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SEQUENCES, and POLLEN STRUCTURE of REPRESENTATIVES of the FAMILY Amaranthaceae Juss

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SEQUENCES, and POLLEN STRUCTURE of REPRESENTATIVES of the FAMILY Amaranthaceae Juss CONTENTS REVIEWS Bardakhivska K. I. Gurina N. M. Іmmunoadsorption for therapy Kuchmerovska T. M. of autoimmune diseases . .9 Nikolaev V. G. The cellulose degrading systems of microorganisms: Borzova N. V. biosyntesis, properties structural and Varbanets L. D. functional characteristics . .23 Microbial αglucosidases: classification, substrate Borzova N. V. specificity and mechanism of action . .42 Prylutska S. V. Remeniak О. V. Carbon nanotubes as a new class of materials for Honcharenko Yu. V. nanobiotechnology . .55 Prylutskyy Yu. I. Grape phenols: structure, antioxidant activity Baraboi V. A. applications . .67 EXPERIMENTAL ARTICLES Labyntsev А. Yu. Oliinyk O. S. Kaberniuk A. A. Optimizing protein Acolloidal gold conjugates Chunihin O. Yu. synthesis conditions and developing approaches Gorchev V. F. for their characterization . .78 Kyrchenko T. O. Chernushov V. I. Kolibo D. V. Stezhka V. A. Leonenko O. B. Effect of nanoparticles of amorphous highly dispersed Zinchenko V. Н. SiO2 on blood system and prooxidantantioxidant Matveeva О. Yu. balance of the rats tissues . .86 Movchan V. О. Martyniuk O. O. Nalian A. G. Phylogenetic assay of maturase K, ribulosebisphosphate Van6Kley J. E. carboxylase (rbcL) sequences, and pollen structure Martynova6Van6 of representatives of the family Amaranthaceae Juss. .98 Kley A. V. 7 Estimation of lyophilization stress effects accordind Romanko M. Ye. to lipoperoxidation intensity and of protein oxidative modification in mycoplasma cell membranes . .105 Gojster О. S. Khmelnitsky G. O. T2 toxin determination by surface Dzyadevych S. V. plasmon resonance . .111 Nasarenko W. I. Minchenko O. Н. NEWS . .118 NEW PUBLICATIONS ON BIOTECHNOLOGY AND ADJOINING BRANCHES OF SCIENCE . .130 CONFERENCES, CONGRESSES, SYMPOSIA, EXHIBITIONS . .139 8 UDK 581.33:582.663:575.113:575.21 PHYLOGENETIC ASSAY OF MATURASE K, RIBULOSE@BISPHOSPHATE CARBOXYLASE (rbcL) SEQUENCES, AND POLLEN STRUCTURE OF REPRESENTATIVES OF THE FAMILY Amaranthaceae Juss. O. O. Martyniuk A. G. Nalian J. E. Van<Kley Stephen F. Austin State University, Nacogdoches, TX, USA O. V. Martynova<Van<Kley E<mail: [email protected] Amino acid sequences of the mitochondrial protein maturase K (matK) and the plastid protein ribulose<bisphos< phate carboxylase (rbcL) from different Amaranthaceae Juss. species were retrieved from the NCBI (National Center for Biotechnology Information), and used for phylogenetic analysis. A correspondence was found between phyloge netic trees derived from molecular data and those based on palynomorphological data. Clustering patterns in the trees obtained from both protein sequences support the idea of two main pollen types (Amaranthustype and Gomphrenatype) as described in 1952 by G. Erdtman. The results also indicate that some species, which according to traditional classification, are from different subfamilies and tribes of Amaranthaceae Juss. may in fact be closely related. Thus molecular data support the idea that palynomorphological data can be used in systematic and phyloge netic studies of Amaranthaceae. Key words: bioinformatics, maturase K, ribulose<bisphosphate carboxylase, phylogeny, Amaranthaceae, palynomorphology. In recent years, biodiversity and conserva by various bioinformatics programs and tools. tion have been globally recognized as one of Bioinformatics analysis using data from these the critical issues facing humanity. In light of databases thus provides an inexpensive and this problem, biologists are emphasizing eco powerful method for investigation of DNA logical and environmental studies. However, polymorphism and its origin. it is not possible to study biological objects The flowering plant family Amaranthaceae without naming and describing them, i.e. sensu stricto (s.s.) which corresponds to the without taxonomy and nomenclature, which classical family Amaranthaceae Juss. (69 gen explores relationships within and between dif era and 772 species [1]) as well as the twicelarg ferent groups of organisms. er related family Chenopodiaceae Ventenat By combining methods used by several dif have been subject to repeated taxonomical revi ferent disciplines such as traditional morphol sions from the time they were first described ogy, anatomy, biochemistry, bioinformatics, (1789 and 1799 respectively [2, 3]) to the pre and molecular biology, a new powerful identi sent. Recently it has been proposed to combine fication tool has been developed. Using the them into one large family: Amaranthaceae unique sequences of genes from different sensu lato (s.l.) as a result of molecular analy organisms it is now possible to identify many sis [4]. organisms and determine their relationships The morphology of pollen grains, which with others. DNA, RNA, and protein sequen are the male generative (gametophyte) stage of ces also enable us to evaluate classical methods seed plants, is an important source of informa of identification of organisms and to improve tion for plant systematics. In certain cases, them. Existing sequences for taxa of interest palynological data have been crucial for taxo obtained from international databases such as nomic conclusions [5–13]. The often complex the NCBI (National Center for Biotechnology structure of the pollen wall varies across taxa Information) can be compared and evaluated and is considered to be a conservative, taxo 98 Експериментальні статті nomically meaningful feature. However, the 4.1.1.39), 18S and 16S small subunit riboso< rate and direction of pollen wall structure evo mal RNA, and the internal transcribed spacer lution is not always parallel to the macroevo rRNA (ITS) gene. Since matK and rbcL lution of (sporophyte) seed plants. That is why sequences from Amaranthaceae were the most similar pollen grains might belong to plants abundant in GeneBank, they were chosen for from different taxonomical groups, and one our study. taxon might have a variety of pollen grains among its representatives. Before the advent Materials and methods of molecular bioinformatics tools, scientists had to guess which morphological features: Specimens and microscopy palynological or macromorphological were Pollen grains of 60 species from 14 Ama< most reliable. However, molecular data might ranthaceae genera (100 samples) were exam now serve as arbitrators in such cases. ined using light microscopy (LM), and pollen Both the Amaranthaceae and Chenopodia< grains of 120 species from 32 Amaranthaceae ceae have panporate pollen of the Amaranthus genera (140 samples) along with 5 species of and Gomphrena types [14]. The existence of the genus Corispermum (Chenopodiaceae) were these two pollen types supports, with certain examined using scanning electron microscopy exceptions, the division of the Amaranthaceae (SEM). These pollen samples were taken from into two subfamilies, Amaranthoideae and voucher specimens from the following institu Gomphrenoideae, which were described tions: M. G. Kholodny Institute of Botany of according to macromorphological data, large the National Academy of Sciences of Ukraine, ly anther structure. However, exceptions in Kiev, Ukraine (KW); V.L. Komarov Botanical pollen grain structure of some representatives Institute of the Russian Academy of Sciences, of both subfamilies have lead researchers to St. Petersburg, Russia (LE); and the Main conclude that pollen grain data are not useful Botanical Garden of the Russian Academy of as a taxonomical feature for these taxa. Sciences, Moscow, Russia (MHW). The mater Within the Amaranthus<type pollen there is a ial for LM and portions of the material for small group of pollen grains with an unusual SEM were acetolysed according to the method stellate ornamentation of their opercula [15]. described by G. Erdtman [16]. For LM, pollen Pollen grains of this type also sometimes occur grains were mounted in glycerin jelly. For in plants from Gomphrenoideae. However, SEM, pollen grains were placed in a drop of such complex and unique pollen structure does 96% ethyl alcohol, and vacuumcoated with not suggest accidental parallelism in these two gold. In our study we used a «Biolar» micro subfamilies but rather it is more likely that scope (for LM) and a JEOL JSM35C micro these groups of plants share an ancestor with scope (for SEM). Data from literature sources genes coding for both of these pollen structures. on the pollen wall structure of Amaranthaceae Additionally, certain genera of Amarantho< were also consulted. Thirty features were used ideae possess Gomphrenatype pollen. to characterize the evolutionary pattern of Why are both pollen types not spread pollen types. Pollen wall structure from a total equally through both subfamilies? We have of 213 species from 60 genera was analyzed [17]. assumed that the ancestors of genera with both Gomphrenatype pollen and pollen with Sequence analysis and phylogeny stellate opercula have their common ancestor All available amino acid sequences of matu< within Amaranthoideae. If so, Amarantho< rase K (matK) and ribulose<bisphosphate carbo< ideae should be divided into two parts, and xylase (rbcL) from Amaranthaceae were genera with Gomphrenatype pollen as well as obtained from the NCBI database genera from the Amaranthoideae with stellate (http://www.ncbi.nlm.nih.gov/Genomes/). ornamentation of the opercula should be Multiple sequence alignment and phylogenetic placed into the Gomphrenoideae. If true, bioin analysis were performed with the Molecular formatics analysis of molecular sequences Evolutionary Genetics Analysis (MEGA ver would support this conclusion. Such is the aim sion 3.0) program
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