A novel pex2 mutant: catalase-deficient but temperature-sensitive PTS1 and PTS2 import

We searched for Chinese hamster ovary (CHO) cell mutants defective in peroxisome biogenesis by using peroxisome targeting sequence (PTS) of Pex3p (amino acid residues 1-40)-fused enhanced green fluorescent protein (EGFP). From mutagenized wild-type CHO-K1 cells stably expressing rat Pex2p and Pex3p(1-40)-EGFP, cell colonies resistant to the 9-(1(')-pyrene)nonanol/ultraviolet treatment were examined for intracellular location of peroxisomal proteins, including EGFP chimera, catalase, and matrix proteins with PTS types 1 and 2. One clone, ZPEG309, showed a distinct phenotype: import defect of catalase, but normal transport of PTS1 and PTS2 proteins at 37 degrees C. PTS1 and PTS2 import was abrogated when ZPEG309 was cultured at 39 degrees C. Genetic defect of ZPEG309 was a nonsense point mutation in a codon for Arg50 in CHO PEX2 and a mutation resulting in a C-terminal truncation of the introduced rat Pex2p. Therefore, ZPEG309 is a novel pex2, catalase-deficient mutant with temperature-sensitive PTS1 and PTS2 import.     

The Candida albicans UBI3 gene encoding a hybrid ubiquitin fusion protein involved in ribosome biogenesis is essential for growth

We have constructed a conditional null mutant Candida albicans strain for the UBI3 gene which encodes a ubiquitin fusion protein involved in ribosome biogenesis. A one-step gene disruption procedure, using the plasmid pCaDis, was designed to place the second copy of the UBI3 gene under the control of the tightly regulated MET3 promoter in a C. albicans heterozygous strain (UBI3/Deltaubi3::hisG), previously isolated in the first step of the ura-blaster protocol. Analysis of the conditional null mutant in repressing and inducing conditions indicates that UBI3 is an essential gene whose expression is required for growth of C. albicans.     

Chloroplast DNA restriction site variation and phylogeny of the Berberidaceae

Comparative restriction site mapping of the chloroplast genome was performed to examine phylogenetic relationships among 27 species representing 16 genera of the Berberidaceae and two outgroups. Chloroplast genomes of the species included in this study showed no major structural rearrangements (i.e., they are collinear to tobacco cpDNA) except for the extension of the inverted repeat in species of Berberis and Mahonia. Excluding several regions that exhibited severe length variation, a total of 501 phylogenetically informative sites was mapped for ten restriction enzymes. The strict consensus tree of 14 equally parsimonious trees indicated that some berberidaceous genera (Berberis, Mahonia, Diphylleia) are not monophyletic. To explore phylogenetic utility of different parsimony methods phylogenetic trees were generated using Wagner, Dollo, and weighted parsimony for a reduced data set that included 18 species. One of the most significant results was the recognition of the four chromosomal groups, which were strongly supported regardless of the parsimony method used. The most notable difference among the trees produced by the three parsimony methods was the relationships among the four chromosomal groups. The cpDNA trees also strongly supported a close relationship of several generic pairs (e.g., Berberis-Mahonia, Epimedium-Vancouveria, etc.). Maximum likelihood values were computed for the four different tree topologies of the chromosomal groups, two Wagner, one Dollo, and one weighted topology. The results indicate that the weighted tree has the highest likelihood value. The lowest likelihood value was obtained for the Dollo tree, which had the highest bootstrap and decay values. Separate analyses using only the Inverted Repeat (IR) region resulted in a tree that is identical to the weighted tree. Poor resolution and/or support for the relationships among the four chromosomal lineages of the Berberidaceae indicate that they may have radiated from an ancestral stock in a relatively short evolutionary time.     

The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group

Phylogenetic resolution is often low within groups of recently diverged taxa due to a paucity of phylogenetically informative characters. We tested the relative utility of seven noncoding cpDNA regions and a pair of homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons (Gossypium) as a model system. The five tetraploid species of Gossypium are a monophyletic assemblage derived from an allopolyploidization event that probably occurred within the last 0.5-2 million years. Previous analysis of cpDNA restriction site data provided only partial resolution within this clade despite a large number of enzymes employed. We sequenced three cpDNA introns (rpl16, rpoC1, ndhA) and four cpDNA spacers (accD-psaI, trnL-trnF, trnT-trnL, atpB-rbcL) for a total of over 7 kb of sequence per taxon, yet obtained only four informative nucleotide substitutions (0.05%) resulting in incomplete phylogenetic resolution. In addition, we sequenced a 1.65-kb region of a homoeologous pair of nuclear-encoded alcohol dehydrogenase (Adh) genes. In contrast with the cpDNA sequence data, the Adh homoeologues yielded 25 informative characters (0.76%) and provided a robust and completely resolved topology that is concordant with previous cladistic and phenetic analyses. The enhanced resolution obtained using the nuclear genes reflects an approximately three- to sixfold increase in nucleotide substitution rate relative to the plastome spacers and introns.     

Characterization of a cDNA encoding a novel plant poly(A) polymerase

We have isolated cDNA clones encoding a novel factor (PAP-I) that is a component of a multi-subunit poly(A) polymerase from pea seedlings. The encoded protein, when isolated from appropriately engineered Escherichia coli, was active as a poly(A) polymerase, either with an associated RNA binding cofactor (PAP-III) or with free poly(A) as an RNA substrate. The latter observation indicates that PAP-I is in fact a poly(A) polymerase. PAP-I bore a striking resemblance to an as yet uncharacterized cyanobacterial protein. This observation suggested a possible chloroplast localization for PAP-I. This hypothesis was tested and found to be substantiated; immunoblot analysis identified PAP-I in chloroplast but not nuclear extracts. Our results suggest that PAP-I is a component of the machinery that adds poly(A) to chloroplast RNAs.     

EVIDENCE FOR A LACK OF PHOTOSYSTEM SEGREGATION IN CHLAMYDOMONAS REINHARDTII (CHLOROPHYCEAE)

The distribution of photosystems I and II (PSI and PSII) in cells of Chlamydomonas reinhardtii Dangeard was studied by immunogold electron microscopy using cultures grown autotrophically at moderate irradiance and harvested in the middle of the light period. Sections of Lowicryl-embedded cells were labeled with monospecific heterologous antisera raised against the reaction center proteins of PSI (CP1-e) or the core antenna proteins of PSII (CP40 and CP47). All three antisera labeled both the appressed and the nonappressed thylakoid membranes at essentially similar densities. Labeling with both PSI and PSII antisera was slightly more concentrated over the outer nonappressed membranes of the thylakoid bands (1.7- to 2.4-fold with anti-CP1- e and 1.5- to 1.8-fold with anti-CP47 and anti-CP40). However, since appressed membranes comprised 73% of the total thylakoid membranes, 50%–62% of the PSI and 58%–65% of the PSII labeling were localized on appressed membranes. We conclude that photosystem distribution in C. reinhardtii is similar to that reported for other algae and different from the lateral heterogeneity observed in higher plants.     

Paternally biased cpDNA inheritance in Turnera ulmifolia (Turneraceae)

We end-labeled Hin fI restriction digests of a PCR-amplified plastid encoded gene, the large subunit of ribulose bisphosphate carboxylase, to investigate patterns of cpDNA inheritance in Turnera ulmifolia. A total of 70 progeny from crosses among plants taken from ten populations revealed varying patterns of inheritance. A majority of progeny inherited the paternal cpDNA (64%), while 19% exhibited maternal and 17% biparental inheritance. Eight variegated progeny showed biparental inheritance and were analyzed in greater detail. We extracted and analyzed the cpDNA content of light- vs. dark- green leaf sectors from these plants. The results showed that vegetative segregation of cpDNA had occurred for seven of the eight plants.     

Ingestion and digestion of epilithic algae by larval insects in a heavily grazed montane stream

1. Epilithic algae grown on elevated or non-elevated ceramic tiles were exposed (to produce assemblages with different grazing histories) in a heavily grazed, montane stream in New Mexico, U.S.A. to Ameletus nymphs (Ephemeroptera) and Ecclisomyia larvae (Trichoptera) and the algal composition in insect faeces was compared to that on the tiles. Differences in grazing and digestion efficiency between grazers were then assessed and also differences in susceptibility to ingestion and digestibility among common algae. 2. Ordination of tile and faecal samples, using the relative abundance of common algae, revealed that: (i) algal assemblages on elevated vs. non-elevated tiles differed only slightly; (ii) the taxonomic composition of algae in faeces of both caddis and mayflies differed substantially from that on the tiles, indicating low grazing efficiency for some algal taxa; and (iii) the algal composition of faeces produced by caddis larvae and mayflies was similar, indicating little difference in grazing efficiency between them. However, some algal taxa were more susceptible to ingestion by caddisfly larvae when occurring on elevated tiles than on non-elevated tiles, suggesting that previous exposure to caddis grazing influenced assemblage attributes. 3. Although Ameletus and Ecclisomyia differed little in grazing efficiency, the percentage of diatoms that were dead after passage through the gut was greatest in the mayfly treatment, suggesting that mayflies digested diatoms more efficiently than the caddis. Analyses of differences in the condition of chloroplasts within diatoms in tile and faecal samples showed that losses of ’live‘ diatom cells (i.e. those containing full chloroplasts) during gut passage through mayflies equalled the increase, in faeces, of ’dead‘ (empty frustules) cells of all common diatoms. In contrast, some diatoms were digested inefficiently by caddis larvae. 4. Algae on elevated tiles contained a higher proportion of dead diatoms than those on non-elevated tiles, possibly because mayflies visited raised tiles more often and, consequently, ingested and defaecated cells at a higher rate in the absence of caddis larvae. Moreover, diatom taxa differed in the percentage of cells that were dead within tile assemblages, with populations of typically grazer-resistant taxa (e.g. Achnanthidium minutissimum, Planothidium lanceolatum and Cocconeis placentula var. euglypta) containing significantly more dead cells than grazer-susceptible taxa [e.g. small, chain-forming Fragilaria (= Staurosirella)]. This result suggests that a trade-off exists between ingestion vs. digestion resistance of microalgae. Both the ingestion and digestion efficiency of algivorous macroinvertebrates could influence the structure and function of algal assemblages. In heavily grazed systems, where algal cells are probably processed through grazer guts repeatedly, differential resistance to digestion among algae may be particularly important.