The confirmation of the denatured structure of pyrrolidone carboxyl peptidase under nondenaturing conditions: difference in helix propensity of two synthetic peptides with single amino acid substitution

In the denatured state (D(1) state) of cystein-free pyrrolidone carboxyl peptidase (PCP-0SH) from Pyrococcus furiosus, a hyperthermophile under nondenaturing conditions, a fairly stable alpha-helix (alpha6-helix) has been determined from H/D exchange-NMR experiments. On the other hand, the alpha6-helix region of the proline-mutant at position 199 (A199P) was unstructured in the D(1) state unlike that of the wild-type PCP-0SH, although the folded conformations of both proteins were almost identical to each other. This finding has been deduced from the information regarding the remaining amide hydrogens in the HSQC spectra after H/D exchanges in the D(1) state. To confirm this inference, we examined the helical propensities of two synthetic peptides from their NMR structural analysis in the presence of trifluoroethanol (TFE). One is an 18-residue peptide called the wild-type H6-peptide corresponding to the alpha6-helix (from Ser188 to Glu205) of the wild-type PCP-0SH, and the other is the mutant H6-peptide corresponding to the alpha6-helix region of A199P. The NOE-contact information obtained from the 2D-(1)H-NOESY spectra measured for both peptides in the presence of 30% TFE clearly demonstrated that the wild-type H6-peptide had a high helical propensity, but the mutant H6-peptide was almost totally unstructured. The TFE-induced helical propensities for these peptide fragments confirmed the conclusions deduced from the H/D exchange data measured in the D(1) states of two proteins.     

Effects of glycosylation on swimming ability and flagellar polymorphic transformation in Pseudomonas syringae pv. tabaci 6605

The role of flagellin glycosylation on motility was investigated in Pseudomonas syringae pv. tabaci. The swimming activity of glycosylation-defective mutants was prominently decreased in a highly viscous medium. The mutants showed differences in polymorphic transitions and in the bundle formation of flagella, indicating that glycosylation stabilizes the filament structure and lubricates the rotation of the bundle.     

Identification of a putative acetyltransferase gene, MMP0350, which affects proper assembly of both flagella and pili in the archaeon Methanococcus maripaludis

Glycosylation is a posttranslational modification utilized in all three domains of life. Compared to eukaryotic and bacterial systems, knowledge of the archaeal processes involved in glycosylation is limited. Recently, Methanococcus voltae flagellin proteins were found to have an N-linked trisaccharide necessary for proper flagellum assembly. Current analysis by mass spectrometry of Methanococcus maripaludis flagellin proteins also indicated the attachment of an N-glycan containing acetylated sugars. To identify genes involved in sugar biosynthesis in M. maripaludis, a putative acetyltransferase was targeted for in-frame deletion. Deletion of this gene (MMP0350) resulted in a flagellin molecular mass shift to a size comparable to that expected for underglycosylated or completely nonglycoslyated flagellins, as determined by immunoblotting. Assembled flagellar filaments were not observed by electron microscopy. Interestingly, the deletion also resulted in defective pilus anchoring. Mutant cells with a deletion of MMP0350 had very few, if any, pili attached to the cell surface compared to a nonflagellated but piliated strain. However, pili were obtained from culture supernatants of this strain, indicating that the defect was not in pilus assembly but in stable attachment to the cell surface. Complementation of MMP0350 on a plasmid restored pilus attachment, but it was unable to restore flagellation, likely because the mutant ceased to make detectable flagellin. These findings represent the first report of a biosynthetic gene involved in flagellin glycosylation in archaea. Also, it is the first gene to be associated with pili, linking flagellum and pilus structure and assembly through posttranslational modifications.     

The patch mosaic of an old-growth warm-temperate forest: patch-level descriptions of 40-year gap-forming processes and community structures

Old-growth forests consist of various types of small patches that reflect their own gap-forming process, which includes changes in environmental conditions occurring over several decades. We reconstructed the gap-forming processes that had occurred during a 40-year period for eight representative patches of an old-growth evergreen broad-leaved forest in Japan, and examined the current community structure. The selected patches were based on (1) changes in canopy heights estimated from aerial photographs taken in four different years, (2) long-term ecological research (LTER) monitoring records, and (3) a recent field survey, so that they sufficiently covered characteristic gap-forming processes such as a new gap, an old gap and consistently closed canopy. Height and diameter at breast height (DBH) were measured on all living trees taller than 1.3 m. In their height distributions, currently almost closed patches that were open in 1966 show a rotated sigmoid, whereas their DBH distributions are an inverse J-shape. In contrast, patches that have been consistently under a closed canopy exhibit gentle inverse J-shapes for both distributions. For species composition, there are no clear contrasts associated with the past gap-forming processes except for the existence of fast-growing deciduous species in large currently open patches. Our results suggested that the variation in several decades of gap-forming processes played a central role in the high patch diversity and the complex patch mosaic of the forest. Diverse gap-forming processes created micro-environmental heterogeneity both vertically and horizontally, and contributed to the maintenance of the species-rich, warm-temperate old-growth forest.     

Identification of genes involved in the assembly and attachment of a novel flagellin N-linked tetrasaccharide important for motility in the archaeon Methanococcus maripaludis

Recently, the flagellin proteins of Methanococcus maripaludis were found to harbour an N -linked tetrasaccharide composed of N -acetylgalactosamine, di-acetylated glucuronic acid, an acetylated and acetamidino-modified mannuronic acid linked to threonine, and a novel terminal sugar [( 5S )-2-acetamido-2,4-dideoxy-5-O-methyl-α-L- erythro -hexos-5-ulo-1,5-pyranose]. To identify genes involved in the assembly and attachment of this glycan, in-frame deletions were constructed in putative glycan assembly genes. Successful deletion of genes encoding three glycosyltransferases and an oligosaccharyltransferase (Stt3p homologue) resulted in flagellins of decreased molecular masses as evidenced by immunoblotting, indicating partial or completely absent glycan structures. Deletion of the oligosaccharyltransferase or the glycosyltransferase responsible for the transfer of the second sugar in the chain resulted in flagellins that were not assembled into flagella filaments, as evidenced by electron microscopy. Deletions of the glycosyltransferases responsible for the addition of the third and terminal sugars in the glycan were confirmed by mass spectrometry analysis of purified flagellins from these mutants. Although flagellated, these mutants had decreased motility as evidenced by semi-swarm plate analysis with the presence of each additional sugar improving movement capabilities.     

Flagellar Formation in C-Ring-Defective Mutants by Overproduction of FliI,the ATPase Specific for Flagellar Type III Secretion

The flagellar cytoplasmic ring (C ring), which consists of three proteins, FliG, FliM, and FliN, is located on the cytoplasmic side of the flagellum. The C ring is a multifunctional structure necessary for flagellar protein secretion, torque generation, and switching of the rotational direction of the motor. The deletion of any one of the fliG, fliM, and fliN genes results in a Fla⁻ phenotype. Here, we show that the overproduction of the flagellum-specific ATPase FliI overcomes the inability of basal bodies with partial C-ring structures to produce complete flagella. Flagella made upon FliI overproduction were paralyzed, indicating that an intact C ring is essential for motor function. In FliN- or FliM-deficient mutants, flagellum production was about 10% of the wild-type level, while it was only a few percent in FliG-deficient mutants, suggesting that the size of partial C rings affects the extent of flagellation. For flagella made in C-ring mutants, the hook length varied considerably, with many being markedly shorter or longer than that of the wild type. The broad distribution of hook lengths suggests that defective C rings cannot control the hook length as tightly as the wild type even though FliK and FlhB are both intact.The flagellum is the ultrastructure for motility in many bacterial species (1). Flagellar assembly requires about 50 genes, among which about 20 gene products are incorporated in the complete flagellum (12). Most structural proteins and others necessary for assembly are exported through a flagellum-specific type III secretion apparatus housed within the basal body. The apparatus consists of at least six integral membrane proteins: FlhA, FlhB, FliP, FliQ, FliR, and FliO (for salmonellae and other species) (1, 12). Other proteins are also involved. FliI is the only known ATPase among flagellar proteins (2). FliI interacts with FliJ, which is of unknown function, and with a dimer of FliH, an inhibitor of FliI. The apparatus can be visualized by quick-freeze electron microscopy and has been termed the C (cytoplasmic) rod by virtue of its appearance and membrane-proximal location inside the C ring (7). The C ring is composed of three component proteins: FliG, FliM, and FliN (3). Mutations or deletions of any of these proteins cause a nonflagellate (Fla⁻) phenotype, strongly suggesting that the C ring is necessary for flagellar protein export (6, 22, 26). The trimer FliH₂-FliI specifically binds FliN (4, 15), suggesting that FliI docks at the periphery of the C ring through interactions with FliN-bound FliH, standing ready to escort export substrates to the secretion gate that is probably composed by FlhA, FlhB, and others (15).The C ring has long been studied with respect to motor function rather than export function. It has been proposed that FliG plays a major role in torque generation in concert with MotAB complexes, leaving the other two proteins, FliM and FliN, in minor and supporting roles (10, 11). However, as mentioned above, all three components are required for flagellar protein export (6, 22, 26). Together with the C ring, FliI pushes export substrates into the gate using the energy of ATP hydrolysis. Just recently, it was shown that FliI ATPase activity is not absolutely necessary for protein export and that increasing proton motive force (PMF) or reversion mutations in FlhA and FlhB can compensate for its absence (17, 21).In order to elucidate the roles that FliG, FliM, and FliN play in export, we employed C-ring-defective mutants. Here, we show that the overproduction of FliI allows flagellar formation in C-ring-defective mutants. We closely examined flagella formed in those mutants by electron microscopy, noting percentages of flagellation in each population, analyzing partially formed structures, and measuring hook length.     

Different Minimal Signal Peptide Lengths Recognized by the Archaeal Prepilin-Like Peptidases FlaK and PibD

In Archaea, the preflagellin peptidase (a type IV prepilin-like peptidase designated FlaK in Methanococcus voltae and Methanococcus maripaludis) is the enzyme that cleaves the N-terminal signal peptide from preflagellins. In methanogens and several other archaeal species, the typical flagellin signal peptide length is 11 to 12 amino acids, while in other archaea preflagellins possess extremely short signal peptides. A systematic approach to address the signal peptide length requirement for preflagellin processing is presented in this study. M. voltae preflagellin FlaB2 proteins with signal peptides 3 to 12 amino acids in length were generated and used as a substrate in an in vitro assay utilizing M. voltae membranes as an enzyme source. Processing by FlaK was observed in FlaB2 proteins containing signal peptides shortened to 5 amino acids; signal peptides 4 or 3 amino acids in length were unprocessed. In the case of Sulfolobus solfataricus, where the preflagellin peptidase PibD has broader substrate specificity, some predicted substrates have predicted signal peptides as short as 3 amino acids. Interestingly, the shorter signal peptides of the various mutant FlaB2 proteins not processed by FlaK were processed by PibD, suggesting that some archaeal preflagellin peptidases are likely adapted toward cleaving shorter signal peptides. The functional complementation of signal peptidase activity by FlaK and PibD in an M. maripaludis ΔflaK mutant indicated that processing of preflagellins was detected by complementation with either FlaK or PibD, yet only FlaK-complemented cells were flagellated. This suggested that a block in an assembly step subsequent to signal peptide removal occurred in the PibD complementation.The bacterial type IV prepilin peptidase (TFPP) is a well-characterized enzyme belonging to a family of novel aspartic acid proteases (20). It is responsible for the cleavage of N-terminal signal peptides from prepilins and pseudopilins, prior to their incorporation into the type IV pilus structure (22, 30, 31). The prepilin peptidase is also responsible for the processing of prepilin-like proteins needed for type II secretion (22). In Archaea, the existence of bacterial TFPP-like enzymes has also been reported, and they have been most extensively studied in relation to the assembly of the archaeal flagellum. In the euryarchaeotes Methanococcus maripaludis and Methanococcus voltae, the preflagellin peptidase FlaK was demonstrated to be responsible for cleaving the N-terminal signal peptide from the preflagellin prior to its incorporation into the growing flagellar filament, a step essential to flagellar assembly (6, 7, 26). In Sulfolobus solfataricus, an acidophilic crenarchaeote, the equivalent enzyme, PibD, was also shown to process preflagellins (4). Site-directed mutagenesis of FlaK and PibD demonstrated that both aspartic acid residues that aligned with aspartic acid residues essential for bacterial TFPP activity were also essential in the archaeal enzymes (6, 32), indicating that the two archaeal peptidases belong with the bacterial TFPPs in this novel family of aspartic acid proteases (20). More recently, an additional archaeal TFPP was found to be required for cleavage of the prepilin substrates (33) that are assembled into the unique pili of M. maripaludis (37).The substrate specificity of the archaeal preflagellin peptidase remains an open question. Like prepilin peptidases, FlaK in M. voltae has stringent requirements for the amino acids surrounding the cleavage site of the substrate, especially the −1 glycine, −2 and −3 lysines, and the +3 glycine (numbers given relative to the cleavage site) (35); the last position was conserved in all archaeal flagellins (25). Upon N-terminal sequence alignment of all available archaeal flagellin amino acid sequences at the predicted cleavage site, it was found that most archaeal preflagellin signal peptides are quite conserved in length, with the typical flagellin signal peptide being 11 to 12 amino acids in length (Table ​(Table1).1). It is speculated that while a certain amount of flexibility might exist, some optimum and minimum length probably exists that is crucial for the juxtaposition of the signal peptide and signal peptidase with respect to each other and the membrane (18). A recent study examining possible type IV pilin-like substrates in archaea using the FlaFind program indicated that such substrates may be more widespread than initially thought (33). Since in Methanococcus the pilins are processed by a second TFPP (EppA) (33), it is very possible that the preflagellins might be the only substrates of FlaK in these archaea.

TABLE 1.

N-terminal amino acid alignment of selected archaeal flagellin sequences^a

Day–night fluctuations in floral scent and their effects on reproductive success in <Emphasis Type="Italic">Lilium auratum</Emphasis>

We examined the contribution of diurnal and nocturnal pollination to male and female reproductive success in Lilium auratum. Plants were bagged for either 12 h during the day or at night to allow either only nocturnal or only diurnal visitors to forage throughout the flowering period. We found that there was no significant difference in the seed:ovule ratio among diurnally pollinated, nocturnally pollinated, or control flowers. However, in terms of male reproductive success, it was more advantageous for the plants to be pollinated both diurnally and nocturnally: the numbers of pollen grains remaining in diurnally pollinated or nocturnally pollinated flowers were significantly greater than those in control flowers. The total amount of floral volatiles of L. auratum was significantly higher at night than during the day. The constituents of floral scent of all time series examined were mostly monoterpenoids, many of which serve as attractants for nocturnal hawkmoths. Such nocturnally biased floral scent emission of L. auratum might achieve male reproductive success by attracting nocturnal visitors, which may suggest that the relative contribution of floral scent in this species is biased towards male reproductive success.     

Improving conditional random field model for prediction of protein-RNA residue-base contacts

Background: For understanding biological cellular systems, it is important to analyze interactions between protein residues and RNA bases. A method based on conditional random fields (CRFs) was developed for predicting contacts between residues and bases, which receives multiple sequence alignments for given protein and RNA sequences, respectively, and learns the model with many parameters involved in relationships between neighboring residue-base pairs by maximizing the pseudo likelihood function. Methods: In this paper, we proposed a novel CRF-based model with more complicated dependency relationships between random variables than the previous model, but which takes less parameters for the sake of avoidance of overfitting to training data. Results: We performed cross-validation experiments for evaluating the proposed model, and took the average of AUC (area under receiver operating characteristic curve) scores. The result suggests that the proposed CRF-based model without using L₁-norm regularization (lasso) outperforms the existing model with and without the lasso under several input observations to CRFs. Conclusions: We proposed a novel stochastic model for predicting protein-RNA residue-base contacts, and improved the prediction accuracy in terms of the AUC score. It implies that more dependency relationships in a CRF could be controlled by less parameters.     

A comparison of the peri-implant bone stress generated by the preload with screw tightening between ‘bonded’ and ‘contact’ model

A number of finite element analyses (FEAs) for the dental implant were performed without regard for preload and with all interfaces ‘fixed-bonded’. The purpose of this study was comparing the stress distributions between the conventional FEA model with all contacting interfaces ‘fixed-bonded’ (bonded model) and the model with the interfaces of the components in ‘contact’ with friction simulated as a preloaded implant (contact model). We further verified the accuracy of the result of the FEA using model experiment. In the contact model, the stress was more widely distributed than in the bonded model. From the model study, the preload induced by screw tightening generated strain at the peri-implant bone, even before the application of external force. As a result, the bonded model could not reproduce the mechanical phenomena, whereas the contact model is considered to be appropriate for analysing mechanical problems.