Biological Communications 2018-07-11T19:52:59+03:00 Yegor B. Malashichev Open Journal Systems <p>Biological Communications is a rebranded new title of the former journal «Vestnik of Saint Petersburg University. Series 3. Biology». The journal was founded as «Vestnik of Leningrad University» in 1946.&nbsp;Since 1953, it was published under several series. In 1956 the series «Biology» was first established.&nbsp;As its predecessors, Biological Communications is published at a quarterly&nbsp;basis.</p> A century and a half of plant physiology in Saint Petersburg 2018-07-11T19:52:57+03:00 Farida Minibayeva Maria Shishova 2018-06-08T00:00:00+03:00 ##submission.copyrightStatement## Department of Plant Physiology and Biochemistry of Saint Petersburg State University celebrates 150<sup>th</sup> anniversary 2018-07-11T19:52:58+03:00 Sergei Medvedev Gregory Pozhvanov <p>The Department of Plant Physiology and Biochemistry of St. Petersburg State University is one of the oldest in the Faculty of Biology, and has just recently celebrated its 150<sup>th</sup> anniversary. Here we present a short overview of its history, from its establishment in 1867 to the current date. The history of the department is comprised of individual paths of scientists who worked here over the course of fifteen decades. We highlight the major breakthroughs and scientific discoveries made by the remarkable scholars who chaired the department and co-authored research, starting with Famintsyn, Neljubow, Palladin and Kostychev in the end of the 19<sup>th</sup> — beginning of the 20<sup>th</sup> century, then through the Soviet times to the present; we also give an overview of the department’s current scientific and educational activities.</p> 2018-06-08T00:00:00+03:00 ##submission.copyrightStatement## The role of organic acids in heavy metal tolerance in plants 2018-07-11T19:52:58+03:00 Natalia Osmolovskaya Dung Viet Vu Ludmila Kuchaeva <p>Organic acid metabolism is of fundamental importance at the cellular and at the whole plant level. In recent years there has been increased attention in the role of organic acids in modulating adaptation to the environment, including organic acids participation in the detoxification of heavy metals. The basis of the phenomenon is the ability of acids such as citrate, malate, oxalate, malonate, aconitate and tartrate to form strong bonds with heavy metal ions through metal chelatation with carboxyl groups carrying the function of donor oxygen in metal-ligands. This review deals with aspects of extracellular and intracellular chelation of heavy metal ions with the involvement of organic acids. We consider the role of metal-induced secretion of malate, citrate and oxalate by roots of various plant species in extracellular complexation of heavy metals and in the reduction of their bioavailability for plants. We also review the possible mechanisms of stimulation of metals uptake by plants under the influence of exogenous application of organic acids in the soil. The efficiency of intracellular chelation of heavy metal ions with the participation of organic acids is considered due to the importance of this strategy in hyperaccumulators and non-hyperaccumulators to improve metal tolerance in plants.</p> 2018-06-08T00:00:00+03:00 ##submission.copyrightStatement## The study of plant adaptation to oxygen deficiency in Saint Petersburg University 2018-07-11T19:52:58+03:00 Tamara Chirkova Vladislav Yemelyanov <p>The first studies on plant anaerobiosis started at the Department of Plant Physiology at St. Petersburg University in the beginning of the XXth century, but interest in this subject became most intensive during the investigations of the ecological plant physiology group under the supervision of Prof. T. V. Chirkova. Their first step was focused on the mechanisms of transport of gases from the aerated aboveground part of the plant to the flooded root system. Further interest shifted towards clarifying the biochemistry of respiratory metabolism, pathways of reoxidation of the reduced cofactors, and protein and lipid metabolism of plants under anoxic conditions. The group’s studies have always distinguished the comparative approach, in which the changes taking place in plants differing in resistance to oxygen deficiency were analyzed. In many ways, this research was pioneering and was recognized throughout the world. For the first time the possibility of hydrogen peroxide formation in plants under total anoxia was demonstrated. The role of cell membranes in adaptation processes was revealed. Pioneering investigations distinguished the features of photosynthesis in an oxygen-free environment and the work of an antioxidant system under conditions of anoxia and post-anoxic oxidative effects. Now, the plant ecophysiology group of the Department of Plant Physiology and Biochemistry of St. Petersburg State University concentrates on the mechanisms of anaerobic signal transduction and reveals how plant hormones regulate adaptation to anoxic and post-anoxic stresses.</p> 2018-06-08T00:00:00+03:00 ##submission.copyrightStatement## Proton pump and plant cell elongation 2018-07-11T19:52:58+03:00 Anastasia Kirpichnikova Tingzhuo Chen Serafima Teplyakova Maria Shishova <p>Plant cell elongation growth is an integral process involved in different plant movements (tropisms); it provides the possibility to reach different resources of energy, water and nutrition and is therefore important for metabolism and development. Cell multiple enlargement along the longitudinal axis is commonly accepted to be under the control of the phytohormone auxin. One of the key enzymes involved in elongation is the plasma membrane H<sup>+</sup>-ATPase, which is known to acidify the cell wall. Investigation of the role of the proton pump at the plasma membrane was initiated by Prof. Vsevolod V. Polevoi and still is in progress in the group of Prof. Maria F. Shishova at the Department of Plant Physiology and Biochemistry, St. Petersburg State University. Different mechanisms of post-translation regulation of H<sup>+</sup>-pump activity are discussed in this review. We also suggest a possible scheme of elongation growth based on the shift in plant cell sensitivity to auxin and on its facility to elongate.</p> 2018-06-08T00:00:00+03:00 ##submission.copyrightStatement## Mining seed proteome: from protein dynamics to modification profiles 2018-07-11T19:52:58+03:00 Andrej Frolov Tatiana Mamontova Christian Ihling Elena Lukasheva Mikhail Bankin Veronika Chantseva Maria Vikhnina Alena Soboleva Julia Shumilina Gregory Mavropolo-Stolyarenko Tatiana Grishina Natalia Osmolovskaya Vladimir Zhukov Wolfgang Hoehenwarter Andrea Sinz Igor Tikhononovich Ludger Wessjohann Tatiana Bilova Galina Smolikova Sergei Medvedev <p>In the modern world, crop plants represent a major source of daily consumed foods. Among them, cereals and legumes — i.e. the crops accumulating oils, carbohydrates and proteins in their seeds — dominate in European agriculture, tremendously impacting global protein consumption and biodiesel production. Therefore, the seeds of crop plants attract the special attention of biologists, biochemists, nutritional physiologists and food chemists. Seed development and germination, as well as age- and stress-related changes in their viability and nutritional properties, can be addressed by a variety of physiological and biochemical methods. In this context, the methods of functional genomics can be applied to address characteristic changes in seed metabolism, which can give access to stress-resistant genotypes. Among these methods, proteomics is one of the most effective tools, allowing mining metabolism changes on the protein level. Here we discuss the main methodological approaches of seed proteomics in the context of physiological changes related to environmental stress and ageing. We provide a comprehensive comparison of gel- and chromatographybased approaches with a special emphasis on advantages and disadvantages of both strategies in characterization of the seed proteome.</p> 2018-06-08T00:00:00+03:00 ##submission.copyrightStatement## Visualization and analysis of actin cytoskeleton organization in plants 2018-07-11T19:52:59+03:00 Gregory Pozhvanov <p>The plant cytoskeleton is a highly dynamic system that consists of two components: microfilaments and microtubules. Actin microfilaments are essential for polar growth, cytoplasmic streaming, directing polar growth, anchoring the nucleus, gravity sensing, signalling pathway integration and a number of other functions. Actin morphology and dynamics are orchestrated by a variety of small actin binding proteins, and some of them have become a source of actin interaction domains widely used as markers for microfilaments in fusions with fluorescent reporter proteins. However, older techniques are still employed for actin visualization. In this short review, we will focus on the diversity of fluorescent reporter fusions for F-actin and on approaches and existing free software for the analysis of cytoskeleton organization, mainly in <em>Arabidopsis</em>. Abbreviations: MF ― microfilament, MT ― microtubule, GFP ― green fluorescent protein, MFA ― Microfilament Analyzer.</p> 2018-06-08T00:00:00+03:00 ##submission.copyrightStatement## Physiological functions of phlorotannins 2018-07-11T19:52:59+03:00 Valeriya Lemesheva Elena Tarakhovskaya <p>Phlorotannins are the most abundant group of metabolites specific for brown algae. These substances contribute both to the primary and secondary metabolism of the algal cells and have practical relevance as biologically active compounds. The list of their presumable physiological functions is still not exhaustive and includes wound healing, chelation of heavy metal ions, bioadhesion, contribution to the processes of algal early embryogenesis and sporogenesis, etc. Similar to higher plant phenolics, phlorotannins also have antioxidant properties, provide chemical defense against herbivores and contribute to cell wall rigidification. The complex and diverse composition of natural phlorotannins hampers investigation of their physiological roles and leads to inconsistencies in the obtained data. Further study of the correlation between the structure of these substances and their functions is needed to take a new look at known information, thus providing better performance in the fields of both fundamental algal physiology and applied phycology.</p> 2018-06-08T00:00:00+03:00 ##submission.copyrightStatement## Ascorbate in the apoplast of elongating plant cells 2018-07-11T19:52:59+03:00 Elena Sharova Aleksandra Romanova <p>It was shown that basipetal retardation of cell elongation in the growth zone of etiolated maize mesocotyls correlates with a steep decrease in the apoplastic ascorbic acid (ASC) concentration (50 μM → 10 μM) and ascorbate redox state (17 % → 5 %). Exogenous ASC (0.3 mM) not only inhibits peroxidase-dependent oxidation of phenols in vitro. It also exerts a highly specific effect on the secretion of peroxidases by stimulating the release of some isoforms while inhibiting the release of others to the cell walls. This effect points to the hypothetic signaling function of apoplastic ascorbate. Previously, we described a basipetal decrease in hydrogen peroxide concentration in the apoplast (from 5.1 to 2.0 μM) and a two-times increase in cell wall peroxidase potential activity (Sharova et al., 2012). Summarizing found gradients, we can assume that the conditions in the apoplast of the upper mesocotyl segment are favorable for the occurrence of the Fenton reaction (high ASC and hydrogen peroxide concentrations) and unfavorable for the oxidation of phenols (high ASC concentration and low potential peroxidase activity), which contributes to cell wall extensibility and rapid cell elongation.</p> 2018-06-08T00:00:00+03:00 ##submission.copyrightStatement## Coordinated alterations in gene expression and metabolomic profiles of <em>Chlamydomonas reinhardtii</em> during batch autotrophic culturing 2018-07-11T19:52:59+03:00 Roman Puzanskiy Daria Romanyuk Maria Shishova <p><em>Chlamydomonas reinhardtii</em> was grown under autotrophic batch culturing, which is known to be a widely applicable method for both fundamental research and applied purposes. This type of cultivation results in elevation of cell density and fast exhaustion of nutrient resources. We expected the revealed metabolic adaptation to be triggered at the transcriptional level. This investigation focuses on analyzing expression of the genes encoding enzymes involved in primary metabolism and plastid transporters during the exponential phase of <em>C. reinhardtii</em> autotrophic batch culture. About two-thirds of the tested genes demonstrated differential expression during algae growth. Patterns of expression were clustered into 5 groups. Most of the genes were gathered in two large clusters, characterized by peaks of expression at early or later exponential growth (EG). Genes which showed maximal expression in early EG were <em>OMT1, HXK1, AMYB1, ACK1,2, CHLREDRAFT_123419, APE2, PCK1, CHLREDRAFT_195672, CIS2, TPT2</em> and <em>ACLA1</em>. Among the genes with maximal expression in later EG were <em>SBE3, TPIC, CHLREDRAFT_137300, CHLREDRAFT_111372, PPT1</em> and <em>CHLREDRAFT_122970</em>. There were no genes detected with maximal expression at the cessation of proliferation. PCA showed that the expression profiles in the beginning EG were similar, and profiles changed drastically in the middle of exponential growth. PLS-DA revealed the difference between the beginning of EG and later periods linked to PC1 (44 %), between late EG and early stationary linked to PC2 (23 %) and finally between two points at the beginning of growth linked to PC3 (10 %). Mapping of genes and metabolites according to their correlation revealed a graph with two clusters. The first, smaller cluster contains genes that encode plastid exporters, enzymes of starch and carbohydrates metabolism. The expression level of these genes peaked later in EG. These genes are mainly associated with metabolites such as carbohydrates, acylglycerols and fatty acids metabolism. The second cluster is larger and more diverse. It combines genes with maximum expression in the beginning of EG. The core of this cluster is formed by genes encoding enzymes of fatty acids synthesis, energy and plastic pathways, and plastid transporters. This cluster included the majority of amino acids, carboxylic acids and many fatty acids.</p> 2018-06-08T00:00:00+03:00 ##submission.copyrightStatement##