Biodegradation of 2,4,6-trinitrotoluene (TNT) by the white-rot basidiomycete Phlebia radiata

Phlebia radiatatransformed 2,4,6-trinitrotoluene (TNT), as well as its first reduction products, the aminodinitrotoluenes, into 4-hydroxylamino-2,6-dinitrotoluene (4-OHA-2,6-DNT) and 4-amino-2,6-dinitrotoluene (4-A-2,6-DNT). No extracellular peroxidases were involved in this step. The ligninolytic extracellular fluid, assumed to contain peroxidases, did not reduce TNT. However, ligninolytic peroxidases are implicated in the transformation of the first reduction products of TNT.     

Transformation and mineralization of 2,4,6-trinitrotoluene (TNT) by manganese peroxidase from the white-rot basidiomycete Phlebia radiata

The degradation of the nitroaromatic pollutant 2,4,6-trinitrotoluene (TNT) by the manganese-dependent peroxidase (MnP) of the white-rot fungus Phlebia radiata and the main reduction products formed were investigated. In the presence of small amounts of reduced glutathione (10 mM), a concentrated cell-free preparation of MnP from P. radiata exhibiting an activity of 36 nkat/ml (36 nmol Mn(II) oxidized per sec and per ml) transformed 10 mg/l of TNT within three days. The same preparation was capable of completely transforming the reduced derivatives of TNT. When present at 10 mg/l, the aminodinitrotoluenes were transformed in less than two days and the diaminonitrotoluenes in less than three hours. Experiments with ¹⁴C-U-ring labeled TNT and 2-amino-4,6-dinitrotoluene showed that these compounds were mineralized by 22% and 76%, respectively, within 5 days. Higher concentrations of reduced glutathione (50 mM) led to a severe inhibition of the degradation process. It is concluded that Phlebia radiata is a good candidate for the biodegradation of TNT as well as its reduction metabolites.     

The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus Sclerotinia borealis Reveals Multiple Invasions of Introns and Genomic Duplications

Here we report the complete sequence of the mitochondrial (mt) genome of the necrotrophic phytopathogenic fungus Sclerotinia borealis, a member of the order Helotiales of Ascomycetes. The 203,051 bp long mtDNA of S. borealis represents one of the largest sequenced fungal mt genomes. The large size is mostly determined by the presence of mobile genetic elements, which include 61 introns. Introns contain a total of 125,394 bp, are scattered throughout the genome, and are found in 12 protein-coding genes and in the ribosomal RNA genes. Most introns contain complete or truncated ORFs that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Integrations of mobile elements are also evidenced by the presence of two regions similar to fragments of inverton-like plasmids. Although duplications of some short genome regions, resulting in the appearance of truncated extra copies of genes, did occur, we found no evidences of extensive accumulation of repeat sequences accounting for mitochondrial genome size expansion in some other fungi. Comparisons of mtDNA of S. borealis with other members of the order Helotiales reveal considerable gene order conservation and a dynamic pattern of intron acquisition and loss during evolution. Our data are consistent with the hypothesis that horizontal DNA transfer has played a significant role in the evolution and size expansion of the S. borealis mt genome.     

142 Insight Into the Mitochondrial Genome of Emiliania Huxleyi (Haptophyta)

Emiliania huxleyi (Lohmann) Hay et Mohler 1967 (CCMP373) is the most abundant representative of the Haptophyta, and can be found in oceanic and neritic waters from subpolar to tropical latitudes. Blooms of this coccolithophorid may reach cell densities of 2.106 ml⁻¹ and emit vast amounts of DMS (dimethyl sulfide), with the potential to affect the global climate. We report here the DNA sequence of more than 21 kb of the mitochondrial genome of this species, out of an approximate total of 30 kb. Preliminary annotation of the genome using database searches identified at least 16 genes. The data were also compared to the unpublished mitochondrial genome of Pavlova lutheri , another member of the haptophytes, and some important differences were identified. Although the gene content of E. huxleyi mtDNA seems to closely resemble that of P. lutheri mtDNA, the gene order differs substantially. Access to the P. lutheri and E. huxleyi mitochondrial genomes will permit the comparative analysis of two deeply diverging members of an ancient and ecologically significant lineage. Among other potential applications, the data will help to clarify phylogeny within the haptophytes as well as to determine the phylogenetic position of this division in relation to other groups of algae, such as heterokonts, dinoflagellates and cryptophytes.     

大壁虎线粒体基因组全序列及其结构(英文)

采用长PCR扩增、克隆和引物步行等方法,测定了大壁虎(Gekkogecko)线粒体基因组全序列。序列全长16435bp,共有13个蛋白质编码基因、2个rRNA基因和22个tRNA基因。基因组的组成、顺序、编码链的选择、tRNA的结构、较低的碱基G含量、对碱基T的偏好以及GC和AT偏斜,都与大部分脊椎动物相同或相近。但有些特征揭示了壁虎类的原始性蛋白质编码基因密码子第3位表现为对碱基A的偏好,更接近两栖类和鱼类而不是羊膜动物;标准终止密码子(TAA)只出现于3个蛋白质编码基因中,比大部分脊椎动物少。tRNA基因核苷酸长度为63～76nt,除了tRNACys和tRNASer(AGY)缺少D臂,其余的二级结构均呈典型的三叶草状。     

Recombination and Evolution of Duplicate Control Regions in the Mitochondrial Genome of the Asian Big-Headed Turtle,Platysternon megacephalum

Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3′ end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum.     

The Mitochondrial Genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): Considerable Economization in the Length and Structural Features of Encoded Genes

The complete sequence of the mitochondrial genome of the plant parasitic nematode Xiphinema americanum sensu stricto has been determined. At 12626bp it is the smallest metazoan mitochondrial genome reported to date. Genes are transcribed from both strands. Genes coding for 12 proteins, 2 rRNAs and 17 putative tRNAs (with the tRNA-C, I, N, S1, S2 missing) are predicted from the sequence. The arrangement of genes within the X. americanum mitochondrial genome is unique and includes gene overlaps. Comparisons with the mtDNA of other nematodes show that the small size of the X. americanum mtDNA is due to a combination of factors. The two mitochondrial rRNA genes are considerably smaller than those of other nematodes, with most of the protein encoding and tRNA genes also slightly smaller. In addition, five tRNAs genes are absent, lengthy noncoding regions are not present in the mtDNA, and several gene overlaps are present. [Reviewing Editor: Dr. Yues van de Peer] F. Lamberti: Deceased, 2004     

地山雀线粒体基因组全序列的测定和分析

基于长距PCR扩增及保守引物步移法测定并注释了地山雀(Pseudopodoces humilis)的线粒体基因组全序列.结果表明,地山雀线粒体基因组全长1.6 809万bp,A+T含量为52.9%,37个基因排列顺序与红原鸡一致.蛋白质基因的起始密码子中,除COI基因为GTG外,其余均为ATG.NDⅠ和ND5基因终止密码子为AGA:COⅡ基凶为AGG:COⅢ和ND4基因为不完全终止密码子T;其余基因均为典型的TAA或TAG.预测了22个tRNA基闪的二级结构,发现tRNAScr(AGN)缺少DHU臂,tRNAPhe的TψC臂存在一单核苷酸插入.预测的地山雀12S和16S rRNA二级结构分别包括3个结构域47个茎环和6个结构域60个茎环. 控制区位于tRNAGlu和tRNAPhe之间,长度1240 bp.控制区结构为高变Ⅰ区、中央保守Ⅱ区和保守序列Ⅲ区3个结构域.     

Phosphatidylserine Decarboxylase 1 (Psd1) Promotes Mitochondrial Fusion by Regulating the Biophysical Properties of the Mitochondrial Membrane and Alternative Topogenesis of Mitochondrial Genome Maintenance Protein 1 (Mgm1)

Non–bilayer-forming lipids such as cardiolipin, phosphatidic acid, and phosphatidylethanolamine (PE) are proposed to generate negative membrane curvature, promoting membrane fusion. However, the mechanism by which lipids regulate mitochondrial fusion remains poorly understood. Here, we show that mitochondrial-localized Psd1, the key yeast enzyme that synthesizes PE, is required for proper mitochondrial morphology and fusion. Yeast cells lacking Psd1 exhibit fragmented and aggregated mitochondria with impaired mitochondrial fusion during mating. More importantly, we demonstrate that a reduction in PE reduces the rate of lipid mixing during fusion of liposomes with lipid compositions reflecting the mitochondrial membrane. This suggests that the mitochondrial fusion defect in the Δpsd1 strain could be due to the altered biophysical properties of the mitochondrial membrane, resulting in reduced fusion kinetics. The Δpsd1 strain also has impaired mitochondrial activity such as oxidative phosphorylation and reduced mitochondrial ATP levels which are due to a reduction in mitochondrial PE. The loss of Psd1 also impairs the biogenesis of s-Mgm1, a protein essential for mitochondrial fusion, further exacerbating the mitochondrial fusion defect of the Δpsd1 strain. Increasing s-Mgm1 levels in Δpsd1 cells markedly reduced mitochondrial aggregation. Our results demonstrate that mitochondrial PE regulates mitochondrial fusion by regulating the biophysical properties of the mitochondrial membrane and by enhancing the biogenesis of s-Mgm1. While several proteins are required to orchestrate the intricate process of membrane fusion, we propose that specific phospholipids of the mitochondrial membrane promote fusion by enhancing lipid mixing kinetics and by regulating the action of profusion proteins.     

Organization of the Mitochondrial Genome of Mantis Shrimp Pseudosquilla ciliata (Crustacea: Stomatopoda)

We determined the nearly complete mitochondrial genome of Pseudosquilla ciliata (Crustacea, Stomatopoda), including all protein-coding genes and all but one of the transfer RNAs. There were no gene rearrangements relative to the pattern shared by crustaceans and hexapods. Phylogenetic analysis using concatenated amino acid sequences of the mitochondrial protein-coding genes confirmed a basal position of Stomatopoda among Eumalacostraca. Pancrustacean relationships based on mitogenomic data were analyzed and are discussed in relation to crustacean and hexapod monophyly and hexapod affinities to crustacean subtaxa.     

Effects of Glucose Repression on the Transmission and Recombination of Mitochondrial Genes in Yeast (SACCHAROMYCES CEREVISIAE)

Matings of a number of Saccharomyces cerevisiae stocks give different output ratios of mitochondrial genotypes depending on whether the cells are glucose-repressed or derepressed. The effects of glucose repression are independent of cellular mating type and mitochondrial genotype, and take place at least in part after zygotes are formed. An explanation is proposed in terms of changes in the relative numbers of mitochondrial DNA molecules contributed by the a and α parents, modified by selective replication or destruction of molecules inside the zygote.     

修饰的痘苗病毒安卡拉株（MVA）基因组中高频的同源重组

痘苗病毒由于其外源基因容量大,表达产物后加工完善等优势而广泛用于基因工程的研究以及基因治疗,痘苗病毒基因组的同源重组现象为其基因操作带来了方便,也被用于很多痘苗病毒基因结构和功能的研究,痘苗病毒安卡拉株（MVA）是一种修饰的复制限制的痘苗病毒,由于极高的安全性,正在实验室和临床应用的很多领域取代普通的痘苗病毒,为提高重组MVA系统的安全性以及筛选重组MVA的效率,发展了一种暂时选择系统,此系统利用分子内2段同向的相同序列发生同源重组去除选择标记k1l基因,从而消除选择标记对宿主可能的危害。利用此暂时表达系统构建了4个携带编码不同长度外源多蛋白质序列的重组MVA,并估算了每次传代的重组频率,结果显示,MVA同源重组频率虽然比其他痘苗病毒株要低,但仍然是较斋的,将带有k1l基因的重组MVA经3-4次盲传（blind passage),即可获得完全去除选择标记的重组MVA。进一步证明上述利用暂时选择标记k1l基因构建重组MVA的系统具有十分可靠的安全性,适合作为人体活疫苗开发和基因治疗的载体,而且,通过盲传进行筛选,能大大提高去除选择标记的效率,降低鸺建重组MVA的成本。     

Complete Mitochondrial DNA Sequences of the Threadfin Cichlid (Petrochromis trewavasae) and the Blunthead Cichlid (Tropheus moorii) and Patterns of Mitochondrial Genome Evolution in Cichlid Fishes

The cichlid fishes of the East African Great Lakes represent a model especially suited to study adaptive radiation and speciation. With several African cichlid genome projects being in progress, a promising set of closely related genomes is emerging, which is expected to serve as a valuable data base to solve questions on genotype-phenotype relations. The mitochondrial (mt) genomes presented here are the first results of the assembly and annotation process for two closely related but eco-morphologically highly distinct Lake Tanganyika cichlids, Petrochromis trewavasae and Tropheus moorii. The genomic sequences comprise 16,588 bp (P. trewavasae) and 16,590 bp (T. moorii), and exhibit the typical mitochondrial structure, with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region. Analyses confirmed that the two species are very closely related with an overall sequence similarity of 96%. We analyzed the newly generated sequences in the phylogenetic context of 21 published labroid fish mitochondrial genomes. Consistent with other vertebrates, the D-loop region was found to evolve faster than protein-coding genes, which in turn are followed by the rRNAs; the tRNAs vary greatly in the rate of sequence evolution, but on average evolve the slowest. Within the group of coding genes, ND6 evolves most rapidly. Codon usage is similar among examined cichlid tribes and labroid families; although a slight shift in usage patterns down the gene tree could be observed. Despite having a clearly different nucleotide composition, ND6 showed a similar codon usage. C-terminal ends of Cox1 exhibit variations, where the varying number of amino acids is related to the structure of the obtained phylogenetic tree. This variation may be of functional relevance for Cox1 synthesis.     

湾鳄(Crocodylus porosus)线粒体基因组全序列结构分析与鳄类系统发生

该文测序了湾鳄的线粒体基因组全序列,全长为16,917bp。湾鳄mtDNA结构与其他脊椎动物相似,由22个tRNA,2个rRNA和13个蛋白质编码基因及1个非编码的控制区(D-loop)所组成。除NADH6和tRNAGln、tRNAAla、tRNAAsn、tRNACys、tRNATyr、tRNASer(UCN)、tRNAGlu、tRNAPro在L-链上编码之外,其余基因均在H-链编码。基因排列顺序与已测序的鳄类一致,这显示了鳄类线粒体基因排列顺序上的保守性。但鳄类线粒体基因排列顺序与脊椎动物的典型排列方式相比,有较大的差异,尤其是tRNAPhe基因的重排、tRNASer-tRNAHis-tRNALeu基因族的排列方式等。湾鳄mtDNA和已测序的鳄类一样,缺失轻链复制起始点(OLR)。基于17种鳄mtDNA控制区保守区,采用PAUP4.0最大简约法(Maximumparsimony,MP)构建MP树,邻接法(Neighbor-joiningmethod,NJ)构建NJ树,结果显示:食鱼鳄(Gavialisgangeticus)和假食鱼鳄(Tomistomaschlegelii)聚为一支后再与鳄科(Crocodylidae)的其他物种形成姐妹群,这与基于食鱼鳄和假食鱼鳄的线粒体全序列的分析结果一致,支持将食鱼鳄并入鳄科的观点。结果还支持非洲窄吻鳄(Crocodyluscataphractus)与鳄属(Crocodylus)构成姐妹群,可以单独划分为属的观点。     

Mutational Events in the Triplo- and Haplo-Lethal Region (83de) of the DROSOPHILA MELANOGASTER Genome

The Drosophila melanogaster genome contains a single region (at 83DE on the polytene chromosome map) for which both heterozygous deficiency and heterozygous duplication are inviable. Seven EMS-induced mutations have been recovered that are viable in combination with a duplication of this region. Two classes of mutations are reported: (1) Mutations that allow survival of flies with either a duplication or a normal third chromosome. These mutations retain Ki, a closely linked marker on the mutagenized chromosome. They fail to complement, and one has been mapped to the vicinity of 83DE. (2) Mutations that allow survival only in heterozygous combination with a duplication and have lost the Ki marker. These mutations represent new deletions of the dose-sensitive information. The possible structural organization of the 83DE region is discussed in light of these two classes of mutations.     

Characterization and Phylogenetic Analysis of the Mitochondrial Genome of Shiraia bambusicola Reveals Special Features in the Order of Pleosporales

Shiraia bambusicola P. Henn. is a pathogenic fungus of bamboo, and its fruiting bodies are regarded as folk medicine. We determined and analyzed its complete mitochondrial DNA sequence (circular DNA molecule of 39,030 bp, G + C content of 25.19%). It contains the typical genes encoding proteins involved in electron transport and coupled oxidative phosphorylation (nad1-6 and nad4L, cob and cox1-3), one ATP synthase subunit (atp6), 4 hypothetical proteins, and two genes for large and small rRNAs (rnl and rns). There is a set of 32 tRNA genes comprising all 20 amino acids, and these genes are evenly distributed on the two strands. Phylogenetic analyses based on concatenated mitochondrial proteins indicated that S. bambusicola clustered with members of the order Pleosporales, which is in agreement with previous results. The gene arrangements of Dothideomycetes species contained three regions of gene orders partitioned in their mitochondrial genomes, including block 1 (nad6-atp6), block 2 (nad1-cox3) and block 3 (genes around rns). S. bambusicola displayed unique special features that differed from the other Pleosporales species, especially in the coding regions around rns (trnR-trnY). Moreover, a comparison of gene orders in mitochondrial genomes from Pezizomycotina revealed that although all encoded regions are located on the same strand in most Pezizomycotina mtDNAs, genes from Dothideomycetes species had different orientations, as well as diverse positions and colocalization of genes (such as cox3, cox1-cox2 and nad2–nad3); these distinctions were regarded as class-specific features. Interestingly, two incomplete copies of the atp6 gene were found on different strands of the mitogenomic DNA, a finding that has not been observed in the other analyzed fungal species. In our study, mitochondrial genomes from Dothideomycetes species were comprehensively analyzed for the first time, including many species that have not appeared in previous reports.     

Reconstruction of the Mitochondrial Genome of the Ancient Horse from the Ashna-Pando Hillfort (Middle Volga)

Russian Journal of Genetics - Reconstruction of the mitochondrial genome of a horse from the Ashna-Pando hillfort (the Sura River basin, Middle Volga, Ulyanovsk oblast, Russia) was performed using...