Synthesis and repair of 3'-end of tRNA molecule by tRNA nucleotidyltransferase

Enzim ATP(CTP):tRNA-nukleotidil-transferaza (CCA enzim) katalizira posttranskripcijsku sintezu i popravak slijeda CCA na 3'-kraju molekule tRNA, neophodnog u reakcijama translacije i stoga od životne važnosti za stanicu. CCA enzim se razlikuje od standardnih DNA- i RNA-polimeraza u nekoliko karakteristika. Osim što ne treba nukleinsku kiselinu kao kalup, u molekulu tRNA koja služi kao klica ugrađuje strogo određen broj nukleotida, zaustavljajući reakciju visokom efikasnošću i točnošću. Također, CCA enzim za ugradnju odabire isključivo CTP i ATP i jako je selektivan prema strukturama nalik molekuli tRNA kao polimerizacijskim supstratima. Zbog prisutnosti samo jednog aktivnog mjesta, ono mora promijeniti specifičnost ugradnje između ATP-a i CTP-a, ovisno o staničnoj koncentraciji nukleotida i slijedu na 3'-kraju molekule tRNA. Tijekom evolucije došlo je do razvoja dvaju razreda CCA enzima koji se, iako dijele sveukupnu strukturnu organizaciju i obavljaju identične funkcije, izrazito razlikuju u strukturi pojedinačnih domena i posjeduju drugačija mehanistička rješenja. Enzimi razreda 1 prisutni su samo u arhejama, dok su enzimi razreda 2 prisutni u bakterijama i eukariotima. Oba razreda CCA enzima sadrže visoko očuvanu katalitičku srž u domeni glave s tri karboksilata u rasporedu karakterističnom za DNA- i RNA-polimeraze koje koriste mehanizam dvaju metalnih iona za prijenos fosforila. Oba razreda enzima ovise o metalnim ionima, pri čemu primarno koriste Mg2+ i Mn2+ kao produktivne metalne ione. Osim razlike između dvaju razreda enzima, postoje značajne razlike između enzima koji pripadaju istom razredu, što je vidljivo na primjeru ljudskog i CCA enzima iz bakterije E. coli.ATP(CTP):tRNA nucleotidyltransferase (CCA enzyme) is responsible for posstranscriptional synthesis and repair of the 3'-terminal CCA sequence in tRNA trascripts, which is indispensable in translation reactions and therefore of vital importance for the cell. CCA enzyme differs from standard DNA and RNA polymerases in several ways. Apart from the fact that it does not require a nucleic acid template, it incorporates only restricted number of nucleotides in a tRNA primer and then stops reaction at a high efficiency and accuracy. It also selects exclusively CTP and ATP for incorporation and it is highly selective for tRNAlike structures as a polymerization substrate. Because of the existance of single active site, this active site has to change the specificity between ATP i CTP depending on cellular concentrations of nucleotides and the sequence of the tRNA 3' end. CCA enzymes evolved in two classes during evolution, and although this two classes share an overall structural organization and fulfill indentical functions, the individual domains vary extremely and have different mechanistic solutions. Class 1 enzymes are found only in archaea while class2 enzymes are found in bacteria and eukaryotes. Both classes of CCA enzymes have a highly conserved catalytic core within the head domain having three carboxylates in a geometry similar to those of template-dependent DNA and RNA polymerases that use two metal ion mechanism for phosphoryl transfer. Both classes use Mn2+ and Mg2+ as productive metal ions. Except for the differences between two classes, even closely related enzymes that belong to the same class differ substantially

Synthesis and repair of 3'-end of tRNA molecule by tRNA nucleotidyltransferase

Enzim ATP(CTP):tRNA-nukleotidil-transferaza (CCA enzim) katalizira posttranskripcijsku sintezu i popravak slijeda CCA na 3'-kraju molekule tRNA, neophodnog u reakcijama translacije i stoga od životne važnosti za stanicu. CCA enzim se razlikuje od standardnih DNA- i RNA-polimeraza u nekoliko karakteristika. Osim što ne treba nukleinsku kiselinu kao kalup, u molekulu tRNA koja služi kao klica ugrađuje strogo određen broj nukleotida, zaustavljajući reakciju visokom efikasnošću i točnošću. Također, CCA enzim za ugradnju odabire isključivo CTP i ATP i jako je selektivan prema strukturama nalik molekuli tRNA kao polimerizacijskim supstratima. Zbog prisutnosti samo jednog aktivnog mjesta, ono mora promijeniti specifičnost ugradnje između ATP-a i CTP-a, ovisno o staničnoj koncentraciji nukleotida i slijedu na 3'-kraju molekule tRNA. Tijekom evolucije došlo je do razvoja dvaju razreda CCA enzima koji se, iako dijele sveukupnu strukturnu organizaciju i obavljaju identične funkcije, izrazito razlikuju u strukturi pojedinačnih domena i posjeduju drugačija mehanistička rješenja. Enzimi razreda 1 prisutni su samo u arhejama, dok su enzimi razreda 2 prisutni u bakterijama i eukariotima. Oba razreda CCA enzima sadrže visoko očuvanu katalitičku srž u domeni glave s tri karboksilata u rasporedu karakterističnom za DNA- i RNA-polimeraze koje koriste mehanizam dvaju metalnih iona za prijenos fosforila. Oba razreda enzima ovise o metalnim ionima, pri čemu primarno koriste Mg2+ i Mn2+ kao produktivne metalne ione. Osim razlike između dvaju razreda enzima, postoje značajne razlike između enzima koji pripadaju istom razredu, što je vidljivo na primjeru ljudskog i CCA enzima iz bakterije E. coli.ATP(CTP):tRNA nucleotidyltransferase (CCA enzyme) is responsible for posstranscriptional synthesis and repair of the 3'-terminal CCA sequence in tRNA trascripts, which is indispensable in translation reactions and therefore of vital importance for the cell. CCA enzyme differs from standard DNA and RNA polymerases in several ways. Apart from the fact that it does not require a nucleic acid template, it incorporates only restricted number of nucleotides in a tRNA primer and then stops reaction at a high efficiency and accuracy. It also selects exclusively CTP and ATP for incorporation and it is highly selective for tRNAlike structures as a polymerization substrate. Because of the existance of single active site, this active site has to change the specificity between ATP i CTP depending on cellular concentrations of nucleotides and the sequence of the tRNA 3' end. CCA enzymes evolved in two classes during evolution, and although this two classes share an overall structural organization and fulfill indentical functions, the individual domains vary extremely and have different mechanistic solutions. Class 1 enzymes are found only in archaea while class2 enzymes are found in bacteria and eukaryotes. Both classes of CCA enzymes have a highly conserved catalytic core within the head domain having three carboxylates in a geometry similar to those of template-dependent DNA and RNA polymerases that use two metal ion mechanism for phosphoryl transfer. Both classes use Mn2+ and Mg2+ as productive metal ions. Except for the differences between two classes, even closely related enzymes that belong to the same class differ substantially

Synthesis and repair of 3'-end of tRNA molecule by tRNA nucleotidyltransferase

Enzim ATP(CTP):tRNA-nukleotidil-transferaza (CCA enzim) katalizira posttranskripcijsku sintezu i popravak slijeda CCA na 3'-kraju molekule tRNA, neophodnog u reakcijama translacije i stoga od životne važnosti za stanicu. CCA enzim se razlikuje od standardnih DNA- i RNA-polimeraza u nekoliko karakteristika. Osim što ne treba nukleinsku kiselinu kao kalup, u molekulu tRNA koja služi kao klica ugrađuje strogo određen broj nukleotida, zaustavljajući reakciju visokom efikasnošću i točnošću. Također, CCA enzim za ugradnju odabire isključivo CTP i ATP i jako je selektivan prema strukturama nalik molekuli tRNA kao polimerizacijskim supstratima. Zbog prisutnosti samo jednog aktivnog mjesta, ono mora promijeniti specifičnost ugradnje između ATP-a i CTP-a, ovisno o staničnoj koncentraciji nukleotida i slijedu na 3'-kraju molekule tRNA. Tijekom evolucije došlo je do razvoja dvaju razreda CCA enzima koji se, iako dijele sveukupnu strukturnu organizaciju i obavljaju identične funkcije, izrazito razlikuju u strukturi pojedinačnih domena i posjeduju drugačija mehanistička rješenja. Enzimi razreda 1 prisutni su samo u arhejama, dok su enzimi razreda 2 prisutni u bakterijama i eukariotima. Oba razreda CCA enzima sadrže visoko očuvanu katalitičku srž u domeni glave s tri karboksilata u rasporedu karakterističnom za DNA- i RNA-polimeraze koje koriste mehanizam dvaju metalnih iona za prijenos fosforila. Oba razreda enzima ovise o metalnim ionima, pri čemu primarno koriste Mg2+ i Mn2+ kao produktivne metalne ione. Osim razlike između dvaju razreda enzima, postoje značajne razlike između enzima koji pripadaju istom razredu, što je vidljivo na primjeru ljudskog i CCA enzima iz bakterije E. coli.ATP(CTP):tRNA nucleotidyltransferase (CCA enzyme) is responsible for posstranscriptional synthesis and repair of the 3'-terminal CCA sequence in tRNA trascripts, which is indispensable in translation reactions and therefore of vital importance for the cell. CCA enzyme differs from standard DNA and RNA polymerases in several ways. Apart from the fact that it does not require a nucleic acid template, it incorporates only restricted number of nucleotides in a tRNA primer and then stops reaction at a high efficiency and accuracy. It also selects exclusively CTP and ATP for incorporation and it is highly selective for tRNAlike structures as a polymerization substrate. Because of the existance of single active site, this active site has to change the specificity between ATP i CTP depending on cellular concentrations of nucleotides and the sequence of the tRNA 3' end. CCA enzymes evolved in two classes during evolution, and although this two classes share an overall structural organization and fulfill indentical functions, the individual domains vary extremely and have different mechanistic solutions. Class 1 enzymes are found only in archaea while class2 enzymes are found in bacteria and eukaryotes. Both classes of CCA enzymes have a highly conserved catalytic core within the head domain having three carboxylates in a geometry similar to those of template-dependent DNA and RNA polymerases that use two metal ion mechanism for phosphoryl transfer. Both classes use Mn2+ and Mg2+ as productive metal ions. Except for the differences between two classes, even closely related enzymes that belong to the same class differ substantially

The evolutionary history of Neanderthal and Denisovan Y chromosomes

Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.Q.F. was supported by funding from the Chinese Academy of Sciences (XDB26000000) and the National Natural Science Foundation of China (91731303, 41925009, 41630102). A.R. was funded by Spanish government (MICINN/ FEDER) (grant number CGL2016-75109-P). The reassessment of the Spy collection by H.R., I.C., and P.S. was supported by the Belgian Science Policy Office (BELSPO 2004-2007, MO/36/0112). M.V.S., M.B.K., and A.P.D. were supported by the Russian Foundation for Basic Research (RFBR 17-29-04206). This study was funded by the Max Planck Society and the European Research Council (grant agreement number 694707)

New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland).

The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus

The evolutionary history of Neandertal and Denisovan Y chromosomes

Ancient DNA has allowed the study of various aspects of human history in unprecedented detail. However, because the majority of archaic human specimens preserved well enough for genome sequencing have been female, comprehensive studies of Y chromosomes of Denisovans and Neandertals have not yet been possible. Here we present sequences of the first Denisovan Y chromosomes (Denisova 4 and Denisova 8), as well as the Y chromosomes of three late Neandertals (Spy 94a, Mezmaiskaya 2 and El Sidrón 1253). We find that the Denisovan Y chromosomes split around 700 thousand years ago (kya) from a lineage shared by Neandertal and modern human Y chromosomes, which diverged from each other around 370 kya. The phylogenetic relationships of archaic and modern human Y chromosomes therefore differ from population relationships inferred from their autosomal genomes, and mirror the relationships observed on the level of mitochondrial DNA. This provides strong evidence that gene flow from an early lineage related to modern humans resulted in the replacement of both the mitochondrial and Y chromosomal gene pools in late Neandertals. Although unlikely under neutrality, we show that this replacement is plausible if the low effective population size of Neandertals resulted in an increased genetic load in their Y chromosomes and mitochondrial DNA relative to modern humans.Q.F. was supported by funding from the Chinese Academy of Sciences (XDB26000000), and the National Natural Science Foundation of China (91731303, 41925009,41630102). A.R. was funded by Spanish government (MICINN/FEDER), grant number CGL2016-75109-P. The reassessment of the Spy collection by H.R., I.C. and P.S. was supported by the Belgian Science Policy Office (BELSPO 2004-2007, MO/36/0112). M.S., M.K. and A.D. were supported by the Russian Foundation for Basic Research (RFBR 17-29-04206). This study was funded by the Max Planck Society and the European Research Council (grant agreement number 694707).N

Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain

Genetic investigations of Upper Palaeolithic Europe have revealed a complex and transformative history of human population movements and ancestries, with evidence of several instances of genetic change across the European continent in the period following the Last Glacial Maximum (LGM). Concurrent with these genetic shifts, the post-LGM period is characterized by a series of significant climatic changes, population expansions and cultural diversification. Britain lies at the extreme northwest corner of post-LGM expansion and its earliest Late Glacial human occupation remains unclear. Here we present genetic data from Palaeolithic human individuals in the United Kingdom and the oldest human DNA thus far obtained from Britain or Ireland. We determine that a Late Upper Palaeolithic individual from Gough's Cave probably traced all its ancestry to Magdalenian-associated individuals closely related to those from sites such as El Mirón Cave, Spain, and Troisième Caverne in Goyet, Belgium. However, an individual from Kendrick's Cave shows no evidence of having ancestry related to the Gough’s Cave individual. Instead, the Kendrick’s Cave individual traces its ancestry to groups who expanded across Europe during the Late Glacial and are represented at sites such as Villabruna, Italy. Furthermore, the individuals differ not only in their genetic ancestry profiles but also in their mortuary practices and their diets and ecologies, as evidenced through stable isotope analyses. This finding mirrors patterns of dual genetic ancestry and admixture previously detected in Iberia but may suggest a more drastic genetic turnover in northwestern Europe than in the southwest

An infant burial from Arma Veirana in northwestern Italy provides insights into funerary practices and female personhood in early Mesolithic Europe

The evolution and development of human mortuary behaviors is of enormous cultural significance. Here we report a richly-decorated young infant burial (AVH-1) from Arma Veirana (Liguria, northwestern Italy) that is directly dated to 10,211–9910 cal BP (95.4% probability), placing it within the early Holocene and therefore attributable to the early Mesolithic, a cultural period from which well-documented burials are exceedingly rare. Virtual dental histology, proteomics, and aDNA indicate that the infant was a 40–50 days old female. Associated artifacts indicate significant material and emotional investment in the child’s interment. The detailed biological profile of AVH-1 establishes the child as the earliest European near-neonate documented to be female. The Arma Veirana burial thus provides insight into sex/gender-based social status, funerary treatment, and the attribution of personhood to the youngest individuals among prehistoric hunter-gatherer groups and adds substantially to the scant data on mortuary practices from an important period in prehistory shortly following the end of the last Ice Age

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian–Ranisian–Jerzmanowician (LRJ), which has been described in northwestern and central Europe5,6,7,8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period

Analysis of kinship and detection of Kenny - Caffey syndrome in skeletons recovered from midieval grave in Dubrovnik area

Na arheološkom nalazištu Sveti Petar Zvekovica pored Dubrovnika, u kasnosrednjovjekovnom grobu, pronađeni su ostaci odrasle ženske osobe i djeteta. Na kostima odrasle ženske osobe uočene su morfološke promjene karakteristične za Kenny – Caffey sindrom, rijedak kongenitalni poremećaj proporcionalnog patuljastog rasta. Morfološke promjene jedinstvene za Klippel – Feil sindrom, još jedan iznimno rijedak poremećaj, uočene su na kostima djeteta. Kako bi odgovorili na pitanje jesu li dvije osobe u međusobnom srodstvu ili su u isti grob smještene zbog svojih morfoloških obilježja, iz njihovih skeletnih ostataka smo izolirali DNA i analizirali srodnost pomoću PowerPlex® ESI 17 System kita i Investigator® DIPplex kita. Zbog oštećenja molekula DNA, do kojih dolazi nakon smrti svakog organizma, i prisutnosti inhibitora, dobiveni su parcijalni DNA profili na temelju kojih nismo mogli potvrditi roditeljstvo, ali ga ni u potpunosti isključiti. Alelno – specifičnom lančanom reakcijom polimerazom nismo uspjeli potvrditi Kenny – Caffey sindrom na molekularno – genetičkom nivou zbog prevelikog oštećenja molekula DNA.Skeletal remains of a woman and a child were found in a common medieval tomb during excavations at the archaeological site Sveti Petar Zvekovica near the city of Dubrovnik. Morphological analysis of skeletal remains showed that the woman had the main characteristics of the Kenny - Caffey syndrome, a rare congenital disorder of proportionate dwarfism, and the child had morphological features of the Klippel - Feil syndrome, another rare disorder. To answer the question whether the two skeletons belonged to a mother and a child, or if they were placed together in a common tomb because of their morphological features, we extracted DNA from skeletal remains and analyzed kinship using two commercial kits. Due to severe degradation of DNA and presence of inhibitors, we weren't able to confirm kinship nor disprove it and, also, we couldn't prove the Kenny - Caffey syndrome at the molecular level using allele – specific PCR