한국산 꿩의다리속(미나리아재비과)의 cpDNA trnL-F 지역의 분자진화와 유연관계: Indel events의 영향

박성준,박선주,김혁진 한국식물분류학회 2012 식물 분류학회지 Vol.42 No.1

The trnL-F region islocated in the large single-copy region of the chloroplast genome. It consists of the trnL gene, the trnL intron, and the trnL-F IGS. Molecular evolution and phylogenetic relationships in Korean Thalictrum L. were investigated using data from the cpDNA trnL-F region. Bayesian and parsimony analyses of the data set with the gap characteristics recovered well-resolved trees that are topologically similar, with clades supported by some indels evolution. Indel events of cpDNA trnL-F in Korean Thalictrum were interpreted as phylogenetically informative characteristics. Sect. Physocarpum (excluding T. osmorhizoides) was an early-diverging group with in the genus and the remaining section formed strongly supported clades. Korean Thalictrum has various evolutionary patterns, such as the spatial distribution of the nucleotide diversity and transversion-type base substitutions in the trnL-F region. trnL-F 지역은 엽록체 게놈 large single-copy 지역에 위치하며, trnL gene, trnL intron, trnL-F IGS로 구성된다. 본 연구는 한국산 꿩의다리속 내에서 trnL-F 지역의 분자진화와 유연관계를 분석하였다. 갭형질을 이용한 자료의 베이시안과 파시모니 분석에서 몇몇 indels evolution는 분계조를 지지하여 해상력이 좋은 계통수가 나타났다. 한국산 꿩의다리속 내에 cpDNA trnL-F 지역의 indel events는 계통학적으로 유용한 정보를 가지고 있는 것으로 판단된다. 산꿩의다리절(그늘꿩의다리 제외)은 속내에서 가장 먼저 분기한 것으로 나타났고, 나머지 절은 강하게 분계조를 형성하며 분기하였다. 한국산 꿩의다리속 내에 trnL-F 지역은 뉴클레오티드의 다양한 공간적 분포 변이와 주로 transversion에 따른 염기치환 등 다양한 진화적 패턴을 가지고 있었다.

Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence

Kim, Dong Seon,Hahn, Yoonsoo BioMed Central 2012 BMC bioinformatics Vol.13 No.-

<P><B>Background</B></P><P>Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to protein products. Here, we analyzed annotated human protein-coding exons and identified human-specific splice sites that arose after the human-chimpanzee divergence.</P><P><B>Results</B></P><P>We analyzed multiple alignments of the annotated human protein-coding exons and their respective orthologous mammalian genome sequences to identify 85 novel splice sites (50 splice acceptors and 35 donors) in the human genome. The novel protein-coding exons, which are expressed either constitutively or alternatively, produce novel protein isoforms by insertion, deletion, or frameshift. We found three cases in which the human-specific isoform conferred novel molecular function in the human cells: the human-specific IMUP protein isoform induces apoptosis of the trophoblast and is implicated in pre-eclampsia; the intronization of a part of <I>SMOX</I> gene exon produces inactive spermine oxidase; the human-specific NUB1 isoform shows reduced interaction with ubiquitin-like proteins, possibly affecting ubiquitin pathways.</P><P><B>Conclusions</B></P><P>Although the generation of novel protein isoforms does not equate to adaptive evolution, we propose that these cases are useful candidates for a molecular functional study to identify proteomic changes that might bring about novel phenotypes during human evolution.</P>

Gains of ubiquitylation sites in highly conserved proteins in the human lineage

Kim, Dong Seon,Hahn, Yoonsoo BioMed Central 2012 BMC bioinformatics Vol.13 No.-

<P><B>Background</B></P><P>Post-translational modification of lysine residues of specific proteins by ubiquitin modulates the degradation, localization, and activity of these target proteins. Here, we identified gains of ubiquitylation sites in highly conserved regions of human proteins that occurred during human evolution.</P><P><B>Results</B></P><P>We analyzed human ubiquitylation site data and multiple alignments of orthologous mammalian proteins including those from humans, primates, other placental mammals, opossum, and platypus. In our analysis, we identified 281 ubiquitylation sites in 252 proteins that first appeared along the human lineage during primate evolution: one protein had four novel sites; four proteins had three sites each; 18 proteins had two sites each; and the remaining 229 proteins had one site each. PML, which is involved in neurodevelopment and neurodegeneration, acquired three sites, two of which have been reported to be involved in the degradation of PML. Thirteen human proteins, including ERCC2 (also known as XPD) and NBR1, gained human-specific ubiquitylated lysines after the human-chimpanzee divergence. ERCC2 has a Lys/Gln polymorphism, the derived (major) allele of which confers enhanced DNA repair capacity and reduced cancer risk compared with the ancestral (minor) allele. NBR1 and eight other proteins that are involved in the human autophagy protein interaction network gained a novel ubiquitylation site.</P><P><B>Conclusions</B></P><P>The gain of novel ubiquitylation sites could be involved in the evolution of protein degradation and other regulatory networks. Although gains of ubiquitylation sites do not necessarily equate to adaptive evolution, they are useful candidates for molecular functional analyses to identify novel advantageous genetic modifications and innovative phenotypes acquired during human evolution.</P>

Asymmetry of evolution and selection response of subgenomes in Brassica crops

Shengyi Liu 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

Genome polyploidization has provided significant sources of genetic variation for plant adaptive evolution and new species formation. However, the way in which molecular evolution of polyploid genomes builds up genetic architecture underlying speciation is unclear and whether there are any differences in polyploidsubgenomes’s responses to selection is unknown. Brassica is an ideal model to address these questions. Here, we used Arabidopsis thaliana as an outgroup to conduct comparative genome analysis of newly sequenced Brassica oleracea, B. rapaand B. napus. We revealed multi-layered modes of asymmetrical interspecific and intraspecific genome evolution. Between parallel species B. oleracea and B. rapa, these layers include: asymmetrical gene retention rates,asymmetrical TE amplification, asymmetrical tandem duplication of genes and asymmetrically alternative splicing variantsbetween the two sister species; Between subgenomes within species, these layers include: massive and asymmetrical subgenomic gene loss, great variations between paralogs at the DNA sequence level, expression differentiation of triplicated, α-duplicated and tandem duplicated genes across different tissues in the two diploid species, asymmetrical recombination on A and C in B. napus. In addition, the predominant mechanism for gene loss is small deletion, rather than asymmetrical cross-over. These patterns provide new insight into genome evolution underlying speciation and trait formation and will underpin research into genetic improvement of these important crops

일본원숭이의 리보솜 단백질 S4 유전자의 분자적 클로닝 및 진화적 분석

김희수(Heui Soo Kim),(Takashi Kageyama),(Osamu Takenaka) 한국유전학회 2001 Genes & Genomics Vol.23 No.1

N/A We cloned and sequenced the cDNA encoding ribosomal protein S4 (RPS4) from testis cDNA library of the Japanese monkey. The monkey RPS4Y gene encodes a deduced protein of 263 amino acids and share 92.8% and 95.4% amino acid sequence identities with the deduced mouse Rps4 and human RPS4Y. Northern blot analysis of poly (A) mRNA from the Japanese monkey revealed approximately 1.0 kb transcript. Molecular evolutionary rate was 0.2 ∼ 0.3 × 10-9/site/year in the Japanese monkey. This value was at least three fold lower than that of the TSPY and SRY genes of human Y chromosome, suggesting that the RPS4Y gene has been evolved conservatively during primate evolution.

Atomistic simulation analysis of the effects of void interaction on void growth and coalescence in a metallic system

Z.X. Wen,J.P. Wang,Y.W. Wu,K.J. Zhou,Z.F. Yue 한국물리학회 2018 Current Applied Physics Vol.18 No.6

Material deformation caused by the interaction between defects is a significant factor of material fracture failure. The present study employs molecular dynamics simulations of single-void and double-void crystalline Ni atomic systems to investigate inter-void interactions. Furthermore, simulations showing the evolution of dislocations for three different crystallographic orientations are conducted to study the void growth and coalescence. The simulations also consider the effect of the radius of the secondary void on dislocation evolution. The results show that double-void systems are more prone to yield than single-void systems. Further microstructural analysis indicates that the interaction between voids is realized by dislocation reactions. The simulation results of the dislocation evolution of the three orientations reveal that a relationship exists between the evolution of the dislocation density and the stress-strain curve. At the initial stage of dislocation, the dislocation grows slowly, and consists of Shockley partial dislocation. The dislocation growth rate then increases significantly in the sharply declining stage of the stress-strain curve, where most of dislocations are Shockley partial dislocation. Analysis of the dislocation length during the overall simulation indicates that the dislocation length of the [110] orientation is the longest, followed by that of the [111] orientation and the [100] orientation, which has the shortest dislocation length.

Fossil-calibrated molecular dating support a rapid radiation of tribe Aphidini (Hemiptera: Aphididae) in the Tertiary

Hyojoong Kim,Seunghwan Lee 한국응용곤충학회 2009 한국응용곤충학회 학술대회논문집 Vol.2009 No.10

Aphid is relatively young group among insects, which radiated contemporaneously with the host plants in angiosperm. Based on recent molecular phylogenetic studies, the tribe Aphidini has been strongly suggested as a primitive group sister to two other tribes, Macrosiphini and Pterocommatini, in the subfamily Aphidinae which is most diversified aphid group. These ideas have been proposed due to the phylogenetic relationships between the groups and the relatively simple morphological characters. Our study is aimed to confirm the evolutionary process of this primitive group in order to understand the diversification of the modern aphids. Firstly, we obtained the phylogenetic relationships for 59 ingroup species plus 10 outgroup species (6 macrosiphine species, 1 hormaphidine species, and 3 adelgids) based on the combined sequences (2,899 bp) of three mitochondrial genes (COI, COII, CytB) and one nuclear gene (EF1α). The optimal tree topology is obtained by the ML analysis in GARLI 0.95b with Kishino-Hasegawa and Shimodaira-Hasegawa tests in PAUP*4b10, and the posterior probabilities on each node were estimated by MrBayes 3.1.1 under the best fit model (GTR+I+G) tested by MrMODELTEST 3.0. Then, the node ages of the obtained tree were calibrated using the relaxed-clock model implemented in BEAST 1.4.8 and its package programs based on one node fixation of 150 MYA (million years ago) for Aphididae+Adelgidae, and two node constraints as 80-100 MYA for Aphididae crown and 50-70 MYA for Aphidinae crown according to the fossil related publications. As results, we found four major facts on their evolution: 1) Aphidini radiated from the early Eocene in the Tertiary, 2) however, most lineages rapidly radiated during the late Eocene, 3) common ancestor of the subtribe Aphidina maybe fed on herbs or shrubs in asterids, 4) host alternation trait was lately acquired on Rosaceae- or Rhamnaceae-feeding aphids.

Sirtuin/Sir2 Phylogeny, Evolutionary Considerations and Structural Conservation

Sebastian Greiss,Anton Gartner 한국분자세포생물학회 2009 Molecules and cells Vol.28 No.5

The sirtuins are a protein family named after the first identified member, S. cerevisiae Sir2p. Sirtuins are protein deacetylases whose activity is dependent on NAD+ as a cosubstrate. They are structurally defined by two central domains that together form a highly conserved catalytic center, which catalyzes the transfer of an acetyl moiety from acetyllysine to NAD+, yielding nicotinamide, the unique metabolite O-acetyl-ADP-ribose and deacetylated lysine. One or more sirtuins are present in virtually all species from bacteria to mammals. Here we describe a phylogenetic analysis of sirtuins. Based on their phylogenetic relationship, sirtuins can be grouped into over a dozen classes and subclasses. Humans, like most vertebrates, have seven sirtuins: SIRT1-SIRT7. These function in diverse cellular pathways, regulating transcriptional repression, aging, metabolism, DNA damage responses and apoptosis. We show that these seven sirtuins arose early during animal evolution. Conserved residues cluster around the catalytic center of known sirtuin family members.

Distinct evolution of toll‑like receptor signaling pathway genes in cetaceans

Ran Tian,Inge Seim,Zepeng Zhang,Ying Yang,Wenhua Ren,Shixia Xu,Guang Yang 한국유전학회 2019 Genes & Genomics Vol.41 No.12

Background The relatively rapid spread and diversity of marine pathogens posed an initial and ongoing challenge for cetaceans (whales, dolphins, and porpoises), descendants of terrestrial mammals that transitioned from land to sea approximately 56 million years ago. Toll-like receptors (TLRs) play important roles in regulating immunity against pathogen infections by detecting specific molecular patterns and activating a wide range of downstream signaling pathways. The ever-increasing catalogue of mammalian genomes offers unprecedented opportunities to reveal genetic changes associated with evolutionary and ecological processes. Objective This study aimed to explore the molecular evolution of TLR signaling pathway genes in cetaceans. Methods Genes involved in the TLR signaling pathway were retrieved by BLAST searches using human coding sequences as queries. We tested each gene for positive selection along the cetacean branches using PAML and Hyphy. Physicochemical property changes of amino acids at all positively selected residues were assessed by TreeSAAP and visualized with WebLogo. Bovine and dolphin TLR4 was assessed using human embryonic kidney cell line HEK293, which lacks TLR4 and its co-receptor MD-2. Results We demonstrate that eight TLR signaling pathway genes are under positive selection in cetaceans. These include key genes in the response to Gram-negative bacteria: TLR4, CD14, and LY96 (MD-2). Moreover, 41 out of 65 positively selected sites were inferred to harbor substitution that dramatically changes the physicochemical properties of amino acids, with most of them situated in or adjacent to functional regions. We also found strong evidence that positive selection occurred in the lineage of the Yangtze finless porpoise, likely reflecting relatively recent adaptions to a freshwater milieu. Species-specific differences in TLR4 response were observed between cetacean and terrestrial species. Cetacean TLR4 was significantly less responsive to lipopolysaccharides from a terrestrial E. coli strain, possibly a reflection of the arms race of host–pathogen co-evolution faced by cetaceans in an aquatic environment. Conclusion This study provides further impetus for studies on the evolution and function of the cetacean immune system.

In vitro Constructive Approaches to the Origin of Coding Sequences

Shiba, Kiyotaka Korean Society for Biochemistry and Molecular Biol 1998 Journal of biochemistry and molecular biology Vol.31 No.3

How did nature create the first set of genes at the beginning of life on Earth? One of the goals of molecular biology is to elucidate the fundamental rules governing how genes and, therefore, proteins were created. Through experiments carried out in the emerging field of "in vitro" or "benchtop" evolution studies, we are gaining new insights into the origins of genes and proteins as well as the origins of their functions (e.g., catalysis). In this review, I present an overview of recent experimental approaches to the question of the origin and evolution of genes. In addition, I will introduce a novel in vitro protein emergence system that was recently developed in my laboratory.