Predicted metal binding sites for phytoremediation

Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. The objective of the study is to design and analyze metal binding motifs against the genes involved in phytoremediation. This is being done on the basis of certain pre-requisite amino-acid residues known to bind metal ions/metal complexes in medicinal and aromatic plants (MAP''s). Earlier work on MAP''s have shown that heavy metals accumulated by aromatic and medicinal plants do not appear in the essential oil and that some of these species are able to grow in metal contaminated sites. A pattern search against the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases yielded true positives in each case showing the high specificity of the motifs designed for the ions of nickel, lead, molybdenum, manganese, cadmium, zinc, iron, cobalt and xenobiotic compounds. Motifs were also studied against PDB structures. Results of the study suggested the presence of binding sites on the surface of protein molecules involved. PDB structures of proteins were finally predicted for the binding sites functionality in their respective phytoremediation usage. This was further validated through CASTp server to study its physico-chemical properties. Bioinformatics implications would help in designing strategy for developing transgenic plants with increased metal binding capacity. These metal binding factors can be used to restrict metal update by plants. This helps in reducing the possibility of metal movement into the food chain.     

Genome-Wide Analysis and Experimentation of Plant Serine/ Threonine/Tyrosine-Specific Protein Kinases

Protein tyrosine phosphorylation plays an important role in cell growth, development and oncogenesis. No classical protein tyrosine kinase has hitherto been cloned from plants. Does protein tyrosine kinase exist in plants? To address this, we have performed a genomic survey of protein tyrosine kinase motifs in plants using the delineated tyrosine phosphorylation motifs from the animal system. The Arabidopsis thaliana genome encodes 57 different protein kinases that have tyrosine kinase motifs. Animal non-receptor tyrosine kinases, SRC, ABL, LYN, FES, SEK, KIN and RAS have structural relationship with putative plant tyrosine kinases. In an extended analysis, animal receptor and non-receptor kinases, Raf and Ras kinases, mixed lineage kinases and plant serine/threonine/tyrosine (STY) protein kinases, form a well-supported group sharing a common origin within the superfamily of STY kinases. We report that plants lack bona fide tyrosine kinases, which raise an intriguing possibility that tyrosine phosphorylation is carried out by dual-specificity STY protein kinases in plants. The distribution pattern of STY protein kinase families on Arabidopsis chromosomes indicates that this gene family is partly a consequence of duplication and reshuffling of the Arabidopsis genome and of the generation of tandem repeats. Genome-wide analysis is supported by the functional expression and characterization of At2g24360 and phosphoproteomics of Arabidopsis. Evidence for tyrosine phosphorylated proteins is provided by alkaline hydrolysis, anti-phosphotyrosine immunoblotting, phosphoamino acid analysis and peptide mass fingerprinting. These results report the first comprehensive survey of genome-wide and tyrosine phosphoproteome analysis of plant STY protein kinases.     

PPR蛋白影响植物生长发育的研究进展

植物生长发育是一个极其复杂的生理生化过程,受内外因素共同作用。PPR蛋白是核基因编码的具有重复PPR基序的蛋白,分布广泛,在高等植物中数量巨大。PPR蛋白的靶标一般是线粒体和叶绿体中转录的RNA前体,多数可与MORF互作,参与线粒体和叶绿体基因的RNA编辑。PPR蛋白缺失的突变体植株多数呈现异常表型,影响植物的正常生长发育。本文就近年来发现的PPR蛋白结构、分布,与RNA编辑的关系,及其对植物生长发育的影响进行了综述。     

中国外来植物数据集

搞清楚中国外来植物种类有哪些, 从哪里来, 如何进入中国, 属于什么性质的类群, 它们的生物学特征和生态学特性如何等问题, 是中国外来入侵植物预防和预警机制研究的重要基础。《中国植物志》、Flora of China、各省级植物志书等记载的外来植物信息由于种种原因非常有限, 且目前我国尚没有完整体现中国外来植物信息的数据库。本文通过整合近几年外来植物相关的资料, 并通过文献考证增补外来植物原产地、习性等信息, 利用计算机网络、数据库及大数据分析技术手段, 经信息化处理和分类学校正, 进行分类体系重建, 最终确定中国外来植物的物种名录数据集。该数据集共有数据14,710条, 记载中国外来植物283科3,233属14,710个类群(含13,401原种332杂交种2嵌合体458亚种503变种14变型)。每个类群包括类别、中文科名、科名、中文属名、属名、中文名、别名、学名、命名人、生存状态、生存时间、生活型、原产国家或地区和中国引入省份等基础信息。数据集显示, 外来植物已在中国的植物种类构成中占据了相当大的比例(高达28.19%, 中国境内有维管植物52,177个类群, 其中本土37,464, 外来14,710, 上述数字包含种下等级, 统计截至2021年12月31日); 就生存状态而言, 栽培植物占所有外来植物的比例高达91%, 逃逸植物占7.36%, 归化植物占6.69%, 入侵植物占2.66%; 对于生活型的分析显示, 多年生类群占据了外来植物的绝大多数(13,625种, 约占总数的92.6%), 草本植物(8,937种, 约占总数的60.8%)相较于乔木(2,752种, 约占总数的18.7%)、灌木(4,916种, 约占总数的33.4%)及其他生活型数量要更多; 中国的外来植物大多来自北美洲(4,242种)、非洲(3,707种)、南美洲(3,645种)、亚洲(3,102种), 欧洲(1,690种)和大洋洲(1,305种)相对较少; 而中国具有外来植物最多的前10个省份分别为台湾(6,122种)、北京(5,244种)、福建(3,667种)、广东(3,544种)、云南(3,404种)、上海(2,924种)、江苏(2,183种)、江西(1,789种)、浙江(1,658种)和湖北(973种)。本数据集是第一次对中国外来植物进行全面系统整理, 可供从事外来植物相关研究工作参考, 也可作为植物多样性研究的基础资料, 还可作为农业、林业、草业、园林、草药及自然保护和环境保护人士及高等院校师生的参考数据。     

Environmental regulation and physiological basis of freezing tolerance in woody plants

Cold acclimation of plants is a complex process involving a number of biochemical and physiological changes. The ability to cold acclimate is under genetic control. The development of freezing tolerance in woody plants is generally triggered by non-freezing low temperatures but can also be induced by mild drought or exogenous abscisic acid, as well as by short photoperiod. In nature, the extreme freezing tolerance of woody plants is achieved during sequential stages of cold acclimation the first of which is initiated by short photoperiods and non-freezing low temperatures, and the second by freezing temperatures. Although recent breakthroughs have increased our knowledge on the physiological molecular basis of freezing tolerance in herbaceous species, which acclimate primarily in response to non-freezing low temperatures, very little is known about cold acclimation of woody plants. This article attempts to review our current understanding of the physiological aspects that underline cold acclimation in woody plants.     

The role of interactions between trophic levels in determining the effects of UV-B on terrestrial ecosystems

Understanding the potential impact of ozone depletion on terrestrial ecosystems is constrained by lack of information on the effects of environmentally realistic UV-B doses on terrestrial organisms other than higher plants. Increasing UV-B may alter interactions between plants and consumers through direct effects on consumer organisms (herbivores, phytopathogens, decomposers, etc.). The effects of increasing UV-B on arthropods are not known. Significant UV-B effects on fungi have been reported, and may be either negative (inhibition of spore germination and mycelial growth) or positive (increased growth, induction of reproductive development and sporulation). However, in many cases consumers are unlikely to be directly exposed to UV-B in the field. In addition, UV action spectra for fungi suggest that this major group may be less sensitive to the effects of ozone depletion than higher plants. Host mediated effects of UV-B on consumers may include alterations in plant chemistry. While secondary metabolites such as phenolics may increase under increased UV-B, this is not invariably the case and evidence that such changes have significant effects on consumers is limited. In particular, there is no evidence that increased UV-B increases resistance of higher plants to fungal pathogens. Indeed, increased UV-B prior to inoculation results in no significant effect or increased disease. Such responses may be attributable to UV-B effects on host surface properties or on compounds other than phenolics. However, such changes are poorly known, and their potential effects on phytopathogens, herbivores or decomposers cannot be assessed. Understanding the effects of UV-B on terrestrial ecosystems is further limited since virtually nothing is known of possible impacts on higher trophic levels, i.e. predators, parasites or pathogens.     

The right motifs for plant cell adhesion: what makes an adhesive site?

Cells of multicellular organisms are surrounded by and attached to a matrix of fibrous polysaccharides and proteins known as the extracellular matrix. This fibrous network not only serves as a structural support to cells and tissues but also plays an integral part in the process as important as proliferation, differentiation, or defense. While at first sight, the extracellular matrices of plant and animals do not have much in common, a closer look reveals remarkable similarities. In particular, the proteins involved in the adhesion of the cell to the extracellular matrix share many functional properties. At the sequence level, however, a surprising lack of homology is found between adhesion-related proteins of plants and animals. Both protein machineries only reveal similarities between small subdomains and motifs, which further underlines their functional relationship. In this review, we provide an overview on the similarities between motifs in proteins known to be located at the plant cell wall—plasma membrane—cytoskeleton interface to proteins of the animal adhesome. We also show that by comparing the proteome of both adhesion machineries at the level of motifs, we are also able to identify potentially new candidate proteins that functionally contribute to the adhesion of the plant plasma membrane to the cell wall.     

Host plant utilization by butterfly larvae in the Andaman and Nicobar Islands (Indian Ocean)

The larval food plants of the butterflies of the Andaman and Nicobar islands have not been studied, although the butterfly fauna per se is fairly well known. For the first time we report the food plants of the larvae of 120 species of butterflies from these islands on the basis of laboratory rearing and field studies. This information is essential for the formulation of management programmes for butterfly conservation on these islands which are known to harbour critical swallowtail and (possibly) danaine faunas.     

小麦长链非编码RNA的预测及功能分析

生物体有部分基因被转录成RNA,但是不编码相应蛋白质,称为长链非编码RNA(lncRNA)。它们参与基因的表观调控,这一过程对动物、植物的生长发育都有重要作用,但是,目前植物中发现和研究的lncRNA较少。为了研究lncRNA在植物中的功能,本研究建立了基于小麦全长cDNA的lncRNA识别程序。从6162条小麦全长cDNA中发现了231条lncRNAs,并从中鉴定出两个新miRNAs,这表明lncRNAs可以通过形成miRNAs前体基因形成其功能。此外,通过序列富集分析,我们从小麦lncRNAs中鉴定出三个保守的调控元件,结果显示小麦lncRNAs可能通过和其它蛋白质或DNA等分子作用,进而参与小麦生长、发育等过程的调控,这些结果对进一步研究植物体内的lncRNA的功能和作用机制具有重要意义。     

Chromium in a series of Portuguese plants used in the herbal treatment of diabetes

Chromium (Cr³⁺) is an essential micronutrient for humans. Its main action is thought to be the regulation of blood sugar, because chromium deficiency is associated with diabetic-like symptoms, and chromium supplementation is correlated with increased glucose tolerance and insulin sensivity. Some Portuguese aromatic plants are utilized as tisanes by diabetic people as medicinal plants. Their active principle is not yet known, and the importance of their chromium content in the claimed therapeutic properties should not be discarded. Therefore, determination of chromium in some Portuguese medicinal plants was performed by flameless atomic absorption. All the analyzed plants contain chromium at the normal level for this element, but the plants used to prepare tisanes to help diabetic conditions contain higher levels (2.2 μg/g dry wt ±0.88;n=11) than the others (0.88 μg/g dry wt±0.18;n=17).     

14-3-3 proteins: eukaryotic regulatory proteins with many functions

The enigmatically named 14-3-3 proteins have been the subject of considerable attention in recent years since they have been implicated in the regulation of diverse physiological processes, in eukaryotes ranging from slime moulds to higher plants. In plants they have roles in the regulation of the plasma membrane H⁺-ATPase and nitrate reductase, among others. Regulation of target proteins is achieved through binding of 14-3-3 to short, often phosphorylated motifs in the target, resulting either in its activation (e.g. H⁺-ATPase), inactivation (e.g. nitrate reductase) or translocation (although this function of 14-3-3 proteins has yet to be demonstrated in plants). The native 14-3-3 proteins are homo- or heterodimers and, as each monomer has a binding site, a dimer can potentially bind two targets, promoting their association. Alternatively, target proteins may have more than one 14-3-3-binding site. In this mini review, we present a synthesis of recent results from plant 14-3-3 research and, with reference to known 14-3-3-binding motifs, suggest further subjects for research.     

Medicinal plants for helminth parasite control: facts and fiction

The use of medicinal plants for the prevention and treatment of gastro-intestinal parasitism has its origin in ethnoveterinary medicine. Although until recently the majority of the evidence on the antiparasitic activity of medicinal plants was anecdotal and lacked scientific validity, there is currently an increasing number of controlled experimental studies that aim to verify and quantify such plant activity. There are indeed a large number of plants whose anthelmintic activity has been demonstrated under controlled experimentation, either through feeding the whole plant or administering plant extracts to parasitised hosts. However, contrary to traditional expectation, there are also a great number of plants with purported antiparasitic properties, which have not been reproduced under experimental conditions. In this paper, we discuss the source of such inconsistencies between ethnoveterinary wisdom and scientific experimentation. We focus on the strengths and weaknesses of the existing methodologies used in the controlled studies to determine the activity of antiparasitic plants. We discuss issues like the seasonal and environmental variability of the plant composition, and how this can affect their antiparasitic properties and highlight the importance of identifying the mechanisms of action of such plants and the target parasite species. In addition to their antiparasitic properties, medicinal plants may also have anti-nutritional properties, which can affect animal performance and behaviour. For this reason, we emphasise the need for considering additional dimensions when evaluating medicinal plants. We also question whether using similar criteria as those used for the evaluation of anthelmintics is the way forward. We propose that a holistic approach is required to evaluate the potential of medicinal plants in parasite control and maximise their benefits on parasitised hosts.     

Cadmium Toxicity in Plants: Is There any Analogy to its Carcinogenic Effect in Mammalian Cells?

Cadmium is a heavy metal, which is classified as a human carcinogen and is known to be toxic to plants. However, plants do not respond to this metal by massive cell proliferation. In this review the various aspects of cadmium toxicity in plants are compared to related processes in mammalian cells. The following issues are discussed: cellular uptake of Cd ions, their intracellular transport, the effects on cellular signaling, nucleic acids and proteins, modification of gene expression, cell cycle control and apoptosis. Reviewed data suggest that such features as: ability to remove the oxidized proteins, slightly different regulation of cell cycle genes, specific pattern of apoptosis, makes plants resistant to Cd²⁺-induced uncontrolled cell proliferation.     

Carnivorous pitcher plants: insights in an old topic

Plant insect interactions are usually recognized as a scenario where herbivorous insects feed on a host plant. However, also the opposite situation is known, where plants feed on insects. Carnivorous pitcher plants of the genus Nepenthes as well as other pitcher plants obtain many nutrients from caught insect prey. Special features of the pitcher traps’ surface are responsible for attraction and trapping insects. Once caught, the prey is digested in the fluid of the pitchers to release nutrients and make them available for the plant. Nutrients are taken up by special glands localized on the inner surface of the pitchers. These glands also secrete the hydrolyzing enzymes into the digestion fluid. Although this is known for more than 100 years, our knowledge of the pitcher fluid composition is still limited. Only in recent years some enzymes have been purified from the pitcher fluid and their corresponding genes could be identified. Among them, many pathogenesis-related proteins have been identified, most of which exhibiting hydrolytic activities. The role of these proteins as well as the role of secondary metabolites, which have been identified in the pitcher fluid, is discussed in general and in the context of further studies on carnivorous plants that might give answers to basic questions in plant biology.     

Phytogenesis of halomethanes: A product ofselection or a metabolic accident?

Phytoplankton (microalgae), seaweeds(macroalgae), higher plants and fungi producehalomethanes. Algae and fungi produce bothmethyl halides and polyhalomethanes, whereasplants are known to produce only methylhalides. Why these organisms producehalomethanes is a question frequently asked bychemists and biologists. This question impliesthat halomethanes have a function and have aselective value to the producing organism.Except for some fungi, the evolutionaryadvantage of producing halomethanes may notpresently exist. Polyhalomethanes areby-products of halogenation of certain organiccompounds by haloperoxidases in marine algaeand perhaps some fungi, and they may beindirectly produced in aquatic environments byalgal release of oxidized halogen species. Amain function of this enzyme is to rid the cellof harmful oxidants such as hydrogen peroxide.Monohalomethanes (methyl halides) are productsof methyltransferase activity. It has beenproposed that methyl halide production mayprovide a mechanism to regulate chloride levelsin halotolerant plants. The examination of halidecellular concentrations, halomethane productionrates, and enzyme characteristics raisesquestions about this possible function. Inalgae, plants and some fungi, methyl halidesmay be a result of the insertion of ubiquitoushalides into the active site of numerousmethyltransferases. Therefore, halomethanes maybe by-products or `accidents' of metabolism.     

Resurrection Plants: The Puzzle of Surviving Extreme Vegetative Desiccation

Tolerance to near complete desiccation of vegetative organs is a widespread capability in bryophytes and is also shared by a small group of vascular plants known as resurrection plants. To date more than 300 species, belonging to pteridophytes and angiosperms, have been identified that possess this kind of desiccation-tolerance. The vegetative desiccation-tolerance of resurrection plants is an inductive process displayed only under environmental stress with or without the involvement of abscisic acid as molecular signal. The different problems associated with desiccation encountered by resurrection plants render the employment of many interacting mechanisms necessary. Preservation of cell order and correct structure of membranes and macromolecules is underpinned by the synthesis of large amounts of sugars, amino acids, and small polypeptides such as late embryogenesis abundant (LEA) proteins and dehydrins. Some of these compatible solutes, such as sucrose and LEA proteins, are also involved in cytoplasm vitrification, which occurs during the last phase of desiccation. Mechanical damage due to vacuole shrinkage in dehydrating cells is avoided by cell wall folding or by replacing the water in vacuoles with nonaqueous substances. Oxidative stress, due to enhanced production of reactive oxygen species (ROS) especially by chloroplasts, is minimized through two different strategies. The homoiochlorophyllous resurrection plants, which conserve chloroplasts with chlorophylls and thylakoids upon drying, fold leaf blades and synthesize anthocyanins, as both sunscreens and free radical scavengers, and additionally increase the activity of antioxidant systems in cells. In contrast, the chloroplasts in poikilochlorophyllous species degrade chlorophylls and thylakoid membranes yielding desiccoplasts that are devoid of any internal structures. These adaptive mechanisms preserve cells from damage by desiccation and allow them to resume vital functions once rehydrated. Even if based mainly on cell protection during drying, the vegetative desiccation-tolerance of resurrection plants also relies on systems of cell recovery and repair upon rehydration. However, most of these systems are prepared during cell dehydration.     

The binding motifs for Ac transposase are absolutely required for excision of Ds1 in maize

A reverse genetic system for studying excision of the transposable elementDs1 in maize plants has been established previously. In this system, theDs1 element, as part of the genome of maize streak virus (MSV), is introduced into maize plants via agroinfection. In the presence of theAc element, excision ofDs1 from the MSV genome results in the appearance of viral symptoms on the maize plants. Here, we used this system to study DNA sequences requiredin cis for excision ofDs1. TheDs1 element contains theAc transposase binding motif AAACGG in only one of its subterminal regions (defined here as the 5′ subterminal region). We showed that mutation of these motifs abolished completely the excision capacity ofDs1. This is the first direct demonstration that the transposase binding motifs are essential for excision. Mutagenesis with oligonucleotide insertions in the other (3′) subterminal region resulted in elements with either a reduced or an increased excision efficiency, indicating that this subterminal region also has an important function.     

BiP and zein binding domains within the delta zein protein

Zeins are alcohol soluble seed storage proteins synthesized within the endosperm of maize and subsequently deposited into endoplasmic reticulum (ER) derived protein bodies. The genes encoding the beta and delta zeins were previously introduced into tobacco with the expectation of improving the nutritional quality of plants (Bagga et al. in Plant Physiol 107:13, 1997). Novel protein bodies are produced in the leaves of transgenic plants accumulating the beta or delta zein proteins. The mechanism of protein body formation within leaves is unknown. It is also unknown how zeins are retained in the ER since they do not contain known ER retention motifs. Retention may be due to an interaction of zeins with an ER chaperone such as binding luminal protein (BiP). We have demonstrated protein–protein interactions with the delta zeins, beta zeins, and BiP proteins using an E. coli two-hybrid system. In this study, four putative BiP binding motifs were identified within the delta zein protein using a BiP scoring program (Blond-Elguindi et al. in Cell 75:717, 1993). These putative binding motifs were mutated and their effects on protein interactions were analyzed in both a prokaryotic two-hybrid system and in plants. These mutations resulted in reduced BiP–zein protein interaction and also altered zein–zein interactions. Our results indicate that specific motifs are necessary for BiP–delta zein protein interactions and that there are specific motifs which are necessary for zein–zein interactions. Furthermore, our data demonstrates that zein proteins must be able to interact with BiP and zeins for their stability and ability to form protein bodies.     

基因组学: 理解植物入侵性的重要工具

入侵植物基因组学是一个新兴的研究领域, 它利用基因组学方法研究与植物入侵性相关的分子基础和表达调控机制, 甄别入侵性基因型, 进而在基因组水平上揭示外来种入侵性产生和进化的分子机制。本文扼要综述了可用于植物入侵生物学研究的主要基因组学方法, 包括比较基因组学、群体基因组学和表观基因组学等方法; 运用基因组学技术研究入侵植物除草剂抗性和根状茎发育的分子基础已取得了重要进展。然而, 入侵植物基因组学仍处于发展初期, 选择理想的入侵植物模式种, 建立入侵性研究的模式系统, 是当前亟待解决的问题。本文还提出了入侵植物基因组学研究值得关注的几个发展方向, 包括基因组信息的完善、不同环境条件下入侵植物的分子响应机制以及入侵性的系统生物学研究等。