Transcriptional mapping of ribosomal RNA genes of the chloroplast and nucleus of Chlamydomonas reinhardi

Reminiscences of Robert Paul Levine (1927-2022)

I present my personal reminiscence of Paul Levine-a highly innovative scientist who did seminal work in photosynthesis. He was among the first to initiate and use a genetic approach toward photosynthesis. He greatly helped in establishing the green unicellular alga Chlamydomonas reinhardtii as a powerful model system not only for understanding the function of the photosynthetic apparatus but also for studying its biogenesis and regulation. During the period he spent at Harvard, he made several ground-breaking contributions such as identifying and establishing the order of some components of the photosynthetic electron transport chain as well as determining their genetic origin. He trained many students and post-doctoral fellows several of whom later became prominent in this field and in other areas of plant science.

Historical perspective on Chlamydomonas as a model for basic research: 1950-1970

During the period 1950-1970, groundbreaking research on the genetic mapping of Chlamydomonas reinhardtii and the use of mutant strains to analyze photosynthesis was conducted in the laboratory of R. Paul Levine at Harvard University. An account of this era, based in part on interviews with Levine, is presented.

Comparative analysis of the biogenesis of photosystem II in the wild-type and Y-1 mutant of Chlamydomonas reinhardtii

Expression of the genes of the photosystem II (PSII) core polypeptides D1 and D2, of three proteins of the oxygen evolving complex of PSII and of the light harvesting chlorophyll a/b binding proteins (LHCP) has been compared in wild-type (wt) and in the y-1 mutant of Chlamydomonas reinhardtii. Since wt, but not y-1 cells produce a fully developed photosynthetic system in the dark, comparison of the two has allowed us to distinguish the direct effect of light from the influence of plastid development on gene expression. The PSII core polypeptides and LHCP are nearly undetectable in dark-grown y-1 cells but they accumulate progressively during light induced greening. The levels of these proteins in wt are the same in the light and the dark. The amounts of the proteins of the oxygen evolving complex do not change appreciably in the light or in the dark for both wt and y-1. Steady state levels of chloroplast mRNA encoding the core PSII polypeptides remain nearly constant in the light or the dark and are not affected by the developmental stage of the plastid. Levels of nuclear encoded mRNAs for the oxygen evolving proteins and of LHCP increase during light growth in wt and y-1. In contrast to wt, synthesis of LHCP proteins is not detectable in y-1 cells in the dark but starts immediately after transfer to light, indicating that LHCP synthesis is controlled by a light-induced factor or process. While the rates of synthesis of D1 and D2 are immediately enhanced by light in wt, this increase occurs only after a lag in y-1 and thus must be dependent on an early light-induced event in the plastid. These results show that the biosynthesis of PSII is affected by light directly, by the stage of plastid development, and by the interaction of light and events associated with plastid development.

Regulation of genes encoding the large subunit of ribulose-1,5-bisphosphate carboxylase and the photosystem II polypeptides D-1 and D-2 during the cell cycle of Chlamydomonas reinhardtii

Synthesis of the major chloroplast proteins is temporally regulated in light-dark-synchronized Chlamydomonas cells. We have used cloned chloroplast DNA probes, and in vitro and in vivo protein synthesis to examine the cell cycle regulation of photosystem II polypeptides D-1 and D-2, and the large subunit of ribulose-1,5-bisphosphate carboxylase (RuBPCase LS). Synthesis and accumulation of D-1 and D-2 mRNAs occurs during the first half of the light period (G1), correlating with increasing synthesis of the polypeptides. Rifampicin, added immediately before the light period, inhibited the normal increase in D-1, D-2 polypeptide synthesis. During the dark period D-1, D-2 mRNAs persist at high levels despite reduced rates of mRNA synthesis and translation during this period. Cell-free translation analyses indicate that the D-1 mRNA present during the dark period is efficient at directing synthesis of the D-1 precursor in vitro. We conclude that expression of the psbA (D-1) and psbD (D-2) genes are regulated primarily at the transcriptional level during the light-induction period but at the translational level for the remainder of the cell cycle. Transcripts of the RuBPCase LS gene (rbcL) are also found at high levels during the light and dark periods but, unlike D-1 and D-2, LS mRNA levels do not increase until the last half of the light period and measurable synthesis and accumulation of this mRNA occurs during the dark. Furthermore, induction of LS polypeptide synthesis during the light period is insensitive to rifampicin. We conclude that LS production is regulated primarily at the translational level during the cell cycle.

Complete nucleotide sequence of the 23S rRNA gene of the Cyanobacterium, Anacystis nidulans

The nucleotide sequence of the Anacystis nidulans 23S rRNA gene, including the 5'- and 3'-flanking regions has been determined. The gene is 2876 nucleotides long and shows higher primary sequence homology to the 23S rRNAs of plastids (84.5%) than to that of E. coli (79%). The predicted rRNA transcript also shares many secondary structural features with those of plastids, reinforcing the endosymbiont hypothesis for the origin of these organelles.

Sequencing of the 16S-23S spacer in a ribosomal RNA operon of Zea mays chloroplast DNA reveals two split tRNA genes

The nucleotide sequence of th 16S-23S spacer from a ribosomal RNA operon of Zea mays chloroplast DNA has been determined. It contains two tRNA genes, coding for tRNAlle (AUCU) and tRNAAla (GCGA), which are split by intervening sequences of 949 and 806 base pairs, respectively. Homology between the two introns suggests that they have a common origin.

An RNA-dependent ATPase from Chlamydomonas reinhardII

An RNA-dependent ATPase has been isolated from extracts of Chlamydomonas reinhardii. The enzyme catalyzes the hydrolysis of ATP, dATP, CTP and dCTP to the corresponding nucleoside diphosphate and Pi in the presence of Mg2+ or Mn2+ and an RNA cofactor. In 1 mM MgCl2 it displays the greatest activity with poly(A), poly(I) and poly(U); and somewhat lower activity with poly(C) and T7 RNA. Although the enzyme is active with single-stranded DNA, all the single-stranded RNAs tested were significantly more effective cofactors than any of the single or double-stranded DNAs tested. A comparison of this ATPase with other RNA-dependent ATPases indicates that is has more in common with the ATPase isolated from the nuclei of animal cells than with the RNA synthesis termination protein rho, the major RNA-dependent ATPase from Escherichia coli. Although chloroplasts of C. reinhardii are known to contain many bacterial-like gene expression components, the presence of an enzyme with close homology to the E. coli rho protein was not detected.

Sub-thylakoid fractions containing ribosomes

A sub-membrane fraction which contains a large portion of any thylakoid-bound ribosomes can be obtained when thylakoids are treated with the detergents Nonidet P-40, or Triton X-100. These 'pseudopolysome' fractions contain 50% of thylakoid-bound ribosomes, but less than 0.5% of thylakoid chlorophyll. Triton and Nonidet psuedopolysomes contain about 10%, and 3% of thylakoid protein, respectively. Pseudopolysomes, prepared from thylakoids with low levels of ribosomes, contain about the same proportion of thylakoid protein but proportionately less ribosomes. Pseudopolysomes contain thylakoid polypeptides in addition to chlorophyll, but lack a major membrane polypeptide of Mr 50 000. Pseudopolysome chlorophyll, and RNA band at the same buoyant density. However, they band at different densities after pseudopolysomes are treated with trypsin (a procedure which strips thylakoids of ribosomes). Pseudopolysome fractions from thylakoids with low levels of ribosomes have a lower density than the corresponding fractions from thylakoids with high levels of ribosomes. Ribosomes are released from thylakoids, and pseudopolysomes by the same treatments. Subunits are released with KCl and puromycin. Polysomes are released with trypsin. It was concluded the pseudopolysomes consist of ribosomes and a membrane fragment containing the sites to which ribosomes are bound.

The synthesis of chloroplast high-molecular-weight ribosomal ribonucleic acid in spinach

Illuminated suspensions of chloroplasts isolated from young spinach leaves show incorporation of [3H]uridine into several species of RNA. One such RNA species of Mr 2.7 x 10(6) shows sequence homology with both the chloroplast 23-S rRNA (Mr = 1.05 x 10(6)) and 16-S rRNA (Mr = 0.56 x 10(6)), as judged by DNA/RNA competition hybridization. Leaves labelled in vivo with [32P]orthophosphate in the presence of chloramphenicol accumulate labelled RNAs of Mr 1.28 x 10(6), 0.71/0.75 x 10(6) and 0.47 x 10(6). The 1.28 x 10(6)-Mr RNA shows 80.5% sequence homology with the 1.05 x 10(6)-Mr rRNA and the 0.71/0.75 x 10(6)-Mr RNA mixture shows 76% sequence homology with the 0.56 x 10(6)-Mr rRNA. We conclude that the pathway of rRNA maturation in spinach chloroplasts is similar to that of Escherichia coli.

Synthesis of chloroplast ribonucleic acid in Chlamydomonas reinhardtii toluene-treated cells

Chlamydomonas reinhardtii cells treated with toluene at 0 degrees C and 25 degrees C incorporate ribonucleoside triphosphates (NTPs) into chloroplast RNA at 25 degrees C and also at 35 degrees C. The incorporation requires all four NTPs and Mg2+, and is completely inhibited by DNase, RNase, actinomycin D (40 microgram/ml) and rifampicin (350 microgram/ml). However, the incorporation is almost totally insensitive to both alpha-amanitin and streptolydigin at 200 microgram/ml.

Effects of erythromycin on membrane-bound chloroplast ribosomes from wild-type Chlamydomonas reinhardi and erythromycin-resistant mutants

1. Treatment of wild-type cells of Chlamydomonas reinhardi with high concentrations of erythromycin results in increased recovery of membrane-bound chloroplast ribosomes, presumably by preventing polysomal runoff during harvesting of cells. No such membrane-retention effect is detected if erythromycin is added after harvesting of cultures, before cell breakage. 2. Growth of wild-type cells is inhibited by 10 microgram/ml erythromycin, but a concentration twice as high is required to increase recovery of membrane-bound wild-type ribosomes. On the other hand, the concentrations of erythromycin which inhibit growth of mutant ery-M1b produce a membrane-retention effect. Mutant ery-U1a is resistant to high concentrations of erythromycin and no membrane-retention effect is detectable at concentrations which produce one in wild type and ery-M1b. 3. These results can be reconciled by a two-point model of the mechanism of erythromycin action on chloroplast ribosomes in Chlamydomonas.

Blue light-dependent regulation of cytoplasmic ribosomal RNA synthesis in Chlorella

Effect of blue and red light on ribosomal RNA synthesis in autotrophic synchronous cultures of Chlorella pyrenoidosa (strain 211-8b) is studied by pulse labeling experiments with tritiated guanosine. Nucleic acids were separated by electrophoresis on polyacrylamide gels. Compared with darkness and red light (679 nm), blue light (457 nm) of equal quantum flux (0.5-5x10(-10) Einstein cm-2 s-1) stimulates incorporation into ribosomal RNA. This blue light effect is observed in the cytoplasmic ribosomal RNA after 5 min of illumination, whereas the stimulation of chloroplast ribosomal RNA synthesis by blue light appears later. Maturation of chloroplast ribosomal RNA is slower than that of cytoplasmic ribosomal RNA. The blue light effect on the cytoplasmic ribosomal RNA formation does not require chloroplast RNA or protein synthesis as shown by inhibitor studies with rifampicin or lincomycin. The blocking of cytoplasmic protein synthesis by cycloheximide inhibits the blue light effect on ribosomal RNA formation. It is concluded that the cytoplasmic ribosomal RNA transcription is controlled by a blue light sensitive system.

Temporal programming of chloroplast and cytoplasmic ribosomal RNA transcription in the synchronous cell cycle of Chlamydomonas reinhardtii

Approximately 90% of the Chlamydomonas reinhardtii chloroplast and cytoplasmic rRNAs was transcribed in the nuclear G1 phase, which occurred during the light period under an alternating light-dark synchronization regime of 12 h each. The remaining 10% of chloroplast and cytoplasmic rRNAs was transcribed from its respective DNAs in the dark period, in the midst of an apparent turnover of a transcription appeared to be prokaryotic in sophistication. The transcription was not interrupted during chloroplast DNA synthesis which occurred during the light period. However, transcription of the nuclear DNA was repressed severely during the nuclear S phase in the dark period. The patterns of incorporation of 32P into chloroplast and cytoplasmic rRNA species in the cell cycle were similar to those of the actual rRNA synthesis as measured optically. However, the quantity of 32P incorporation per unit amount of rRNA synthesized varied considerably during the cell cycle, increasing in all rRNA's during the dark period. 32P incorporation data obtained from continuous and pulse 32P-labeling experiments also revealed a turnover of a small amount of both cytoplasmic and chloroplast rRNAs at the end of the S phase. The 32P incorporation into cytoplasmic and chloroplast rRNAs was well matched temporally with the 32P incorporation into their corresponding ribosomes, indicating that the newly synthesized rRNA molecules are utilized without delay throughout the cell cycle in the assembly of ribosomes.

A mutant strain of Chlamydomonas reinhardi exhibiting altered ribulosebisphosphate carboxylase

A mutant, ac i72, of Chlamydomonas reinhardi possessing an altered ribulosebisphosphate carboxylase and unable to grow on minimal medium has been isolated and characterized. Comparison of ribulosebisphosphate carboxylase purified from both wild type and ac i72 strains is given. The enzyme from ac i72 shows alterations in several characteristics: (a) the specific activity is reduced to 35% that of wild type, (b) the V for both substrates is reduced 3-6 fold, (c) the Mg2+ requirement for maximal activity is 3 times greater, (d) the inhibitory effect of Cl- is greater, and (e) the isoelectric point is changed (6.0 for wild type and 5.8 for ac i72). However, the ribulosebisphosphate carboxylase from ac i72 is identical to that from wild type with respect to pH requirement, temperature sensitivity, subunit structure, and sedimentation characteristic. Other photosynthetic properties of wild type and ac i72 cells were also compared. CO2 fixation in ac i72 in vivo is reduced proportionally to the reduction in activity of the enzyme, but the level of O2 evolution is the same as in wild-type cells. Photosynthetic electron transport, 70-S ribosome content, and chlorophyll content are unaltered in ac i72. The chloroplast ultrastructure of ac i72 cells is distinctly different from that of wild-type cells. The inheritance of the mutation is Mendelian.

Inhibitor effects during the cell cycle in Chlamydomonas reinhardtii. Determination of transition points in asynchronous cultures

A wide variety of inhibitors (drugs, antibiotics, and antimetabolites) will block cell division within an ongoing cell cycle in autotrophic cultures of Chlamydomonas reinhardtii. To determine when during the cell cycle a given inhibitor is effective in preventing cell division, a technique is described which does not rely on the use of synchronous cultures. The technique permits the measurement of transition points, the cell cycle stage at which the subsequent cell division becomes insensitive to the effects of an inhibitor. A map of transition points in the cell cycle reveals that they are grouped into two broad periods, the second and fourth quarters. In general, inhibitors which block organellar DNA, RNA, and protein synthesis have second-quarter transition points, while those which inhibit nuclear cytoplasmic macromolecular synthesis have fourth-quarter transition points. The specific grouping of these transition points into two periods suggests that the synthesis of organellar components is completed midway through the cell cycle and that the synthesis of nonorganellar components required for cell division is not completed until late in the cell cycle.

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.

On the prokaryotic nature of red algal chloroplasts

The sequences of oligonucleotides released by T1 ribonuclease digestion of 32-P-labeled 16S (chloroplast) and 18S (cytoplasmic) ribosomal RNAs from a marine species of Porphyridium (Rhodophyta) have been determined. The resultant catalogs have been compared to those obtained for three prokaryotes:Escherichia coli, Bacillus subtilis, and Anacystis nidulans (a blud-green alga). There is extensive sequence homology between the Porphyridium chloroplast 16S ribosomal RNA and each of the prokaryotic 16S ribosomal RNAs, but little homology between the Porphyridium cytoplasmic 18S ribosomal RNA and any of the 16S species. These data provide a measure of the evolutionary distance separating existing chloroplasts from contemporary bacteria and blue-green algae, and are discussed in terms of the hypothesis that these organelles evolved from endosymbiotic photosynthetic prokaryotes.

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.

[Precursors of chloroplast ribosomal RNA and their maturation in Chlorella]

In Chlorella pyrenoidosa, tritiated uridine is incorporated specifically into the RNA of the chloroplast. The 16 S and 23 S ribosomal RNA become labeled after at least 15 min. Short pulse labeling of 5 min results in peaks of radioactivity in the 17 S region and at the heavy side of the 23 S peak, as shown by polyacrylamide electrophoresis.During chase treatment with unlabeled uridine after the pulse labeling, a shift of radioactivity from the 17 S to the 16 S region is observed. At the same time, the radioactivity over the 23 S speak becomes symmetrical. In the 17 S region, there are at least two peaks which appear and disappear during chase treatment. From data of specific radioactivity a precursor-end product relation can be deduced.After blocking of the chloroplast translation with spectinomycin, the RNA in the 17 S region is accumulated. This product is not stringently the same as that from pulse labeling experiments, because it migrates slightly faster than 17 S RNA. Removal of the antibiotic results in a shift of the radioactivity to the 16 S region. At the same time, the previously blocked chloroplast ribosome synthesis is reinitiated.Attempts have been made to localize the precursor molecules of 17 S and 23 S within the cell. By means of differential centrifugation it has been shown that the precursor RNA components are located in ribosomal particles. No free precursor molecules are found in the ribosome-free supernatant. This is the case in normal as well as in spectinomycin-treated cells.The results are discussed in view of the possible role of chloroplast ribosomal particles as processing agents for the maturation of chloroplast ribosomal RNA.

Chloroplast ribosome biogenesis in Chlamydomonas. Selection and characterization of mutants blocked in ribosome formation

Chloroplast protein synthesis in Chlamydomonas reinhardtii is dispensable when cells are provided acetate as a carbon source. Mutants defective in synthesis, assembly, or function of chloroplast ribosomes are therefore conditionally viable. Positive selection of nonphotosynthetic cells on arsenate has been combined with a simple screening procedure to isolate mutants with a broad spectrum of defects in chloroplast protein synthesis. Eight new mutants deficient in chloroplast ribosomes have been isolated. Three of these have been characterized genetically and phenotypically, and compared with two previously described ribosome mutants, ac-20 and cr-1. A working model of ribosome assembly is proposed which suggests possible biochemical roles for these five Mendelian gene loci.

[Synthesis of chlorophyll and of chloroplast structure in Chlorella without participation of chloroplast ribosomes]

The unicellular green alga Chlorella pyrenoidosa shows normal heterotrophic growth and pigment synthesis in the presence of inhibitors of chloroplast transcription and translation.Cells treated with 100 μg/ml of rifampin, 25 μg/ml of lincomycin or 25 μg/ml of spectinomycin for 48 h do not contain any chloroplast ribosomes, 16 S or 23 S RNA as shown with cell fractionation and gel electrophoresis. Labeling experiments with [5(-3) H]uridine indicate that rifampin blocks completely the formation of 16 S and 23 S RNA whilst cytoplasmic rRNA synthesis is unaffected.Production of dry matter and of cell nitrogen are unaffected by treatment of the cells with antibiotics. Chlorophyll production is almost normal as compared with the untreated control culture. The release of daughter cells is partially inhibited by rifampin treatment. In such cultures, giant cells can be observed among cells of normal size.The O2-production of rifampin-treated cells remains unaffected up to 24 h after application of the drug. Later on, the oxygen evolution declines and, after 72 h, oxygen is consumed even during illumination. The O2-consumption in the dark is markedly enhanced after rifampin treatment.Electron microscopy of rifampin-treated Chlorella shows that apparently normal chloroplast membranes are formed. The thylakoids are arranged in grana-like structures whereas in untreated cells they form only stacks of two or three thylakoids. In the chloroplasts of rifampin-treated Chlorella cells, no more ribosomes are found.The cellular location of synthesis of some chloroplast constituents is discussed.