Reduction of Paraoxonase Expression Followed by Inactivation across Independent Semiaquatic Mammals Suggests Stepwise Path to Pseudogenization

Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages-Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding-level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best associated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.

A large open reading frame (orf1995) in the chloroplast DNA of Chlamydomonas reinhardtii encodes an essential protein

An open reading frame potentially encoding a protein of 1995 amino acids (orf1995) has been found in the chloroplast genome of the green alga Chlamydomonas reinhardtii. Besides having a short hydrophobic N-terminal domain with five putative transmembrane helices, the predicted orf1995 product is highly basic. orf1995 might be a homologue of the ycf1 gene in land plants, whose function has not yet been determined. Mutants of C. reinhardtii transformed with a disruption of orf1995 remain heteroplasmic for the wild-type and disrupted alleles of this gene, indicating that the orf1995 product is essential for cell survival.

Survival following traumatic rupture of the heart in a child

Blunt force trauma to the chest can result in rupture of the heart. We report the youngest survivor of this injury, followed by a literature review, description of the epidemiology, and mechanism and guidelines for diagnosis and aggressive management.

Transcription and translation of the chloroplast atpB-gene and assembly of ATP synthase subunit beta

In vitro transcription and subsequent translation of the cloned Chlamydomonas chloroplast atpB gene was used to study assembly of ATP synthase. Translation in the presence of thylakoids resulted in association of the beta subunit with the membrane. The in vitro synthesized polypeptide bound to the membrane copurified with CF1 on sucrose gradients. This provides more evidence for the self-assembly of CF1.

Translational regulation of chloroplast gene expression during the light-dark cell cycle of Chlamydomonas: evidence for control by ATP/energy supply

In Chlamydomonas reinhardtii growing synchronously under a light-dark cycle, the major chloroplast mRNAs are constitutively present but are translated only during the light period. We show that translation of these mRNAs can be induced during the normal dark period by light or by acetate and the induction is blocked by an inhibitor of ATP synthesis, CCCP. Moreover, ATP levels in synchronous cells were found to be 2-5-fold lower during the dark than in the light period; the administration of acetate or light at the mid-dark period increased the ATP level 2-3-fold. These results exclude cell-cycle mediated control and suggest that the regulation of chloroplast translation in light-dark grown Chlamydomonas is mediated, at least in part, by ATP levels.

Cell cycle-dependent transcriptional and post-transcriptional regulation of chloroplast gene expression in Chlamydomonas reinhardtii

The regulated expression of five chloroplast genes in Chlamydomonas reinhardtii during a 24 hour cell cycle (12 hours light, 12 hours dark) was analyzed. Transcription rates of the genes encoding the two reaction center proteins of Photosystem I (psaA, psaB), the subunits alpha and beta (atpA, atpB) of chloroplast ATP synthase and for chloroplast elongation factor tu (EF-tu) were measured during the cell cycle. All genes are maximally transcribed at the beginning of the light period. Transcription was induced before the onset of illumination by a light-independent mechanism. Transcript abundance of the same genes during the cell cycle was determined by quantification of Northern blots hybridized with gene-specific probes. The atpA, atpB and psaB mRNAs were most abundant in the first 6 hours of the light period and decreased to about 15% of maximum in the dark. The abundance of psaA mRNA showed less variation and was maximal around the middle of the cell cycle. The EF-tu mRNA showed a maximum early in the light period, but decreased to almost undetectable levels in the second half of the light period. Because of the similar transcriptional patterns observed, the differential steady state levels of these chloroplast transcripts appeared to be regulated at the post-transcriptional level.

Synthesis of EF-Tu and distribution of its mRNA between stroma and thylakoids during the cell cycle of Chlamydomonas reinhardii

In Chlamydomonas reinhardii the elongation factor EF-Tu is encoded in the chloroplast DNA. We identified EF-Tu in the electrophoretic product pattern of chloroplast-made proteins and showed that this protein is only synthesized in the first half of the light period in synchronized cells. The newly synthesized EF-Tu contributed little to the almost invariable content of EF-Tu in chloroplasts during the light period of the cell cycle. However, increasing cell volume and the lack of EF-Tu synthesis in the second half of the light period led to a decrease in the concentration of EF-Tu in chloroplasts. At different times in the vegetative cell cycle, the RNA was extracted from whole chloroplasts and from free and thylakoid-bound chloroplast polysomes. The content of mRNA of EF-Tu in chloroplasts and the distribution between stroma and thylakoids were determined. During the light period, the content of the mRNA for EF-Tu varied in parallel to the rate of EF-Tu synthesis. However, in the dark, some mRNA was present even in the absence of EF-Tu synthesis. Most of the mRNA was bound to thylakoids during the whole cell cycle. This suggests that synthesis of EF-Tu is associated with thylakoid membranes.

In vitro synthesis, assembly and function of a photosynthetic membrane protein

Cell-free translation of Chlamydomonas reinhardtii RNA in the presence of photosynthetic membranes resulted in association of the herbicide binding (Qb) protein with membranes. Incubation of recovered membranes with high salt did not extract the polypeptide from membranes. Tryptic digestion of in vivo labeled membranes or membranes recovered from in vitro translation mixtures showed that Qb had similar orientation. In vitro translation in the presence of chloroplast membranes from cells exposed to high light intensity restored the membrane associated kinase activity lost by photoinhibition. Thus, in vitro synthesis resulted in functional integration of the Qb protein within the photosynthetic membrane.

Labeling of neural cells by gold-filled Sendai virus envelopes before intracerebral transplantation

Gold-filled Sendai virus envelopes were fused with cell suspensions from the basal forebrain of fetal rat donors, and the resulting gold-labeled cells were transplanted into the neocortex of adult rat recipients. Not only did large numbers of labeled cells remain intact through 3 months in the neocortex, but sizable numbers migrated subcortically to the recipient's lesioned nucleus basalis region (a distance of 4 to 5 millimeters). Since this technique is capable of labeling most transplanted cells for long periods of time, it may be useful in determining the survival, migration, and connectivity of intracerebrally transplanted tissues.

Adaptation to CO(2) Level and Changes in the Phosphorylation of Thylakoid Proteins during the Cell Cycle of Chlamydomonas reinhardtii

The photosynthetic performance of synchronously grown Chlamydomonas reinhardtii alternated rhythmically during the cell cycle. The activity of the "CO(2) concentrating mechanism" including the ability to accumulate CO(2) internally and the activity of carbonic anhydrase peaked after 6 to 9 hours of light and reached minimum after 6 to 9 hours of dark. Consequently, the apparent photosynthetic affinity to extracellular CO(2) alternated rhythmically. At the end of the dark period the cells behaved as if they were adapted to high CO(2) even though they were continuously aerated with air. Results from experiments in which the light or dark periods were extended bear on the interaction between the internal (cell cycle or biological clock) and the external (light) signal. The observed rhythmical alterations in photosynthetic V(max) may result from changes in PSII activity. The latter may be partly explained by the capacity for phosphorylation of thylakoid proteins, which reached maximum after 9 hours of light and decreased toward the dark period.

In vitro synthesis and assembly of the peripheral subunits of coupling factor CF1 (alpha and beta) by thylakoid-bound ribosomes

Bispecific antisera were prepared to a mixture of thylakoid membrane polypeptides 4.1 and 4.2. The identity of these polypeptides as the alpha and beta subunits of coupling factor (CF1) was established based on the cross-reactivity of the antisera toward CF1 from peas and by an analysis of the thm-24 mutant of Chlamydomonas which lacks the CF1 ATPase. Photochemical labeling of thylakoid membranes with hydrophobic and hydrophilic fluorescent probes indicated that these polypeptides did not significantly penetrate the membrane bilayer. Immunoprecipitation of the translation products of thylakoid-bound and soluble ribosomes showed the thylakoids to be the major site of synthesis of the polypeptides. Immunoprecipitation of the products of translation of total cellular RNA in a reticulocyte lysate showed no evidence for substantially higher molecular weight precursors. Further analysis of the thylakoid-bound synthesis of alpha and beta revealed that some of the in vitro synthesized polypeptides had been incorporated into the CF0-CF1 complex based on their release from membranes with trypsin and copurification with the CF0-CF1 ATPase.

Respiratory and calcium transport properties of spiny lobster hepatopancreas mitochondria

Mitochondria were isolated from the hepatopancreas of the Florida spiny lobster Panulirus argus using a high osmolarity medium containing 600 mM mannitol, 83 mM sucrose, 5 mM 4-morpholinepropanesulfonic acid, pH 7.6, 0.5% bovine serum albumin (BSA), and 1 mM EDTA. O2 uptake and Ca2+ transport were measured by electrode methods in similar media (plus 4 mM KPi, 3.3 mM MgCl2, and 0.67 mg/ml BSA, with 80 mM KCl replacing a portion of the osmotic support). Substrate-supported respiration was observed to be coupled to phosphorylation of ADP or uptake of Ca2+ ions. State 3 rates (nanogram atoms O X minute-1 X milligram protein-1 +/- SEM (N)) were: 49.2 +/- 3.9 (19), succinate; 30.9 +/- 3.9 (6), DL-palmitoyl carnitine; 29.0 +/- 2.7(9), L-malate; 40.0 +/- 2.3(3), L-glutamate; 27.7 +/- 2.2(5), D-3-hydroxybutyrate; and 26.4 +/- 2.4 (18), L-proline +/- pyruvate. alpha-Glycerol phosphate was not oxidized. Ca2+ uptake driven by succinate oxidation proceeded with Ca:O ratios of 4.0 +/- 0.2 (SEM). Hepatopancreas mitochondria were not uncoupled by Ca2+ uptake in excess of 1100 ng atoms X mg protein-1. Ca2+ efflux could be induced by ruthenium red, indicating the presence of an active Ca2+ cycle. These mitochondria may provide a favorable model system in which to study regulation of the Ca2+ cycle.

Isolation and characterization of the mitochondrial DNA from the florida spiny lobster, Panulirus argus

1. Mitochondria and mitochondrial DNA were isolated from the digestive gland of Panulirus argus. 2. The mitochondrial DNA has an average contour length of 5.13 microns which corresponds to a molecular weight of 10.10 X 10(6) daltons. 3. The molecular weight based on agarose gel electrophoresis of restricted individual DNA samples ranges from 10.04 to 10.4 X 10(6) daltons. 4. Restriction endonuclease analysis with Bam H1 and Eco R1 demonstrate variation in nucleotide sequence between individual lobsters.

Tryptic digestion of membrane proteins synthesized on chloroplast ribosomes in Chlamydomonas reinhardtii

Chloroplast membranes of the green alga Chlamydomonas reinhardtii have been isolated from cells incubated in the presence of cycloheximide. The proteins produced under these conditions are formed on chloroplastic ribosomes. Fluorography of the polypeptides separated on polyacrylamide gels shows ten major protein species associated with the membranes that are produced on chloroplast ribosomes. These membranes were subjected to differential proteolysis. The change in electrophoretic mobility of the membrane proteins after controlled digestion indicates that proteins of molecular weight 55 000, 43 000 and 30 000 are either buried in the membrane or protected by association with other proteins. Most, if not all, of the chloroplast-synthesized thylakoid proteins contain trypsin-sensitive sites accessible from the stromal (out)-side of the isolated membrane vesicle. Thus, most chloroplast-synthesized membrane proteins are asymmetrically distributed in the thylakoid.

Free and membrane-bound chloroplast polyribosomes Chlamydomonas reinhardtii

Over half of the chloroplast ribosomes isolated from growing cultures of Chlamydomonas reinhardtii are bound to chloroplast thylakoid membranes if completion of nascent polypeptide chains is prevented by chloramphenicol. The free chloroplast ribosomes are recovered in homogenate supernatants, and presumably originate from the chloroplast stroma. Only about 10% of these free chloroplast ribosomes are polyribosomes, even under conditions when 70% of free cytoplasm ribosomes are recovered as polyribosomes. The nonionic detergent Nonidet P-40 liberates atypical polyribosomes (Type I), from membranes, which require both ribonuclease and proteases for complete conversion to monomeric ribosomes. Thus Type I particles are held together by mRNA but are also held together by peptide bonds. These Type I polyribosomes probably are not bound to intact membrane, but might be bound to some protein-containing sub-membrane particle. The Type I polyribosomes are dissociated to ribosomal subunits by puromycin and high salt, and contained 0.2 to 1 nascent chain per ribosome. If membranes are treated with Nonidet and proteases at the same time, polyribosomes which are digested to monomeric ribosomes by ribonuclease alone (Type II) are obtained. Type II polyribosomes are smaller than Type I, and probably represent the true size distribution of polyribosomes on the membranes. At least 50% of the membrane-bound ribosomes are polyribosomes, since that much membrane bound chloroplast RNA is recovered as Type I or Type II polyribosomes.

Amino acid incorporation into protein by ribosomes bound to chloroplast thylakoid membranes: formation of discrete products

A system which incorporates amino acids into proteins of chloroplast membranes of Chlamydomonas reinhardti is described. It consists of chloroplast ribosomes bound to thylakoid membranes and cell extract. mRNA is present in this thylakoid-ribosome complex, since neither initiation nor RNA synthesis seems to be required for amino acid incorporation. Incorporation requires ATP, GTP and a soluble portion of cell extract. It is inhibited by chloramphenicol, but not cycloheximide. Most incorporated radioactivity remains bound to the membranes. Although a large portion of this labeled membrane-bound protein occurs as nascent polypeptides, a portion appears at least four products of discrete molecular weights. The major in vitro product migrates as a polypeptide of 23 000 daltons. We conclude that a portion of chloroplast membrane proteins is not only made within the chloroplast, but directly on the membranes. We had previously observed that release of membrane-bound ribosomes is partially dependent on puromycin, and concluded that some membrane-bound ribosomes were attached to the membranes through nascent protein chains. Thus, our results suggest that some chloroplast membrane proteins are inserted into the membranes as they are synthesized. This chloroplast membrane amino acid incorporation system offers a promising tool for studying biosynthesis of membrane proteins, and how they become inserted into chloroplast thylakoids to form functional membranes.

Ribosomes bound to chloroplast membranes in Chlamydomonas reinhardtii

The amount of chloroplast ribosomal RNAs of Chlamydomonas reinhardtii which sediment at 15,000 g is increased when cells are treated with chloramphenicol. Preparations of chloroplast membranes from chloramphenicol-treated cells contain more chloroplast ribosomal RNAs than preparations from untreated cells. The membranes from treated cells also contain more ribosome-like particles, some of which appear in polysome-like arrangements. About 50% of chloroplast ribosomes are released from membranes in vitro as subunits by 1 mM puromycin in 500 mM KCl. A portion of chloroplast ribosomal subunits is released by 500 mM KCl alone, a portion by 1 mM puromycin alone, and a portion by 1 mM puromycin in 500 mM KCl. Ribosomes are not released from isolated membranes by treatment with ribonuclease. Membranes in chloroplasts of chloramphenicol-treated cells show many ribosomes associated with membranes, some of which are present in polysome-like arrangements. This type of organization is less frequent in chloroplasts of untreated cells. Streptogramin, an inhibitor of initiation, prevents chloramphenicol from acting to permit isolation of membrane-bound ribosomes. Membrane-bound chloroplast ribosomes are probably a normal component of actively growing cells. The ability to isolate membrane-bound ribosomes from chloramphenicol-treated cells is probably due to chloramphenicol-prevented completion of nascent chains during harvesting of cells. Since chloroplasts synthesize some of their membrane proteins, and a portion of chloroplast ribosomes is bound to chloroplast membranes through nascent protein chains, it is suggested that the membrane-bound ribosomes are synthesizing membrane protein.

Ultrastructural Changes in Euglena After Ultraviolet Irradiation

The structural changes associated with the ultraviolet-induced bleaching of light-grown cells of Euglena gracilis were investigated. Our light- and electron-microscopic observations of the bleaching process indicate that there is a continuity of plastid structure in cells 5 generations after receiving a bleaching dose of ultraviolet light. There seems to be a continuous dilution of the plastid thylakoids and a decrease in plastid size in the bleaching cells. There also seems to be a change in the position of the plastids in relation to the mitochondria in the bleaching cells. The plastids and possibly the mitochondria are the only organelles which are affected by the ultraviolet irradiation. The continuity of plastids in bleaching cells of Euglena is discussed in relation to the proposed effect of the ultraviolet light.