A.N. Tikhonov

Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species

Octaheme nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio paradoxus was isolated and characterized. A comparative structural and functional analysis of two homologous octaheme nitrite reductases from closely related Thioalkalivibrio species was performed. It was shown that both enzymes have similar catalytic properties, owing to high structural similarity. Both enzymes are characterized by specific structural features distinguishing them from pentaheme cytochrome c nitrite reductases, such as the Tyr‐Cys bond in the active site, the hexameric structure resulting in the formation of a void space inside the hexamer, and the product channel that opens into the void interior space of the hexamer. It is suggested that these specific structural features are responsible for the higher nitrite reductase activity, the greater preference for nitrite than for sulfite as a substrate, and the wider pH range of the catalytic activity of octaheme nitrite reductases than of pentaheme homologs.

Preliminary analyses of the frozen mummies of mammoth (Mammuthus primigenius), bison (Bison priscus) and horse (Equus sp.) from the Yana‐Indigirka Lowland, Yakutia, Russia

The frozen bodies of a young woolly mammoth (Mammuthus primigenius), a wild horse (Equus sp.) and a steppe bison (Bison priscus) were recently found in the northern Yakutia (northeastern Siberia). All specimens have preserved bones, skin and soft tissues. Whereas the woolly mammoth and the Pleistocene horse were represented by partial frozen bodies, the steppe bison body was recovered in an absolutely complete state. All specimens were found frozen in the permafrost, with some of the tissues mummified. The wild horse and steppe bison are of Holocene age, and the mammoth is of Late Pleistocene age.

The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis

Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.

Molecular phylogeny of the Dacnomys division (Rodentia, Muridae): the taxonomic positions of Saxatilomys and Leopoldamys.

The central position in the division belongs to genera of Leopoldamys and Niviventer, which includes 6 and 17 species, respecc tively; the other genera are monotypic. Based on mitoo chondrial and nuclear genes phylogenetic analysis, the division Dacnomys is a monophyletic group [2] closely related to the divisions Rattus and Maxomys. Recently, genetic and morphological variability of Niviventer spp. have been investigated, as well as those of some taxa of genus Leopoldamys [3–6]. The data on other genera (Dacnomys, Chiromyscus, and Srilankamys) are scrappy; Anonymomys and Saxatilomys are included into the division only based on their morphological characteristics; i.e., they are not genetically characterr ized yet [1, 7]. The monotypic genus Saxatilomys was first described from central Laos in 2005 [7]; the phyloo genetic relationships of this genus with the other genera from the Rattini tribe have not been studied yet. The study presents an original the data and genetic analysis of Saxatilomys paulinae, as well as on the composition and phylogenetic relationships within division Dacnomys; and on the species composition of genus Leopoldamys for continental Indochina. The analysis was based on 87 samples, including Leopoldamys spp. (73 individuals), Dacnomys milliardi (2 specimens), Chiromyscus chiropus (2 specimens) sampled in different regions of Vietnam, and Saxatiloo mys paulinae (10 individuals) from Khammouane provv ince, central Laos (the type locality of species, [7]). Total DNA was extracted from liver or muscle tiss sues according to routine phenoll chloroform method. Three genes were used for the analysis; they were usuu ally used for phylogeny studies of Muroidea. These genes included cytochrome b gene (Cyt b, 680–1143 bp), part of exon of subunit of 1 gene of interphotoree ceptor retionoid binding protein (IRBP, 1010–1610 bp), and the proximal part of the first subunit of cytoo chromoxydase (COI, 680–730 bp); the last one usually used for the species identification in DNA Barcoding Project. These genes were amplified [4, 5] and sequenced (by both chains) in an Applied Biosystems 3130 sequenator. All the primary nucleotide sequences were deposited in the GenBank database (COI: JQ755811–JQ755858; Cyt b: JQ755859–JQ755934; IRBP: JQ755935–JQ755965). The analysis also included all the sequences currently available for the species, Leopoldamys (72 individuals), Chiromyscus (1 specimen), Dacnomys (1 specimen), Srilankamys (1 specimen), and some other representatives of the Rattini tribe, used as outgroups for comparison. The nucleotide sequences (150 for Cyt b, 80 for COI gene, and 61 for IRBP) were aligned using the Clustal …

Structural adaptations of octaheme nitrite reductases from haloalkaliphilic Thioalkalivibrio bacteria to alkaline pH and high salinity

Bacteria Tv. nitratireducens and Tv. paradoxus from soda lakes grow optimally in sodium carbonate/NaCl brines at pH range from 9.5 to 10 and salinity from 0.5 to 1.5 M Na+. Octaheme nitrite reductases (ONRs) from haloalkaliphilic bacteria of genus Thioalkalivibrio are stable and active in a wide range of pH (up to 11) and salinity (up to 1 M NaCl). To establish adaptation mechanisms of ONRs from haloalkaliphilic bacteria a comparative analysis of amino acid sequences and structures of ONRs from haloalkaliphilic bacteria and their homologues from non-halophilic neutrophilic bacteria was performed. The following adaptation strategies were observed: (1) strategies specific for halophilic and alkaliphilic proteins (an increase in the number of aspartate and glutamate residues and a decrease in the number of lysine residues on the protein surface), (2) strategies specific for halophilic proteins (an increase in the arginine content and a decrease in the number of hydrophobic residues on the solvent-accessible protein surface), (3) strategies specific for alkaliphilic proteins (an increase in the area of intersubunit hydrophobic contacts). Unique adaptation mechanism inherent in the ONRs from bacteria of genus Thioalkalivibrio was revealed (an increase in the core in the number of tryptophan and phenylalanine residues, and an increase in the number of small side chain residues, such as alanine and valine, in the core).

Dynamics of Escherichia coli type I-E CRISPR spacers over 42 000 years.

CRISPR‐Cas are nucleic acid‐based prokaryotic immune systems. CRISPR arrays accumulate spacers from foreign DNA and provide resistance to mobile genetic elements containing identical or similar sequences. Thus, the set of spacers present in a given bacterium can be regarded as a record of encounters of its ancestors with genetic invaders. Such records should be specific for different lineages and change with time, as earlier acquired spacers get obsolete and are lost. Here, we studied type I‐E CRISPR spacers of Escherichia coli from extinct pachyderm. We find that many spacers recovered from intestines of a 42 000‐year‐old mammoth match spacers of present‐day E. coli. Present‐day CRISPR arrays can be reconstructed from palaeo sequences, indicating that the order of spacers has also been preserved. The results suggest that E. coli CRISPR arrays were not subject to intensive change through adaptive acquisition during this time.

Bighorn sheep from Yakutia

244 The living bighorn sheep Ovis (Pachyceros) nivicola Eschscholtz, 1829 is an exclusively mountain animal. Its geographical range includes some mountain ridges of northeastern and southern Yakutia and adjacent regions (Stanovoi Mountain Range, Dzhugdzhur), the Chukchi Peninsula (Anyui and Chukchi plateaus), Koryak Plateau, and Kamchatka Peninsula. An iso lated population of this species inhabits the Putorana Plateau [1–4]. It was repeatedly indicated that, previ ously, O. nivicola had a larger range. Fossil specimens of the bighorn sheep dated Late Pleistocene come from a number of localities outside the modern species range, i.e., southern Western Siberia [5, 6], upper reaches of the Yenisei River [7], Transbaikalia and Baikal Region [2, 5, 7, 8], Yakutia [2, 9], and Sakhalin [10]. In central Yakutia, the fossil bighorn sheep has been found on the Vilyui River in the vicinity of the town of Verkhnevilyuisk (Vilyui River), Yakutsk (Lena River), and the village of Kachikattsy (Buotama River) [2, 9].

A study of a frozen mummy of a wild horse from the Holocene of Yakutia, East Siberia, Russia

The paper presents a description of a rare finding of the partial frozen corpse of the Yukagir horse. Discovered from thawing deposits in northern East Siberia (Yakutia, Russia), its age is confirmed to be Mid-Holocene (about 4600 BP). The mummy had a preserved head with the neck and the back of the torso with the legs and tail. The Yukagir horse was relatively short, with short ears and tail. Compared to the modern breeds, including the Yakutian domestic horse, wild Przewalski’s horse, and extinct Lena horse, Equus lenensis, the Yukagir horse was closest to the latter, which was also confirmed by studies of the hair microstructure. The pollen and plant remains from the horse’s intestines indicated a preference to grasses. The late geological age of the Yukagir horse is an indication that this species survived the Pleistocene–Holocene crisis and lived through the Mid-Holocene in northern Eastern Siberia.