Adrian K. Clarke

A novel α-type carbonic anhydrase associated with the thylakoid membrane in Chlamydomonas reinhardtii is required for growth at ambient CO2

A 29.5 kDa intracellular α‐type carbonic anhydrase, designated Cah3, from the unicellular green alga Chlamydomonas reinhardtii is the first of this type discovered inside a photosynthetic eukaryote cell. We describe the cloning of a cDNA which encodes the protein. Immunoblot studies with specific antibodies raised against Cah3 demonstrate that the polypeptide is associated exclusively with the thylakoid membrane. The putative transit peptide suggests that Cah3 is directed to the thylakoid lumen, which is confirmed further by the presence of mature sized Cah3 after thermolysin treatment of intact thylakoids. Complementation of the high inorganic carbon concentration‐requiring mutant, cia‐3, with a subcloned cosmid containing the cah3 gene yielded transformants that grew on atmospheric levels of CO2 (0.035%) and contained an active 29.5 kDa α‐type carbonic anhydrase. Although, cia‐3 has reduced internal carbonic anhydrase activity, unexpectedly the level of Cah3 was similar to that of the wild‐type, suggesting that the mutant accumulates an inactive Cah3 polypeptide. Genomic sequence analysis of the mutant revealed two amino acid changes in the transit peptide. Results from photosynthesis and chlorophyll a fluorescence parameter measurements show that the cia‐3 mutant is photosynthetically impaired. Our results indicate that the carbonic anhydrase, extrinsically located within the chloroplast thylakoid lumen, is essential for growth of C.reinhardtii at ambient levels of CO2, and that at these CO2 concentrations the enzyme is required for optimal photosystem II photochemistry.

New insights into the ATP-dependent Clp protease : Escherichia coli and beyond

Proteolysis functions as a precise regulatory mechanism for a broad spectrum of cellular processes. Such control impacts not only on the stability of key metabolic enzymes but also on the effective removal of terminally damaged polypeptides. Much of this directed protein turnover is performed by proteases that require ATP and, of those in bacteria, the Clp protease from Escherichia coli is one of the best characterized to date. The Clp holoenzyme consists of two adjacent heptameric rings of the proteolytic subunit known as ClpP, which are flanked by a hexameric ring of a regulatory subunit from the Clp/Hsp100 chaperone family at one or both ends. The recently resolved three‐dimensional structure of the E. coli ClpP protein has provided new insights into its interaction with the regulatory/chaperone subunits. In addition, an increasing number of studies over the last few years have recognized the added complexity and functional importance of ClpP proteins in other eubacteria and, in particular, in photosynthetic organisms ranging from cyanobacteria to higher plants. The goal of this review is to summarize these recent findings and to highlight those areas that remain unresolved.

Plant mitochondria contain proteolytic and regulatory subunits of the ATP-dependent Clp protease

The proteolytic machinery of plant organelles is largely unknown, although indications so far point to several proteases of bacterial origin. In this study an Arabidopsis thaliana cDNA was isolated that encodes a homologue of bacterial ClpX, a molecular chaperone and regulatory subunit of the ATP-dependent, serine-type Clp protease. Computer analysis of the predicted plant ClpX revealed a putative mitochondrial transit peptide at the N-terminus, as well as overall sequence similarity to other eukaryotic ClpX homologues. Specific polyclonal antibodies were made to the Arabidopsis ClpX protein and used to confirm its localization in plant mitochondria. In addition to ClpX, a ClpP protein located in mitochondria was also identified from the numerous ClpP isomers in Arabidopsis. Localization of this nuclear-encoded protein, termed ClpP2, was determined first by its close sequence similarity to mitochondrial ClpP human, and later experimentally using ClpP2-specific antibodies with isolated plant organellar fractions. In Arabidopsis, transcripts for both clpX and clpP2 genes were detected in various tissues and under different growth conditions, with no significant variation in mRNA level (i.e. 2-fold) for each gene between samples. Using β-casein as a substrate, plant mitochondria were found to possess an ATP-stimulated, serine-type proteolytic activity that could be strongly inhibited by antibodies specific for ClpX or ClpP2, suggesting an active ClpXP protease. The recent discovery of homologous mitochondrial ClpX and ClpP proteins in mammals suggests that this type of protease may be common to multicellular eukaryotes.

The ATP‐dependent Clp protease is essential for acclimation to UV‐B and low temperature in the cyanobacterium Synechococcus

ClpP is the proteolytic subunit of the ATP‐dependent Clp protease in eubacteria, mammals and plant chloroplasts. Cyanobacterial ClpP protein is encoded by a multigene family, producing up to four distinct isozymes. We have examined the importance of the first ClpP protein (ClpP1) isolated from the cyanobacterium Synechococcus sp. PCC 7942 for acclimation to ecologically relevant UV‐B and low‐temperature regimens. When the growth light of 50 μmol photons m−2 s−1 was supplemented with 0.5 W m−2 UV‐B for 8 h, the constitutive level of ClpP1 rose eightfold after an initial lag of 1 h. Wild‐type cells readily acclimated to this UV‐B level, recovering after the initial stress to almost the same growth rate as that before UV‐B exposure. Growth of a clpP1 null mutant (ΔclpP1), however, was severely inhibited by UV‐B, being eight times slower than the wild type after 8 h. In comparison, ClpP1 content increased 15‐fold in wild‐type cultures shifted from 37°C to 25°C for 24 h. Wild‐type cultures readily acclimated to 25°C after 24 h, whereas the ΔclpP1 strain did not and eventually lost viability with prolonged cold treatment. During acclimation to either UV‐B or cold, photosynthesis in the wild type was initially inhibited upon the shift but then recovered. Photosynthesis in ΔclpP1 cultures, however, was more severely inhibited by the stress treatment and failed to recover. Acclimation was also monitored by examining the exchange of photosystem II reaction centre D1 proteins that occurs in wild‐type Synechococcus during conditions of excitation stress. During both cold and UV‐B shifts, wild‐type cultures replaced the acclimative form of D1 (D1:1) with the alternative D1 form 2 (D1:2) within the first hours. Once acclimated to either 25°C or 0.5 W m−2 UV‐B, D1:2 was exchanged back for D1:1. In ΔclpP1 cultures, this second exchange between D1 forms did not occur, with D1:2 remaining the predominant D1 form. Our results demonstrate that the ATP‐dependent Clp protease is an essential component of the cold and UV‐B acclimation processes of Synechococcus.

The cyanobacterium Synechococcus modulates Photosystem II function in response to excitation stress through D1 exchange

In this minireview we discuss effects of excitation stress on the molecular organization and function of PS II as induced by high light or low temperature in the cyanobacterium Synechococcus sp. PCC 7942. Synechococcus displays PS II plasticity by transiently replacing the constitutive D1 form (D1:1) with another form (D1:2) upon exposure to excitation stress. The cells thereby counteract photoinhibition by increasing D1 turn over and modulating PS II function. A comparison between the cyanobacterium Synechococcus and plants shows that in cyanobacteria, with their large phycobilisomes, resistance to photoinhibition is mainly through the dynamic properties (D1 turnover and quenching) of the reaction centre. In contrast, plants use antenna quenching in the light-harvesting complex as an important means to protect the reaction center from excessive excitation.

Dynamic responses of photosystem II and phycobilisomes to changing light in the cyanobacterium Synechococcus sp. PCC 7942

We have examined the molecular and photosynthetic responses of a planktonic cyanobacterium to shifts in light intensity over periods up to one generation (7 h). Synechococcus sp. PCC 7942 possesses two functionally distinct forms of the D1 protein, D1∶1 and D1∶2. Photosystem II (PSII) centers containing D1∶1 are less efficient and more susceptible to photoinhibition than are centers containing D 1∶2. Under 50 μmol photons· m−2·s−1, PSII centers contain D1∶1, but upon shifts to higher light (200 to 1000 μmol photons·m−2·s−1), D1∶1 is rapidly replaced by D 1∶2, with the rate of interchange dependent on the magnitude of the light shift. This interchange is readily reversed when cells are returned to 50 μmol photons·m−2·s−1. If, however, incubation under 200 μmol photons·m−2·s−1 is extended, D1∶1 content recovers and by 3 h after the light shift D1∶1 once again predominates. Oxygen evolution and chlorophyll (Chl) fluorescence measurements spanning the light shift and D1 interchanges showed an initial inhibition of photosynthesis at 200 μmol photons·m−2·s−1, which correlates with a proportional loss of total D1 protein and a cessation of growth. This was followed by recovery in photosynthesis and growth as the maximum level of D 1∶2 is reached after 2 h at 200 μmol photons·m−2·s−1. Thereafter, photosynthesis steadily declines with the loss of D1∶2 and the return of the less-efficient D1∶1. During the D1∶1/D1∶2 interchanges, no significant change occurs in the level of phycocyanin (PC) and Chl a, nor of the phycobilisome rod linkers. Nevertheless, the initial PC/Chl a ratio strongly influences the magnitude of photo inhibition and recovery during the light shifts. In Synechococcus sp. PCC 7942, the PC/Chl a ratio responds only slowly to light intensity or quality, while the rapid but transient interchange between D1∶1 and D 1∶2 modulates PSII activity to limit damage upon exposure to excess light.

Identification and expression of the chloroplast clpP gene in the conifer Pinus contorta

The clpP gene from the conifer Pinus contorta was identified and isolated from a chloroplast genomic library by heterologous hybridisation to the second exon of the chloroplast clpP gene in tobacco. DNA sequencing of two overlapping clones revealed an uninterrupted 615 bp open-reading frame with 41 to 65% similarity to the clpP genes in five other chloroplast genomes and Escherichia coli. The 615 bp sequence in P. contorta contained perfectly matched motifs for the serine and histidine active sites of the ClpP protease in E. coli. The location of the clpP gene was determined using a physical map of the P. contorta chloroplast genome, and was found to lie within a 10 kb region between the psbE/F and rpoB genes. Sequencing of the regions adjacent to the clpP gene revealed the first exon of the rps12 gene located 135 bp downstream. The genomic position of the first exon of the rps12 gene in relation to the clpP gene is conserved for all other chloroplast clpP genes identified so far. Northern blot analysis showed that the clpP gene in both P. contorta and P. sylvestris was present in several transcript of different length, ranging from 0.8 to 2.4 kb. The two longer transcripts in P. contorta also included the first exon of the rps12 gene. Mapping of the 5′ end of the clpP transcripts by primer extension, however, revealed a single transcription initiation site 53 bp upstream of the first ATG codon. Analysis of total RNA isolated from the two pine species grown in darkness or moderate light conditions (250 μmol photons m-2 s-1) showed no significant difference in the level of expression of the clpP gene. The results suggest that the clpP gene in conifers is part of an operon which includes the first exon of the rps12 and the entire rpl20 gene, and is expressed in a light-independent manner as a polycistronic precursor which later undergoes post-transcriptional processing to give the mature monocistronic clpP mRNA.

Protection of Photosystem II Against UV‐A and UV‐B Radiation in the Cyanobacterium Plectonema boryanum: The Role of Growth Temperature and Growth Irradiance¶

Abstract Plectonema boryanum UTEX 485 cells were grown at 29°C and 150 μmol m−2 s−1 photosynthetically active radiation (PAR) and exposed to PAR combined with ultraviolet-A radiation (UV-A) at 15°C. This induced a time-dependent inhibition of photosystem II (PSII) photochemistry measured as a decrease of the chlorophyll a fluorescence ratio, Fv/Fm, to 50% after 2 h of UV-A treatment compared to nontreated control cells. Exposure of the same cells to PAR combined with UV-A + ultraviolet-B radiation (UV-B) caused only a 30% inhibition of PSII photochemistry relative to nontreated cells. In contrast, UV-A and UV-A + UV-B irradiation of cells cultured at 15°C and 150 μmol m−2 s−1 had minimal effects on the Fv/Fm values. However, cells grown at 15°C and lower PAR irradiance (6 μmol m−2 s−1) exhibited similar inhibition patterns of PSII photochemistry as control cells. The decreased sensitivity of PSII photochemistry of P. boryanum grown at 15°C and 150 μmol m−2 s−1 to subsequent exposure to UV radiation relative to either control cells or cells grown at low temperature but low irradiance was correlated with the following: (1) a reduced efficiency of energy transfer to PSII reaction centers; (2) higher levels of a carotenoid tentatively identified as myxoxanthophyll; (3) the accumulation of scytonemin and mycosporine amino acids; and (4) the accumulation of ATP-dependent caseinolytic proteases. Thus, acclimation of P. boryanum at low temperature and moderate irradiance appears to confer significant resistance to UV-induced photoinhibition of PSII. The role of excitation pressure in the induction of this resistance to UV radiation is discussed.

Inactivation of the clpP1 gene for the proteolytic subunit of the ATP-dependent Clp protease in the cyanobacterium Synechococcus limits growth and light acclimation

ClpP functions as the proteolytic subunit of the ATP-dependent Clp protease in eubacteria, mammals and plant chloroplasts. We have cloned a clpP gene, designated clpP1, from the cyanobacterium Synechococcus sp. PCC 7942. The monocistronic 591 bp gene codes for a protein 80% similar to one of four putative ClpP proteins in another cyanobacterium, Synechocystis sp. PCC 6803. The constitutive ClpP1 content in Synechococcus cultures was not inducible by high temperatures, but it did rise fivefold with increasing growth light from 50 to 175 µmol photons m-2 s-1. A clpP1 inactivation strain (ΔclpP1) exhibited slower growth rates, especially at the higher irradiances, and changes in the proportion of the photosynthetic pigments, chlorophyll a and phycocyanin. Many mutant cells (ca. 35%) were also severely elongated, up to 20 times longer than the wild type. The stress phenotype of ΔclpP1 when grown at high light was confirmed by the induction of known stress proteins, such as the heat shock protein GroEL and the alternate form of PSII reaction center D1 protein, D1 form 2. ClpP1 content also rose significantly during short-term photoinhibition, but its loss in ΔclpP1 did not exacerbate the extent of inactivation of photosynthesis, nor affect the inducible D1 exchange mechanism, indicating ClpP1 is not directly involved in D1 protein turnover.

The cyanobacterium Synechococcus sp. PCC 7942 possesses a close homologue to the chloroplast ClpC protein of higher plants

The Clp family consists of large, ubiquitous proteins that function as molecular chaperones and/or regulators of ATP-dependent proteolysis. A single copy gene coding for one of these proteins, ClpC, was cloned from the unicellular cyanobacterium Synechococcus sp. PCC 7942. The predicted polypeptide is most similar (ca. 88%) to the chloroplast-localized ClpC protein from higher plants. Using degenerate PCR primers specific for the two distinct ATP-binding domains characteristic of all ClpA-C proteins, partial sequences homologous to clpC from Synechococcus were also identified in five other cyanobacterial strains. The Synechococcus clpC gene is transcribed under standard growth conditions as a monocistronic message of around 2.7 kb. The level of this message, however, decreases slightly after a shift from 37 to 47.5°C for 2 h, similar to expression previously observed for clpC mRNA from heat-shocked higher plants. At the protein level, the amount of ClpC remains relatively unchanged during the high temperature shift, while that of the known heat shock protein GroEL rises considerably. In contrast, the constitutive level of ClpC in Synechococcus increases considerably under conditions of rapid growth, both with increasing light intensities or CO2 concentrations. This, and the fact that attempts to inactivate clpC expression fail to produce a viable phenotype, suggest that ClpC activity is essential for growth in this obligate photoautotrophic cyanobacterium.