Proteolysis in protein import and export: Signal peptide processing in eu-and prokaryotes

Numerous proteins in pro-and eukaryotes must cross cellular membranes in order to reach their site of function. Many of these proteins carry signal sequences that are removed by specific signal peptidases during, or shortly after, membrane transport. Signal peptidases have been identified in the rough endoplasmic reticulum, the matrix and inner membrane of mitochondria, the stroma and thylakoid membrane of chloroplasts, the bacterial plasma membrane and the thylakoid membrane of cyanobacteria. The composition of these peptidases varies between one and several subunits. No site-specific inhibitors are known for the majority of these enzymes. Accordingly, signal peptidases recognize structural motifs rather than linear amino acid sequences. Such motifs have become evident by employing extensive site-directed mutagenesis to investigate the anatomy of signal sequences. Analysis of the reaction specificities and the primary sequences of several signal peptidases suggests that the enzymes of the endoplasmic reticulum, the inner mitochondrial membrane and the thylakoid membrane of chloroplasts all have evolved from bacterial progenitors.     

Function and evolution of channels and transporters in photosynthetic membranes

Chloroplasts from land plants and algae originated from an endosymbiotic event, most likely involving an ancestral photoautotrophic prokaryote related to cyanobacteria. Both chloroplasts and cyanobacteria have thylakoid membranes, harboring pigment-protein complexes that perform the light-dependent reactions of oxygenic photosynthesis. The composition, function and regulation of these complexes have thus far been the major topics in thylakoid membrane research. For many decades, we have also accumulated biochemical and electrophysiological evidence for the existence of solute transthylakoid transport activities that affect photosynthesis. However, research dedicated to molecular identification of the responsible proteins has only recently emerged with the explosion of genomic information. Here we review the current knowledge about channels and transporters from the thylakoid membrane of Arabidopsis thaliana and of the cyanobacterium Synechocystis sp. PCC 6803. No homologues of these proteins have been characterized in algae, although similar sequences could be recognized in many of the available sequenced genomes. Based on phylogenetic analyses, we hypothesize a host origin for most of the so far identified Arabidopsis thylakoid channels and transporters. Additionally, the shift from a non-thylakoid to a thylakoid location appears to have occurred at different times for different transport proteins. We propose that closer control of and provision for the thylakoid by products of the host genome has been an ongoing process, rather than a one-step event. Some of the proteins recruited to serve in the thylakoid may have been the result of the increased specialization of its pigment-protein composition and organization in green plants.     

Biogenesis of bacterial inner-membrane proteins

All cells must traffic proteins into and across their membranes. In bacteria, several pathways have evolved to enable protein transfer across the inner membrane, the periplasm, and the outer membrane. The major route of protein translocation in and across the cytoplasmic membrane is the general secretion pathway (Sec-pathway). The biogenesis of membrane proteins not only requires protein translocation but also coordinated targeting to the membrane beforehand and folding and assembly into their protein complexes afterwards to function properly in the cell. All these processes are responsible for the biogenesis of membrane proteins that mediate essential functions of the cell such as selective transport, energy conversion, cell division, extracellular signal sensing, and motility. This review will highlight the most recent developments on the structure and function of bacterial membrane proteins, focusing on the journey that integral membrane proteins take to find their final destination in the inner membrane.     

Biogenesis of β-barrel membrane proteins in bacteria and eukaryotes: evolutionary conservation and divergence

Membrane-embedded β-barrel proteins span the membrane via multiple amphipathic β-strands arranged in a cylindrical shape. These proteins are found in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. This situation is thought to reflect the evolutionary origin of mitochondria and chloroplasts from Gram-negative bacterial endosymbionts. β-barrel proteins fulfil a variety of functions; among them are pore-forming proteins that allow the flux of metabolites across the membrane by passive diffusion, active transporters of siderophores, enzymes, structural proteins, and proteins that mediate protein translocation across or insertion into membranes. The biogenesis process of these proteins combines evolutionary conservation of the central elements with some noticeable differences in signals and machineries. This review summarizes our current knowledge of the functions and biogenesis of this special family of proteins.     

Inner nuclear membrane proteins: functions and targeting

We summarize the properties of integral membrane proteins that reside in the inner nuclear membrane, including lamin B receptor (LBR), lamina-associated polypeptide (LAP) 1, LAP2, emerin, MAN1 and nurim. Most of these proteins interact with lamins and chromatin. Some data also suggest more speculative functions such as gene regulation and possibly sterol metabolism. Mutations in emerin and nuclear lamins have been associated with muscular dystrophies and lipodystrophy, raising new questions about the functions of inner nuclear membrane proteins. Integral proteins of the inner nuclear membrane are synthesized on the rough endoplasmic reticulum (ER) and reach the inner nuclear membrane by lateral diffusion in the connected ER and nuclear envelope membranes. Associations with nuclear ligands retain them in the inner nuclear membrane. Further investigation of the functions and targeting of inner nuclear membrane proteins are needed to determine how they are involved in human disease.     

Spore germination

Despite being relatively insensitive to environmental insult, the spore is responsive to low concentrations of chemical germinants, which induce germination. The process of bacterial spore germination involves membrane permeability changes, ion fluxes and the activation of enzymes that degrade the outer layers of the spore. A number of components in the spore that are required for the germination response have been identified, including a spore-specific family of receptor proteins (the GerA family), an ion transporter and cortex lytic enzymes. The germinant traverses the outer layers of the spore and interacts with its receptor in the inner membrane to initiate the cascade of germination events, but the molecular details of this signal transduction process remain to be identified.     

The ancient claudin Dni2 facilitates yeast cell fusion by compartmentalizing Dni1 into a membrane subdomain

Dni1 and Dni2 facilitate cell fusion during mating. Here, we show that these proteins are interdependent for their localization in a plasma membrane subdomain, which we have termed the mating fusion domain. Dni1 compartmentation in the domain is required for cell fusion. The contribution of actin, sterol-dependent membrane organization, and Dni2 to this compartmentation was analysed, and the results showed that Dni2 plays the most relevant role in the process. In turn, the Dni2 exit from the endoplasmic reticulum depends on Dni1. These proteins share the presence of a cysteine motif in their first extracellular loop related to the claudin GLWxxC(8–10 aa)C signature motif. Structure–function analyses show that mutating each Dni1 conserved cysteine has mild effects, and that only simultaneous elimination of several cysteines leads to a mating defect. On the contrary, eliminating each single cysteine and the C-terminal tail in Dni2 abrogates Dni1 compartmentation and cell fusion. Sequence alignments show that claudin trans-membrane helixes bear small-XXX-small motifs at conserved positions. The fourth Dni2 trans-membrane helix tends to form homo-oligomers in Escherichia plasma membrane, and two concatenated small-XXX-small motifs are required for efficient oligomerization and for Dni2 export from the yeast endoplasmic reticulum. Together, our results strongly suggest that Dni2 is an ancient claudin that blocks Dni1 diffusion from the intercellular region where two plasma membranes are in close proximity, and that this function is required for Dni1 to facilitate cell fusion.     

Light-harvesting complexes of vascular plants

Light-harvesting complexes (LHCs) located in the thylakoid membrane of plant chloroplasts are the collectors of solar radiation that fuel photosynthesis, and thus enable life on our planet. They consist of pigments that are non-covalently bound to light-harvesting proteins (Lhc proteins), which form a family whose members share a significant sequence identity. Due to their central role in photosynthesis, LHCs belong in several respects to the best-analysed membrane proteins. In the past decade, tremendous progress has been made in identifying new members of the Lhc family, in localising the LHCs within the photosystems, and in elucidating the structure and function of LHCs, which is summarised in this review. By contrast, gaining insight into the assembly process and the degradation of the LHCs could not keep pace. Therefore, topics for the next decade will be the elucidation of the location(s) and the operating mode of steps in the assembly and degradation process. Received 15 June 2008; received after revision 1 July 2008; accepted 10 July 2008     

Molecular biology of chloroplast biogenesis: gene expression, protein import and intraorganellar sorting

The chloroplast is the hallmark organelle of plants. It performs photosynthesis and is therefore required for photoautotrophic plant growth. The chloroplast is the most prominent member of a family of related organelles termed plastids which are ubiquitous in plant cells. Biogenesis of the chloroplast from undifferentiated proplastids is induced by light. The generally accepted endosymbiont hypothesis states that chloroplasts have arisen from an internalized cyanobacterial ancestor. Although chloroplasts have maintained remnants of the ancestral genome (plastome), the vast majority of the genes encoding chloroplast proteins have been transferred to the nucleus. This poses two major challenges to the plant cell during chloroplast biogenesis: First, light and developmental signals must be interpreted to coordinately express genetic information contained in two distinct compartments. This is to ensure supply and stoichiometry of abundant chloroplast components. Second, developing chloroplasts must efficiently import nuclear encoded and cytosolically synthesized proteins. A subset of proteins, including such encoded by the plastome, must further be sorted to the thylakoid compartments for assembly into the photosynthetic apparatus. Received 1 September 2000; received after revision 27 October 2000; accepted 1 November 2000     

Annotating proteins from endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes

The sub-cellular localization of a native protein constitutes one coarse-grained aspect of its function. Transport between compartments is often regulated through short sequence motifs. Here, we analyzed experimentally characterized endoplasmic reticulum (ER)/ Golgi retrieval motifs and investigated the accuracy of homology-transfer. Only the C-terminal ER retrieval motifs KDEL, HDEL and AIAKE were sufficiently specific. However, even unspecific motifs may help, provided we know the probability for localization given the motif. We provided such estimates. We also rigorously estimated the accuracy and coverage for inferring ER and Golgi localization through homology-transfer by sequence similarity. In entire proteomes, we could thereby annotate 3304 ER (3182 membrane) and 1853 Golgi (759 membrane) proteins. We identified another putative 5157 globular and 3941 membrane ER or Golgi proteins. Each experimental annotation yielded, on average, one to three high-accuracy and five to six low-accuracy homology-transfers in the six proteomes. These numbers will increase with each new experimental annotation.Received 6 January 2004; received after revision 10 March 2004; accepted 29 March 2004     

Biogenesis of prokaryotic pores.

The prokaryotic pore-forming proteins are synthesized in the cytoplasm, and are assembled in their functional form in the outer membrane. They begin to traverse the cytoplasmic membrane via the SecY/SecA export pathway, which is shared also by periplasmic proteins. The sorting signals that direct these proteins to the outer membrane could be present in the three-dimensional conformations of the proteins, but some results suggest that they may be present in short, contiguous sequences. Outer membrane proteins share a rather hydrophilic amino acid composition, and appear to be rich in beta-sheets (with the exception of lipoproteins). This observation as well as the demonstration of periplasmic export intermediates favor the secretion pathway through the periplasm, as opposed to export through fusion sites between the inner and the outer membrane, but such intermediates have not yet been observed with the wild type proteins under physiological conditions.     

Gene structure and function of the 2'-5'-oligoadenylate synthetase family

2'-5'-Oligoadenylate synthetase was among the first interferon-induced antiviral enzymes to be discovered. This family of enzymes plays an important role in the mechanisms of action of interferon antiviral activity, but is also involved in other cellular processes such as apoptosis and growth control. We have reviewed the function and genomic structure of this class of at least nine proteins. By studying the recently available data in the human genome database and the human Expressed Sequence Tag database, we have been able to build a comprehensive picture of the 2'-5'-oligoadenylate synthetase gene family and its precise location on chromosome 12. Chromosomal localization as well as the intron/exon structure of all four genes has been established and an overview of the splice variant forms of the 2'-5'-oligoadenylate synthetases arising from expression of the four genes is presented. Alignments of the human 2'-5'-oligoadenylate synthetase sequences with non-human 2'-5'-oligoadenylate synthetase sequences suggest that the exon structure and several amino acid sequence motifs have been conserved during evolution.     

Functional significance of the lipid-protein interface in photosynthetic membranes

The functional significance of the lipid-protein interface in photosynthetic membranes, mainly in thylakoids, is reviewed with emphasis on membrane structure and dynamics. The lipid-protein interface is identified primarily by the restricted molecular dynamics of its lipids as compared with the dynamics in the bulk lipid phase of the membrane. In a broad sense, lipid-protein interfaces comprise solvation shell lipids that are weakly associated with the hydrophobic surface of transmembrane proteins but also include lipids that are strongly and specifically bound to membrane proteins or protein assemblies. The relation between protein-associated lipids and the overall fluidity of the thylakoid membrane is discussed. Spin label electron paramagnetic resonance spectroscopy has been identified as the technique of choice to characterize the protein solvation shell in its highly dynamic nature; biochemical and direct structural methods have revealed an increasing number of protein-bound lipids. The structural and functional roles of these protein-bound lipids are mustered, but in most cases they remain to be determined. As suggested by recent data, the interaction of the non-bilayer-forming lipid, monogalactosyldyacilglycerol (MGDG), with the main light-harvesting chlorophyll a/b-binding protein complexes of photosystem-II (LHCII), the most abundant lipid and membrane protein components on earth, play multiple structural and functional roles in developing and mature thylakoid membranes. A brief outlook to future directions concludes this review.     

Calcium signalling: a historical account, recent developments and future perspectives

Ca2+ is a uniquely important messenger that penetrates into cells through gated channels to transmit signals to a large number of enzymes. The evolutionary choice of Ca2+ was dictated by its unusual chemical properties, which permit its reversible complexation by specific proteins in the presence of much larger amounts of other potentially competing cations. The decoding of the Ca2+ signal consists in two conformational changes of the complexing proteins, of which calmodulin is the most important. The first occurs when Ca2+ is bound, the second (a collapse of the elongated protein) when interaction with the targeted enzymes occurs. Soluble proteins such as calmodulin contribute to the buffering of cell Ca2+, but membrane intrinsic transporting proteins are more important. Ca2+ is transported across the plasma membrane (channel, a pump, a Na+/Ca2+ exchanger) and across the membrane of the organelles. The endoplasmic reticulum is the most dynamic store: it accumulates Ca2+ by a pump, and releases it via channels gated by either inositol 1,4,5-trisphosphate (IP3) and cyclic adenosine diphosphate ribose (cADPr). The mitochondrion is more sluggish, but it is closed-connected with the reticulum, and senses microdomains of high Ca2+ close to IP3 or cADPr release channels. The regulation of Ca2+ in the nucleus, where important Ca(2+)-sensitive processes reside, is a debated issue. Finally, if the control of cellular Ca2+ homeostasis somehow fails (excess penetration), mitochondria 'buy time' by precipitating inside Ca2+ and phosphate. If injury persists, Ca2(+)-death eventually ensues.     

Phylogenetic relationship of organisms obtained by ribosomal protein comparison

The evolutionary relationships of ribosomal proteins from eubacteria, archaea, eukaryotes, chloroplasts and mitochondria were examined by their degree of conservation, their structural and functional properties and by the occurrence of conserved structural elements. The structural domains formed by the different protein families were studied. The occurrence of monophyletic groups was investigated for each protein family within the archaea. Phylogenetic trees were constructed between these organisms and together with the homologous sequences of the other phylogenetic domains. All organisms belonging to the archaea clearly formed a monophyletic group. The conserved sequence motifs were checked for the potential to form similar secondary structural elements. Received 24 October 1996; accepted 30 October 1996     

Ultrastructure of 30–40 million year old leaflets from Dominican amber (Hymenaea protera,Fabaceae: Angiospermae)

Hymenaea protera leaflet fossils entombed in amber, dated at 30 to 40 million years (mine strata and exomethylene dating) were observed by both light and transmission electron microscopy. Ultrastructure preservation in these leaflets shows the presence of chloroplasts with thylakoid membranes, cell walls, mitochondria with associated endoplasmic reticulum, nuclei, and xylem tissue. Tissues show varying degrees of degradation; however, natural resin, which has perfused the cells, seems to maintain the structural integrity of the membranes and walls. We conclude that preservation of amber entombed organisms results from dehydration and slow fixative properties leaving the ultrastructure in excellent condition. These findings parallel reports on the exceptional preservation of amino acids and of DNA in amber-entombed organisms.     

Bacterial nonspecific acid phosphohydrolases: physiology, evolution and use as tools in microbial biotechnology

Bacterial nonspecific acid phosphohydrolases (NSAPs) are secreted enzymes, produced as soluble periplasmic proteins or as membrane-bound lipoproteins, that are usually able to dephosphorylate a broad array of structurally unrelated substrates and exhibit optimal catalytic activity at acidic to neutral pH values. Bacterial NSAPs are monomeric or oligomeric proteins containing polypeptide components with an M _r of 25 – 30 kDa. On the basis of amino acid sequence relatedness, three different molecular families of NSAPs can be distinguished, indicated as molecular class A, B and C, respectively. Members of each class share some common biophysical and functional features, but may also exhibit functional differences. NSAPs have been detected in several microbial taxa, and enzymes of different classes can be produced by the same bacterial species. Structural and phyletic relationships exist among the various bacterial NSAPs and some other bacterial and eucaryotic phosphohydrolases. Current knowledge on bacterial NSAPs is reviewed, together with analytical tools that may be useful for their characterization. An overview is also presented concerning the use of bacterial NSAPs in biotechnology. Received 21 November 1997; received after revision 10 March 1998; accepted 10 March 1998     

The role of adapter proteins in T cell activation

Engagement of antigen receptors on lymphocytes leads to a myriad of complex signal transduction cascades. Recently, work from several laboratories has led to the identification and characterization of novel adapter molecules, proteins with no intrinsic enzymatic activity but which integrate signal transduction pathways by mediating protein-protein interactions. Interestingly, it appears that many of these adapter proteins play as critical a role as the effector enzymes themselves in both lymphocyte development and activation. This review describes some of the biochemical and molecular features of several of these newly identified hematopoietic cell-specific adapter molecules highlighting their importance in regulating (both positively and negatively) signal transduction mediated by the T cell antigen receptor.