Active transcription of the pseudogene for subunit 7 of the NADH dehydrogenase in Marchantia polymorpha mitochondria

A pseudogene, ψnad7, which has significant sequence similarity (66.7% amino acid identity) with the bovine nuclear gene for a 49 kDa subunit of the NADH dehydrogenase (NADH:ubiquinone oxidoreductase, EC 1.6.99.3), has been identified on the mitochondrial genome of the liverwort Marchantia polymorpha. The predicted coding region, which includes six termination codons, is actively transcribed into RNA molecules of 16 and 9.6 kb in length, but RNA splicing products were not detected in the liverwort mitochondria. Genomic DNA blot analysis and RNA blot analysis using poly(A)⁺ RNA suggest that a structurally related nuclear gene encodes the mitochondrial ND7 polypeptide. These results imply that this ψnad7 is a relic of a gene transfer event from the mitochondrial genome into the nuclear genome during mitochondrial evolution in M. polymorpha.     

Interorganellar gene transfer in bryophytes: the functional nad7 gene is nuclear encoded in Marchantia polymorpha

The nad7 gene, encoding subunit 7 of NADH dehydrogenase, is mitochondrially encoded in seed plants. In the liverwort, Marchantia polymorpha, only a pseudogene is located in the mitochondrial genome. We have now identified the functional nad7 gene copy in the nuclear genome of Marchantia, coding for a polypeptide of 468 amino acids. The nuclear-encoded nad7 has lost the two group II introns present in the mitochondrial pseudogene copy. Instead, a typical nuclear intron is found to split an exon encoding the presumptive mitochondrial targeting signal peptide and the mature subunit 7 of NADH dehydrogenase. These results suggest that RNA-mediated gene transfer from the mitochondrial into the nuclear genome occurs not only in seed plants but also in bryophytes. Received: 11 March 1997 / Accepted: 20 August 1997     

Interorganellar gene transfer in bryophytes: the functional nad7 gene is nuclear encoded in Marchantia polymorpha

The nad7 gene, encoding subunit 7 of NADH dehydrogenase, is mitochondrially encoded in seed plants. In the liverwort, Marchantia polymorpha, only a pseudogene is located in the mitochondrial genome. We have now identified the functional nad7 gene copy in the nuclear genome of Marchantia, coding for a polypeptide of 468 amino acids. The nuclear-encoded nad7 has lost the two group II introns present in the mitochondrial pseudogene copy. Instead, a typical nuclear intron is found to split an exon encoding the presumptive mitochondrial targeting signal peptide and the mature subunit 7 of NADH dehydrogenase. These results suggest that RNA-mediated gene transfer from the mitochondrial into the nuclear genome occurs not only in seed plants but also in bryophytes.     

Cotranscriptional expression of mitochondrial genes for subunits of NADH dehydrogenase, nad5, nad4, nad2, in Marchantia polymorpha

Three genes for the subunits of the NADH dehydrogenase (nad5, nad4, and nad2) are tandemly clustered on the liverwort mitochondrial genome. Their gene products showed high levels of amino acid sequence identity with the corresponding subunits from higher plant mitochondria (82.8–84.4%), and significant levels of identity with those from liverwort chloroplast (32.0–33.5%), Podospora anserina mitochondria (21.4–45.9%), and human mitochondria (18.4–27.9%). In addition, these three subunits from liverwort mitochondria have conserved amino acid residues in their central regions. The gene nad5 is interrupted by a 672 by group I intron, while genes nad4 and nad2 are interrupted by group II introns of 899 by and 1418 bp, respectively. Northern blot analysis using exon-intron specific probes indicated that these three genes are transcribed as a single precursor mRNA of 9.6 kb in length and are processed into mature mRNA molecules in liverwort mitochondria. Several regions of this nad gene cluster are repeated in the liverwort mitochondrial genome.Communicated by R.G. Herrmann     

Organization of Methanobacterium thermoautotrophicum bacteriophage psi M1 DNA

Summary M1 is a virulent bacteriophage of Methanobacterium thermoautotrophicum strain Marburg. Restriction enzyme analysis of the linear, 30.4 kb phage DNA led to a circular map of the 27.1 kb M1 genome. M1 is thus circularly permuted and exhibits terminal redundancy of approximately 3 kb. Packaging of M1 DNA from a concatemeric precursor initiates at the pac site which was identified at coordinate 4.6 kb on the circular genome map. It proceeds clockwise for at least five packaging rounds. Headful packaging was also shown for M2, a phage variant with a 0.7 kb deletion at coordinate 23.25 on the map.     

Structural and Functional Rearrangements of Mesophyll as a Probable Basis for the Cytokinin-Dependent Assimilate Translocation in Detached Leaves

The effects of benzyladenine (BA) on the mesophyll functioning, such as osmotic potential (), the effect of the inhibitors of ⁺-ATPase on the influx of ¹⁴C-sucrose, the direction of carbon metabolism, and the rate of dark respiration, were followed in the detached leaves of pumpkin (Cucurbita pepo L.) and broad beans (Vicia faba L.). BA elevated and established a gradient of (_p) between the treated and untreated leaf regions. The inhibitors of H⁺-ATPase did not affect the BA-induced influx of ¹⁴C-sucrose. The changes were accompanied with the elevated synthesis of starch and other polymeric compounds and the diminished synthesis of the substances of relatively low molecular weight. The stimulation of dark respiration was short and inconsiderable. The author concludes that the BA-induced transport was a passive process related to a increase. Leaf expansion accompanied by the synthesis of high-molecular-weight substances essential for cell growth and by starch synthesis apparently increased the sink capacity of the BA-treated detached leaves. The diminished efflux from the leaf blade was probably related to a lowered level of the transportable carbon compounds restricting their entry into the phloem. The influx induction could result from the activation of growth and metabolic processes, the decline in the number of organic molecules per cell volume unit, and the development of _p between the source and sink leaf regions.     

DNA polymorphisms in the ψβ1- and β-globin gene regions in asian macaques

DNA polymorphisms in the ₁--globin gene region in nine Asian macaques(Macaca fuscata, M. mulatta, M. nemestrina, M. cyclopis, M. fascicularis, M. arctoides, M. radiata, M. maura, andM. assamensis) were examined using several restriction endonucleases and the human ₁, IVS2, and IVS2 probes. TheBamHI site 3 to the -globin gene was polymorphic inM. fuscata andM. mulatta, while the HincII site and the EcoRI site in the ₁-globin gene region was highly polymorphic inM. fuscata andM. mulatta, respectively. These polymorphic sites also seem to be present in other Asian macaques. The present study of the polymorphism at theBamHI site 3 to the -globin gene in Asian macaques supports, at the nuclear DNA level, the idea that thefascicularis group includingM. fuscata, M. mulatta, M. cyclopis, andM. fascicularis is different from other Asian macaque groups.This study was supported in part by the Cooperation Research Program of the Primate Research Institute, Kyoto University.     

Using bacteria to analyze sequences involved in chloroplast gene expression

The complete nucleotide sequence of chloroplast DNA from a liverwort, Marchantia polymorpha has made clear the entire gene organization of the chloroplast genome. Quite a few genes encoding components of photosynthesis and protein synthesis machinery have been identified by comparative computer analysis. Other genes involved in photosynthesis, respiratory electron transport, and membrane-associated transport in chloroplasts were predicted by the amino acid sequence homology and secondary structure of gene products. Thirty-three open reading frames in the liverwort chloroplast genome remain unidentified. However, most of these open reading frames are also conserved in the chloroplast genomes of two species, a liverwort, Marchantia polymorpha, and tobacco, Nicotiana tabacum, indicating their active functions in chloroplasts.Abbreviations bp base pair - kDa kilodalton - IR inverted repeat - ORF open reading frame - DALA -aminolevulinate     

Leaf osmotic potentials of 104 plant species in relation to habitats and plant functional types in Hunshandak Sandland,Inner Mongolia,China

Leaf osmotic potentials ( _s) of 104 plant species from different habitats, i.e., fixed sand dunes, lowland and wetlands in Hunshandak Sandland, Inner Mongolia, China, were investigated. The values of _s were strongly species-specific, and varied from –6.54 MPa ( Caragana microphylla), to –0.44 MPa ( Digitaria ischaemum); 75% of plants investigated had _s from –1.01 to –3.0 MPa. Shrubs were found to have the lowest _s, with an average value of –3.19 MPa, while grasses showed the highest _s. The order of plant _s is shrubs<trees<grasses. The result may relate to anatomical features of shrubs. C₄ photosynthetic pathway plants showed lower _s values. The _s values of 104 species were negatively correlated with their rooting depths ( r ²=0.42; P <0.001). High hydraulic pressure resulting from the deep roots may well explain this trend. The value of _s increased as the environment became wetter, ranging from –0.79 MPa in wetlands to –2.09 MPa in fixed sand dunes. Although soil salt content was higher in wetlands, we did not find any effect on _s.An erratum to this article can be found at     

Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome.

Analysis of the mitochondrial DNA of a liverwort Marchantia polymorpha by electron microscopy and restriction endonuclease mapping indicated that the liverwort mitochondrial genome was a single circular molecule of about 184,400 base-pairs. We have determined the complete sequence of the liverwort mitochondrial DNA and detected 94 possible genes in the sequence of 186,608 base-pairs. These included genes for three species of ribosomal RNA, 29 genes for 27 species of transfer RNA and 30 open reading frames (ORFs) for functionally known proteins (16 ribosomal proteins, 3 subunits of H(+)-ATPase, 3 subunits of cytochrome c oxidase, apocytochrome b protein and 7 subunits of NADH ubiquinone oxidoreductase). Three ORFs showed similarity to ORFs of unknown function in the mitochondrial genomes of other organisms. Furthermore, 29 ORFs were predicted as possible genes by using the index of G + C content in first, second and third letters of codons (42.0 +/- 10.9%, 37.0 +/- 13.2% and 26.4 +/- 9.4%, respectively) obtained from the codon usages of identified liverwort genes. To date, 32 introns belonging to either group I or group II intron have been found in the coding regions of 17 genes including ribosomal RNA genes (rrn18 and rrn26), a transfer RNA gene (trnS) and a pseudogene (psi nad7). RNA editing was apparently lacking in liverwort mitochondria since the nucleotide sequences of the liverwort mitochondrial DNA were well-conserved at the DNA level.     

Altered genetic code in Paramecium mitochondria: Possible evolutionary trends

Summary The sequence and presumptive structure of a tRNA trp gene from Paramecium tetraaurelia are given. The gene is located 1,500 bp downstream from the 13S rRNA gene, in about the middle of the genome. Paramecium tRNA trp has a completely normal TC loop and stem, however its anticodon (UCA) constitutes an alteration in the universal genetic code, similar to those seen in fungal and mammalian mitochondria. Most features of Paramecium tRNA trp resemble other mitochondrial counterparts; however, its sequence is more homologous to the unaltered tRNA trp (anticodon CCA) from E. coli. Paramecium mitochondria may resemble a primitive stage of organelle evolution.     

Relationships between leaf water status and transpiration of cowpea with progressive soil drying

Summary It was previously reported that leaf water status of cowpea (Vigna unguiculata) exhibited only small changes with progressive soil drying over extended periods of time. In these studies, under field conditions, it was demonstrated that when soil water was not limiting, xylem pressure potential ( _x ) exhibited a linear relationship with transpirational flux density with no obvious hysteresis. With progressive soil drying, values of _x and transpiration rate fell below the regression line established for nonlimiting soil conditions. It is proposed that paired measurements of _x and transpirational flux density made between midday and sunset can provide a measure of the extent to which soil conditions are limiting water uptake. The relation between _x and transpiration exhibits a family of curves, with more negative slopes and decreases in maximum transpiration rate indicating progressive limitation due to soil drying.     

Carbon isotope discrimination and foliar nutrient status of Larrea tridentata (creosote bush) in contrasting Mojave Desert soils

We investigated the relationships between foliar stable carbon isotope discrimination (), % foliar N, and predawn water potentials (_pd) and midday stomatal conductance (g _s) of Larrea tridentata across five Mojave Desert soils with different age-specific surface and sub-surface horizon development and soil hydrologies. We wished to elucidate how this long-lived evergreen shrub optimizes leaf-level physiological performance across soils with physicochemical characteristics that affect the distribution of limiting water and nitrogen resources. We found that in young, coarse alluvial soils that permit water infiltration to deeper soil horizons, % foliar N was highest and , g _s and _pd were lowest, while %N was lowest and , g _s and _pd were highest in fine sandy soils; Larrea growing in older soils with well-developed surface and sub-surface horizons exhibited intermediate values for these parameters. showed negative linear relationships with % N (R ²=0.54) and a positive relationship with _pd (R ²=0.14). Multiple regression analyses showed a strong degree of multicolinearity of g _s and with _pd and N, suggesting that soil-mediated distribution of co-limiting water and nitrogen resources was the primary determinant of stomatal behavior, which is the primary limitation to productivity in this shrub. These findings show that subtle changes in the soil medium plays a strong role in the spatial and temporal distribution and utilization of limiting water and nitrogen resources by this long-lived desert evergreen, and that this role can be detected through carbon isotope ratios.     

Complete nucleotide sequence of the mitochondrial DNA from a liverwort,Marchantia polymorpha

Libraries of cosmid and plasmid clones covering the entire region of mtDNA from the liverwortMarchantia polymorpha were constructed. These clones were used for the determination of the complete nucleotide sequence of the liverwort mtDNA totally 186,608 bp (GenBank no. M68929) and including genes for 3 species of ribosomal RNAs, 29 genes for 27 species of transfer RNAs, and 30 genes for functionally known proteins (16 ribosomal proteins, 3 subunits of cytochromec oxidase, apocytochromeb protein, 3 subunits of H⁺-ATPase, and 7 subunits of NADH ubiquinone oxidoreductase). The genome also contains 32 unidentified open reading frames. Thus the complete nucleotide sequences from both chloroplast and mitochondrial genomes have been determined in the same organism. Plasmid clones are available upon the request. Gene names are represented according to Lonsdale and Leaver (1988) with modifications recommended by Lonsdale (personal communication).     

Chloroplast volume: cell water potential relationships and acclimation of photosynthesis to leaf water deficits

Studies were undertaken to determine if there is an association between nonstomatally-mediated acclimation of photosynthesis to low water potential (w) and the maintenance of chloroplast volume during water stress. Spinach plants either kept well watered throughout their growth (non-acclimated), or subjected to water stress such that leaf w dropped to -1.5 megapascals (MPa) and then were rewatered (acclimated) were subjected to drought episodes. During these stress periods, photosynthesis was maintained to a greater extent in acclimated plants as compared to non-acclimated plants at w below -1 MPa.Estimates of internal leaf [CO₂] suggested that photosynthetic acclimation to low w was not primarily due to altered stomatal response. As w dropped from initial values, a decline in steady state levels of ribulose 1,5-bisphosphate (RuBP) occurred in both non-acclimated and acclimated plants. RuBP decline was less severe in acclimated plants.Low w effects on chloroplast volume in non-acclimated and acclimated plants were estimated by measuring the volume of intact chloroplasts isolated from plants in solutions which were made isotonic to declining leaf osmotic potential during the drought episodes. Chloroplast volume was maintained to a greater extent at low w in acclimated, as compared with non-acclimated plants. Although substantial osmotic adjustment occurred in both non-acclimated and acclimated plants, the extent of osmotic adjustment was the same. These data were interpreted as supporting the hypothesis that cellular-level acclimation to low w is associated with chloroplast volume maintenance, and this physiological acclimation is correlated with enhanced photosynthetic capacity of the leaf at low w.Abbreviations [CO₂]_i internal leaf CO₂ concentration - s osmotic potential - RWC relative water content - RuBP ribulose 1,5-bisphosphate - w water potential     

Identification of a novel cytoplasmic male sterile line M2BS induced by partial-length <Emphasis Type="Italic">HcPDIL5-2a</Emphasis> transformation in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

A cytoplasmic male sterile line (designated as M2BS) was obtained from an indica rice maintainer M2B induced by partial-length HcPDIL5-2a (Hibiscus cannabinus protein disulfide isomerase-like) transformation. The anther of M2BS was short, slender, hygrophanous, and fissured. I2-KI staining method showed that there was typical and spherical abortion in pollen grains. M2BS was found abortive at middle and late stage of monocyte by the modified carbol fuchsin stained observation and paraffin section observation. The tapetum was observed pre-degenerated in M2BS. Hereditary analysis indicated that the male sterility of M2BS was a maternally inherited inability after six backcross generations with M2B and the combinations of M2BS hybridized with other two male fertile materials. The M2BS could be affirmed a cytoplasmic male sterile (CMS) type. Moreover, it was a transgenic plant confirmed by PCR, Southern blot and RT-PCR detection. M2BS could be distinguished from M2B and its CMS line M2A by RFLP analysis. The overall mitochondrial genome sequencing results showed, that in M2BS, the main differences of mitochondrial gene sequence were located in nad4, nad5, nad7, orf194 and intergenic region, relatively to those of M2A. The obtained results indicate that M2BS is a novel cytoplasmic male sterile line.     

Water relations and growth of shrubs before and after fire in a semi-arid woodland

Summary Plant water relations and shoot growth rate of shrubs resprouting after fire or unburnt were measured in a semi-arid poplar box (Eucalyptus populnea) shrub woodland of eastern Australia. In vegetation unburnt for about 60 years, the dawn xylem water potential (_x) of the dominant shrub species was about-1.0 MPa when the soil was wet and-8.0 MPa when the soil was very dry. At any one time, the dominant shrub species,Eremophila mitchellii, E. sturtii, Geijera parviflora andCassia nemophila, were similar in _x butAcacia aneura andDodonaea viscosa were consistently higher in _x than this group when the soil was moist and lower when the soil was dry. The dominant tree species,Eucalyptus populnea andE. intertexta, appeared to have access to additional water beneath the hardpan which is located 60–80 cm below the surface. When shrubs were under extreme water stress (_x of-8 MPa), the trees had a _x of-3 to-3.6 MPa. Following a fire, both _x and leaf stomatal conductance (g _s) of resprouting shrubs were higher for about 5 years than comparable-aged unburnt vegetation, with relative differences in _x increasing with drought stress. Elongation rate of resprouts was positively linked to prefire shrub height in 3 of 4 species. However, shrubs resprouting after high intensity fires had substantially higher rates of shoot elongation than after low intensity fires which were in turn higher than for foliar expansion of unburnt shrubs. It is concluded that the growth rate of resprouting shrubs is primarily determined by physiological/ morphological factors associated with plant size but is also assisted by greater availability of water and possibly nutrients for a period after fire.     

Bryophyte 5S rDNA was inserted into 45S rDNA repeat units after the divergence from higher land plants

The 5S ribosomal RNA genes (5S rDNA) are located independently from the 45S rDNA repeats containing 18S, 5.8S and 26S ribosomal RNA genes in higher eukaryotes. Southern blot and fluorescence in situ hybridization analyses demonstrated that the 5S rDNAs are encoded in the 45S rDNA repeat unit of a liverwort, Marchantia polymorpha, in contrast to higher plants. Sequencing analyses revealed that a single-repeat unit of the M. polymorpha nuclear rDNA, which is 16103 bp in length, contained a 5S rDNA downstream of 18S, 5.8S and 26S rDNA. To our knowledge, this is the first report on co-localization of the 5S and 45S rDNAs in the rDNA repeat of land plants. Furthermore, we detected a 5S rDNA in the rDNA repeat of a moss, Funaria hygrometrica, by a homology search in a database. These findings suggest that there has been structural re-organization of the rDNAs after divergence of the bryophytes from the other plant species in the course of evolution.