Characterisation of a chloroplast-encoded secY homologue and atpH from a chromophytic alga. Evidence for a novel chloroplast genome organisation

The Sec translocase

The vast majority of proteins trafficking across or into the bacterial cytoplasmic membrane occur via the translocon. The translocon consists of the SecYEG complex that forms an evolutionarily conserved heterotrimeric protein-conducting membrane channel that functions in conjunction with a variety of ancillary proteins. For posttranslational protein translocation, the translocon interacts with the cytosolic motor protein SecA that drives the ATP-dependent stepwise translocation of unfolded polypeptides across the membrane. For the cotranslational integration of membrane proteins, the translocon interacts with ribosome-nascent chain complexes and membrane insertion is coupled to polypeptide chain elongation at the ribosome. These processes are assisted by the YidC and SecDF(yajC) complex that transiently interacts with the translocon. This review summarizes our current understanding of the structure-function relationship of the translocon and its interactions with ancillary components during protein translocation and membrane protein insertion. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.

The protein-conducting channel SecYEG

In bacteria, the translocase mediates the translocation of proteins into or across the cytosolic membrane. It consists of a membrane embedded protein-conducting channel and a peripherally associated motor domain, the ATPase SecA. The channel is formed by SecYEG, a multimeric protein complex that assembles into oligomeric forms. The structure and subunit composition of this protein-conducting channel is evolutionary conserved and a similar system is found in the endoplasmic reticulum of eukaryotes and the cytoplasmic membrane of archaea. The ribosome and other membrane proteins can associate with the protein-conducting channel complex and affect its activity or functionality.

PROTEIN TARGETING TO THE THYLAKOID MEMBRANE

▪ Abstract  The assembly of the photosynthetic apparatus at the thylakoid begins with the targeting of proteins from their site of synthesis in the cytoplasm or stroma to the thylakoid membrane. Plastid-encoded proteins are targeted directly to the thylakoid during or after synthesis on plastid ribosomes. Nuclear-encoded proteins undergo a two-step targeting process requiring posttranslational import into the organelle from the cytoplasm and subsequent targeting to the thylakoid membrane. Recent investigations have revealed a single general import machinery at the envelope that mediates the direct transport of preproteins from the cytoplasm to the stroma. In contrast, at least four distinct pathways exist for the targeting of proteins to the thylakoid membrane. At least two of these systems are homologous to translocation systems that operate in bacteria and at the endoplasmic reticulum, indicating that elements of the targeting mechanisms have been conserved from the original prokaryotic endosymbiont.

Chloroplast SecA functions as a membrane-associated component of the Sec-like protein translocase of pea chloroplasts

Protein cross-linking studies with a thylakoid membrane translocation intermediate were used to demonstrate that chloroplast SecA functions as a membrane-associated component of the Sec-like ATP-dependent protein translocase of pea chloroplasts. In assays with isolated thylakoids, it was observed that translocation of the 33-kDa protein of the oxygen-evolving complex of photosystem II (OE33) decreased when the ATP concentration was low, and that the protein accumulated as a bound precursor. The bound precursor was able to be translocated into the lumen when the ATP concentration was raised, indicating that the precursor was bound to the translocation apparatus. Inclusion of apyrase in the import reaction prevented translocation but did not affect precursor binding to the membrane. When this translocation intermediate was treated with the cross-linking agent disuccinimidyl suberate, a single predominant cross-linked product of 120 kDa was produced. This conjugate could be immunoprecipitated with antibodies to pea chloroplast SecA, identifying the cross-linking partner as SecA. This provides direct evidence for a functional interaction between a thylakoid precursor protein and a component of the thylakoid protein-translocation apparatus.

A model for the evolution of the plastid sec apparatus inferred from secY gene phylogeny

Plastids possess a bacteria-like sec apparatus that is involved in protein import into the thylakoid lumen. We have analyzed one of the genes essential for this process, secY. A secY gene from the unicellular red alga Cyanidium caldarium was found to be transcriptionally active, demonstrating for the first time that secY is functional in a plastid. Unlike the situation seen in bacteria the C. caldarium gene is transcribed monocistronically, despite the fact that it is part of a large ribosomal gene cluster that resembles bacterial spc operons. A molecular phylogeny is presented for 8 plastid-encoded secY genes, four of which have not been published yet. In this analysis plastid secY genes fall into two classes. One of these, comprising of genes from multicellular red algae and Cryptophyta, clusters in a neighbour-joining tree with a cyanobacterial counterpart. Separated from the aforesaid are secY genes from Chromophyta, Glaucocystophyta and a unicellular red alga. All plastid and cyanobacterial sequences are located on the same branch, separated from bacterial homologues. We postulate that the two classes of secY genes are paralogous, i.e. their gene products are involved in different protein translocation processes. Based on this assumption a model for the evolution of the plastid sec apparatus is presented.

SecYEG and SecA are the stoichiometric components of preprotein translocase

The transport of large preproteins across the Escherichia coli plasma membrane is catalyzed by preprotein translocase, comprised of the peripherally bound SecA subunit and an integrally bound heterotrimeric domain consisting of the SecY, SecE, and SecG subunits. We have now placed the secY, secE, and secG genes under the control of an arabinose-inducible promoter on a multicopy plasmid. Upon induction, all three of the proteins are strongly overexpressed and recovered in the plasma membrane fraction. These membranes show a strong enhancement of 1) translocation ATPase activity, 2) preprotein translocation, 3) capacity for SecA binding, and 4) formation of the membrane-inserted form of SecA. These data establish that SecY, SecE, and SecG constitute the integral membrane domain of preprotein translocase.

SecA homolog in protein transport within chloroplasts: evidence for endosymbiont-derived sorting

The SecA protein is an essential, azide-sensitive component of the bacterial protein translocation machinery. A SecA protein homolog (CPSecA) now identified in pea chloroplasts was purified to homogeneity. CPSecA supported protein transport into thylakoids, the chloroplast internal membrane network, in an azide-sensitive fashion. Only one of three pathways for protein transport into thylakoids uses the CPSecA mechanism. The use of a bacteria-homologous mechanism in intrachloroplast protein transport provides evidence for conservative sorting of proteins within chloroplasts.

Genetic analysis of SecY: additional export-defective mutations and factors affecting their phenotypes

A number of secY mutants of Escherichia coli showing protein export defects were isolated by a combination of localized mutagenesis and secA-lacZ screening. Most of them were cold sensitive and contained single base substitutions in secY leading to amino acid replacements in various parts of the SecY protein, mainly in the cytoplasmic and the transmembrane domains. A temperature-sensitive mutant with an export defect had the same base substitution as secY24, which was characterized previously. Many cold-sensitive secY mutants exhibited rapid responses to temperature lowering but their apparent defects varied at the permissive temperature. Others exhibited delayed responses to the temperature shift. Some secY mutations, including secY39, interfered with protein export when expressed from a multicopy plasmid, even in the presence of wild-type secY on the chromosome. Such "dominant negative" mutations, including secY-d1, which was studied previously, were all located in either cytoplasmic domain 5 or 6, which is consistent with our previous proposal that the C-terminal region of SecY is important for its function as a protein translocator. We also studied the phenotypes of strains in which one of the secY mutations was combined with the components of the secD operon. Overexpression of secD partially suppressed the secY39 mutation, while overexpression of secF exacerbated the export defects of secY122 and secY125 mutations. Overexpression of "yajC", located within the secD operon, suppressed secY-d1. Although yajC itself proved to be dispensable, its disruption impaired the growth of the secY39 mutant at 42 degrees C. These observations suggest that SecY interacts with SecD, SecF, and the product of yajC.

Cloning and sequencing of the secY homolog from Coryneform bacteria

A conserved domain of the secY genes from Bacillus subtilis, Mycoplasma capricolum and Escherichia coli was used to design degenerate oligodeoxyribonucleotides. These synthetic DNA sequences were used to screen a lambda library of Brevibacterium flavum MJ233. A 1.5-kb KpnI fragment of a recombinant lambda phage containing the secY homology from Br. flavum MJ233 was subsequently subcloned into plasmid pUC118. The complete nucleotide (nt) sequence of the cloned fragment indicated that the deduced gene product of the Br. flavum secY homolog is composed of 440 amino acids (aa) with a deduced M(r) of 47,871. Comparison of this aa sequence to the corresponding sequences from E. coli and B. subtilis revealed a high degree of conservation, and suggested that the Br. flavum secY homolog is a membrane protein containing ten transmembrane segments. In addition, we could identify, downstream from secY, a putative coding sequence of the enzyme adenylate kinase. This gene organization is identical to that observed in the B. subtilis genome.

Glutamate synthase is plastid-encoded in a red alga: implications for the evolution of glutamate synthases

An actively transcribed gene (glsF) encoding for ferredoxin-dependent glutamate synthase (Fd-GOGAT) was found on the plastid genome of the multicellular red alga Antithamnion sp. Fd-GOGAT is not plastid-encoded in chlorophytic plants, demonstrating that red algal plastid genomes encode for additional functions when compared to those known from green chloroplasts. Moreover, our results suggest that the plant Fd-GOGAT has an endosymbiotic origin. The same may not be true for NADPH-dependent GOGAT. In Antithamnion glsF is flanked upstream by cpcBA and downstream by psaC and is transcribed monocistronically. Implications of these results for the evolution of GOGAT enzymes and the plastid genome are discussed.

SecA is plastid-encoded in a red alga: implications for the evolution of plastid genomes and the thylakoid protein import apparatus

Partial sequence analysis of the plastid DNA (ptDNA) from a red alga, Antithamnion sp., revealed the presence of a homologue to the Escherichia coli secA gene as well as two open reading frames (ORF 510, ORF 179). In addition a sec Y homologue has been detected on the plastid genome by heterologous hybridization. None of these genes has been found in completely sequenced chlorophytic plastid genomes. SecA and secY gene copies were also detected in the ptDNA of a chromophytic alga, indicating that secA Y may be ubiquitous in rhodophytes and chromophytes. The significance of these findings for the evolution of plastid genomes and the thylakoid protein import mechanism is discussed.

Cloning and characterization of the secY gene from the cyanobacterium Synechococcus PCC7942

The secY gene product is an essential component of the Escherichia coli cytoplasmic membrane, which mediates the protein translocation across the membrane. We found a gene homologous to secY in the genome of the cyanobacterium Synechococcus PCC7942. The deduced amino acid sequence, 439 amino acids long, shows 43% homology with that of the E. coli secY. The hydrophobic profile suggests that the Synechococcus SecY protein is an integral membrane protein containing ten membrane-spanning segments, which are closely related to the E. coli counterpart. The SecY protein may participate in the protein translocation across the cytoplasmic or thylakoid membrane in Synechococcus PCC7942.

Identification of a chloroplast-encoded secA gene homologue in a chromophytic alga: possible role in chloroplast protein translocation

SecA is one of seven Sec proteins that comprise the prokaryotic protein translocation apparatus. A chloroplast-encoded secA gene has been identified from the unicellular chromophytic alga Pavlova lutherii. The gene predicts a protein that is related to the SecA proteins of Escherichia coli and Bacillus subtilis. The presence of secA, as well as the previously described secY and hsp70 genes, on the chloroplast genome of P. lutherii suggests that this eukaryotic organism utilises protein translocation mechanisms similar to those of bacterial cells.