Rubisco evolution in C4 eudicots: an analysis of Amaranthaceae sensu lato

BACKGROUND Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO₂. In C₄ plants CO₂ is supplied to Rubisco by an auxiliary CO₂-concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C₄ Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C₃ enzyme. Specific amino-acids in Rubisco are associated with C₄ photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots. METHODOLOGY/PRINCIPAL FINDINGS We investigated Rubisco evolution in Amaranthaceae sensu lato (including Chenopodiaceae), the third-largest family of C₄ plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast rbcL gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C₄ Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C₄ plant groups, such as C₄ monocots, illustrating a striking parallelism in molecular evolution. CONCLUSIONS/SIGNIFICANCE Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco.This research was funded by NERC (http://www.nerc.ac.uk/; grant number NE/H007741/1)

Widespread positive selection in the photosynthetic Rubisco enzyme

Background: Rubisco enzyme catalyzes the first step in net photosynthetic CO2 assimilation and photorespiratory carbon oxidation and is responsible for almost all carbon fixation on Earth. The large subunit of Rubisco is encoded by the chloroplast rbcL gene, which is widely used for reconstruction of plant phylogenies due to its conservative nature. Plant systematicists have mainly used rbcL paying little attention to its function, and the question whether it evolves under Darwinian selection has received little attention. The purpose of our study was to evaluate how common is positive selection in Rubisco among the phototrophs and where in the Rubisco structure does positive selection occur. Results: We searched for positive selection in rbcL sequences from over 3000 species representing all lineages of green plants and some lineages of other phototrophs, such as brown and red algae, diatoms, euglenids and cyanobacteria. Our molecular phylogenetic analysis found the presence of positive selection in rbcL of most analyzed land plants, but not in algae and cyanobacteria. The mapping of the positively selected residues on the Rubisco tertiary structure revealed that they are located in regions important for dimer-dimer, intradimer, large subunit-small subunit and Rubisco-Rubisco activase interactions, and that some of the positively selected residues are close to the active site. Conclusion: Our results demonstrate that despite its conservative nature, Rubisco evolves under positive selection in most lineages of land plants, and after billions of years of evolution Darwinian selection still fine-tunes its performance. Widespread positive selection in rbcL has to be taken into account when this gene is used for phylogenetic reconstructions. </p

Molecular Adaptation during Adaptive Radiation in the Hawaiian Endemic Genus Schiedea

BACKGROUND: “Explosive” adaptive radiations on islands remain one of the most puzzling evolutionary phenomena. The rate of phenotypic and ecological adaptations is extremely fast during such events, suggesting that many genes may be under fairly strong selection. However, no evidence for adaptation at the level of protein coding genes was found, so it has been suggested that selection may work mainly on regulatory elements. Here we report the first evidence that positive selection does operate at the level of protein coding genes during rapid adaptive radiations. We studied molecular adaptation in Hawaiian endemic plant genus Schiedea (Caryophyllaceae), which includes closely related species with a striking range of morphological and ecological forms, varying from rainforest vines to woody shrubs growing in desert-like conditions on cliffs. Given the remarkable difference in photosynthetic performance between Schiedea species from different habitats, we focused on the “photosynthetic” Rubisco enzyme, the efficiency of which is known to be a limiting step in plant photosynthesis. RESULTS: We demonstrate that the chloroplast rbcL gene, encoding the large subunit of Rubisco enzyme, evolved under strong positive selection in Schiedea. Adaptive amino acid changes occurred in functionally important regions of Rubisco that interact with Rubisco activase, a chaperone which promotes and maintains the catalytic activity of Rubisco. Interestingly, positive selection acting on the rbcL might have caused favorable cytotypes to spread across several Schiedea species. SIGNIFICANCE: We report the first evidence for adaptive changes at the DNA and protein sequence level that may have been associated with the evolution of photosynthetic performance and colonization of new habitats during a recent adaptive radiation in an island plant genus. This illustrates how small changes at the molecular level may change ecological species performance and helps us to understand the molecular bases of extremely fast rate of adaptation during island adaptive radiations

Evaluation of the exposure to a ferroalloy plant for forest ecosystems by bioindication methods

Большинство металлургических предприятий оказывает негативное воздействие на лесные насаждения прилегающих к нему территорий. Одним из таких участков являются лесные насаждения вблизи п. Двуреченск Свердловской области, окружающие ферросплавный завод ПАО «КЗФ». Известно, что поллютанты металлургических предприятий оказывают влияние на все компоненты биогеоценоза, в частности на лесную растительность. Завод в последние десятилетия не работает на полную мощность и в значительной степени отвечает современным экологическим требованиям. Однако так было не всегда: очистные сооружения завода не обеспечивали задержание вредных выбросов, в результате чего накопление поллютантов на прилегающих территориях проводилось более полувека. Цель настоящей работы – оценка воздействия ферросплавного завода на лесные экосистемы зоны влияния, определение их состояния и выявление значимости индикаторов оценки. В работе проведены исследования по определению состояния лесных насаждений с использованием методов биоиндикации. Исследования проводились на временных пробных площадях (ВПП), заложенных на трансектах, которые располагаются в северном, восточном, южном и западном направлениях. На ВПП было определено санитарное состояние древостоев, средний возраст хвои сосны обыкновенной, произведен анализ на фитотоксичность проб почвы и талой снеговой воды. С целью оценки экологической ситуации от возможного воздействия завода определялось количество лишайников в лесном насаждении (метод лихеноиндикации). Оценка воздействия ферросплавного завода на лесные экосистемы выявила, что насаждения находятся в ослабленном состоянии. Достаточно четко прослеживается связь санитарного состояния древостоев с фитотоксичностью почв и талой снеговой воды, данными лихеноиндикации. В наибольшей степени влияние завода на состояние древостоя прослеживается в северной и восточной частях зоны.Most metallurgical enterprises have a negative impact on forest stands adjacent to it. One of these sites is forest plantations near the village of Dvurechensk, Sverdlovsk Region, surrounding the ferroalloy plant of PJSC «KZF». It is known that pollutants of metallurgical enterprises infl uence all components of the biogeocenosis, in particular, forest vegetation. Over the past decade, the plant has not been operating at full capacity and largely meets modern environmental requirements. However, this was not always the case — the treatment facilities of the plant did not provide for the containment of harmful emissions; as a result of the accumulation of pollutants in the adjacent territories, more than half a century was spent. The purpose of this work: to assess the impact of the ferroalloy plant on the forest ecosystems of the zone of infl uence, determine their condition and identify the signifi cance of the assessment indicators. The study conducted studies to determine the state of forest stands using bioindication methods. The studies were carried out on temporary trial plots (TTP) laid on transects located in the north, east, south and west. The TTP determined the sanitary condition of the stands, the average age of pine needles, and analyzed the phytotoxicity of soil and snowmelt samples. In order to assess the environmental situation from the possible impact of the plant, the number of lichens in the forest stands was determined (lichenoindication method). An assessment of the impact of the ferroalloy plant on forest ecosystems revealed that the stands are in a weakened state. The relationship between the sanitary state of the stands and the phytotoxicity of soils and melt snow water, lichenoindication, is quite clearly traced. The infl uence of the plant on the state of the stand is most pronounced in the northern and eastern parts of the zone

Maximum Matching in Turnstile Streams

We consider the unweighted bipartite maximum matching problem in the one-pass turnstile streaming model where the input stream consists of edge insertions and deletions. In the insertion-only model, a one-pass $2$-approximation streaming algorithm can be easily obtained with space $O(n \log n)$, where $n$ denotes the number of vertices of the input graph. We show that no such result is possible if edge deletions are allowed, even if space $O(n^{3/2-\delta})$ is granted, for every $\delta > 0$. Specifically, for every $0 \le \epsilon \le 1$, we show that in the one-pass turnstile streaming model, in order to compute a $O(n^{\epsilon})$-approximation, space $\Omega(n^{3/2 - 4\epsilon})$ is required for constant error randomized algorithms, and, up to logarithmic factors, space $O( n^{2-2\epsilon} )$ is sufficient. Our lower bound result is proved in the simultaneous message model of communication and may be of independent interest

Sparse {Fourier Transform} by Traversing {Cooley-Tukey FFT} Computation Graphs

Computing the dominant Fourier coefficients of a vector is a common task in many fields, such as signal processing, learning theory, and computational complexity. In the Sparse Fast Fourier Transform (Sparse FFT) problem, one is given oracle access to a $d$-dimensional vector $x$ of size $N$, and is asked to compute the best $k$-term approximation of its Discrete Fourier Transform, quickly and using few samples of the input vector $x$. While the sample complexity of this problem is quite well understood, all previous approaches either suffer from an exponential dependence of runtime on the dimension $d$ or can only tolerate a trivial amount of noise. This is in sharp contrast with the classical FFT algorithm of Cooley and Tukey, which is stable and completely insensitive to the dimension of the input vector: its runtime is $O(N\log N)$ in any dimension $d$. In this work, we introduce a new high-dimensional Sparse FFT toolkit and use it to obtain new algorithms, both on the exact, as well as in the case of bounded $\ell_2$ noise. This toolkit includes i) a new strategy for exploring a pruned FFT computation tree that reduces the cost of filtering, ii) new structural properties of adaptive aliasing filters recently introduced by Kapralov, Velingker and Zandieh'SODA'19, and iii) a novel lazy estimation argument, suited to reducing the cost of estimation in FFT tree-traversal approaches. Our robust algorithm can be viewed as a highly optimized sparse, stable extension of the Cooley-Tukey FFT algorithm. Finally, we explain the barriers we have faced by proving a conditional quadratic lower bound on the running time of the well-studied non-equispaced Fourier transform problem. This resolves a natural and frequently asked question in computational Fourier transforms. Lastly, we provide a preliminary experimental evaluation comparing the runtime of our algorithm to FFTW and SFFT 2.0

Optoelectronic Methods of IR-Photometry in Solving Thermal and Physical Problems

Results of the application of optoelectronic IR-photometry methods for solving the actual thermophysical problems using high-speed photodiode temperature (pyrometric) sensors are presented. The latest achievements of the Ioffe Institute in the field of middle IR spectral range (3-6 μm) photodiode production technology are used in the sensor development. The above-mentioned middle-IR photodiode sensors are based on heterostructures from A3B5 solid solutions and they do not require forced cooling. New data on thermophysical processes taking place under the complex experimental conditions, including dynamically changing properties of the object, have been obtained. The new experimental results are based on high-speed non-contact measurements of the absolute temperature of objects directly in the exposure region of laser radiation and / or powerful electromagnetic fields. In the context of creating new experimental techniques for determining the thermophysical parameters of new promising materials the efficiency of middle- IR photodiode temperature sensors has been shown. In particular, a simple and effective measuring method for determining the heat transfer coefficient of solid objects and the pyroelectric coefficient of ferro- and pyroelectric materials is offered. The measuring method is based on laser thermowave techniques and direct noncontact measurements of the sample surface temperature under the pulsed / periodic laser action. The proposed experimental techniques make it possible to significantly improve the accuracy of measurements of thermophysical parameters of materials, and in particular, to eliminate a considerable spread of data on the parameters of the pyroelectric effect in ferroelectric materials. Keywords: Pyrometric sensors, mid-IR photodiodes, laser thermowave techniques, heat transfer coefficient, pyroelectric coefficien

Resource-efficient modular space greenhouse with LED lighting

The main goal of this project is the developing a design and configuration suitable for growing plants in microgravity conditions. For a decision, a block-modular design has been developed that will maximize the efficiency of using the growing surface due to the location of the plants on all faces. The resulting cubes can be cascaded to link with each other, increasing the desired volume. As a result, the installation will use less space at the station, than the modern using analogues. Design development was made by Autodesk Inventor software

Surveying Rubisco diversity and temperature response to improve crop photosynthetic efficiency.

The threat to global food security of stagnating yields and population growth makes increasing crop productivity a critical goal over the coming decades. One key target for improving crop productivity and yields is increasing the efficiency of photosynthesis. Central to photosynthesis is ribulose-1,5-bisphosphate carboxylase/oxygenase, Rubisco, which is a critical but often rate-limiting component. Here we present full Rubisco catalytic properties measured at three temperatures for 75 plants species representing both crops and undomesticated plants from diverse climates. Some newly characterised Rubiscos were naturally 'better' compared to crop enzymes and have the potential to improve crop photosynthetic efficiency. The temperature response of the various catalytic parameters was largely consistent across the diverse range of species, though absolute values showed significant variation in Rubisco catalysis, even between closely related species. An analysis of residue differences amongst the species characterised identified a number of candidate amino acid substitutions that will aid in advancing engineering of improved Rubisco in crop systems. This study provides new insights on the range of Rubisco catalysis and temperature response present in nature, and provides new information to include in models from leaf to canopy and ecosystem scale