2009

How antibodies fold

Trends in Biochemical Sciences, 2009, doi:10.1016/j.tibs.2009.11.005, Volume 35, Issue 4, 189-198 published on 22.12.2009
Trends in Biochemical Sciences, online article
B cells use unconventional strategies for the production of a seemingly unlimited number of antibodies from a very limited amount of DNA. These methods dramatically increase the likelihood of producing proteins that cannot fold or assemble appropriately. B cells are therefore particularly dependent on ‘quality control’ mechanisms to oversee antibody production. Recent in vitro experiments demonstrate that Ig domains have evolved diverse folding strategies ranging from robust spontaneous folding to intrinsically disordered domains that require assembly with their partner domains to fold; in vivo experiments reveal that these different folding characteristics form the basis for cellular checkpoints in Ig transport. Taken together, these reports provide a detailed understanding of how B cells monitor and ensure the functional fidelity of Ig proteins.

166 How antibodies fold_b__500



ATPase domain and interdomain linker play a key role in aggregation of mitochondrial Hsp70 chaperone Ssc1

Mol. Biol. Cell, in press, doi:10.1074/jbc.M109.061697 published on 10.12.2009
J. Biol. Chem., online article
The co-chaperone Hep1 is required to prevent the aggregation of mitochondrial Hsp70 proteins. We have analyzed the interaction of Hep1 with mitochondrial Hsp70 (Ssc1) and the determinants in Ssc1 which make it prone to aggregation. The ATPase and the peptide binding domain (PBD) of Hsp70 proteins are connected by a linker segment that mediates interdomain communication between the domains. We show here that the minimal Hep1 binding entity of Ssc1 consists of the ATPase domain and the interdomain linker. In the absence of Hep1, the ATPase domain with interdomain linker had the tendency to aggregate, in contrast to the ATPase domain with mutated linker segment or without linker, and in contrast to the PBD. The closest homolog of Ssc1, bacterial DnaK, and a Ssc1 chimera, in which a segment of the ATPase domain of Ssc1 was replaced by the corresponding segment from DnaK, did not aggregate in Δhep1 mitochondria. The propensity to aggregate appears to be a specific property of the mitochondrial Hsp70 proteins. The ATPase domain in combination with the interdomain linker is crucial for aggregation of Ssc1. In conclusion, our results suggest that interdomain communication makes Ssc1 prone to aggregation. Hep1 counteracts aggregation by binding to this aggregation-prone conformer.

Neupert4_500



Superior Protective Immunity against Murine Listeriosis by Combined Vaccination with CpG DNA and Recombinant Salmonella enterica Serovar Typhimurium

Infection and Immunity, 2009, 77, 12, 5501 - 08 published on 01.12.2009
Infection and Immunity, online article
Preexisting antivector immunity can severely compromise the ability of Salmonella enterica serovar Typhimurium live vaccines to induce protective CD8 T-cell frequencies after type III secretion system-mediated heterologous protein translocation in orally immunized mice. To circumvent this problem, we injected CpG DNA admixed to the immunodominant p60217-225 peptide from Listeria monocytogenes subcutaneously into BALB/c mice and coadministered a p60-translocating Salmonella strain by the orogastric route. The distribution of tetramer-positive p60217-225-specific effector and memory CD8 T cells was analyzed by costaining of lymphocytes with CD62L and CD127. In contrast to the single oral application of recombinant Salmonella or single immunization with CpG and p60, in the spleens from mice immunized with a combination of both vaccine types a significantly higher level of p60-specific CD8 T cells with a predominance of the effector memory T-cell subset was detected. In vivo protection studies revealed that this CD8 T-cell population conferred sterile protective immunity against a lethal infection with L. monocytogenes. However, p60-specific central memory CD8 T cells induced by single vaccination with CpG and p60 were not able confer effective protection against rapidly replicating intracellular Listeria. In conclusion, we provide compelling evidence that the combination of Salmonella type III-mediated antigen delivery and CpG immunization is an attractive novel vaccination strategy to modulate CD8 differentiation patterns toward distinct antigen-specific T-cell subsets with favorable protective capacities.

endres_heesemann_infect_immuni_09_500



Alb4 of Arabidopsis Promotes Assembly and Stabilization of a Non Chlorophyll-Binding Photosynthetic Complex, the CF1CF0–ATP Synthase

Mol. Plant, 2009, 2(6), 1410-1424, doi:10.1093/mp/ssp095 published on 01.11.2009
Molecular Plant, online article
All members of the YidC/Oxa1/Alb3 protein family are evolutionarily conserved and appear to function in membrane protein integration and protein complex stabilization. Here, we report on a second thylakoidal isoform of Alb3, named Alb4. Analysis of Arabidopsis knockout mutant lines shows that Alb4 is required in assembly and/or stability of the CF1CF0–ATP synthase (ATPase). alb4 mutant lines not only have reduced steady-state levels of ATPase subunits, but also their assembly into high-molecular-mass complexes is altered, leading to a reduction of ATP synthesis in the mutants. Moreover, we show that Alb4 but not Alb3 physically interacts with the subunits CF1β and CF0II. Summarizing, the data indicate that Alb4 functions to stabilize or promote assembly of CF1 during its attachment to the membrane-embedded CF0 part.

Soll3_500



The mitA gene of Aspergillus fumigatus is required for mannosylation of inositol-phosphorylceramide, but is dispensable for pathogenicity

Fungal Genet. Biol., 2010, 47(2), 169-178, doi:10.1016/j.fgb.2009.10.001 published on 12.10.2009
Fungal Genetics and Biology, online article
GDP-mannose:inositol-phosphorylceramide (MIPC)-derived glycosphingolipids are important pathogen-associated molecular patterns (PAMP) of Candida albicans and according to recently published data also of Aspergillus fumigatus. MIPC transferases are essential for the synthesis of MIPC, but have so far been studied only in Saccharomyces cerevisiae and C. albicans. Here, we have identified MitA as the only MIPC transferase in A. fumigatus. The ΔmitA mutant lacks MIPC and MIPC-derived glycosphingolipids and accumulates the precursor IPC. The mutant grows normally, shows no defects in cell wall or membrane organization and a normal resistance to different stressors. It is, however, sensitive to high Ca2+ concentrations, especially during germination. Germination of ΔmitA mutant conidia is also decelerated under normal growth conditions, but neither the virulence of this mutant in a systemic model of infection nor its ability to trigger a cytokine response in macrophages is impaired, arguing against a role of MIPC-derived glycosphingolipids as important A. fumigatus PAMPs.

Heesemann2_500



The Folding Pathway of the Antibody VL Domain

J. Mol. Biol., 2009, 392(5), 1326-1338, doi:10.1016/j.jmb.2009.07.075 published on 09.10.2009
J. Mol. Biol., online article
Antibodies are modular proteins consisting of domains that exhibit a β-sandwich structure, the so-called immunoglobulin fold. Despite structural similarity, differences in folding and stability exist between different domains. In particular, the variable domain of the light chain VL is unusual as it is associated with misfolding diseases, including the pathologic assembly of the protein into fibrillar structures. Here, we have analysed the folding pathway of a VL domain with a view to determine features that may influence the relationship between productive folding and fibril formation. The VL domain from MAK33 (murine monoclonal antibody of the subtype κ/IgG1) has not previously been associated with fibrillisation but is shown here to be capable of forming fibrils. The folding pathway of this VL domain is complex, involving two intermediates in different pathways. An obligatory early molten globule-like intermediate with secondary structure but only loose tertiary interactions is inferred. The native state can then be formed directly from this intermediate in a phase that can be accelerated by the addition of prolyl isomerases. However, an alternative pathway involving a second, more native-like intermediate is also significantly populated. Thus, the protein can reach the native state via two distinct folding pathways. Comparisons to the folding pathways of other antibody domains reveal similarities in the folding pathways; however, in detail, the folding of the VL domain is striking, with two intermediates populated on different branches of the folding pathway, one of which could provide an entry point for molecules diverted into the amyloid pathway.

162_500



The charged linker region is an important regulator of Hsp90 function

J. Biol. Chem., 2009, 284(34), 22559–22567, doi:10.1074/jbc.M109.031658 published on 09.10.2009
J. Biol. Chem., online article
Hsp90 is an ATP-dependent molecular chaperone which assists the maturation of a large set of target proteins. Members of the highly conserved Hsp90 family are found from bacteria to higher eukaryotes, with homologues in different organelles. The core architecture of Hsp90 is defined by the N-terminal ATP-binding domain, followed by the middle domain and the C-terminal dimerization domain. A long, highly charged linker between the N-terminal domain and the middle domain is a feature characteristic for Hsp90s of eukaryotic organisms. We set out to clarify the function of this linker by studying the effects of deletions in this region in vivo and in vitro. Here we show that increasing deletions in the charged linker region lead to defects ranging from mild temperature-sensitivity to a lethal phenotype. The lethal deletion variants investigated in this study still exhibit ATPase activity. Further, we observed that deletion of the charged linker ultimately causes a loss of Hsp90 regulation by co-chaperones, as the sensitivity for Aha1-mediated ATPase acceleration declines, and binding of p23/Sba1 is lost in non-viable deletion constructs. In vivo client assays additionally demonstrated that the deletion of the linker had a pronounced effect on the ability of Hsp90 to facilitate client activation. A partial reconstruction of the linker-sequence showed that the supplementation by artificial sequences can rescue the functionality of Hsp90 and restore the conformational flexibility of the protein, required for the processing of client proteins.

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Arabidopsis Tic62 and Ferredoxin-NADP(H) Oxidoreductase Form Light-Regulated Complexes That Are Integrated into the Chloroplast Redox Poise

Plant Cell, 2009, doi:10.1105/tpc.109.069815 published on 29.09.2009
The Plant Cell, online article
Translocation of nuclear-encoded preproteins across the inner envelope of chloroplasts is catalyzed by the Tic translocon, consisting of Tic110, Tic40, Tic62, Tic55, Tic32, Tic20, and Tic22. Tic62 was proposed to act as a redox sensor of the complex because of its redox-dependent shuttling between envelope and stroma and its specific interaction with the photosynthetic protein ferredoxin-NADP(H) oxidoreductase (FNR). However, the nature of this close relationship so far remained enigmatic. A putative additional localization of Tic62 at the thylakoids mandated further studies examining how this feature might be involved in the respective redox sensing pathway and the interaction with its partner protein. Therefore, both the association with FNR and the physiological role of the third, thylakoid-bound pool of Tic62 were investigated in detail. Coexpression analysis indicates that Tic62 has similar expression patterns as genes involved in photosynthetic functions and protein turnover. At the thylakoids, Tic62 and FNR form high molecular weight complexes that are not involved in photosynthetic electron transfer but are dynamically regulated by light signals and the stromal pH. Structural analyses reveal that Tic62 binds to FNR in a novel binding mode for flavoproteins, with a major contribution from hydrophobic interactions. Moreover, in absence of Tic62, membrane binding and stability of FNR are drastically reduced. We conclude that Tic62 represents a major FNR interaction partner not only at the envelope and in the stroma, but also at the thylakoids of Arabidopsis thaliana and perhaps all flowering plants. Association with Tic62 stabilizes FNR and is involved in its dynamic and light-dependent membrane tethering.

Soll4_500



Arabidopsis OBG-Like GTPase (AtOBGL) Is Localized in Chloroplasts and Has an Essential Function in Embryo Development

Mol. Plant, 2009, 1-11, doi:10.1093/mp/ssp073 published on 02.09.2009
Molecular Plant, online article
OBG-like GTPases, a subfamily of P-loop GTPases, have divers and important functions in bacteria, including initiation of sporulation, DNA replication, and protein translation. Homologs of the Bacillus subtilis spo0B GTP-binding protein (OBG) can be found in plants and algae but their specific function in these organisms has not yet been elucidated. Here, it is shown that AT5G18570 encodes an Arabidopsis thaliana OBG-like protein (AtOBGL) that is localized in chloroplasts. In contrast to the bacterial members of this protein family, AtOBGL and other OBG-like proteins from green algae and plants possess an additional N-terminal domain, indicating functional adaptation. Disruption of the gene locus of ATOBGL by TDNA insertion resulted in an embryo-lethal phenotype and light microscopy using Normarski optics revealed that embryo maturation in the atobgl mutant is arrested at the late globular stage before development of a green embryo. Expression of 35S::ATOBGL within the atobgl mutant background could rescue the mutant phenotype, confirming that embryo-lethality is caused by the loss of AtOBGL. Together, the data show that the bacterial-derived OBG-like GTPases have retained an essential role in chloroplasts of plants and algae. They furthermore corroborate the significance of chloroplast functions for embryo development — an important stage within the Arabidopsis lifecycle.

Vothknecht3_500



Calcium regulation in endosymbiotic organelles of plants

PSB, 2009, 4 Issue 9, 805-8 published on 01.09.2009
Plant Signaling & Behavior, online article
In plant cells calcium-dependent signaling pathways are involved in a large array of biological processes in response to hormones, biotic/abiotic stress signals and a variety of developmental cues. This is generally achieved through binding of calcium to diverse calcium-sensing proteins, which subsequently control downstream events by activating or inhibiting biochemical reactions. Regulation by calcium is considered as a eukaryotic trait and has not been described for prokaryotes. Nevertheless, there is increasing evidence indicating that organelles of prokaryotic origin, such as chloroplasts and mitochondria, are integrated into the calcium-signaling network of the cell. An important transducer of calcium in these organelles appears to be calmodulin. In this review we want to give an overview over present data showing that endosymbiotic organelles harbour calcium-dependent biological processes with a focus on calmodulin-regulation.

vothknecht_psb_09_500



Formation of She2p tetramers is required for mRNA binding, mRNP assembly, and localization

RNA, 2009, 15, 2002-2012, doi:10.1261/rna.1753309 published on 26.08.2009
RNA, online article
In eukaryotic cells, dozens to hundreds of different mRNAs are localized by specialized motor-dependent transport complexes. One of the best-studied examples for directional mRNA transport is the localization of ASH1 mRNA in Saccharomyces cerevisiae. For transport, ASH1 mRNA is bound by the unusual RNA-binding protein She2p. Although previous results indicated that She2p forms dimers required for RNA binding and transcript localization, it remained unclear if the dimer constitutes the minimal RNA-binding unit assembling in vivo. By using analytical ultracentrifugation we found that She2p forms larger oligomeric complexes in solution. We also identified a point mutant that shows impaired oligomer formation. Size-exclusion chromatography suggests that She2p forms defined tetramers at physiological concentrations. Subsequent structural studies by small-angle X-ray scattering confirmed this finding and demonstrated that the previously observed She2p dimers interact in a head-to-head conformation to form an elongated tetrameric complex. This She2p tetramer suggests the generation of large continuous RNA-binding surfaces at both sides of the complex. Biochemical studies and immunostaining of cells confirmed that She2p tetramer formation is required for RNA binding, efficient mRNP assembly, and mRNA localization in vivo. Our finding on She2p tetramerization resolves previously raised questions on complex formation and mRNP function.

161_500



Hsp90 is regulated by a switch point in the C-terminal domain

EMBO reports, 2009, 10, 1147-1153, doi:10.1038/embor.2009.153 published on 21.08.2009
EMBO reports, online article
Heat shock protein 90 (Hsp90) is an abundant, dimeric ATP-dependent molecular chaperone, and ATPase activity is essential for its in vivo functions. S-nitrosylation of a residue located in the carboxy-terminal domain has been shown to affect Hsp90 activity in vivo. To understand how variation of a specific amino acid far away from the amino-terminal ATP-binding site regulates Hsp90 functions, we mutated the corresponding residue and analysed yeast and human Hsp90 variants both in vivo and in vitro. Here, we show that this residue is a conserved, strong regulator of Hsp90 functions, including ATP hydrolysis and chaperone activity. Unexpectedly, the variants alter both the C-terminal and N-terminal association properties of Hsp90, and shift its conformational equilibrium within the ATPase cycle. Thus, S-nitrosylation of this residue allows the fast and efficient fine regulation of Hsp90.

159_500



Structural and functional diversity in the family of small heat shock proteins from the parasite Toxoplasma gondii

Biochim. Biophys. Acta, 2009, 1793(11), 1738-1748, doi:10.1016/j.bbamcr.2009.08.005 published on 19.08.2009
Biochim. Biophys. Acta, online article
Small heat shock proteins (sHsps) are ubiquitous molecular chaperones which prevent the nonspecific aggregation of non-native proteins. Five potential sHsps exist in the parasite Toxoplasma gondii. They are located in different intracellular compartments including mitochondria and are differentially expressed during the parasite's life cycle. Here, we analyzed the structural and functional properties of all five proteins. Interestingly, this first in vitro characterization of sHsps from protists showed that all T. gondii sHsps exhibit the characteristic properties of sHsps such as oligomeric structure and chaperone activity. However, differences in their quaternary structure and in their specific chaperone properties exist. On the structural level, the T. gondii sHsps can be divided in small (12–18 subunits) and large (24–32 subunits) oligomers. Furthermore, they differ in their interaction with non-native proteins. While some bind substrates tightly, others interact more transiently. The chaperone activity of the three more mono-disperse T. gondii sHsps is regulated by temperature with a decrease in temperature leading to the activation of chaperone activity, suggesting an adaption to specific steps of the parasite's life cycle.

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NMR Structure of a Monomeric Intermediate on the Evolutionarily Optimized Assembly Pathway of a Small Trimerization Domain

J. Mol. Biol., 2009, 389(1), 103-114, doi:10.1016/j.jmb.2009.03.073 published on 19.08.2009
J. Mol. Biol., online article
Efficient formation of specific intermolecular interactions is essential for self-assembly of biological structures. The foldon domain is an evolutionarily optimized trimerization module required for assembly of the large, trimeric structural protein fibritin from phage T4. Monomers consisting of the 27 amino acids comprising a single foldon domain subunit spontaneously form a natively folded trimer. During assembly of the foldon domain, a monomeric intermediate is formed on the submillisecond time scale, which provides the basis for two consecutive very fast association reactions. Mutation of an intermolecular salt bridge leads to a monomeric protein that resembles the kinetic intermediate in its spectroscopic properties. NMR spectroscopy revealed essentially native topology of the monomeric intermediate with defined hydrogen bonds and side-chain interactions but largely reduced stability compared to the native trimer. This structural preorganization leads to an asymmetric charge distribution on the surface that can direct rapid subunit recognition. The low stability of the intermediate allows a large free-energy gain upon trimerization, which serves as driving force for rapid assembly. These results indicate different free-energy landscapes for folding of small oligomeric proteins compared to monomeric proteins, which typically avoid the transient population of intermediates.

Habazettl et al w supporting_500



The eye lens chaperone alpha-crystallin forms defined globular assemblies

PNAS, 2009, doi: 10.1073/pnas.0902651106, published on 27.07.2009
PNAS, online article
alpha-Crystallins are molecular chaperones that protect vertebrate eye lens proteins from detrimental protein aggregation. alpha B-Crystallin, 1 of the 2 alpha-crystallin isoforms, is also associated with myopathies and neuropathological diseases. Despite the importance of alpha-crystallins in protein homeostasis, only little is known about their quaternary structures because of their seemingly polydisperse nature. Here, we analyzed the structures of recombinant alpha-crystallins using biophysical methods. In contrast to previous reports, we show that alpha B-crystallin assembles into defined oligomers consisting of 24 subunits. The 3-dimensional (3D) reconstruction of alpha B-crystallin by electron microscopy reveals a spherelike structure with large openings to the interior of the protein. Alpha A-Crystallin forms, in addition to complexes of 24 subunits, also smaller oligomers and large clusters consisting of individual oligomers. This propensity might explain the previously reported polydisperse nature of alpha-crystallin.

buchner_weinkauf_pnas_09_500



Full View

Distinct roles of the two isoforms of the dynamin-like GTPase Mgm1 in mitochondrial fusion

FEBS Lett., 2009, 583(13), 2237-2243, doi:10.1016/j.febslet.2009.05.053 published on 07.07.2009
FEBS Letters, online article
The mitochondrial dynamin-like GTPase Mgm1 exists as a long (l-Mgm1) and a short isoform (s-Mgm1). They both are essential for mitochondrial fusion. Here we show that the isoforms interact in a homotypic and heterotypic manner. Their submitochondrial distribution between inner boundary membrane and cristae was markedly different. Overexpression of l-Mgm1 exerts a dominant negative effect on mitochondrial fusion. A functional GTPase domain is required only in s-Mgm1 but not in l-Mgm1. We propose that l-Mgm1 acts primarily as an anchor in the inner membrane that in concert with the GTPase activity of s-Mgm1 mediates the fusion of inner membranes.

Neupert5_500



Preprotein Import into Chloroplasts via the Toc and Tic Complexes Is Regulated by Redox Signals in Pisum sativum

Mol. Plant, 2009, doi:10.1093/mp/ssp043, published on 06.07.2009
Molecular Plant, online article
The import of nuclear-encoded preproteins is necessary to maintain chloroplast function. The recognition and transfer of most precursor proteins across the chloroplast envelopes are facilitated by two membrane-inserted protein complexes, the translocons of the chloroplast outer and inner envelope (Toc and Tic complexes, respectively). Several signals have been invoked to regulate the import of preproteins. In our study, we were interested in redox-based import regulation mediated by two signals: regulation based on thiols and on the metabolic NADP1/NADPH ratio. We sought to identify the proteins participating in the regulation of these transport pathways and to characterize the preprotein subgroups whose import is redox-dependent. Our results provide evidence that the formation and reduction of disulfide bridges in the Toc receptors and Toc translocation channel have a strong influence on import yield of all tested preproteins that depend on the Toc complex for translocation. Furthermore, the metabolic NADP1/NADPH ratio influences not only the composition of the Tic complex, but also the import efficiency of most, but not all, preproteins tested. Thus, several Tic subcomplexes appear to participate in the translocation of different preprotein subgroups, and the redox-active components of these complexes likely play a role in regulating transport.

soll_molplant_09_500



Arabidopsis ATPase family gene 1-like protein 1 is a calmodulin-binding AAA+-ATPase with a dual localization in chloroplasts and mitochondria

The FEBS Journal, 2009, 276, 14, 3870 - 80 published on 01.07.2009
The FEBS Journal,  online article
Members of the AAA+-ATPase superfamily (ATPases associated with various cellular activities) are found in all kingdoms of life and they are involved in very diverse cellular processes, including protein degradation, membrane fusion or cell division. The Arabidopsis genome encodes approximately 140 different proteins that are putative members of this superfamily, although the exact function of most of these proteins remains unknown. Using affinity chromatography on calmodulin-agarose with chloroplast proteins, we purified a 50 kDa protein encoded by AT4G30490 with similarity to the ATPase family gene 1 protein from yeast. Structural analysis showed that the protein possesses a single AAA-domain characteristic for members of the AAA+-ATPase superfamily and that this contains all features specific to proteins of the ATPase family gene 1-like subfamily. In vitro pull-down as well as cross-linking assays corroborate calcium-dependent binding of the protein to calmodulin. The calmodulin binding domain could be located to a region of 20 amino acids within the AAA-domain in close proximity to the Walker A motif. Our analysis further showed that the protein is localized in both mitochondria and chloroplasts, further supporting the incorporation of both endosymbiotic organelles into the calcium-signaling network of the cell. Localization of the same calmodulin-binding protein into mitochondria and chloroplasts could be a means to provide a coordinated regulation of processes in both organelles by calcium signals.

vothknecht_febs_09_500



A search for factors influencing etioplast - chloroplast transition

PNAS, 2009, doi: 10.1073/pnas.0902145106, published on 30.06.2009
PNAS,  online article
Chloroplast biogenesis in angiosperm plants requires the light-dependent transition from an etioplast stage. A key factor in this process is NADPH:protochlorophyllide oxidoreductase A (PORA), which catalyzes the light-dependent reduction of protochlorophyllide to chlorophyllide. In a recent study the chloroplast outer envelope channel OEP16 was described to be involved in etioplast to chloroplast transition by forming the translocation pore for the precursor protein of PORA [Pollmann et al. (2007) Proc Natl Acad Sci USA 104:2019–2023]. This hypothesis was based on the finding that a single OEP16.1 knockout mutant in Arabidopsis thaliana was severely affected during seedling de-etiolation and PORA protein was absent in etioplasts. In contrast, in our study the identical T-DNA insertion line greened normally and showed normal etioplast to chloroplast transition, and mature PORA was present in etioplasts [Philippar et al. (2007) Proc Natl Acad Sci USA 104:678–683]. To address these conflicting results regarding the function of OEP16.1 for PORA import, we analyzed several lines segregating from the original OEP16.1 T-DNA insertion line. Thereby we can unequivocally show that the loss of OEP16.1 neither correlates with impaired PORA import nor causes the observed de-etiolation phenotype. Furthermore, we found that the mutant line contains at least 2 additional T-DNA insertions in the genes for the extracellular polygalacturonase converter AroGP1 and the plastid-localized chorismate mutase CM1. However, detailed examination of the de-etiolation phenotype and a genomewide transcriptional analysis revealed no direct influence of these genes on etioplast to chloroplast transition in Arabidopsis cotyledons.

soll_pnas_09_500



Formation of cristae and crista junctions in mitochondria depends on antagonism between Fcj1 and Su e/g

J. Cell Biol., 2009, 185(6), 1047-1063, doi:10.1083/jcb.200811099 published on 15.06.2009
J. Cell Biol., online article
Crista junctions (CJs) are important for mitochondrial organization and function, but the molecular basis of their formation and architecture is obscure. We have identified and characterized a mitochondrial membrane protein in yeast, Fcj1 (formation of CJ protein 1), which is specifically enriched in CJs. Cells lacking Fcj1 lack CJs, exhibit concentric stacks of inner membrane in the mitochondrial matrix, and show increased levels of F1FO–ATP synthase (F1FO) supercomplexes. Overexpression of Fcj1 leads to increased CJ formation, branching of cristae, enlargement of CJ diameter, and reduced levels of F1FO supercomplexes. Impairment of F1FO oligomer formation by deletion of its subunits e/g (Su e/g) causes CJ diameter enlargement and reduction of cristae tip numbers and promotes cristae branching. Fcj1 and Su e/g genetically interact. We propose a model in which the antagonism between Fcj1 and Su e/g locally modulates the F1FO oligomeric state, thereby controlling membrane curvature of cristae to generate CJs and cristae tips.

Neupert3_500



An Unfolded CH1 Domain Controls the Assembly and Secretion of IgG Antibodies

Molecular Cell, 2009, 34, 5, 569- 79 published on 12.06.2009
Molecular Cell, online article
A prerequisite for antibody secretion and function is their assembly into a defined quaternary structure, composed of two heavy and two light chains for IgG. Unassembled heavy chains are actively retained in the endoplasmic reticulum (ER). Here, we show that the CH1 domain of the heavy chain is intrinsically disordered invitro, which sets it apart from other antibody domains. It folds only upon interaction with the light-chain CL domain. Structure formation proceeds via a trapped intermediate and can be accelerated by the ER-specific peptidyl-prolyl isomerase cyclophilin B. The molecular chaperone BiP recognizes incompletely folded states of the CH1 domain and competes for binding to the CL domain. In vivo experiments demonstrate that requirements identified for folding the CH1 domain invitro, including association with a folded CL domain and isomerization of a conserved proline residue, are essential for antibody assembly and secretion in the cell.

buchner_kessler_cell_09_500



Graduate School Life Science Munich (LSM)

published on 29.05.2009
http://www.lsm.bio.lmu.de/
In order to promote future scientists the best way we can, CIPSM decided to form an own Graduate School. The Graduate School Life Science Munich (LSM) of the Ludwig-Maximilians-University Munich (LMU) offers an international doctoral program in life sciences covering areas of anthropology, biochemistry and cell biology, ecology, evolution, genetics, microbiology, plant sciences, systematics and zoology to outstanding motivated and qualified researchers. The program, which will be complemented by lectures, seminars and workshops, provides comprehensive scientific training in one of Germany´s highest ranking universities. It is open for students that hold a Master´s or Diploma´s degree. Applicants will be selected based on academic qualification, research experience and motivation. Additionally, the LSM accepts outstanding students with a Bachelor´s degree. Bachelor graduates will be enrolled in a preparatory program, which is covered by a stipend of 643 Euro per month for living expenses.

 

If you are interested, please visit our website www.lsm.bio.lmu.de for further information and online application.

 

lsm_500



Interaction of human heat shock protein 70 with tumor-associated peptides

Biological Chemistry, 2009, 390 , 4, 305-312, doi:10.1515/BC.2009.038 published on 01.04.2009
Biological Chemistry, online article
Molecular chaperones of the heat shock protein 70 (Hsp70) family play a crucial role in the presentation of exogenous antigenic peptides by antigen-presenting cells (APCs). In a combined biochemical and immuno-logical approach, we characterize the biochemical interaction of tumor-associated peptides with human Hsp70 and show that the strength of this interaction determines the efficacy of immunological cross-presentation of the antigenic sequences by APCs. A fluorescein-labeled cytosolic mammalian Hsc70 binding peptide is shown to interact with human Hsp70 molecules with high affinity (Kd=0.58 [mu]M at 25[degrees]C). Competition experiments demonstrate weaker binding by Hsp70 of antigenic peptides derived from the tumor-associated proteins tyrosinase (Kd=32 [mu]M) and melanoma antigen recognized by T cells (MART-1) (Kd=2.4 mM). Adding a peptide sequence (pep70) with high Hsp70 binding affinity (Kd=0.04 mM) to the tumor-associated peptides enables them to strongly interact with Hsp70. Presentation of tumor-associated peptides by B cells resulting in T cell activation in vitro is enhanced by Hsp70 when the tumor-associated peptides contain the Hsp70 binding sequence. This observation has relevance for vaccine design, as augmented transfer of tumor-associated antigens to APCs is closely linked to the vaccine's efficacy of T cell stimulation.

kessler_biolchem_09_500



Full View

The large conformational changes of Hsp90 are only weakly coupled to ATP hydrolysis

Nature Structual & Molecular Biology, 2009, 16, 281 - 86 published on 01.03.2009
www.nature.com, online article
The molecular chaperone heat-shock protein 90 (Hsp90) is one of the most abundant proteins in unstressed eukaryotic cells. Its function is dependent on an exceptionally slow ATPase reaction that involves large conformational changes. To observe these conformational changes and to understand their interplay with the ATPase function, we developed a single-molecule assay that allows examination of yeast Hsp90 dimers in real time under various nucleotide conditions. We detected conformational fluctuations between open and closed states on timescales much faster than the rate of ATP hydrolysis. The compiled distributions of dwell times allow us to assign all rate constants to a minimal kinetic model for the conformational changes of Hsp90 and to delineate the influence of ATP hydrolysis. Unexpectedly, in this model ATP lowers two energy barriers almost symmetrically, such that little directionality is introduced. Instead, stochastic, thermal fluctuations of Hsp90 are the dominating processes.

hugel_buchner_nsmb_mar09_500



Rapid Matrix-Assisted Refolding of Histidine-Tagged Proteins

ChemBioChem, 2009, 10(5), 869 - 876, doi:10.1002/cbic.200800697 published on 23.02.2009
ChemBioChem, online article
Matrix refolded: The formation of inclusion bodies, which are amorphous aggregates of misfolded insoluble protein, during recombinant protein expression, is one of the biggest bottlenecks in protein science. We report a stepwise, rational optimization procedure for refolding of insoluble proteins (see scheme). In comparison to refolding in-solution, this parallelized, matrix-assisted approach allows the refolding of various proteins in a fast and efficient manner.

152_folding_500



Dissection of the ATP-induced conformational cycle of the molecular chaperone Hsp90

Nature Structual & Molecular Biology, 2009, 16, 287 - 93 published on 22.02.2009
www.nature.com, online article
The molecular chaperone heat-shock protein 90 (Hsp90) couples ATP hydrolysis to conformational changes driving a reaction cycle that is required for substrate activation. Recent structural analysis provided snapshots of the open and closed states of Hsp90, which mark the starting and end points of these changes. Using fluorescence resonance energy transfer (FRET), we dissected the cycle kinetically and identified the intermediates on the pathway. The conformational transitions are orders of magnitude slower than the ATP-hydrolysis step and thus are the limiting events during the reaction cycle. Furthermore, these structural changes can be tightly regulated by cochaperones, being completely inhibited by Sti1 or accelerated by Aha1. In fact, even in the absence of nucleotide, Aha1 induces Hsp90 rearrangements that speed up the conformational cycle. This comprehensive reconstitution of the Hsp90 cycle defines a controlled progression through distinct intermediates that can be modulated by conformation-sensitive cochaperones.

buchner_nsmb_mar09_500



Calcium depletion and calmodulin inhibition affect the import of nuclear-encoded proteins into plant mitochondria

The Plant Journal, 2009, 58, 694-705 published on 19.02.2009
The Plant Journal, online article
Many metabolic processes essential for plant viability take place in mitochondria. Therefore, mitochondrial function has to be carefully balanced in accordance with the developmental stage and metabolic requirements of the cell. One way to adapt organellar function is the alteration of protein composition. Since most mitochondrial proteins are nuclear encoded, fine-tuning of mitochondrial protein content could be achieved by the regulation of protein translocation. Here we present evidence that the import of nuclear-encoded mitochondrial proteins into plant mitochondria is influenced by calcium and calmodulin. In pea mitochondria, the calmodulin inhibitor ophiobolin A as well as the calcium ionophores A23187 and ionomycin inhibit translocation of nuclear-encoded proteins in a concentration-dependent manner, an effect that can be countered by the addition of external calmodulin or calcium, respectively. Inhibition was observed exclusively for proteins translocating into or across the inner membrane but not for proteins residing in the outer membrane or the intermembrane space. Ophiobolin A and the calcium ionophores further inhibit translocation into mitochondria with disrupted outer membranes, but their effect is not mediated via a change in the membrane potential across the inner mitochondrial membrane. Together, our results suggest that calcium/ calmodulin influences the import of a subset of mitochondrial proteins at the inner membrane. Interestingly, we could not observe any influence of ophiobolin A or the calcium ionophores on protein translocation into mitochondria of yeast, indicating that the effect of calcium/calmodulin on mitochondrial protein import might be a plant-specific trait.

voethknecht_pj_08_500



Protein import machineries in endosymbiotic organelles

Cell. Mol. Life Sci., 2009, 66(11-12), 1903-1923, doi:10.1007/s00018-009-8644-2 published on 05.02.2009
Cellular and Molecular Life Sciences, online article
Chloroplast and mitochondria, the two organelles with an accepted endosymbiotic origin, have developed multiple translocation pathways to ensure the subcellular allocation of proteins synthesized by cytosolic ribosomes, and to guarantee their assembly into functional complexes in coordination also with organellar-encoded subunits. The evolution of different protein import machineries was thus essential for the development of these two organelles within cells. A general overview of the translocation machineries in chloroplast and mitochondrial membranes involved in targeting and import of nuclearencoded proteins, with special focus on plant cells where the two organelles coexist, is expounded.

Soll1_500



Protein transport in organelles: The composition, function and regulation of the Tic complex in chloroplast protein import

FEBS J., 2009, 276(5), 1166-1176, doi:10.1111/j.1742-4658.2009.06874.x published on 31.01.2009
FEBS Journal, online article
It is widely accepted that chloroplasts derived from an endosymbiotic event in which an early eukaryotic cell engulfed an ancient cyanobacterial prokaryote. During subsequent evolution, this new organelle lost its autonomy by transferring most of its genetic information to the host cell nucleus and therefore became dependent on protein import from the cytoplasm. The so-called 'general import pathway' makes use of two multisubunit protein translocases located in the two envelope membranes: the Toc and Tic complexes (translocon at the outer/inner envelope membrane of chloroplasts). The main function of both complexes, which are thought to work in parallel, is to provide a protein-selective channel through the envelope membrane and to exert the necessary driving force for the translocation. To achieve high efficiency of protein import, additional regulatory subunits have been developed that sense, and quickly react to, signals giving information about the status and demand of the organelle. These include calcium-mediated signals, most likely through a potential plastidic calmodulin, as well as redox sensing (e.g. via the stromal NADP+/NADPH pool). In this minireview, we briefly summarize the present knowledge of how the Tic complex adapted to the tasks outlined above, focusing more on the recent advances in the field, which have brought substantial progress concerning the motor function as well as the regulatory potential of this protein translocation system.

Soll5_500



The Native 3D Organization of Bacterial Polysomes

Cell, 2009, 136, 2, 261-71 published on 23.01.2009
Cell, online article
Recent advances have led to insights into the structure of the bacterial ribosome, but little is knownabout the 3D organization of ribosomes in the context of translating polysomes. We employed cryoelectron tomography and a template-matching approach to map 70S ribosomes in vitrified bacterial translation extracts and in lysates of active E. coli spheroplasts. In these preparations, polysomal arrangements were observed inwhich neighboring ribosomesare densely packed and exhibit preferred orientations. Analysis of characteristic examples of polysomes reveals a staggered or pseudohelical organization of ribosomes along the mRNA trace, with the transcript being sequestered on the inside, the tRNA entrance sites being accessible, and the polypeptide exit sites facing the cytosol. Modeling of elongating nascent polypeptide chains suggests that this arrangement maximizes the distance between nascent chains on adjacent ribosomes, thereby reducing the probability of intermolecular interactions thatwould give rise to aggregation and limit productive folding.

hartl_baumeister_cell_09_500



Role of Tim50 in the Transfer of Precursor Proteins from the Outer to the Inner Membrane of Mitochondria

Mol. Biol. Cell, 2009, 20(5), 1400-1407, doi:10.1091/mbc.E08-09-0934 published on 14.01.2009
Molecular Biology of the Cell, online article
Transport of essentially all matrix and a number of inner membrane proteins is governed, entirely or in part, by N-terminal presequences and requires a coordinated action of the translocases of outer and inner mitochondrial membranes (TOM and TIM23 complexes). Here, we have analyzed Tim50, a subunit of the TIM23 complex that is implicated in transfer of precursors from TOM to TIM23. Tim50 is recruited to the TIM23 complex via Tim23 in an interaction that is essentially independent of the rest of the translocase. We find Tim50 in close proximity to the intermembrane space side of the TOM complex where it recognizes both types of TIM23 substrates, those that are to be transported into the matrix and those destined to the inner membrane, suggesting that Tim50 recognizes presequences. This function of Tim50 depends on its association with TIM23. We conclude that the efficient transfer of precursors between TOM and TIM23 complexes requires the concerted action of Tim50 with Tim23.

Neupert2_500



Local conformational dynamics in alpha-helices measured by fast triplet transfer

PNAS, 2009, doi: 10.1073/pnas.0808581106, published on 08.01.2009
PNAS, online article
Coupling fast triplet–triplet energy transfer (TTET) between xanthone and naphthylalanine to the helix–coil equilibrium in alanine-based peptides allowed the observation of local equilibrium fluctuations in α-helices on the nanoseconds to microseconds time scale. The experiments revealed faster helix unfolding in the terminal regions compared with the central parts of the helix with time constants varying from 250 ns to 1.4 μs at 5 °C. Local helix formation occurs with a time constant of ≈400 ns, independent of the position in the helix. Comparing the experimental data with simulations using a kinetic Ising model showed that the experimentally observed dynamics can be explained by a 1-dimensional boundary diffusion with position-independent elementary time constants of ≈50 ns for the addition and of ≈65 ns for the removal of an α-helical segment. The elementary time constant for helix growth agrees well with previously measured time constants for formation of short loops in unfolded polypeptide chains, suggesting that helix elongation is mainly limited by a conformational search.

kiefhaber_pnas_09_500



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