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Novel cyclic peptide antibiotics A21459 A and B are produced by a member of the genus Actinoplanes sp. These antibiotics inhibit bacterial protein synthesis and have selective antimicrobial activity against clostridia, mycoplasma and some Gram-negative bacteria.
Solvent accessibility (Lee, B. & Richards, F.M. (1971) J. Mol. Biol. 55, 379-400) was calculated for each atom of a bacterial protein proteinase inhibitor SSI (Streptomyces subtilisin inhibitor) based on crystallographic coordinates. Mainly based on this information, various chemical and spectroscopic (UV, Raman, NMR) observations made on the microenvironments of cystines, methionines, tryptophan, histidines, and tyrosines of SSI in solution were evaluated. Crystallographic data and the latter two sets of data were mainly at least qualitatively consistent with each other. These data include (1) the conformation of the two disulfide bridges, (2) the flexibility of the three methionyl side chains, (3) the extent of exposure of the indole ring of a tryptophan, (4) the environment of the two histidines, (5) the environment of the tyrosines, and (6) the hydrogen-deuterium exchangeability of peptide NH's. However, the extents of exposure of tyrosines deduced by solvent perturbation UV difference spectroscopy were significantly larger than those based on solvent accessibility calculations. Possible reasons for this discrepancy are discussed.
The chemical composition of the meat and liver of pigs fattened under production conditions was established with the addition of 3, 4, and 5 per cent bacterial protein to three experimental groups of animals, respectively. A control group of pigs was also used fed with no biomass in their feed. The trial lasted 104 days, the liveweight of the animals in the beginning of the experiment being about 35-40 kg, and at the end of it--100--115 kg. It was found that by the contents of water, total, extractable and protein nitrogen, fats, ash, essential and common proteins, tryptophane, and hydroxyproline and the index of their ratio, the pH value and calories as well as by organoleptic evaluation the samples of the investigated m. longissimus dorsi and liver of the test animals did not differ essentially (P greater than 0.05) from the respective values of the controls.
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A novel antibiotic, GE2270 A, was isolated from the fermentation broth of a strain of Planobispora rosea. The product was found to inhibit bacterial protein synthesis. Structural characteristics showed similarities between GE2270 A and thiazolyl peptides such as micrococcin which is known to inhibit protein synthesis by acting directly on the ribosome. Despite this similarity GE2270 A showed functional analogy to kirromycin-like antibiotics and pulvomycin, as its molecular target was found to be elongation factor Tu (EF-Tu). GE2270 A is active against Gram-positive microorganism and anaerobes and differs from the other EF-Tu inhibitors in its spectrum of antimicrobial activity.
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The 44-kDa envelope polypeptides are active components of the plastid translocon, but their role in plastid protein import remains elusive. One form from Brassica napus (bnToc36B) was previously observed to exert a significant overall effect on bacterial protein translocation, but the nature of the influence requires further characterization. The experimental strategies employed in this study thus focus specifically on the nature of the bnToc36B-bacterial Sec translocon relationship to gain an understanding of Toc36's function. BnToc36B's presence in bacteria created a number of effects related to the protein transport process that together point to functional interactions with the bacterial Sec translocon. These effects are (1) reduced sensitivity to azide impairment as measured by a higher recovery rate from azide treatment, (2) reduced sensitivity to suboptimal temperatures manifesting as sustained levels of protein synthesis and translocation, (3) sustained levels of growth and beta-lactamase transport in high ampicillin concentrations, and (4) evidence for a physical affinity for the bacterial translocon. A reduction in overall SecA levels and a more stable SecA profile, when subjected to azide treatment, was observed in bnToc36B-containing bacteria. The implications of the bacterial data are discussed.
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Crystallization of membrane proteins, a prerequisite for their X-ray crystallographic analysis, remains difficult. Here, we demonstrate that the crystallization of the cytochrome c oxidase from Paracoccus denitrificans can be mediated by co-crystallization with an antibody Fv fragment. The crystals obtained contain all four subunits of this membrane protein complex and the Fv fragment. The approach of co-crystallizing membrane proteins with antibody fragments should be useful in obtaining well-ordered crystals of membrane proteins in general.
Many species of Gram-negative bacteria are pathogenic bacteria that can cause disease in a host organism. This pathogenic capability is usually associated with certain components in Gram-negative cells. Therefore, developing an automated method for fast and reliable prediction of Gram-negative protein subcellular location will allow us to not only timely annotate gene products, but also screen candidates for drug discovery. However, protein subcellular location prediction is a very difficult problem, particularly when more location sites need to be involved and when unknown query proteins do not have significant homology to proteins of known subcellular locations. PSORT-B, a recently updated version of PSORT, widely used for predicting Gram-negative protein subcellular location, only covers five location sites. Also, the data set used to train PSORT-B contains many proteins with high degrees of sequence identity in a same location group and, hence, may bear a strong homology bias. To overcome these problems, a new predictor, called "Gneg-PLoc", is developed. Featured by fusing many basic classifiers each being trained with a stringent data set containing proteins with strictly less than 25% sequence identity to one another in a same location group, the new predictor can cover eight subcellular locations; that is, cytoplasm, extracellular space, fimbrium, flagellum, inner membrane, nucleoid, outer membrane, and periplasm. In comparison with PSORT-B, the new predictor not only covers more subcellular locations, but also yields remarkably higher success rates. Gneg-PLoc is available as a Web server at http://202.120.37.186/bioinf/Gneg. To support the demand of people working in the relevant areas, a downloadable file is provided at the same Web site to list the results identified by Gneg-PLoc for 49 907 Gram-negative protein entries in the Swiss-Prot database that have no subcellular location annotations or are annotated with uncertain terms. The large-scale results will be updated twice a year to cover the new entries of Gram-negative bacterial proteins and reflect the new development of Gneg-PLoc.
In experiments with dairy cows provided with rumen fistulas and duodenal re-entrant canulas, the order of feeding roughage (chopped forage and pellets) and concentrates (maize and barley) was found to influence carbohydrate digestion and bacterial protein synthesis in the rumen. Feeding the roughage 90 min. before the concentrate caused a wider C2:C3 ratio and a sustained course of the pH-value (greater than 6.5) than the ratio other way round. This favoured cellulose digestion in the rumen when feeding chopped roughage. When feeding roughage before concentrates, the nonbacterial N-proportion in the duodenal contents proved greater than in the reverse order and revealed the highest values for roughage fed in pelleted form. Feeding structured roughage as first component of the diet with concentrates given afterwards is, therefore, recommended for dairy cows.
The replication of bacteria, when unchecked, may lead to morbidity or mortality in a susceptible host. The majority of antimicrobial agents either modify or inhibit the synthesis of key substances and are reflected by morphologic, if not lethal, changes. Activity occurs during synthesis of the bacterial cell wall and synthesis of bacterial protein. These two events are described in terms of the local mechanism of action of different classes of antibiotics. The role of antibacterial agents in the replication of bacteria should be clearly understood before antibiotic therapy is administered.
BACKGROUND: Shewanella oneidensis MR-1 is a facultative, gram-negative bacterium capable of coupling the oxidation of organic carbon to a wide range of electron acceptors such as oxygen, nitrate and metals, and has potential for bioremediation of heavy metal contaminated sites. The complete 5-Mb genome of S. oneidensis MR-1 was sequenced and standard sequence-comparison methods revealed approximately 42% of the MR-1 genome encodes proteins of unknown function. Defining the functions of hypothetical proteins is a great challenge and may need a systems approach. In this study, by using integrated approaches including whole genomic microarray and proteomics, we examined knockout effects of the gene encoding SO1377 (gi24372955), a member of the conserved, hypothetical, bacterial protein family COG2268 (Clusters of Orthologous Group) in bacterium Shewanella oneidensis MR-1, under various physiological conditions. RESULTS: Compared with the wild-type strain, growth assays showed that the deletion mutant had a decreased growth rate when cultured aerobically, but not affected under anaerobic conditions. Whole-genome expression (RNA and protein) profiles revealed numerous gene and protein expression changes relative to the wild-type control, including some involved in iron metabolism, oxidative damage protection and respiratory electron transfer, e. g. complex IV of the respiration chain. Although total intracellular iron levels remained unchanged, whole-cell electron paramagnetic resonance (EPR) demonstrated that the level of free iron in mutant cells was 3 times less than that of the wild-type strain. Siderophore excretion in the mutant also decreased in iron-depleted medium. The mutant was more sensitive to hydrogen peroxide and gave rise to 100 times more colonies resistant to gentamicin or kanamycin. CONCLUSION: Our results showed that the knock-out of SO1377 gene had pleiotropic effects and suggested that SO1377 may play a role in iron homeostasis and oxidative damage protection in S. oneidensis MR-1.
Among the potential T cell determinants contained in a protein antigen, the T cell response only focuses on a few immunodominant T cell determinants, whereas cryptic epitopes remain hidden to the immune system. In the present work, we have studied the antigen processing and presentation of the C3:93-115 sequences of Mahoney poliovirus VP1 protein, which is immunodominant in H-2d but cryptic in H-2s and H-2q mouse MHC haplotypes. For this purpose, we genetically inserted the C3 determinant into five internal sites of a bacterial protein, the maltose binding protein of Escherichia coli (MalE). In four out of five insertion sites of MalE, the C3 determinant retained its immunodominance when the purified hybrid proteins were injected to BALB/c (H-2d) mice. Moreover, in SJL/J (H-2s) mice, in three out of five MalE-C3 constructs, the new structural environment of the cryptic C3 epitope rescued its processing and its in vivo presentation to T cells. In contrast, in DBA/1 (H-2q) mice, although MalE-C3 chimeric proteins were correctly processed in vitro, the C3 epitope remained cryptic in vivo. In this case, the impairment to stimulate a T cell response in vivo was correlated with a short time persistence of C3 peptides bound to Aq molecules at the surface of live antigen-presenting cells. These results emphasize the role of flanking residues on the lack of processing of cryptic determinants and the importance of the life span of peptide-MHC complexes to stimulate T cell responses.
In the evolution of eukaryotic genes, introns are believed to have played a major role in increasing the probability of favorable duplication events, chance recombinations, and exon shuffling resulting in functional hybrid proteins. As a rule, prokaryotic genes lack introns, and the examples of prokaryotic introns described do not seem to have contributed to gene evolution by exon shuffling. Still, certain protein families in modern bacteria evolve rapidly by recombination of genes, duplication of functional domains, and as shown for protein PAB of the anaerobic bacterial species Peptostreptococcus magnus, by the shuffling of an albumin-binding protein module from group C and G streptococci. Characterization of a protein PAB-related gene in a P. magnus strain with less albumin-binding activity revealed that the shuffled module was missing. Based on this fact and observations made when comparing gene sequences of this family of bacterial surface proteins interacting with albumin and/or immunoglobulin, a model is presented that can explain how this rapid intronless evolution takes place. A new kind of genetic element is introduced: the recer sequence promoting interdomain, in frame recombination and acting as a structure-less flexibility-promoting spacer in the corresponding protein. The data presented also suggest that antibiotics could represent the selective pressure behind the shuffling of protein modules in P. magnus, a member of the indigenous bacterial flora.
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