种浓度的钆与另一种稀土元素铒（Erbium，Er）相比，离子半径较小的铒离子对根瘤菌的抑制作用更加明显。 　　比较不同浓度的钆对酿酒酵母YM4271的影响，发现酵母对稀土元素的反应不及根瘤菌敏感，对数生长初期的酵母经钆处理12小时或24小时后均无显著变化。 　　本研究首次用蛋白质组学的方法研究稀土元素对微生物的作用，鉴定了一些有价值的蛋白质，并得到了它们的表达特点和相关数据，为更好地理解稀土元素的生物效应提供了有力的分子生物学证据。 　　

Release of Flavonoids by the Soybean Cultivars McCall and Peking and Their Perception as Signals by the Nitrogen-Fixing Symbiont Sinorhizobium fredii1

Sinorhizobium fredii strain USDA191 forms N-fixing nodules on the soybean (Glycine max L. Merr.) cultivars (cvs) McCall and Peking, but S. fredii strain USDA257 nodulates only cv Peking. We wondered whether specificity in this system is conditioned by the release of unique flavonoid signals from one of the cultivars or by differential perception of signals by the strains. We isolated flavonoids and used nodC and nolX, which are nod-box-dependent and -independent nod genes, respectively, to determine how signals activate genes in the microsymbionts. Seeds of cv McCall and cv Peking contain the isoflavones daidzein, genistein, and glycitein, as well as their glucosyl and malonylglucosyl glycosides. Roots exude picomolar concentrations of daidzein, genistein, glycitein, and coumestrol. Amounts are generally higher in cv Peking than in cv McCall, and the presence of rhizobia markedly influences the level of specific signals. Nanomolar concentrations of daidzein, genistein, and coumestrol induce expression of nodC and nolX in strain USDA257, but the relative nolX-inducing activities of these signals differ in strain USDA191. Glycitein and the conjugates are inactive. Strain USDA257 deglycosylates daidzin and genistin into daidzein and genistein, respectively, thereby converting inactive precursors into active inducers. Although neither soybean cultivar contains unique nod-gene-inducing flavonoids, strain- and cultivar-specific interactions are characterized by distinct patterns of signal release and response.

快生型大豆根瘤菌（Rhizobium fredii）与野大豆（Glycine soja）相互作用的研究

快生型大豆根瘤菌（Rhizobium fredii）能浸染野大豆（Glycine soja）和栽培大豆（Glycine max）根部并形成固氮的根瘤。本文研究了R.fredii对野大豆的识别和侵染。通过研究R.fredii与大豆植物凝集素（SBL）结合和根毛吸附，R. fredii的EPS缺失突变株结瘤能力分析。结瘤；能力下降的突变株表面多糖分析等。发现了R.fredii与野大豆识别和侵染过程的特殊性。研究表明，（1）发现R.fredii与B.Jiaponicum和宿主的识别有不同的方式， 这在世界上是首次证明同一豆科宿主对不同的共生根瘤菌有不同的识别机制。这对认识宿主牧民性控制，研究扩大结瘤固氮范围等有重要意义；（2）第一个进行了R.fredii的Exo~-突变型的分离和鉴定。发现R. fredii的EPS产量和组成的严重发迹并不影响识别和侵染。说明在其他一些根瘤菌中发现的EPS作为宿主防御机制的保护层的作用。在R.fredii-野大豆和栽培大豆的共生结瘤中并不着急丰富了对根瘤菌EPS功能的新认识。并提出EPS作为保护层的作用与宿主植物类型有关的假设；（3）首次获得了LPS发生变化的R. fredii突变株Exol。并研究了其结瘤能力下降的现象与侵染能力和表面多糖变化的关系。提出R. fredii SG2的LPS可能在野大豆根毛郑曲和根瘤菌侵染过程中起重要作用。

Estabilización y sobrevivencia de suspensiones de Sinorhizobium meliloti, efecto de la concentración de exopolisacáridos

p.185-190

Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome

The number of solute-binding protein-dependent transporters in rhizobia is dramatically increased compared with the majority of other bacteria so far sequenced. This increase may be due to the high affinity of solute-binding proteins for solutes, permitting the acquisition of a broad range of growth-limiting nutrients from soil and the rhizosphere. The transcriptional induction of these transporters was studied by creating a suite of plasmid and integrated fusions to nearly all ATP-binding cassette (ABC) and tripartite ATP-independent periplasmic (TRAP) transporters of Sinorhizobium meliloti. In total, specific inducers were identified for 76 transport systems, amounting to approximate to 47% of the ABC uptake systems and 53% of the TRAP transporters in S. meliloti. Of these transport systems, 64 are previously uncharacterized in Rhizobia and 24 were induced by solutes not known to be transported by ABC- or TRAP-uptake systems in any organism. This study provides a global expression map of one of the largest transporter families (transportome) and an invaluable tool to both understand their solute specificity and the relationships between members of large paralogous families.

Identification of lumichrome as a Sinorhizobium enhancer of alfalfa root respiration and shoot growth

Sinorhizobium meliloti bacteria produce a signal molecule that enhances root respiration in alfalfa (Medicago sativa L.) and also triggers a compensatory increase in whole-plant net carbon assimilation. Nuclear magnetic resonance, mass spectrometry, and ultraviolet–visible absorption identify the enhancer as lumichrome, a common breakdown product of riboflavin. Treating alfalfa roots with 3 nM lumichrome increased root respiration 21% (P < 0.05) within 48 h. A closely linked increase in net carbon assimilation by the shoot compensated for the enhanced root respiration. For example, applying 5 nM lumichrome to young alfalfa roots increased plant growth by 8% (P < 0.05) after 12 days. Soaking alfalfa seeds in 5 nM lumichrome before germination increased growth by 18% (P < 0.01) over the same period. In both cases, significant growth enhancement (P < 0.05) was evident only in the shoot. S. meliloti requires exogenous CO2 for growth and may benefit directly from the enhanced root respiration that is triggered by lumichrome. Thus Sinorhizobium–alfalfa associations, which ultimately form symbiotic N2-reducing root nodules, may be favored at an early developmental stage by lumichrome, a previously unrecognized mutualistic signal. The rapid degradation of riboflavin to lumichrome under many physiological conditions and the prevalence of riboflavin release by rhizosphere bacteria suggest that events demonstrated here in the S. meliloti–alfalfa association may be widely important across many plant–microbe interactions.

Galactosides in the rhizosphere: Utilization by Sinorhizobium meliloti and development of a biosensor

Identifying the types and distributions of organic substrates that support microbial activities around plant roots is essential for a full understanding of plant–microbe interactions and rhizosphere ecology. We have constructed a strain of the soil bacterium Sinorhizobium meliloti containing a gfp gene fused to the melA promoter which is induced on exposure to galactose and galactosides. We used the fusion strain as a biosensor to determine that galactosides are released from the seeds of several different legume species during germination and are also released from roots of alfalfa seedlings growing on artificial medium. Galactoside presence in seed wash and sterile root washes was confirmed by HPLC. Experiments examining microbial growth on α-galactosides in seed wash suggested that α-galactoside utilization could play an important role in supporting growth of S. meliloti near germinating seeds of alfalfa. When inoculated into microcosms containing legumes or grasses, the biosensor allowed us to visualize the localized presence of galactosides on and around roots in unsterilized soil, as well as the grazing of fluorescent bacteria by protozoa. Galactosides were present in patches around zones of lateral root initiation and around roots hairs, but not around root tips. Such biosensors can reveal intriguing aspects of the environment and the physiology of the free-living soil S. meliloti before and during the establishment of nodulation, and they provide a nondestructive, spatially explicit method for examining rhizosphere soil chemical composition.

The Sinorhizobium meliloti EmrR Regulator Is Required for Efficient Colonization of Medicago sativa Root Nodules

The nitrogen-fixing bacterium Sinorhizobium meliloti must adapt to diverse conditions encountered during its symbiosis with leguminous plants. We characterized a new symbiotically relevant gene, emrR (SMc03169), whose product belongs to the TetR family of repressors and is divergently transcribed from emrAB genes encoding a putative major facilitator superfamily-type efflux pump. An emrR deletion mutant produced more succinoglycan, displayed increased cell-wall permeability, and exhibited higher tolerance to heat shock. It also showed lower tolerance to acidic conditions, a reduced production of siderophores, and lower motility and biofilm formation. The simultaneous deletion of emrA and emrR genes restored the mentioned traits to the wild-type phenotype, except for survival under heat shock, which was lower than that displayed by the wild-type strain. Furthermore, the ΔemrR mutant as well as the double ΔemrAR mutant was impaired in symbiosis with Medicago sativa; it formed fewer nodules and competed poorly with the wild-type strain for nodule colonization. Expression profiling of the ΔemrR mutant showed decreased expression of genes involved in Nod-factor and rhizobactin biosynthesis and in stress responses. Expression of genes directing the biosynthesis of succinoglycan and other polysaccharides were increased. EmrR may therefore be involved in a regulatory network targeting membrane and cell wall modifications in preparation for colonization of root hairs during symbiosis.

根瘤菌在植物内的迁移运动及其与植物相互作用的蛋白质组学研究

根瘤菌不但可以在豆科植物的根部形成共生固氮的根瘤，而且还可以在自然条件下与重要的谷类作物的根形成内生的联合作用。尽管内生菌在植物中广泛存在，但是关于根瘤菌在植物根内的定殖方式还有许多未知。根瘤菌作为内生菌与水稻相互作用的分子机制目前还不清楚。本研究应用显微镜观察、分子生物学和蛋白质组学的研究技术，对内生根瘤菌与植物相互作用，并促进生长的机制进行了探索。 我们用带有gfp标记的根瘤菌分别接种非豆科植物水稻、烟草和豆科植物，应用激光共聚焦显微镜和平板分离，检测其在健康植物组织内的侵染、定殖和分布过程及其对植物生长生理的影响。结果表明： 1．根瘤菌对水稻的侵染是一个动态的过程，它开始于根际表面的定殖，然后从根的裂隙进入根内，向上迁移到叶鞘和叶部分，并且发展为较高的群体密度。水稻接种不同种类的根瘤菌，显著增加了根和地上部分的生物量，提高了光合速率、气孔导度、蒸腾速率、水分利用效率和旗叶的叶面积，并且在植物体内积累了更高浓度的植物激素（生长素和赤霉素）。 2．根瘤菌同样可以在烟草体内由根部向植物地上部分的茎、叶迁移，并从叶的气孔溢出到叶的表面，具有附生－内生－附生生活方式的转换。同时，根瘤菌还可以沿植物的表面从根到地上部分迁移。在植物的生殖生长阶段，内生根瘤菌仍然保持活动性，可以进入烟草子房的子房壁、胎座和胚珠内，暗示根瘤菌通过种子向子代垂直传播的可能性。 3．根瘤菌与豆科植物形成共生固氮根瘤的同时，还可以以内生菌的生态方式定殖于豆科植物中，同样有类似于水稻、烟草的方式在体内由根向地上部分迁移。这种定殖和迁移与根瘤菌胞外多糖和鞭毛的有和无没有关系。 内生根瘤菌促进植物生长的原因是人们一直关心的问题。将根瘤菌固氮正调控基因nifA的启动子与gfp基因构建成融合质粒，设计其他nif相关基因的引物，对有内生根瘤菌的水稻和豆科植物的RNA，进行RT-PCR，表明，虽然定殖于豆科植物体内的内生根瘤菌nifA基因有表达，但是其他的nif基因不表达，因而内生根瘤菌对植物的促生作用不是固氮作用的结果。 我们还用蛋白质组学的方法，分析了Sinorhizobium meliloti 1021和Azorhizobium caulinodans ORS 571接种水稻根部后的植物根、叶鞘和叶组织的蛋白质表达的差异变化。结果表明Sinorhizobium meliloti 1021接种水稻引起的差异蛋白在根内有21个，叶鞘内有19个，叶内有12个;Azorhizobium caulinodans ORS 571接种水稻引起的差异蛋白在根内有7个，叶鞘内有 8个，叶内有8个。蛋白功能的归类中有防卫反应、光合作用、植物生长素、碳和能量代谢及氮代谢相关蛋白的变化。特别是光合作用、植物生长素等相关蛋白的表达，与生理测定光合作用和生长素有提高是一致的，为内生根瘤菌促进水稻生长提供了一个方面的分子证据。 综上所述，表明内生根瘤菌和植物的联合作用比以前所认识的更为复杂，更具有侵染力和动态性。因此，本研究提高了人们对根瘤菌的新认识，不仅与豆科植物根部结瘤，进行共生固氮，而且以内生菌与水稻等植物联合，提高光合作用和生长素含量，促进生长，从另一个方面补充了根瘤菌对植物的有益作用，为根瘤菌作为广谱生物肥料的发展策略奠定分子基础，对可持续农业有重要意义。

大豆根瘤菌种群多样性及结瘤特性研究

环境因子及土著根瘤菌是影响人工接种根瘤菌剂接种效果的两个主要因素。论文分为二部分。第一部分首先考察了外界因素对根瘤菌剂接种效果的影响。应用GUS（葡萄糖苷酶）基因标记技术将标记基因GUS导入受体菌S.fredii 8855，标记菌体形成的根瘤可被GUS染色缓冲液染成兰色，而土著菌形成的根瘤不能着色，由此即可十分简便地确定土著菌的影响程度。盆栽实验表明，S.fredii 8855的结瘤抗酸碱能力高于土著菌，能在土壤中较大范围内迁移。当它的根瘤占有率不小于43％时，接种能显著提高大豆产量。大豆产量与根瘤根瘤占有率呈正相关(r = 0.98)，而与总瘤数关系不大(r = 0.13)。土壤氮素显著抑制其结瘤，补加磷能缓解这种抑制作用。研究发现应用快生型大豆根瘤菌剂为保证接种效果，接种量至少应为土著根瘤菌数量的10~5倍，同时施用磷肥会提高接种效果。只有当接种根瘤菌的占瘤率在40％以上时接种才可能达到增产目的。第二部分较为系统地考察了新疆主要大豆产区耕作土中大豆根瘤菌种群数量、种群结构及种群共生、遗传多样性。新疆大豆地耕作土中含有数量较高的大豆根瘤菌，数量每克土大多在10~5-10~6之间，种群结构大多以快生型根瘤菌为主。对分离的28株根瘤共生及遗传多样性进行了分析，土著大豆根瘤菌菌株间结瘤能力有一定差异，快生型大豆根瘤菌总体结瘤能力高于慢生型，但差异不显著(p <= 0.05)，形成的根瘤大小也有较大差异。根瘤菌种群中菌株间为植物提供的生物固氮量存在明显差别，但仅有20％的菌株能明显促进植物生长，有1/3的菌株具有较高的固氮能力。慢生型大豆根瘤菌固氮能力明显高于快生型，但二者之间差异未达到显著水平(p < 0.05)。根瘤菌结瘤力与固氮活性之间的相关性分析发现许多根瘤菌形成的根瘤为无效根瘤。重复序列（重复基因外回文REP和肠细菌重复基因间共同序列ERIC）结合聚合酶链式反应(ERP和ERIC－PCR)用于大豆根瘤菌染色体指纹分析，分析结果表明新疆土著大豆根瘤菌具有复杂的遗传多样性，遗传相近程度具有一定的地域性，来自同一地区的根瘤菌株具有较高的遗传相似性。新疆土著大豆根瘤菌在相似水平0.5可分为两大类群，一个类群包括所有慢生型根瘤菌，另一类群为所有快生型根瘤菌。在相似水平0.6大豆根瘤菌可分为5个聚群，快生型根瘤菌分为二个主要聚群和一个次要类群，慢生型根瘤菌分为二个次要类群。主要聚群中一个聚群结瘤能力较高但固氮能力较低，另一聚群结瘤能力和固氮量均较低；次要聚群中快生型和一个慢生型聚群固氮能力较高但结瘤力低，另一慢生型聚群固氮能力和结瘤力均较高。以上研究表明，新疆绿洲农业生态系统中大豆根瘤菌具有一定种质特异性，尽管次要类群具有相对较高的因氮活性，但由于多数根瘤菌形成的根瘤为固氮活性很低的无效根瘤，占优势的主要聚群固氮活性较低，因此土著根瘤菌生物固氮量不能满足作物对氮素的需求，在新疆人工施用根瘤菌剂具有现实意义，但接种的根瘤菌剂可能受到对环境适应性强、结瘤能力高的土著根瘤菌优势类群强有力的竞争。

苜蓿根瘤菌聚羟丁酸代谢突变体的竞争生长和结瘤能力以及外源生物素的影响

对苜蓿根瘤菌(Sinorhizobium meliloti)聚羟丁酸(PHB)代谢突变体与野生型菌株之间,以及不同突变体之间的竞争生长和竞争结瘤能力在不同培养条件下进行了测定,并研究了外源生物素对各突变体竞争生长和竞争结瘤能力的影响。结果表明:①PAbC 突变体菌株与野生型菌株共培养,不论培养基中添加、不添加外源生物素,pAbC 突变体均表现出生长竞争能力的严重缺陷;竞争结瘤实验也显示,该突变体同野生型菌株竞争结瘤能力大幅下降;说明 PHB 合成能力的缺陷影响了菌株的竞争生长和竞争结瘤能力。②bdhA 突变体与野生型菌株共培养,在不添加外源生物素的情况下,bdhA 突变体同野生菌株竞争生长的能力有明显缺陷,但在添加外源生物素的情况下,其竞争生长能力有明显提高;bdhA::Tn5突变体与 phbC::Tn5-233突变体共培养,如培养基中不添加外源生物素,二者间的竞争生长能力无大的差异;但若添加外源生物素,则 bdhA 突变体的竞争生长能力明显高于 phbC 突变体;表明外源生物素对 bdhA 突变体的竞争生长能力有重要作用。