A deviant mitochondrial genetic code in prymnesiophytes (yellow-algae): UGA codon for tryptophan

The sequence of a representative mitochondrial gene COXI, encoding cytochrome c oxidase subunit I, was determined in five species that cover all the orders of the Prymnesiophyta with the exception of the Pavlovales. Through this analysis, we noticed that the `stop' codon UGA appears frequently and, specifically, at conserved tryptophan (Trp) sites of the gene. We showed these sites were not edited in the corresponding mRNA in one of these species, Isochrysis galbana. Therefore, it is most likely that the UGA codon is used for Trp, and not as a stop codon, in prymnesiophytes. All the analyzed prymnesiophytes made a tight cluster on the COXI phylogenetic tree which includes representative species of green-algae, land plants, yellow-green algae, eustigmatophytes and a red-alga. This suggests a monophyletic origin for the prymnesiophytes. The same deviant genetic code, i.e. UGA for Trp, has also been found in the red-alga, Chondrus crispus. In spite of the fact that this red-alga and the prymnesiophytes, share the same deviant genetic code for Trp, close affinity between the two groups was not statistically supported by the phylogenetic analysis of COXI sequences. Received: 23 December 1996 / 23 June 1997     

UAG is a sense codon in several chlorophycean mitochondria

 The mitochondrial genetic code of those land plants and green algae that have been examined does not deviate from the universal one. A red alga, Chondrus crispus, is the sole reported example throughout the algae that uses a deviant (non-universal) mitochondrial genetic code (UGA=Trp). We have analyzed 366-bp DNA sequences of the gene for mitochondrial cytochrome oxidase subunit I (COXI) from ten chlorophyceaen algae, and detected 3–8 in-frame UAG codons in the sequences of five species. Comparisons of these sequences with those of other algae and land plants have shown that most of the UAG sites in Hydrodictyon reticulatum, Pediastrum boryanum and Tetraedron bitridens correspond to alanine, and those of Coelastrum microporum and Scenedesmus quadricauda to leucine. The three species in which UAG probably codes for alanine are characterized by zoospore formation in asexual reproduction and form a clade in the COXI phylogenetic tree. The two species in which UAG codes for leucine are known to form daughter coenobia and pair in the tree. This is the first report on a deviant mitochondrial genetic code in green algae. Mutational change(s) in the release factor corresponding to UAG would be involved in these code changes. No genetic code deviation has been found in five other species examined. Received: 23 October/6 December 1995     

Complete sequence of the mitochondrial genome of a diatom alga Synedra acus and comparative analysis of diatom mitochondrial genomes

The first two mitochondrial genomes of marine diatoms were previously reported for the centric Thalassiosira pseudonana and the raphid pennate Phaeodactylum tricornutum. As part of a genomic project, we sequenced the complete mitochondrial genome of the freshwater araphid pennate diatom Synedra acus. This 46,657 bp mtDNA encodes 2 rRNAs, 24 tRNAs, and 33 proteins. The mtDNA of S. acus contains three group II introns, two inserted into the cox1 gene and containing ORFs, and one inserted into the rnl gene and lacking an ORF. The compact gene organization contrasts with the presence of a 4.9-kb-long intergenic region, which contains repeat sequences. Comparison of the three sequenced mtDNAs showed that these three genomes carry similar gene pools, but the positions of some genes are rearranged. Phylogenetic analysis performed with a fragment of the cox1 gene of diatoms and other heterokonts produced a tree that is similar to that derived from 18S RNA genes. The introns of mtDNA in the diatoms seem to be polyphyletic. This study demonstrates that pyrosequencing is an efficient method for complete sequencing of mitochondrial genomes from diatoms, and may soon give valuable information about the molecular phylogeny of this outstanding group of unicellular organisms.     

Intracellular distribution of the reductive and oxidative pentose phosphate pathways in two diatoms

Diatoms contribute a large proportion to the worldwide primary production and are particularly effective in fixing carbon dioxide. Possibly because diatom plastids originate from a secondary endocytobiosis, their cellular structure is more complex and metabolic pathways are rearranged within diatom cells compared to cells containing primary plastids. We annotated genes encoding isozymes of the reductive and oxidative pentose phosphate pathways in the genomes of the centric diatom Thalassiosira pseudonana and the pennate diatom Phaeodactylum tricornutum and bioinformatically inferred their intracellular distribution. Prediction results were confirmed by fusion of selected presequences to Green Fluorescent Protein and expression of these constructs in P. tricornutum. Calvin cycle enzymes for the carbon fixation and reduction of 3‐phosphoglycerate are present in single isoforms, while we found multiple isoenzymes involved in the regeneration of ribulose‐1,5‐bisphosphate. We only identified one cytosolic sedoheptulose‐1,7‐bisphosphatase in both investigated diatoms. The oxidative pentose phosphate pathway seems to be restricted to the cytosol in diatoms, since we did not find stromal glucose‐6‐phosphate dehydrogenase and 6‐phosphogluconolactone dehydrogenase isoforms. However, the two species apparently possess a plastidic phosphogluconolactonase. A 6‐phosphogluconolactone dehydrogenase is apparently plastid associated in P. tricornutum and might be active in the periplastidic compartment, suggesting that this compartment might be involved in metabolic processes in diatoms. Abbreviations: AL: aldolase, ATP: adenosine triphosphate, Chl: Chlorophyll, DIC: Normanski differential interference contrast, ER: endoplasmic reticulum, EST: expressed sequence tag, FBA: fructose‐1,6‐bisphosphate aldolase, FBPase: fructose‐1,6‐bisphosphatase, GAPDH: glycerinaldehyd‐3‐phosphate dehydrogenase, GFP: enhanced Green Fluorescent Protein, GPDH: glucose‐6‐phosphate dehydrogenase, GPI: glucose‐6‐phosphate isomerase, HMM: Hidden Markov Models, JGI: Joint Genome Institute, NADPH: nicotinamide adenine dinucleotide phosphate, NN: Neuronal networks, OPP: oxidative pentose phosphate pathway, PCR: Polymerase Chain Reaction, PGDH: 6‐phosphogluconolactone dehydrogenase, PGK: phosphoglycerate kinase, PGL: phosphogluconolactonase, Phatr2: version 2.0 of the Phaeodactylum tricornutum genome, PRK: phosphoribulokinase, RPE: ribulose‐phosphate epimerase, RPI: ribose‐5‐phosphate isomerase, RuBisCO: ribulose‐1,5‐bisphosphate carboxylase/oxygenase, SBPase: sedoheptulose‐1,7‐bisphosphatase, TAL: transaldolase, Thaps3: version 3.0 of the Thalassiosira pseudonana genome, TKL: transketolase, TPI: triosephosphate isomerase, UGGtransferase: UDP glucose‐starch glycosyl transferase. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Transfer RNA genes and the genetic code in Chlamydomonas reinhardtii mitochondria

Summary Only three tRNA genes are present within a sequenced 12.35 kbp region of the 15.8 kbp mtDNA of Chlamydomonas reinhardtii, a unicellular green alga. The corresponding tRNAs, whose anticodons are specific for TGG (Trp), CAA/G (Gln) and ATG (Met) codons, all display conventional secondary structures. The tRNA^Met gene encodes an elongator rather than initiator species. The standard genetic code is used in C. reinhardtii mitochondria, but codon distribution is highly biased: in a collection of six identified protein coding genes, nine codons (including TGA) are not used at all, while four other sense codons occur very infrequently. In spite of the absence of certain codons, a minimum of 23 tRNAs (assuming separate initiator and elongator tRNAs^Met are used) is needed to translate the C. reinhardtii mitochondrial genetic code. It appears unlikely that this minimal tRNA set is encoded by C. reinhardtii mtDNA.     

The occurrence of epibionts of Gordiida (Nematomorpha) in Catamarca,Argentina

The presence of larvae and pupae of the genus Metrichia (Trichoptera, Hydroptilidae), larvae of the genus Macrelmis and Phanocerus (Coleoptera, Elmidae), three diatom genera Achnanthes, Cocconeis, Gomphonema, and some specimens of very small diatoms that could not be determined to species or genus level, were recorded for the first time as epibionts for Chordodes brasiliensis (Gordiida, Nematomorpha). Such epibionts were found on the body surface of this species of hairworms, captured from El Tala stream, Catamarca, Argentina.     

The peculiar distribution of class I and class II aldolases in diatoms and in red algae

Diatom plastids probably evolved by secondary endocytobiosis from a red alga that was up by a eukaryotic host cell. Apparently, this process increased the complexity of the intracellular distribution of metabolic enzymes. We identified genes encoding fructose-bisphosphate aldolases (FBA) in two centric (Odontella sinensis, Thalassiosira pseudonana) and one pennate (Phaeodactylum tricornutum) diatoms and found that four different aldolases are present in both groups: two plastid targeted class II enzymes (FBAC1 and FBAC2), one cytosolic class II (FBA3) and one cytosolic class I (FBA4) enzyme. The pennate Phaeodactylum possesses an additional plastidic class I enzyme (FBAC5). We verified the classification of the different aldolases in the diatoms by enzymatic characterization of isolated plastids and whole cell extracts. Interestingly, our results imply that in plastids of centric and pennate diatoms mainly either class I or class II aldolases are active. We also identified genes for both class I and class II aldolases in red algal EST databases, thus presenting a fascinating example of the reutilization and recompartmentalization of different aldolase isoenzymes during secondary endocytobiosis but as well demonstrating the limited use of metabolic enzymes as markers for the interpretation of phylogenetic histories in algae. The nucleotide sequences have been deposited at Genbank under the accession numbers AY116588, AY191866 and AY212505     

Inheritance of mitochondrial and chloroplast genome markers in backcrosses of Chlamydomonas eugametos x Chlamydomonas moewusii hybrids

Summary Southern blot analysis of AvaI-digested total cellular DNA from the interfertile species Chlamydomonas eugametos and Chlamydomonas moewusii with a coxI mitochondrial gene probe from Chlamydomonas reinhardtii revealed single hybridizing fragments of 5.0 and 3.5 kb, respectively. The transmission of these mitochondrial DNA physical markers along with that of chloroplast genetic markers for resistance to streptomycin and resistance to erythromycin was studied in the fourth backcrosses of F₁ hybrids to one or the other parent. Viability in these backcrosses is high in contrast to the cross C. eugametos x C. moewusii and its reciprocal which are associated with considerable meiotic product lethality. The resulting zygospores were found to transmit the mitochondrial and chloroplast genome markers uniparentally or preferentially from the mating-type-plus parent. Thus the species pair C. eugametos and C. moewusii differs from the pair Chlamydomonas reinhardtii and Chlamydomonas smithii in which mitochondrial genome markers are transmitted uniparentally by the mating-type minus parent, while the chloroplast genome markers are transmitted uniparentally by the opposite parental mating-type (Boynton et al. 1987).     

广州地区自然水域水中常见硅藻形态图谱及其分布特点

目的制作广州地区自然水域水中常见硅藻图谱并分析其分布特点。方法在广州地区自然水域抽取水样,离心沉淀,用硝酸消化处理沉淀物,去酸去盐并涂片镜检,观察、分析其中硅藻的形态并拍摄照片。结果在2010年3～8月间在测水域共检出硅藻50多种,并制作成图谱;硅藻分布特点：水中硅藻的密度或种类构成比例在同源而分隔的两个水域间可存在明显差异,在水体流动性不强的同一片水域中不同局域间也存在差异,存在潮汐性的河段水体中,这种差异相对较小。结论硅藻在自然静溢的水体中分布呈局域性,水体自身的来回流动及受到的外来扰动是使水中硅藻分布趋向均匀分布的重要原因。     

The effect of bacteria on diatom community structure--the 'antibiotics' approach

To investigate the effect of bacteria on diatoms at the community level, sediment samples from an intertidal tropical environment were treated with penicillin (a β-lactam antibiotic that can affect diatoms only through bacteria). Streptomycin (an aminoglycoside) and chloramphenicol, antibiotics that can potentially affect protein synthesis in diatom organelles and photosynthesis, were also used for comparison. The changes in diatom community structure and the resistant and tolerant bacterial fractions were analyzed through microscopy, culture techniques and denaturing gradient gel electrophoresis. The reduction in bacterial abundance when treated with penicillin resulted in suppression of Amphora coffeaeformis, a dominant diatom in the study area. The bacterial community preferred the ‘tolerance’ strategy over ‘resistance’ in response to treatment with penicillin; these changes in bacterial dynamics were probably linked to concurrent changes in diatom community structure. The observations with penicillin differed from those with streptomycin that did not seem to significantly affect diatoms, and chloramphenicol, which consistently inhibited diatoms. Overall, the results of this study highlight the significance of bacteria in structuring benthic diatom communities and call for the inclusion of the ‘antibiotics’ approach in studies addressing diatom-bacterial interactions at the community level.     

Molecular characterization of muscle-parasitizing didymozoids in marine fishes

Classification and identification of muscle-parasitizing didymozoids found in marine fish is difficult because of their novel parasitism and morphology. Recent sequence analysis has helped, but only seven sequences are available. Therefore, the usefulness of molecular methods for differentiation of muscle-parasitizing didymozoids, as well as genetic differences between the muscle and the other site-parasitizing didymozoids are quite unclear. In the present study, six unidentified didymozoid isolates from the trunk muscles of four marine fish species (Diagramma pictum, Plectorhinchus cinctus, Pagrus major and Cypselurus heterurus) were examined genetically using sequence analysis (18S rDNA, 28S rDNA, ITS-2 and coxI). All isolates were placed phylogenetically as a lineage independent of other site-parasitizing didymozoids at 18S rDNA, ITS-2 and coxI. They were grouped into three distinct lineages. The present and the previous unidentified or identified didymozoids from trunk muscles were found to differ clearly for every host species by sequence analysis, suggesting that muscle-parasitizing didymozoids are host-specific. This report is the first describing the molecular characteristics of muscle-parasitizing didymozoids by sequence analysis targeting the nuclear and mitochondrial DNA loci, which is proposed as a superior method for didymozoid differentiation.     

The genetic fine structure of nonsense suppressors in Schizosaccharomyces pombe

Summary Meiotic and mitotic fine-structure maps of two efficient UGA suppressors of Schizosaccharomyces pombe which are known (sup3-e) or inferred (sup9-e) to code for two serine tRNAs carrying the mutant anticodon U*CA (Kohli et al. 1979a, b, Rafalski et al. 1979) are presented. Maps based on spontaneous meiotic, spontaneous mitotic and MMS induced mitotic recombination between the primary site of the anticodon mutation and a number of inactivating second-site mutations are similar. Specific marker effects, which drastically increase the frequency of spontaneous meiotic and mitotic recombination in crosses involving one or the other of four exceptional sites (including the anticodon sites of both sup3-e and sup9-e), disappear when mapping is based on MMS induced mitotic recombination. The meiotic marker effect characterizing the anticodon site of one of the two efficient UGA suppressors (sup3-e) also disappears upon further mutation to an inefficient UAA suppressor allele (sup3-i), as shown by its absence in a fine-structure map based on meiotic recombination between the anticodon mutation of this ochre suppressor allele and a new set of inactivating second-site mutations derived from it.     

First‐impression bias effects on mismatch negativity to auditory spatial deviants

Internal models of regularities in the world serve to facilitate perception as redundant input can be predicted and neural resources conserved for that which is new or unexpected. In the auditory system, this is reflected in an evoked potential component known as mismatch negativity (MMN). MMN is elicited by the violation of an established regularity to signal the inaccuracy of the current model and direct resources to the unexpected event. Prevailing accounts suggest that MMN amplitude will increase with stability in regularity; however, observations of first‐impression bias contradict stability effects. If tones rotate probabilities as a rare deviant (p = .125) and common standard (p = .875), MMN elicited to the initial deviant tone reaches maximal amplitude faster than MMN to the first standard when later encountered as deviant—a differential pattern that persists throughout rotations. Sensory inference is therefore biased by longer‐term contextual information beyond local probability statistics. Using the same multicontext sequence structure, we examined whether this bias generalizes to MMN elicited by spatial sound cues using monaural sounds (n = 19, right first deviant and n = 22, left first deviant) and binaural sounds (n = 19, right first deviant). The characteristic differential modulation of MMN to the two tones was observed in two of three groups, providing partial support for the generalization of first‐impression bias to spatially deviant sounds. We discuss possible explanations for its absence when the initial deviant was delivered monaurally to the right ear.     

Biochemical analysis of encapsulated and non-encapsulated species of<Emphasis Type="Italic"> Trichinella</Emphasis> (Nematoda,Trichinellidae) from cold- and warm-blooded animals reveals a high genetic divergence in the genus

Multilocus enzyme electrophoresis was used to analyse genetic variation in the genus Trichinella. Twenty-eight isolates belonging to eight species and six genotypes were analysed for 12 enzyme systems, producing 19 different phenotypes. According to Jaccards similarity index, the isolates clustered into two main groups, specifically, encapsulated species/genotypes and non-encapsulated species/genotypes. Furthermore, the non-encapsulated species clustered into two other groups: the species infecting mammals and birds (Trichinella pseudospiralis) and those infecting mammals and reptiles (Trichinella papuae and Trichinella zimbabwensis). The encapsulated species/genotypes, which only infect mammals, clustered into four main groups: the cosmopolitan species Trichinella spiralis, the species/genotypes of the temperate regions (Trichinella britovi, Trichinella murrelli , Trichinella T8, and Trichinella T9), the species/genotype of the arctic region (Trichinella nativa and Trichinella T6), and the equatorial species Trichinella nelsoni. These results are consistent with biological, epidemiological, and molecular data, which show a high genetic divergence in this genus.     

Modifiers of ochre suppressors in Saccharomyces cerevisiae that exhibit ochre suppressor-dependent amber suppression

Summary Mutants of Saccharomyces cerevisiae were selected that would interact with ochre (UAA) suppressors so as to allow ochre -suppressor dependant amber (UAG) suppression, but which do not exhibit opal (UGA) suppression. Strains mutant at four distinct loci were isolated, and two of these are recessive mutations while the other two behave as dominants or semidominants. MOS3 has some suppressor activity in the absence of a resident SUP4-o gene and shares other characteristics with previously described omnipotent suppressors. MOS4, mos1 and mos2, on the other hand, exhibit no suppressor activity in the absence of a resident SUP4-o gene but do exhibit suppression of UAG alleles when there is a resident SUP4-o gene. These latter modifier strains do not interact with a SUP4-o gene to suppress UGA alleles. By genetic and physiological criteria the MOS4, mosl, and most mutations appear to be different than previously described allosuppressors or modifiers of suppression.     

Karyotype evolution and phylogenetic relationships of hamsters (Cricetidae, Muroidea, Rodentia) inferred from chromosomal painting and banding comparison

The evolutionary success of rodents of the superfamily Muroidea makes this taxon the most interesting for evolution studies, including study at the chromosomal level. Chromosome-specific painting probes from the Chinese hamster and the Syrian (golden) hamster were used to delimit homologous chromosomal segments among 15 hamster species from eight genera: Allocricetulus, Calomyscus, Cricetulus, Cricetus, Mesocricetus, Peromyscus, Phodopus and Tscherskia (Cricetidae, Muroidea, Rodentia). Based on results of chromosome painting and G-banding, comparative maps between 20 rodent species have been established. The integrated maps demonstrate a high level of karyotype conservation among species in the Cricetus group (Cricetus, Cricetulus, Allocricetulus) with Tscherskia as its sister group. Species within the genera Mesocricetus and Phodopus also show a high degree of chromosomal conservation. Our results substantiate many of the conclusions suggested by other data and strengthen the topology of the Muroidea phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. The derivation of the muroids karyotypes from the putative ancestral state involved centric fusions, fissions, addition of heterochromatic arms and a great number of inversions. Our results provide further insights into the karyotype relationships of all species investigated.     

Association study of COL9A2 with lumbar disc disease in the Japanese population

Lumbar disc disease (LDD) is a common musculo-skeletal disease with strong genetic determinants. In a Finnish population, a single nucleotide polymorphism (SNP) causing an amino-acid substitution (Trp2 allele) in COL9A2, which encodes the α2 (IX) chain of type IX collagen, has been reported to associate with LDD. However, replication studies in different populations have produced controversial results. To further investigate the association of COL9A2 with LDD in Japanese, we examined SNPs in COL9A2, including Trp2, in 470 LDD patients (mean age 35) along with 658 controls (mean age 48). We identified a total of 43 sequence variations in COL9A2. Nine SNPs, including Trp2, were selected and genotyped. After Bonferroni’s correction, none of these SNPs showed association. Unlike observations in the Finnish population, Trp2 was common in Japanese, and no association with LDD was apparent. However, we did see association of a COL9A2 specific haplotype with LDD (P=0.025; permutation test); this association is more significant in patients with severe lumbar disc degeneration (P=0.011). Thus, the association of Trp2 with LDD was not replicated, but COL9A2 susceptibility allele(s) other than Trp2 may be present in Japanese LDD.     

Heterogeneity of the <Emphasis Type="Italic">ospA</Emphasis> gene structure from isolates of <Emphasis Type="Italic">Borrelia garinii</Emphasis> and <Emphasis Type="Italic">Borrelia afzelii</Emphasis> from Western Siberia and Mongolia

In this work, identification and analyses of 48 full-length sequences of the ospA gene isolates of Borrelia garinii and Borrelia afzelii from Western Siberia and Mongolia has been made. It was shown that B. garinii isolates was of its high genetic heterogeneity of the ospA gene. Four genetic groups of the ospA gene from the Ixodes persulcatus tick collected in of Western Siberia and Mongolia were defined. The basic differences in the genetic variants of the ospA gene considered are seen in regions which code for antibody determinants of thhe OspA protein.