Transposable elements in plants: Recent advancements,tools and prospects

Transposable elements (TEs) have long been considered junk DNA; however, the availability of genome sequences and the growth of omics databases have accelerated the study of TEs, and they are now considered evolutionary signatures. TEs, essential genetic elements in plant genomes, can move around the genome by either “cut-paste” (DNA transposons) or “copypaste” mechanisms (RNA transposons). TEs often affect host genome size and interact with host genes, resulting in altered gene expression and regulatory networks. Several genes have been identified to be influenced/modified by the action of TEs. TEs have diverse structures and functions. Plants are capable of using TEs as promoters and enhancers to drive epigenetic mechanisms in a tissue-specific manner. However, our knowledge about TEs remains poor despite extensive research in plants. Plant physiological functions associated with TEs have been challenging to analyse due to a lack of focused research. Another limitation is the lack of sufficient genetic information. The different functions displayed by plant genomes are genetically regulated, which opens up opportunities in areas such as genomic evolution and epigenetic modification. Indeed, understanding the contribution of TEs in the plant genome is indispensable to assess the diversity of evolutionary adaptability in plant taxa. In this study, we review the applications of TEs and discuss the value of genetic information in the plant genome. Genomic information about TEs has a significant value in high throughput research, including forward and reverse genetics. We discuss current strategies in using TEs for the genetic dissection of plant genomes. This review covers opportunities to use different TEs databases to increase the productivity of economically important plants for sustainable development

     

Current genetic engineering strategies for the production of antihypertensive ACEI peptides

Hypertension is a major and highly prevalent risk factor for various diseases. Among the most frequently prescribed antihypertensive first-line drugs are synthetic angiotensin I-converting enzyme inhibitors (ACEI). However, since  their use in hypertension therapy has been linked to various side effects, interest in the application of food-derived ACEI peptides (ACEIp) as antihypertensive agents is rapidly growing. Although promising, the industrial production of ACEIp through conventional methods such as chemical synthesis or enzymatic hydrolysis of food proteins has been proven troublesome. We here provide an overview of current antihypertensive therapeutics, focusing on ACEI, and illustrate how biotechnology and bioengineering can overcome the limitations of ACEIp large-scale production. Latest advances in ACEIp research and current genetic engineering-based strategies for heterologous production of ACEIp (and precursors) are also presented. Cloning approaches include tandem repeats of single ACEIp, ACEIp fusion to proteins/polypeptides, joining multivariate ACEIp into bioactive polypeptides, and producing ACEIp-containing modified plant storage proteins. Although bacteria have been privileged ACEIp heterologous hosts, particularly when testing for new genetic engineering strategies, plants and microalgae-based platforms are now emerging. Besides being generally safer, cost-effective and scalable, these “pharming” platforms can perform therelevant posttranslational modifications and produce (and eventually deliver) biologically active protein/peptide-based antihypertensive medicines.     

组蛋白修饰调控植物对胁迫的记忆与警备抗性的研究进展

植物扎根土壤,面对不利的环境胁迫无法逃避。然而,植物已经进化出对环境胁迫的记忆(stress memory)与警备抗性(或防御警备defense priming)等机制适应环境。环境胁迫在短时间内无法改变植物的DNA碱基序列,因此表观遗传被认为是植物对环境胁迫产生记忆和产生防御警备的主要机制,而组蛋白修饰被认为是最重要的机制,为胁迫记忆提供了可能。本文综述了非生物和生物胁迫下植物分别以胁迫记忆和防御警备机制为主导的组蛋白修饰参与抵御不良环境的最新进展,并提出该研究领域存在的问题和今后研究的重点与方向。深入探究组蛋白修饰与植物适应环境胁迫的关系,可为提高植物抗性、植物表型塑造、器官再生和作物改良等方面提供理论和技术指导。     

Genome instability and epigenetic modification--heritable responses to environmental stress?

As sessile organisms, plants need to continuously adjust their responses to external stimuli to cope with changing growth conditions. Since the seed dispersal range is often rather limited, exposure of progeny to the growth conditions of parents is very probable. The plasticity of plant phenotypes cannot be simply explained by genetic changes such as point mutations, deletions, insertions and gross chromosomal rearrangements. Since many environmental stresses persist for only one or several plant generations, other mechanisms of adaptation must exist. The heritability of reversible epigenetic modifications that regulate gene expression without changing DNA sequence makes them an attractive alternative mechanism. In this review, we discuss recent advances in understanding how changes in genome stability and epigenetically mediated changes in gene expression could contribute to plant adaptation. We provide examples of environmentally induced transgenerational epigenetic effects that include the appearance of new phenotypes in successive generations of stressed plants. We also describe several cases in which exposure to stress leads to nonrandom heritable but reversible changes in stress tolerance in the progeny of stressed plants.     

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.     

May the proton motive force be with you: A plant transporter review

As our ecosystems experience challenges associated with climate change, an improved understanding of the fundamental biochemical processes governing plant physiology is needed. Strikingly, current structural information on plant membrane transporters is severely limited compared to other kingdoms of life, with only 18 unique structures in total. To advance future breakthroughs and insight in plant cell molecular biology, structural knowledge of membrane transporters is indispensable.This review summarizes the current status of structural knowledge in the plant membrane transporter field. Plants utilize the proton motive force (PMF) to drive secondary active transport. We discuss the PMF, how it relates to secondary active transport and provide a classification of PMF driven secondary active transport, discussing recently published structures of symporters, antiporters, and uniporters from plants.     

Perspectives for epigenetic editing in crops

Site-specific nucleases (SSNs) have drawn much attention in plant biotechnology due to their ability to drive precision mutagenesis, gene targeting or allele replacement. However, when devoid of its nuclease activity, the underlying DNA-binding activity of SSNs can be used to bring other protein functional domains close to specific genomic sites, thus expanding further the range of applications of the technology. In particular, the addition of functional domains encoding epigenetic effectors and chromatin modifiers to the CRISPR/Cas ribonucleoprotein complex opens the possibility to introduce targeted epigenomic modifications in plants in an easily programmable manner. Here we examine some of the most important agronomic traits known to be controlled epigenetically and review the best studied epigenetic catalytic effectors in plants, such as DNA methylases/demethylases or histone acetylases/deacetylases and their associated marks. We also review the most efficient strategies developed to date to functionalize Cas proteins with both catalytic and non-catalytic epigenetic effectors, and the ability of these domains to influence the expression of endogenous genes in a regulatable manner. Based on these new technical developments, we discuss the possibilities offered by epigenetic editing tools in plant biotechnology and their implications in crop breeding.

     

Risposte Fotomorfogeniche Indotte Dalla Radiazione UV-B in Brassica Oleracea var. Capitata

Abstract

Photomorphogenic responses induced by UV-B radiation in Brassica oleracea var. capitata.—Ultraviolet radiation can induce a plethora of “damaging” and “non damaging” effects in higher plants. We analyzed two possible photomorphogenic responses to UV-B radiation, the anthocyanin accumulation and the inhibition of hypocotyl elongation by modifying the UV spectral range with specific cut-off filters, under two levels of photon fluence rate. Experimental results suggest that detrimental effects are due to shorter wavelenghts of UV-B region (less than 305 nm); in contrast some adaptative responses may be induced by longer wavelenghts of UV-B region (between 305 and 320 nm). We attempted to determine the involvment of endogenous anthocyanin content in the UV-B photoprotection. Our experiments suggest a secondary role of anthocyanin accumulation in UV-B plant adaptation.     

The fructan syndrome: Evolutionary aspects and common themes among plants and microbes

Fructans are multifunctional fructose‐based water soluble carbohydrates found in all biological kingdoms but not in animals. Most research has focused on plant and microbial fructans and has received a growing interest because of their practical applications. Nevertheless, the origin of fructan production, the so‐called “fructan syndrome,” is still unknown. Why fructans only occur in a limited number of plant and microbial species remains unclear. In this review, we provide an overview of plant and microbial fructan research with a focus on fructans as an adaptation to the environment and their role in (a)biotic stress tolerance. The taxonomical and biogeographical distribution of fructans in both kingdoms is discussed and linked (where possible) to environmental factors. Overall, the fructan syndrome may be related to water scarcity and differences in physicochemical properties, for instance, water retaining characteristics, at least partially explain why different fructan types with different branching levels are found in different species. Although a close correlation between environmental stresses and fructan production is quite clear in plants, this link seems to be missing in microbes. We hypothesize that this can be at least partially explained by differential evolutionary timeframes for plants and microbes, combined with potential redundancy effects.     

The gamification of elementary school biology: a case study on increasing understanding of plants

ABSTRACT

This study presents a new technique, the “Which plant am I?” game, which helps to increase pupils’ plant knowledge, while motivate them to become familiar with more plants. On the other hand pupils’ plant knowledge was tested in Serbia.

The “Which Plant Am I?“ game was tested with two groups of pupils (in average 11 years old). Pupils in the experimental group took part in outdoor classes and played the ”Which plant am I?” game. Pupils of the control group observed plants only in the classroom. This technique can deliver significant improvement in pupils’ knowledge about plants and motivate them through an active and playful learning process. This technique can be one possible solution of plant blindness.     

OPTIMAL OUTCROSSING IN IPOMOPSIS AGGREGAT A: SEED SET AND OFFSPRING FITNEs

Restricted gene flow and localized selection should establish a correlation between physical proximity and genetic similarity in many plant populations. Given this situation, fitness may decline in crosses between nearby plants (inbreeding depression), and in crosses between more widely separated plants (“outbreeding depression”) mostly as a result of disruption of local adaptation. It follows that seed set and offspring fitness may be greatest in crosses over an intermediate “optimal outcrossing distance.” This prediction was supported for Ipomopsis aggregata, a long-lived herbaceous plant pollinated by hummingbirds. In six replicate pollination experiments, mean seed set per flower was higher with an outcrossing distance of 1–10 m than with selfing or outcrossing over 100 m. A similar pattern appeared in the performance of offspring from experimental crosses grown under natural conditions and censused for a seven-year period. Offspring from 10-m crosses had higher survival, greater chance of flowering, and earlier flowering than those from 1-m or 100-m crosses. As a result, 1-m and 100-m offspring achieved only 47% and 68%, respectively, of the lifetime fitness of 10-m offspring. Offspring fitness also declined with planting distance from the seed parent over a range of 1–30 m, so that adaptation to the maternal environment is a plausible mechanism for outbreeding depression. Censuses in a representative I. aggregata population indicated that the herbaceous vegetation changes over a range of 2–150 m, suggesting that there is spatial variation in selection regimes on a scale commensurate with the observed effects of outbreeding depression and planting distance. We discuss the possibility that differences in seed set might in part reflect maternal mate discrimination and emphasize the desirability of measuring offspring fitness under natural conditions in assessing outcrossing effects.     

Targeted genome engineering via zinc finger nucleases

With the development of next-generation sequencing technology, ever-expanding databases of genetic information from various organisms are available to researchers. However, our ability to study the biological meaning of genetic information and to apply our genetic knowledge to produce genetically modified crops and animals is limited, largely due to the lack of molecular tools to manipulate genomes. Recently, targeted cleavage of the genome using engineered DNA scissors called zinc finger nucleases (ZFNs) has successfully supported the precise manipulation of genetic information in various cells, animals, and plants. In this review, we will discuss the development and applications of ZFN technology for genome engineering and highlight recent reports on its use in plants.     

Vom Klostergarten ins Labor

Changing the genetic setup of plants The history of mankind is closely linked to the success in domesticating plants and animals, while in the beginning – in the “naive era of plant biology” – the successes in changing the genetic setup of plants towards the adaptation of plants to human needs were slow, the re‐discovery of Mendelian rules initiated the era of scientific breeding, culminating in the “green revolution”. Recently, however, classical breeding for the major crop species reached a ceiling as required traits, i.e. resistances against biotic and abiotic stresses could not be found within the crossable gene pools, so novel approaches like genetic engineering were applied to tap foreign gene pools in order to widen the existing gene pools. Some examples are illustrated and discussed in order to create awareness that not the methodology is what is counting, but the result. In that aspect, all agricultural practices have to be compared in order their respective contribution to secure the necessary production increases to feed an ever growing human population.     

Effects of regional origin and genotype on intraspecific root communication in the desert shrub Ambrosia dumosa (Asteraceae)

Previous work has shown that the contact inhibition that occurs among roots of Ambrosia dumosa shrubs has a self/nonself recognition capability. In the current study, we investigated some of the geographic and genotypic dimensions of this recognition capability by using root observation chambers to observe the effects of encounters of individual roots on root elongation rates. We measured such effects in encounters between roots of plants from the same region and compared these to effects in encounters between roots of plants from two different regions. We also measured effects of encounters between roots of plants from the same clones and compared these to effects of encounters of roots of plants from different clones. Roots of plants from the same region (population) showed the usual “nonself” precipitous decline in elongation rates following contact, but when roots of plants from different regions contacted each other, elongation rates continued unchanged. When roots of separate plants from the same clone contacted each other, the same “nonself” precipitous decline in elongation rates as seen in encounters between roots of plants of different clones from the same region occurred. Meanwhile, in these same experiments “self” contacts between sister roots connected to the same plants resulted in no changes in elongation rates. Thus, differences between individuals from two geographically separate populations of Ambrosia dumosa may be sufficient to thwart the “nonself,” population-level recognition of similarity apparently necessary for contact inhibition. Furthermore, the “self” recognition mechanism, which precludes contact inhibition between two roots on the same plant, appears to be physiological rather than genetic in nature.     

Plant anaerobic stress as a novel trend in ecological physiology, biochemistry, and molecular biology: 2. Further development of the problem

This review is a logical development of a previous publication, which summarized the main results of the early period of the systematic and active studying of hypoxic and anoxic stresses in plants. These studies laid a foundation for a new scientific discipline in biology, the investigation relevant to plant anaerobic stress. This review considers a further development of this trend when the investigations embraced a wider set of topics and the discipline acquired an international recognition. The results obtained during last decades by physiologists, biochemists, and molecular biologists engaged in the problem of plant anaerobic stress confirmed the correctness of a concept of the two principal strategies of plant adaptation to hypoxia and anoxia conditions. They are “true” tolerance manifesting at the molecular level under conditions of oxygen deficiency or its absence and “apparent” tolerance, which is realized by avoidance of anaerobiosis due to the long-distance oxygen transport. Therefore, experimental material available now is considered and discussed in this review mainly in the light of these principal notions. Especial attention is paid to the role of stress proteins, which synthesis is induced under hypoxia and anoxia. The results of these experiments confirmed earlier conclusions about the key role of energy (glycolysis and alcoholic fermentation) and carbohydrate (mobilization and utilization of reserved carbohydrates) metabolism in plant adaptation to oxygen deficiency or its absence from the environment. The phenomenon of hypoxic acclimation and its role in plant adaptation to anoxia are also considered. Along with these topics, a further development of pH-stat theory is discussed. A special attention is paid to plant strategy realized by the formation of the net of air-filled spaces (aerenchyma) and long-distance oxygen transport from aerated plant parts to those located in anaerobic environment (apparent tolerance). Among other important aspects, we consider (1) post-anaerobic plant injury by free oxygen radicals; (2) the physiological role of alternative pathways of plant adaptation (nitrate reduction and lipid synthesis); (3) the phenomenon of the adaptation syndrome in plants and possible molecular mechanisms of its realization; and (4) some biotechnological advances in the field of genetic and cell engineering used for the creation of plants more tolerant to anaerobic stress.     

Selection signatures for high-altitude adaptation in ruminants

High-altitude areas are important socio-economical habitats with ruminants serving as a major source of food and commodities for humans. Living at high altitude, however, is extremely challenging, predominantly due to the exposure to hypoxic conditions, but also because of cold temperatures and limited feed for livestock. To survive in high-altitude environments over the long term, ruminants have evolved adaptation strategies, e.g. physiological and morphological modifications, which allow them to cope with these harsh conditions. Identification of such selection signatures in ruminants may contribute to more informed breeding decisions, and thus improved productivity. Moreover, studying the genetic background of altitude adaptation in ruminants provides insights into a common molecular basis across species and thus a better understanding of the physiological basis of this adaptation. In this paper, we review the major effects of high altitude on the mammalian body and highlight some of the most important short-term (coping) and genetically evolved (adaptation) physiological modifications. We then discuss the genetic architecture of altitude adaptation and target genes that show evidence of being under selection based on recent studies in various species, with a focus on ruminants. The yak is presented as an interesting native species that has adapted to the high-altitude regions of Tibet. Finally, we conclude with implications and challenges of selection signature studies on altitude adaptation in general. We found that the number of studies on genetic mechanisms that enable altitude adaptation in ruminants is growing, with a strong focus on identifying selection signatures, and hypothesise that the investigation of genetic data from multiple species and regions will contribute greatly to the understanding of the genetic basis of altitude adaptation.     

Phytoremediation of toxic trace elements in soil and water

Toxic heavy metals and metalloids, such as cadmium, lead, mercury, arsenic, and selenium, are constantly released into the environment. There is an urgent need to develop low-cost, effective, and sustainable methods for their removal or detoxification. Plant-based approaches, such as phytoremediation, are relatively inexpensive since they are performed in situ and are solar-driven. In this review, we discuss specific advances in plant-based approaches for the remediation of contaminated water and soil. Dilute concentrations of trace element contaminants can be removed from large volumes of wastewater by constructed wetlands. We discuss the potential of constructed wetlands for use in remediating agricultural drainage water and industrial effluent, as well as concerns over their potential ecotoxicity. In upland ecosystems, plants may be used to accumulate metals/metalloids in their harvestable biomass (phytoextraction). Plants can also convert and release certain metals/metalloids in a volatile form (phytovolatilization). We discuss how genetic engineering has been used to develop plants with enhanced efficiencies for phytoextraction and phytovolatilization. For example, metal-hyperaccumulating plants and microbes with unique abilities to tolerate, accumulate, and detoxify metals and metalloids represent an important reservoir of unique genes that could be transferred to fast-growing plant species for enhanced phytoremediation. There is also a need to develop new strategies to improve the acceptability of using genetically engineered plants for phytoremediation.