Requirement of the SecB chaperone for export of a non-secretory polypeptide in Escherichia coli

Summary The SecB protein of Escherichia coli is a cytosolic component of the export machinery which can prevent some precursors from prematurely folding into export-incompatible conformations by binding to the newly synthesised polypeptide. The feature(s) of target proteins recognised by SecB, however, are unclear and have been a matter of controversy. Also, it has not been asked if binding of SecB is specific for secretory proteins. We demonstrate here that a non-secretory polypeptide, a fragment of a tail fiber protein of phage T4, fused to the signal peptide of the outer membrane protein OmpA has a very strong SecB requirement for export and that the signal peptide itself cannot, at least not alone, be responsible for this action of SecB. The data reported, together with those of the literature, suggest that SecB recognizes the polypeptide backbone of the target protein.     

CP12: a small nuclear-encoded chloroplast protein provides novel insights into higher-plant GAPDH evolution

Higher-plant chloroplast NAD(P)-glyceraldehyde 3-phosphate dehydrogenase (NAD(P)-GAPDH; EC 1.2.1.13) is composed of two different nuclear-encoded subunits, GAPA and GAPB, forming the highly active heterotetrameric A₂B₂ enzyme. The main difference between these two subunits is a C-terminal extension of about 30 amino acid residues of GAPB. We present cDNA clones for a nuclear-encoded chloroplast protein from pea, spinach and tobacco, which we have named CP12. The mature protein consists of only 74, 75 and 76 amino acid residues, respectively and contains two domains with significant homology to the C-terminal extension of GAPB. Affinity chromatography approaches reveal also a specific interaction between CP12 and chloroplast GAPDH. Northern blot analysis indicates that CP12 is, like plastid GAPDH, expressed in green and also in etiolated leaves. Further homology is observed between CP12 and ORF3, an open reading frame located in the hox gene cluster of Anabaena variabilis. This gene cluster encodes the subunits of the bidirectional NADP⁺-dependent [NiFeS] dehydrogenase. We propose therefore a common evolutionary origin of CP12 and higher-plant chloroplast GAPDH subunit GAPB from the cyanobacterial ORF3.     

The <Emphasis Type="Italic">Chlamydomonas</Emphasis> genome reveals its secrets: chaperone genes and the potential roles of their gene products in the chloroplast

The first draft of the Chlamydomonas nuclear genome was searched for genes potentially encoding members of the five major chaperone families, Hsp100/Clp, Hsp90, Hsp70, Hsp60, the small heat shock proteins, and the Hsp70 and Cpn60 co-chaperones GrpE and Cpn10/20, respectively. This search yielded 34 potential (co-)chaperone genes, among them those 8 that have been reported earlier inChlamydomonas. These 34 genes encode all the (co-)chaperones that have been expected for the different compartments and organelles from genome searches in Arabidopsis, where 74 genes have been described to encode basically the same set of (co-)chaperones. Genome data from Arabidopsis and Chlamydomonas on the five major chaperone families are compared and discussed, with particular emphasis on chloroplast chaperones.     

Yersinia enterocolitica type III secretion chaperone SycD: recombinant expression, purification and characterization of a homodimer

Yersinia species pathogenic to human benefit from a protein transport machinery, a type three secretion system (T3SS), which enables the bacteria to inject effector proteins into host cells. Several of the transport substrates of the Yersinia T3SS, called Yops (Yersinia outer proteins), are assisted by specific chaperones (Syc for specific Yop chaperone) prior to transport. Yersinia enterocolitica SycD (LcrH in Yersinia pestis and Yersinia pseudotuberculosis) is a chaperone dedicated to the assistance of the translocator proteins YopB and YopD, which are assumed to form a pore in the host cell membrane. In an attempt to make SycD amenable to structural investigations we recombinantly expressed SycD with a hexahistidine tag in Escherichia coli. Combining immobilized nickel affinity chromatography and gel filtration we obtained purified SycD with an exceptional yield of 120mg per liter of culture and homogeneity above 95%. Analytical gel filtration and cross-linking experiments revealed the formation of homodimers in solution. Secondary structure analysis based on circular dichroism suggests that SycD is mainly composed of alpha-helical elements. To prove functionality of purified SycD previously suggested interactions of SycD with Yop secretion protein M2 (YscM2), and low calcium response protein V (LcrV), respectively, were reinvestigated.     

Dissecting cellular components of the secretory pathway in filamentous fungi: insights into their application for protein production

Studies on protein production using filamentous fungi have mostly focused on improvement of the protein yields by genetic modifications such as overexpression. Recent genome sequencing in several filamentous fungal species now enables more systematic approaches based on reverse genetics and molecular biology of the secretion pathway. In this review, we summarize recent molecular-based advances in our understanding of vesicular trafficking in filamentous fungi, and discuss insights into their high secretion ability and application for protein production.     

Reconstruction of ancestral FGLamide-type insect allatostatins: a novel approach to the study of allatostatin function and evolution

Allatostatins (ASTs) are a class of regulatory neuropeptides, with diverse functions, found in an array of invertebrate phyla. ASTs have complex gene structure, in which individual ASTs are cleaved from a precursor peptide. Little is known about the molecular evolution of AST structure and function, even in extensively studied groups such as cockroaches. This paper presents the application of a novel technique for the analysis of this system, that of ancestral reconstruction, whereby ancestral amino acid sequences are resurrected in the laboratory. We inferred the ancestral sequences of a well-characterized peptide, AST 7, for the insect ancestor, as well as several cockroach ancestors. Peptides were assayed for in vitro inhibition of JH production in Diploptera punctata and Periplaneta americana. Our results surprisingly, indicate a decrease in potency of the ancestral cockroach AST7 peptide in comparison with more ancient ones such as the ancestral insect peptide, as well as more recently evolved cockroach peptides. We propose that this unexpected decrease in peptide potency at the cockroach ancestor may be related to the concurrent increase in peptide copy number in the lineages leading to cockroaches. This model is consistent with current physiological data, and may be linked to the increased role of ASTs in the regulation of reproductive processes in the cockroaches.     

A novel approach to biological control with entomopathogenic nematodes: Prophylactic control of the peachtree borer, Synanthedon exitiosa

Generally, microbial control agents such as entomopathogenic nematodes are applied in a curative manner for achieving pest suppression; prophylactic applications are rare. In this study, we determined the ability of two Steinernema carpocapsae strains (All and Hybrid) to prophylactically protect peach trees from damage caused by the peachtree borer, Synanthedon exitiosa, which is a major pest of stone fruit trees in North America. In prior studies, the entomopathogenic nematodes S. carpocapsae and Heterorhabditis bacteriophora caused field suppression when applied in a curative manner to established S. exitiosa populations. In our current study, nematodes were applied three times (at 150,000–300,000 infective juveniles/tree) during September and October of 2005, 2006, and 2007. A control (water only) and a single application of chlorpyrifos (at the labeled rate) were also made each year. The presence of S. exitiosa damage was assessed each year in the spring following the treatment applications. Following applications in 2006, we did not detect any differences among treatments or the control (possibly due to a low and variable S. exitiosa infestation of that orchard). Following applications in 2005 and 2007, however, the nematode and chemical treatments caused significant damage suppression. The percentage of trees with S. exitiosa damage in treated plots ranged from 0% damage in 2005 to 16% in plots treated with S. carpocapsae (Hybrid) in 2007. In control plots damage ranged from 25% (2005) to 41% (2007). Our results indicate that nematodes applied in a preventative manner during S. exitios’s oviposition period can reduce insect damage to levels similar to what is achieved with recommended chemical insecticide treatments.     

Drosophila alcohol dehydrogenase: acetate-enzyme interactions and novel insights into the effects of electrostatics on catalysis

Drosophila alcohol dehydrogenase (DADH) is an NAD+-dependent enzyme that catalyzes the oxidation of alcohols to aldehydes/ketones and that is also able to further oxidize aldehydes to their corresponding carboxylic acids. The structure of the ternary enzyme-NADH-acetate complex of the slow alleloform of Drosophila melanogaster ADH (DmADH-S) was solved at 1.6 A resolution by X-ray crystallography. The coenzyme stereochemistry of the aldehyde dismutation reaction showed that the obtained enzyme-NADH-acetate complex reflects a productive ternary complex although no enzymatic reaction occurs. The stereochemistry of the acetate binding in the bifurcated substrate-binding site, along with previous stereochemical studies of aldehyde reduction and alcohol oxidation shows that the methyl group of the aldehyde in the reduction reaction binds to the R1 and in the oxidation reaction to the R2 sub-site. NMR studies along with previous kinetic studies show that the formed acetaldehyde intermediate in the oxidation of ethanol to acetate leaves the substrate site prior to the reduced coenzyme, and then binds to the newly formed enzyme-NAD+ complex. Here, we compare the three-dimensional structure of D.melanogaster ADH-S and a previous theoretically built model, evaluate the differences with the crystal structures of five Drosophila lebanonensis ADHs in numerous complexed forms that explain the substrate specificity as well as subtle kinetic differences between these two enzymes based on their crystal structures. We also re-examine the electrostatic influence of charged residues on the surface of the protein on the catalytic efficiency of the enzyme.     

<Emphasis Type="Italic">Agrobacterium rhizogenes</Emphasis> is a useful transporter for introducing T-DNA of the binary plasmid into the chrysanthemum, <Emphasis Type="Italic">Dendranthema grandiflorum</Emphasis> Kitamura,genome

Agrobacterium rhizogenes was used for efficient transformation of chrysanthemum. Two types of Agrobacterium, A. rhizogenes (A-13) and A. tumefaciens (LBA4404), which harbor pIG121-Hm, were employed for infection. In the A. rhizogenes-infected explants, hairy roots were not observed on any tested medium or culture condition. When explants were cultured on shoot induction medium, calli were formed at the cutting edge within 4–6 weeks of culture, and shoot primordia were observed on the callus surface after 2 weeks of callus formation. Consequently, with gus introduction, a significantly higher transformation rate was observed for A. rhizogenes (6.0%) compared with A. tumefaciens (3.3%). However, only 0.6% of the frequency of rol insertion was exhibited in A. rhizogenes mediation. These results indicate that A. rhizogenes effectively introduces T-DNA of the binary plasmid into the chrysanthemum genome by introducing Ri T-DNA at a low frequency. It also indicates that the system is a useful alternative for the transformation of chrysanthemum.     

New insights into autophagic cell death in the gypsy moth Lymantria dispar: a proteomic approach

Autophagy is an evolutionary ancient process based on the activity of genes conserved from yeast to metazoan taxa. Whereas its role as a mechanism to provide energy during cell starvation is commonly accepted, debate continues about the occurrence of autophagy as a means specifically activated to achieve cell death. The IPLB-LdFB insect cell line, derived from the larval fat body of the lepidoptera Lymantria dispar, represents a suitable model to address this question, as both autophagic and apoptotic cell death can be induced by various stimuli. Using morphological and functional approaches, we have observed that the culture medium conditioned by IPLB-LdFB cells committed to death by the ATPase inhibitor oligomycin A stimulates autophagic cell death in untreated IPLB-LdFB cells. Moreover, proteomic analysis of the conditioned media suggests that, in IPLB-LdFB cells, oligomycin A promotes a shift towards lipid metabolism, increases oxidative stress and specifically directs the cells towards autophagic activity. Electronic Supplementary Material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. This work was supported by an F.A.R. grant from the University of Modena and Reggio Emilia (D.M. and E.O.) and by an “Experimental approaches to the study of evolution” grant from the Department of Animal Biology of the University of Modena and Reggio Emilia (D.M.).     

EFOLD,a New Program Complex for Molecular Modeling: The Use of a Flexible Weighting Coefficient Scheme and the Standard Valence Geometry in Modeling the Enzyme Active Sites

An algorithm was proposed for the representation of biopolymer structures in an internal coordinate system (so-called structure regularization) by minimizing the target function using a flexible weighting coefficient scheme with three components that determine the reliability of deviations of each atom. For the structure regularization, an algorithm for taking into account the temperature factor was suggested for the first time. It was shown by the example of the aspartyl protease rhizopuspepsin that the representation in the internal coordinate system may result in an accurate reproduction of the structural details of separate molecule fragments, such as the enzyme active site region. This algorithm was implemented as one of the modules of EFOLD.     

A new approach for the biolistic method: Bombardment of living nitrogen-fixing bacteria into plant tissues

Summary A new utilization of the biolistic gun was developed for the direct introduction of nitrogen-fixing bacteria (Azotobacter vinelandii) into strawberry (Fragaria x ananassa) tissues. This was the first case of using living bacteria as microprojectiles for the bombardment of plant tissues. Bacterial cells, adhered to tungsten particles, were accelerated by a nitrogen-powered device, and delivered into the target leaves and regenerating shoot meristems. The presence of bacteria in the developing strawberry callus tissues and regenerating plants was detected by microscopy, acetylene reduction assay, and selective polymerase chain reaction. Practically, the elaborated method proved to be suitable for the establishment of artificial intereellular, associations between nitrogen-fixing bacteria and higher plants.     

Adaptogenic activity of a glyco-peptido-lipid fraction from the alcoholic extract of Trichopus zeylanicus Gaertn.

A glyco-peptido lipid fraction ("AF") from the alcoholic extract of Trichopus zeylanicus Gaertn. was evaluated for putative antistress activity in a battery of tests. "AF" exhibited significant antistress activity in dose dependent manner in all the parameters studied, against the different stresses use to induce non-specific stress. Ashwagandha, the commercial extract of Withania somnifera roots was used as control: A preliminary acute toxicity study in mice showed a good margin of safety, as the ALD50 value was more than 3000 mg/kg body wt. p.o. with no signs of abnormalities.     

SC-formation in someAllium species,and a discussion of the significance of SC-associated structures and of the mechanisms for presynaptic alignment

Earlier observations on synaptonemal complex (SC) formation inAllium are supplemented by data from diploidA. sphaerocephalon, pentaploidA. oleraceum and allotetraploidA. senescens. Accumulating information about structures like lateral element thickenings and -doublings allows to draw conclusions about their nature. The occurrence of discrete intercalary and terminal homologous associations prior to synapsis is confirmed for a range ofAllium species and it is argued that they are a general phenomenon. Several hypotheses on homologous recognition and/or attraction are discussed in the light of the observations on homologous alignment inAllium.Gratefully dedicated to my highly respected mentor, Prof. DrElisabeth Tschermak-Woess, on the occasion of her 70th birthday.     

Additional data for nuclear DNA give new insights into the phylogenetic position of Sorex granarius within the Sorex araneus group

Many species contain genetic lineages that are phylogenetically intermixed with those of other species. In the Sorex araneus group, previous results based on mtDNA and Y chromosome sequence data showed an incongruent position of Sorex granarius within this group. In this study, we explored the relationship between species within the S. araneus group, aiming to resolve the particular position of S. granarius. In this context, we sequenced a total of 2447 base pairs (bp) of X-linked and nuclear genes from 47 individuals of the S. araneus group. The same taxa were also analyzed within a Bayesian framework with nine autosomal microsatellites. These analyses revealed that all markers apart from mtDNA showed similar patterns, suggesting that the problematic position of S. granarius is best explained by an incongruent behavior by mtDNA. Given their close phylogenetic relationship and their close geographic distribution, the most likely explanation for this pattern is past mtDNA introgression from S. araneus race Carlit to S. granarius.     

A novel lipase/chaperone pair from<Emphasis Type="Italic"> Ralstonia</Emphasis> sp. M1: analysis of the folding interaction and evidence for gene loss in<Emphasis Type="Italic"> R. solanacearum</Emphasis>

A microbial strain (referred to as M1) that produces an extracellular lipase was isolated from a soil sample in Vietnam, and identified as a Ralstonia species by partial sequencing of its 16S rDNA. A genomic library was constructed from Pst I fragments, and a colony showing lipase activity was selected for further analysis. Sequencing of the 4.7-kb insert in this clone (named M1-72) revealed one incomplete and three complete ORFs, predicted to encode a partial hypothetical glutaminyl tRNA synthetase (304 aa), a hypothetical transmembrane protein (500 aa), a lipase (328 aa) and a lipase chaperone (352 aa), respectively. Alignment of the insert sequence with the corresponding region of the genome of R. solanacearum GMI1000 (GenBank Accession No. AL646081) confirmed the presence in the latter of the genes for the hypothetical transmembrane protein and glutaminyl tRNA synthetase, which exhibited 89–91% identity to their counterparts in M1. However, R. solanacearum GMI1000 lacks the complete lipase-encoding gene and the major part of the chaperone-encoding gene, creating a so-called black hole. The deduced amino acid sequences of the products of the lipase gene lipA and chaperone gene lipB from strain M1 shared 49.3–60.3% and 23.9–32.7% identity, respectively, with those of the Burkholderia lipase/chaperone subfamily I.2. lipB is located downstream of lipA, and separated from it by only 9 bp, and each gene has a putative ribosome binding site. The mature lipase LipA, a His-tagged derivative (LipAhis), the tagged full-length chaperone LipBhis and a truncated form (LipBhis) lacking the 56 N-terminal residues were expressed in Escherichia coli BL21. LipA, LipAhis and LipBhis could be expressed at high levels (70, 15 and 12 mg/g wet cells, respectively) and were easily purified. However, LipBhis was expressed at a much lower level which precluded purification. The specific activity of purified LipAhis, expressed on its own, was very low (<52 U/mg). However, after co-incubation with the purified LipBhis in vitro, the specific activity of the enzyme was markedly enhanced, indicating that the chaperone facilitated correct folding of the enzyme. A lipase:chaperone ratio of 1:10 was found to be optimal, yielding an enzyme preparation with a specific activity of 650 U/mg.Communicated by H. Ikeda     

The association of small heat shock protein Hsp16.3 with the plasma membrane of Mycobacterium tuberculosis: dissociation of oligomers is a prerequisite

Hsp16.3, a small heat shock protein from Mycobacterium tuberculosis (MTB), was originally identified as an immuno-dominant antigen and later found to be a major membrane protein. In vitro studies show that Hsp16.3 exists as nonamers and undergoes dynamic dissociation/re-association equilibrium in solutions. Nevertheless, neither the details nor the physiological implications of the presence of Hsp16.3 in the plasma membrane have been studied. In this study, we demonstrated that the purified Hsp16.3 proteins were able to interact with the MTB plasma membrane in a specific and reversible manner, suggesting that there might be subunit exchange between membrane-bound Hsp16.3 and soluble Hsp16.3 oligomers. The dissociation of Hsp16.3 oligomers appears to be a prerequisite for its membrane binding, which is interesting in view that the dissociation of small heat shock protein oligomers was also found to be necessary for it to bind denaturing substrate proteins. Furthermore, the oligomeric structure of Hsp16.3 seems to be more dynamic and flexible when incubating with the mycobacterium lipids. The physiological implications of these observations for Hsp16.3, and small heat shock proteins in general, are discussed.     

Ventilation and metabolic rate in the platypus: insights into the evolution of the mammalian breathing pattern

The platypus (Ornithorhyncus anatinus) is characterized by a rate of oxygen consumption (V(O2))that is higher than that reported for other similar sized monotremes, similar to marsupials and somewhat lower than eutherians. The platypus is also characterized by a breathing pattern, more typical of a diving mammal, with a high 'inspiratory drive' and a post-inspiratory pause. Further, the platypus reveals an attenuated hyperventilatory response to hypoxia and a reduced hyperpnoea to hypercapnia; such a response to these chemical stimuli is commonly observed in semi-fossorial and diving mammals. Nevertheless, under conditions of normoxia, ventilation (V(E))is matched to (V(O(2)) such that the convection requirement (V(E)/V(O2)) is similar to that reported for other mammals (approx. 37). The apparent consistency of the convection requirement in mammals suggests the blueprint for the design of the mammalian respiratory system has remained an interspecies constant in the three divergent extant sub-classes of mammals.