bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative studies of ribosomal proteins and their genes from Methanococcus vannielii and other organisms
Authors: Köpke Andreas K. E. , Wittmann-Liebold Brigitte
Published: November 2009

Using data from a partial protein sequence analysis of ribosomal proteins derived from the archaebacterium Methanococcus vannielii, oligonucleotide probes were synthesized. The probes enabled us to localize several ribosomal protein genes and to determine their nucleotide sequences. The amino acid sequences that were deduced from the genes correspond to proteins L12 and L10 from the rif operon, according to the genome organization in Escherichia coli, and to proteins L23 and L2, which have comparable locations, as in the Escherichia coli S10 operon. Various degrees of similarity were found when the four proteins were compared with the corresponding ribosomal proteins of prokaryotic or eukaryotic organisms. The highest sequence homology was found in counterparts from other archaebacteria, such as Halobacterium marismortui, Halobacterium halobium, or Sulfolobus. In general, the M. vannielii protein sequences were more related to the eukaryotic kingdom than to the Gram-positive or Gram-negative eubacteria. On the other hand, the organization of the ribosomal protein genes clearly follows the operon structure of the Escherichia coli genome and is different from the monocistronic eukaryotic gene arrangements. The protein coding regions were not interrupted by introns. Furthermore, the Shine–Dalgarno type sequences of methanogenic bacteria are homologous with those of eubacteria, and also their terminator regions are similar.Key words: archaebacteria, ribosomal proteins, evolution, gene organization, Methanococcus vannielii.
Genome mapping in halobacteria
Authors: Charlebois Robert L. , Hofman Jason D. , Schalkwyk Leonard C. , Lam Wan L. , Doolittle W. Ford
Published: November 2009

The goal of our research is to produce an ordered set of cosmid clones for each of several species of halobacteria for use in physical and genetic mapping. These maps will answer questions about genome evolution and about gene organization and regulation in this archaebacterial lineage. Progress in cloning and mapping the genome of Halobacterium volcanii DS2 (synonym Haloferax volcanii DS2) is reported. Overlapping cosmids are recognized by a strategy which makes use of the distinctive restriction fragments around relatively rare restriction sites. Each site recognized by the infrequently cutting restriction enzymes is a landmark from which to identify different regions of the genome. The main advantage of this strategy is that only a small overlap (10–20%) between cosmid clones is required, resulting in a correspondingly small number of cosmid clones to be analyzed. The certainty of overlap is high, and computation is simple. The final 5–10% of each genome is cloned, linked, and identified by chromosome walking methods. Hybridization of cloned homologous or heterologous genes and of stable RNAs to the minimal cosmid set localizes these genes on the physical map. Additional genes have been and will be cloned by complementation of auxotrophic mutants, or as determinants of resistance to antibiotics.Key words: landmark strategy, genome mapping, archaebacteria, cosmid.
Conserved gene structures and expression signals in methanogenic archaebacteria
Authors: Allmansberger Rudolf , Bokranz Martin , Kröckel Lothar , Schallenberg Jürgen , Klein Albrecht
Published: November 2009

A comparative analysis of cotranscribed gene clusters comprising the structural genes mcrA, mcrB, mcrC, mcrD, and mcrG was carried out in three species of methanogens. mcrA, mcrB, and mcrG are the structural genes for the three subunits of methyl coenzyme M reductase, while the two other genes encode polypeptides of unknown functions. The degree of conservation of the mcr gene products among different species of methanogens varies. No correlation was found between the conservation of the G + C contents of the homologous genes and of the amino acid sequences of their products among the different bacteria. The comparison of RNA polymerase core subunit genes of Methanobacterium thermoautotrophicum as evolutionary markers with their equivalents in Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster showed that homologous polypeptide domains are encoded by different numbers of genes suggesting gene fusion of adjacent genes in the course of evolution. The archaebacterial subunits exhibit much stronger homology with their eukaryotic than with their eubacterial equivalents on the polypeptide sequence level. All the analyzed genes are preceded by ribosome binding sites of eubacterial type. In addition to known putative promoter sequences, conserved structural elements of the DNA were detected surrounding the transcription initiation sites of the mcr genes.Key words: archaebacteria, methanogens, gene structure, RNA polymerase, promoter.
Mechanisms of genetic variability in Halobacterium halobium: the purple membrane and gas vesicle mutations
Authors: DasSarma Shiladitya
Published: November 2009

Several phenotypic variants of Halobacterium halobium arise spontaneously at extremely high frequencies (up to 1%) and are readily identified by inspection of bacterial colonies. Two mutant types, those lacking the buoyant gas vesicles or the photosynthetic purple membrane, have been studied in detail by phenotypic and molecular genetic analysis. In the wild-type NRC-1 strain, the bop gene, encoding the purple membrane protein bacterio-opsin, is found on the bacterial chromosome, while the gas vesicle protein genes, gvpA and gvpC, are present on pNRC100, a multicopy plasmid of ~150 kilobase pairs. The gvpA and gvpC genes are on a single transcription unit, while the major bop mRNA is monocistronic. Essentially all of the purple membrane deficient mutants contain insertion sequence (IS) elements into or upstream of the bop gene. Two elements, ISH 1 and ISH 2, account for most (80–90%) of the purple membrane mutations, but at least three other elements, ISH 23, ISH 26, and ISH S1, have also been implicated. The gas vesicle mutants are more heterogeneous, with many displaying partial phenotypes. Three major classes of gas vesicle mutants are distinguishable: class I and class III mutants are the result of large deletions in pNCR100; however, while class I mutants are partially gas vesicle deficient and contain a correspondingly reduced number of gvpAC operon copies, class III mutants contain no detectable copies of the gas vesicle genes and are essentially completely gas vesicle deficient. Class II mutants, like the purple membrane mutants, contain IS elements into or upstream of the gas vesicle genes. At least five different IS elements are involved: ISH 2, ISH 3, ISH 4, ISH 6, and ISH 8.Key words: insertion sequence, transposable element, plasmid, Halobacterium halobium, bacteriorhodopsin, gas vesicle.
Isolation and partial characterization of plasmids found in three Halobacterium volcanii isolates
Authors: Rosenshine Ilan , Mevarech Moshe
Published: November 2009

Three new isolates of Halobacterium volcanii were screened for the presence of plasmids. Each of the different isolates was found to contain one plasmid. These plasmids do not show any homology to each other, nor to the previously isolated plasmid pHV2. Partial restriction maps of these plasmids were determined. One of the plasmids contains chromosomal repetitive sequences as judged by the existence of homologous sequences in the chromosomal DNA of the three isolates. Using the protoplast fusion technique, we showed that at least one of the newly isolated plasmids is compatible with pHV2.Key words: Halobacterium volcanii, archaebacterium, plasmids.
Genome structure of Halobacterium halobium: plasmid dynamics in gas vacuole deficient mutants
Authors: Pfeifer Felicitas , Blaseio Ulrike , Horne Mary
Published: November 2009

Halobacterium halobium contains two gas vacuole protein genes that are located in plasmid pHH1 (p-vac) and in the chromosomal DNA (c-vac). The mutation frequency for these genes is different: the constitutively expressed p-vac gene is mutated with a frequency of 10−2, while the chromosomal gene expressed in the stationary phase of growth is mutated with a frequency of 10−5. The difference in the mutation susceptibility is due to the dynamics of plasmid pHH1. p-vac gene mutations are caused (i) by the integration of an insertion element or (ii) by a deletion event encompassing the p-vac gene region. In contrast, c-vac mutants analyzed to date incurred neither insertion elements nor deletions. Deletion events within pHH1 occur at high frequencies during the development of a H. halobium culture. The investigation of the fusion regions resulting from deletion events indicates that insertion elements are involved. The analysis of pHH1 deletion variants led to a 4 kilobase pair DNA region containing the origin of replication of the pHH1 plasmid.Key words: gas vacuole protein gene, plasmid dynamics, deletions, insertion elements.
A brief note concerning archaebacterial phylogeny
Authors: Olsen Gary J. , Woese Carl R.
Published: November 2009

Critical analysis of the recently proposed alternative to the normal archaebacterial tree, the new eocyte tree, shows that the latter's central topology, in which the eubacteria branch from an entirely different section of the unrooted archaebacterial tree than the eukaryotes, is consistent with an artifact. The effects of the alignment used and the particular composition of the sequence quartets analyzed to infer this tree are discussed in detail.Key words: archaebacteria, molecular phylogeny, 16S ribosomal RNA, evolution, eocyte tree.
The structure and organization of the 16S ribosomal RNA gene from the archaebacterium Thermoplasma acidophilum
Authors: Ree Heesoo K. , Cao Kaiming , Thurlow David L. , Zimmermann Robert A.
Published: November 2009

The complete nucleotide sequence of the 16S rRNA gene from Thermoplasma acidophilum, as well as its 5′ and 3′ flanking regions, were determined by the dideoxynucleotide chain termination method. The 16S rRNA gene encodes 1471 nucleotides. The primary and secondary structures of T. acidophilum 16S rRNA both exhibit typical archaebacterial features. The sequence appears to be more closely related to 16S rRNAs of the methanogen–halophile group than to those of the thermoacidophile group. Secondary-structure comparisons generally support this relationship, although there are several examples in which the single-stranded loops in particular helices of T. acidophilum 16S rRNA more strongly resemble their counterparts in the 16S rRNA of Sulfolobus solfataricus, a member of the thermoacidophile group. In contrast to the polycistronic rRNA operons found in most organisms, the three rRNA genes from T. acidophilum occur in only a single copy per genome and appear to be physically unlinked. Consistent with this, the 16S rRNA gene is flanked by putative promoter and terminator sequences that are comparable to the transcription control signals from other archaebacterial genes. The sequence TATATATA, which is very similar to the archaebacterial promoter consensus TTTAT/AATA, is located 18 bases before the probable site of transcription initiation, TGCACAT. There is a potential transcription termination site immediately downstream from the gene that consists of a relatively stable stem and loop structure followed by stretches of Tresidues.Key words: archaebacteria, thermoacidophile, rRNA sequence, rRNA secondary structure, promoter.
The use of functional analysis of the ribosome as a tool to determine archaebacterial phylogeny
Authors: Amils R. , Ramírez L. , Sanz J. L. , Marín I. , Pisabarro A. G. , Ureña D.
Published: November 2009

Forty different antibiotics with diverse kingdom and functional specificities were used to measure the functional characteristics of the archaebacterial translation apparatus. The resulting inhibitory curves, which are characteristic of the cell-free system analyzed, were transformed into quantitative values that were used to cluster the different archaebacteria analyzed. This cluster resembles the phylogenetic tree generated by 16S rRNA sequence comparisons. These results strongly suggest that functional analysis of an appropriate evolutionary clock, such as the ribosome, is of intrinsic phylogenetic value. More importantly, they indicate that the study of the nexus between genotypic and phenotypic (functional) information may shed considerable light on the evolution of the protein synthetic machinery.Key words: antibiotics, ribosomes, archaebacteria, phylogeny, functional analysis.
Ribosomal protein gene cluster of Halobacterium halobium: nucleotide sequence of the genes coding for S3 and L29 equivalent ribosomal proteins
Authors: Spiridonova V. A. , Akhmanova A. S. , Kagramanova V. K. , Köpke A. K. E. , Mankin A. S.
Published: November 2009

A 1643 base pair fragment encoding the S3 and L29 equivalent ribosomal proteins has been sequenced from the archaebacterium Halobacterium halobium. The incomplete open reading frame present upstream from the S3 gene encodes a protein homologous to the eubacterial ribosomal protein L22. The initiation codons of the S3 and L29 genes overlap with the termination codons of the upstream genes. A tight physical organization suggests that these genes are transcribed as a polycistronic operon. Peculiarities of the protein structure and gene organization are discussed.Key words: archaebacteria, ribosomal protein, halobacteria, gene structure, evolution.
Biosynthesis of pseudomurein: isolation of putative precursors from Methanobacterium thermoautotrophicum
Authors: König Helmut , Kandler Otto , Hammes Walter
Published: November 2009

In aqueous trichloroacetic acid extracts of Methanobacterium thermoautotrophicum the following compounds, which are supposed to be precursors in the biosynthesis of the glycan strand of the pseudomurein, were isolated and identified: (i) a disaccharide (compound II) composed of uridine 5′-diphosphate, N- acetylglucosamine and N-acetyltalosaminuronic acid with N-acetylglucosamine at the reducing end, (ii) uridine 5′-diphospho-N-acetylglucosamine, and (iii) uridine 5′-diphospho-N-acetylgalactosamine. However, the corresponding monomeric derivative of N-acetyltalosaminuronic acid could not be detected. It is assumed that N-acetyltalosaminuronic acid may be formed from N-acetylgalactosamine by epimerisation and oxidation at the disaccharide level. These findings indicate that the biosynthetic pathways of murein and pseudomurein are quite different.Key words: pseudomurein, cell wall, archaebacteria, biosynthesis, methanogens.
Expression and regulation of Halobacterium halobium phage ΦH genes
Authors: Gropp Felix , Palm Peter , Zillig Wolfram
Published: November 2009

In this paper we describe five distinct modes of ΦH gene expression: (i) transcription of phage ΦH during lytic growth on the sensitive host bacterium (Halobacterium halobium strain R,); (ii) transcription of the circularized prophage ΦH1 in strain R124; (iii) transcription of the L region of ΦH present as 12-kilobase-plasmid in the immune strain R1L; (iv) transcription during the lytic growth of phage mutants containing an ISH23/50 in the immune strain R1L; (v) transcription during lytic growth of ISH23/50-insertion mutants in the sensitive host bacterium R1 showing enhancement of early transcripts. The sequential expression of the phage genome is described together with a detailed analysis of the transcription of early lytic, constitutive, and immune genes that map in the L region. The putative promoter sequences determined for several phage genes were compared with the upstream sequences of the H. halobium DNA-dependent RNA polymerase large subunit genes and with the gene for the ribosomal protein S12 homolog of H, halobium. The similarity of these putative promoter elements revealed conserved motifs that are discussed in relation to the TATA-box motif recognized by the eukaryotic DNA-dependent RNA polymerase II.Key words: Halobacterium, phage, gene expression, enhancer, promoter.
Studies on DNA polymerases and topoisomerases in archaebacteria
Authors: Forterre Patrick , Eue Christiane , Sioud Mouldy , Hamal Abdellah
Published: November 2009

We have isolated DNA polymerases and topoisomerases from two thermoacidophilic archaebacteria: Sulfolobus acidocaldarius and Thermoplasma acidophilum. The DNA polymerases are composed of a single polypeptide with molecular masses of 100 and 85 kDa, respectively. Antibodies against Sulfolobus DNA polymerase did not cross react with Thermoplasma DNA polymerase. Whereas the major DNA topoisomerase activity in S. acidocaldarius is an ATP-dependent type I DNA topoisomerase with a reverse gyrase activity, the major DNA topoisomerase activity in T. acidophilum is a ATP-independent relaxing activity. Both enzymes resemble more the eubacterial than the eukaryotic type I DNA topoisomerase. We have found that small plasmids from halobacteria are negatively supercoiled and that DNA topoisomerase II inhibitors modify their topology. This suggests the existence of an archaebacterial type II DNA topoisomerase related to its eubacterial and eukaryotic counterparts. As in eubacteria, novobiocin induces positive supercoiling of halobacterial plasmids, indicating the absence of a eukaryotic-like type I DNA topoisomerase that relaxes positive superturns.Key words: archaebacteria, DNA topoisomerases, DNA polymerases, DNA topology, gyrase.
Structure and evolution of the L11, L1, L10, and L12 equivalent ribosomal proteins in eubacteria, archaebacteria, and eucaryotes
Authors: Ramirez Celia , Shimmin Lawrence C. , Newton C. Hunter , Matheson Alastair T. , Dennis Patrick P.
Published: November 2009

The genes corresponding to the L11, L1, L10, and L12 equivalent ribosomal proteins (L11e, L1e, L10e, and L12e) of Escherichia coli have been cloned and sequenced from two widely divergent species of archaebacteria, Halobacterium cutirubrum and Sulfolobus solfataricus, and the L10 and four different L12 genes have been cloned and sequenced from the eucaryote Saccharomyces cerevisiae. Alignments between the deduced amino acid sequences of these proteins and to other available homologous proteins of eubacteria and eucaryotes have been made. The data suggest that the archaebacteria are a distinct coherent phylogenetic group. Alignment of the proline-rich L11e proteins reveals that the N-terminal region, believed to be responsible for interaction with release factor 1, is the most highly conserved region and that there is specific conservation of most of the proline residues, which may be important in maintaining the highly elongated structure of the molecule. Although L11 is the most highly methylated protein in the E. coli ribosome, the sites of methylation are not conserved in the archaebacterial L11e proteins. The L1e proteins of eubacteria and archaebacteria show two regions of very high similarity near the center and the carboxy termini of the proteins. The L10e proteins of all kingdoms are colinear and contain approximately three fourths of an L12e protein fused to their carboxy terminus, although much of this fusion has been lost in the truncated eubacterial protein. The archaebacterial and eucaryotic L12e proteins are colinear, whereas the eubacterial protein has suffered a rearrangement through what appear to be gene fusion events. Within the L12e derived region of the L10e proteins there exists a repeated module of 26 amino acids, present in two copies in eucaryotes, three in archaebacteria, and one in eubacteria. This modular sequence is apparently also present in the L12e proteins of all kingdoms and may play a role in L12e dimerization, L10e–L12e complex formation, and the function of the L10e–L12e complex in translation.Key words: translation, ribosome.
Development of Entomophaga aulicae protoplasts in synthetic eastern hemlock looper hemolymph
Authors: Dunphy Gary B. , Nolan Richard A.
Published: November 2009

The protoplast stages of Entomophaga aulicae grew in a medium based on the amino acid and amine composition of the hemolymph of the eastern hemlock looper, Lambdina fiscellaria fiscellaria. The optimum temperature and pH ranges for spindle-shaped protoplast growth were 15 to 25 °C and 5.5 to 6.5, respectively. Spindle-shaped protoplast development progressed asynchronously through the formation of mesoprotoplasts, elliptical mesoprotoplasts, and rod-shaped and spherical hyphal bodies. The production of these stages was not influenced by either medium pH or osmolality. Conidia were formed on conidiophores arising from spherical hyphal bodies near the surface of the culture medium. Changes in amino acid and amine levels during growth were correlated with the stage of fungal development. The major amino acids utilized during development included L-glutamine, L-asparagine, L-proline, L-leucine, L-isoleucine, L-tyrosine, and the amine O-phosphoethanolamine.Key words: Entomophaga aulicae, Lambdina fiscellaria fiscellaria, protoplasts, hemolymph, ninhydrin-positive compounds.
The role of an extracellular polysaccharide produced by the marine Pseudomonas sp. S9 in cellular detachment during starvation
Authors: Wrangstadh Michael , Conway Patricia L. , Kjelleberg Staffan
Published: November 2009

An exopolysaccharide polymer is produced by the marine Pseudomonas sp. S9 in response to complete energy and nutrient starvation. The presence of this polysaccharide on the cell surface and its subsequent release have been shown to be associated with both adhesion and detachment of the bacterial cells. Detachment from a hydrophobic surface was correlated to the presence of the exopolysaccharide on detached S9 cells. The exopolysaccharide was detected, using immunofluorescence microscopy, on surface-bound cells after only 15 min of exogenous energy and nutrient deprivation. This technique did not reveal any significant amounts of exopolysaccharide on starving bulk phase cells prior to 3 h of starvation. Cells that detached after 5.5 h of starvation had low cell surface hydrophobicity values and increased amounts of cell-bound exopolysaccharide. In contrast, cells that became detached during the first 5.5 h of starvation showed increasing hydrophobicity values during prolonged bulk phase starvation.
Effects of methanol on the growth of gastrointestinal anaerobes
Authors: Caldwell Daniel R.
Published: November 2009

The effects of methanol on the growth of representative, predominant, anaerobic gut bacteria were studied. Growth yields and rates were determined in a base medium to which methanol was added to produce media with methanol concentrations varying, in twofold steps, over a concentration range of 0.01 to 25%, by volume. The growth of many of the organisms was completely inhibited by a methanol concentration equal to, or less than, 6.2%. Isolates representing cellulolytic species were completely inhibited at a methanol concentration of 3.1%, and inhibitory effects on the yield of some cellulolytic isolates were found at a methanol concentration as small as 0.01%. Although most of the organisms studied were inhibited at relatively small methanol concentrations, isolates of Selenomonas ruminantium, Bacteroides ovatus, and Fusobacterium necrophorum were relatively methanol resistant. A methanol concentration of 12.5% was required to completely inhibit S. ruminantium. Substantial growth of B. ovatus was obtained in media containing 12.5% methanol, and for F. necrophorum, substantial growth occurred in media containing 25% methanol. The yields of F. necrophorum strain B85 and S. ruminantum strain PC18 were enhanced by relatively small methanol concentrations and reduced with further methanol concentration increase. Anaerobic, nonsporing gut bacteria exhibit a diversity of responses to methanol.Key words: methanol, growth, bacteria, anaerobic, gastrointestinal.
Bactericidal action of peptide antibiotic AS-48 against Escherichia coli K-12
Authors: Gálvez A. , Valdivia E. , Martínez M. , Maqueda M.
Published: November 2009

Peptide antibiotic AS-48 exerts a bactericidal mode of action on exponential cultures of Escherichia coli K-12 through a multi-hit kinetics interaction. AS-48 causes a parallel and gradual cessation of all biosynthetic pathways monitored (protein, RNA, DNA, and cell wall synthesis), the rate of incorporation of labeled precursors, the rate of O2 consumption, and cell growth. These effects have been attributed to alterations of cytoplasmic membrane functions.Key words: Escherichia coli, peptide antibiotic, bactericide.
Production of mutacin-like substances by Streptococcus mutans
Authors: Parrot M. , Charest M. , Lavoie M. C.
Published: November 2009

Production of inhibitory substances by strains of the Streptococcus mutans group is well documented, but the nature of the substances implied is often unknown. Of nine laboratory strains known to produce inhibitory substances, the optimal conditions for producing inhibition zones on solid media were found to vary between strains but good production was generally obtained on all-purpose media with Tween 80 at 37 °C after 2–4 days of aerobic incubation. Streptococcus sanguis Ny101 was found to be more sensitive than Streptococcus rattus LG-1 to all inhibitory substances produced by the S. mutans strains tested. While all strains showed some inhibition, only six showed inhibition after neutralization; arginine incorporated in agar at 0.75% completely eliminated all inhibition zones. However 1% arginine in the overlays did not affect the production of inhibition zones by strains of S. mutans C67-1, Ny257, Ny266, and T8. These strains were shown to elaborate (in a reproducible fashion) inhibitory substances which were not organic acids. Inhibitory activity was never obtained in liquid preparations, except for strains Ny257 and T8 where it was found to be very unstable.Key words: mutacin, bacteriocin, inhibitory substance, Streptococcus mutans.
Ethylene is synthesized by vegetative mycelium in surface cultures of Penicillium cyclopium Westling
Authors: Pažout Jaroslav , Pažoutová Sylvie
Published: November 2009

Surface cultures of Penicillium cyclopium, grown in a closed aeration system on a semisolid minimal medium with 2-keto-glutarate, glutamate or glucose as carbon source, produced ethylene in two phases. The first was associated with aerial hyphae formation; the second, with conidiation. The maximum rate of ethylene synthesis coincided with intensive oxygen consumption whereas the cessation and reutilization of ethylene occurred together with a low respiration rate. After the removal of the aerial mycelium, vegetative hyphae continued ethylene production up to 50% of the value reached in intact cultures. Neither detached aerial mycelium with penicilli nor pure conidia produced ethylene. The content of ethylene in the medium of a producing culture was four-fold higher than would correspond to its concentration in the atmosphere above the culture. In the upper agar layer (1.25 mm), a high pH (8.8) and 30 mM [Formula: see text]was found, presumably because of mycelium autolysis. The pH in the layer 3 mm below the surface was 2.4. In lower layers (up to 2 mm beneath the last vegetative hyphae), ammonium ions were completely depleted. The phosphate content was inversely proportional to the hyphal density. We suggest that the low phosphate concentration (0.06 mM) in the upper layers permitted ethylene formation.Key words: conidiation, vegetative hyphae, ethylene, ion gradients, surface culture.
Morphological changes in putrefactive anaerobe 3679 (Clostridium sporogenes) induced by sorbate, hydrochloric acid, and nitrite
Authors: Ronning Irene E. , Frank Hilmer A.
Published: November 2009

Putrefactive anaerobe 3679 (Clostridium sporogenes), a gram-positive bacterium, was examined by light and electron microscopy during normal growth and in a medium containing sorbate (50 mM, pH 6.5), hydrochloric acid (pH of medium adjusted from 7 to 5 with HCl), or nitrite (1 mM, pH 7). During the early exponential growth phase, untreated cells were filamentous and nonseptate, but became septate later and divided when the culture entered the stationary phase. Untreated short and filamentous cells had a double-layered cell wall. Sorbate-treated cells were usually filamentous and nonseptate, but with distorted shapes characterized by numerous bends and bulges. Septation, when present, resulted in minicells. The inner cell wall appeared to be thickened and the outer wall was absent in many areas. Acid-treated cells were similar to sorbate-treated cells but contained septa. Considerable cellular debris was present in the suspension. Nitrite-treated cells were also filamentous, bent, and bulged but the cell wall appeared normal. Considerable cellular debris was also present in suspensions of nitrite-treated cells. Changes in morphology are discussed in relation to possible mechanisms of cell growth regulation and the inhibitory action of sorbate, acid, and nitrite.Key words: putrefactive anaerobe 3679, sorbate, hydrochloric acid, nitrite.
Ammonium ions repress δ-(L-α-aminoadipyl)-L-cysteinyl-D-valine synthetase in Streptomyces clavuligerus NRRL 3585
Authors: Zhang Jinyou , Wolfe Saul , Demain Arnold L.
Published: November 2009

Production of cephems (predominantly cephamycin C) by Streptomyces clavuligerus grown in chemically defined medium supplemented with 120 mM NH4Cl was sharply reduced. This concentration of ammonium ions in the medium repressed δ-(L-α-aminoadipyl)-L-cysteinyl-D-valine (ACV) synthetase formation by about 75%. Of the other cephalosporin synthases, cyclase was repressed by 70%, expandase by 50%, and epimerase only to a very small extent. Inhibition of the action of ACV synthetase was only slight in the presence of 100 mM NH4Cl. Repression of ACV synthetase, cyclase, and expandase appears to be the major factors contributing to the negative effect of ammonium on S. clavuligerus NRRL 3585. ACV synthetase is probably the rate-limiting step of cephalosporin biosynthesis in this strain.Key words: β-lactam biosynthesis, antibiotic biosynthesis, cephalosporins, Streptomyces clavuligerus, ACV synthetase.
Non-nodular endorhizospheric nitrogen fixation in wetland rice
Authors: You Chongbiao , Zhou Fayong
Published: November 2009

Diazotrophic Alcaligenes faecalis strain A15 isolated from rice roots is associated with rice roots and resides in the mucilage layer. On examination by light and electron microscopy, about 10% of the bacteria that accumulated on the surface entered the root cells. Some bacteria were observed to penetrate the cell wall. By using a 10B α-track technique, the presence of bacteria inside the root was also demonstrated after the rice plants were inoculated with A. faecalis. This was further supported by results of an immunofluorescence study. Both single cells and protoplasts were isolated from rice root and its callus. Transmission and scanning electron microscopy showed that A. faecalis grew inside the root cell. Callus, developed from rice root cells inoculated with this bacterium, grew well in nitrogen-free culture medium, while it died within 30 days without inoculation. Nitrogen fixation in the callus was confirmed by 15N tracer methodology and the rate ranged from 18.5 to 35.5 μg N fixed/g dry weight callus per day.Key words: Alcaligenes faecalis, endorhizospheric nitrogen fixation, rice–bacteria symbiont.
Diagnostic biochimique de la présence d'une intoxication par Bacillus thuringiensis sérotype "H3a,3b" chez deux lépidoptères
Authors: Valéro J. R. , Letarte R.
Published: November 2009

A detailed biochemical analysis has shown that during larval development on artificial medium, the amounts of K+, Na+, and Ca2+ in the hemolymph of healthy Choristoneura fumiferana varied from 85 to 110 mg/100 mL, 29 to 33 mg/100 mL, and 4.8 to 7.3 mg/100 mL, respectively. Similar results were obtained with Malacosoma disstria. Intoxication by Bacillus thuringiensis "H3a,3b" (B. t.) considerably modified the amounts of the cations. Thus, after 4 h, the quantity of K+ in M. disstria increased from 99 to 229 mg/100 mL and Na+ from 26.5 to 50.3 mg/100 mL while that of Ca2+ decreased from 5.8 to 1.2 mg/100 mL. Similar results were observed with C. fumiferana, but these variations occurred after 2 to 4 days of B. t. intoxication. The variations detected during the bacillosis, with respect to the cationic composition of the insect hemolymph, are rapidly detectable, well before light microscope observation can confirm the presence of this intoxication. Aspartate aminotransferase, alanine aminotransferase, α-hydroxybutyrate dehydrogenase, and isocitrate dehydrogenase activity fluctuated very slightly in the hemolymph of either healthy or bacillosed larvae of the two insects under study. These results suggest that it is possible to diagnose biochemically the presence of a B. t. intoxication in lepidopteran forest pests following treatments by this biological insecticide for their control.Key words: lepidoptera, Bacillus thuringiensis, intoxication, biochemical diagnosis, cations.
Plant growth responses to bacterization with selected Pseudomonas spp. strains and rhizosphere microbial development in hydroponic cultures
Authors: Peer Ron van , Schippers Bob
Published: November 2009

Increases in root and shoot fresh weight were observed when the nutrient solutions used for growth of tomato, cucumber, lettuce, and potato plants were bacterized with plant growth promoting Pseudomonas strains. It is hypothesized that plant growth promotion is due to the suppression of a deleterious rhizosphere microflora, especially deleterious endorhizosphere bacteria. The composition of the microbial community in artificial substrates, such as nutrient films and rockwool, is thought to be less complex than in soil. Therefore, development of a microflora deleterious for plant growth has to be anticipated. Microbial development in hydrocultures was simulated by preinoculating plant nutrient solutions with rhizosphere suspensions from plants that had been grown for different lengths of time in hydroponic cultures. After 16 days the plants in preinoculated nutrient solutions showed a growth reduction that correlated with the extent of root colonization by fluorescent pseudomonads in the endorhizosphere. Bacterization with plant growth promoting Pseudomonas sp. strain WCS417r counteracted this plant growth reduction. This increase in plant growth was accompanied by a dense colonization of the endorhizosphere by WCS417r and by a consequent displacement of indigenous endorhizosphere-inhabiting pseudomonads.Key words: Pseudomonas, endorhizosphere, hydroponics, plant growth, colonization.
The germination of basidiospores from commercial and wild-collected isolates of Agaricus bisporus (= A. brunnescens)
Authors: Horgen Paul A. , Kokurewicz Karl F. , Anderson James B.
Published: November 2009

A standard set of conditions yielding highly reproducible germination kinetics for basidiospores of the commercial mushroom Agaricus bisporus is described. Spores of three commercial, one wild-collected, and one intraspecies hybrid were examined. The effects of presence or absence of growing mycelium, temperature, culture media, and spore age are described. Cycloheximide completely blocked basidiospore germination and the incorporation of [3H]leucine into protein, whereas actinomycin D had no effect on germ tube emergence. Furthermore, [3H]uridine is not incorporated into spores before or during germination, neither in the presence nor absence of actinomycin D. Two types of basidiospore dormancy exist for A. bisporus: (i) exogenously dormant spores and (ii) constitutively dormant spores, both of the group II type in which protein synthesis precedes RNA synthesis.Key words: spore, germination, Agaricus, basidiomycete.
Aerobic purification of N5,N10-methylenetetrahydromethanopterin dehydrogenase, separated from N5,N10-methenyltetrahydromethanopterin cyclohydrolase, from Methanobacterium thermoautotrophicum strain Marburg
Authors: Mukhopadhyay Biswarup , Daniels Lacy
Published: November 2009

The N5,N10-methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum strain Marburg has been purified with reasonable yield and much higher specific activity than previously reported. For the first time it has been shown that both N5,N10-methylenetetrahydromethanopterin dehydrogenase and N5,N10-methenyltetrahydromethanopterin cyclohydrolase activities were stable under air and could be purified using aerobic operations. The dehydrogenase activity from Methanobacterium thermoautotrophicum Marburg was stable in phosphate buffer with or without glycerol or ammonium sulfate under both aerobic and anaerobic conditions. However, the presence of either 2-mercaptoethanol or dithiothreitol in the enzyme solution destroyed the enzyme activity during both aerobic and anaerobic incubations. Dehydrogenase was purified 62-fold using Phenyl-Sepharose and DEAE-Sephadex chromatography in succession under air. Both of these chromatographic methods separated dehydrogenase activity from N5,N10-methenyltetrahydromethanopterin cyclohydrolase; DEAE-Sephadex provided the best separation. Phenyl-Sepharose chromatography of the supernatant of cell extracts containing ammonium sulfate at 60% of saturation provided a 4.7-fold purification and 98% recovery of cyclohydrolase; this result established the air stability of N5,N10-methenyltetrahydromethanopterin cyclohydrolase from Methanobacterium thermoautotrophicum Marburg.Key words: methylenetetrahydromethanopterin dehydrogenase, methenyltetrahydromethanopterin cyclohydrolase, Methanobacterium, aerobic purification, oxygen stability.
Utilization of D-amino acids by Halobacterium halobium R1mR
Authors: Tanaka Mikiei , Mukohata Yasuo , Yuasa Seiji
Published: November 2009

Halobacterium halobium R1mR required L-amino acids such as methionine, leucine, valine, isoleucine, arginine, and lysine for growth. They also grew, with a lag phase of 15 to 20 days, when phenylalanine or tyrosine was omitted from the medium. This represents the first evidence that halophilic bacteria can grow on either D-methionine, D-phenylalanine, D-tyrosine, or D-leucine, each of which was substituted for the opposite enantiomer in the medium.Key words: halobacteria, D-amino acid.
Effects of selected carbohydrates and the contribution of the prophenoloxidase cascade system to the adhesion of strains of Pseudomonas aeruginosa and Proteus mirabilis to hemocytes of nonimmune larval Galleria mellonella
Authors: Dunphy Gary B. , Chadwick June S.
Published: November 2009

The adhesion of strains of Pseudomonas aeruginosa and Proteus mirabilis to the plasmatocytes and granular cells of non-immune larval Galleria mellonella was influenced by and varied with the type of carbohydrate. Laminarin enhanced prophenoloxidase activation and bacterial adhesion to the hemocytes whereas sucrose suppressed both activities. For all other sugars there was no correlation between bacterial adhesion to the hemocytes and phenoloxidase activity. It is proposed that bacterial adhesion to the hemocytes may be mediated by both lectinlike binding and components of the prophenoloxidase activating system acting like opsonins.Key words: Pseudomonas, Proteus, hemocytes, prophenoloxidase, lectins.
Identification of cytoplasmic membrane protein antigens of Mycobacterium avium, M. intracellular, and M. scrofulaceum
Authors: George Karen L. , Falkinham III Joseph O.
Published: November 2009

The cytoplasmic membrane isolated from representative strains of the Mycobacterium avium, M. intracellular, and M. scrofulaceum (MAIS) group contained approximately 20 proteins, as identified by SDS – polyacrylamide gel electrophoresis. One membrane protein predominated, comprising up to 50% of the total membrane protein. This major cytoplasmic membrane protein (MCMP) had a molecular weight of 31 000 and was surface accessible based on its susceptibility to proteinase digestion. The composition of the culture medium strongly influenced the amount of MCMP in the membrane fraction. Western blot analysis revealed that the MCMP and several other membrane proteins reacted with serum samples from patients infected with M. avium-intracellulare, M. tuberculosis, or other mycobacteria.Key words: Mycobacterium avium, membrane, antigens.
Survival and effects of wild-type, mutant, and recombinant Streptomyces in a soil ecosystem
Authors: Wang Zemin , Crawford Don L. , Pometto III Anthony L. , Rafii Fatemeh
Published: November 2009

In a laboratory simulation, selected wild-type, mutant, and recombinant Streptomyces were released into a silt loam soil. Strains included genetically enhanced lignin decomposers and those expressing recombinant plasmids. Their survival and effects on soil organic carbon mineralization were monitored in sterile and nonsterile soil, with and without lignocellulose supplementation. Survival was followed by viable plate counts on selective media. CO2 evolution was monitored in respiration cabinets. All strains, whether released as spores or mycelia, survived in nonsterile soil for up to 30 days. Selected strains released as spores survived for at least 10 months. With all strains, the numbers of colony-forming units per gram of soil slowly declined until relatively similar, stable population levels were achieved. Spores were more stable than mycelia. Only one recombinant survived significantly better in nonsterile soil than did its corresponding nonrecombinant parent, but only during the 1st to 2nd week after release. With two exceptions, there were no statistically significant short-term effects of release on the rates of carbon mineralization in unamended or lignocellulose-amended sterile and nonsterile soils. One recombinant, Streptomyces lividans TK23-3651, significantly affected the short-term rate of soil organic carbon turnover. After its release, the rate of soil organic carbon mineralization increased, particularly in nonsterile soil amended with lignocellulose. The cumulative amount of CO2 evolved over a 30-day period was significantly higher than for control soils or those inoculated with other Streptomyces. Another recombinant, S. lividans TK23/pSE1, temporarily reduced carbon mineralization rates, but only in nonsterile, unamended soil during the first few days after release. This is the first report of released, genetically altered Streptomyces having a measurable effect on a natural ecosystem. The significant enhancing effect of strain TK23-3651 was transient, and additional studies showed that this strain was genetically unstable in soil.Key words: Streptomyces, recombinant, soil, environment, release.
The effects of varying moisture and nutrient levels on the transfer of a conjugative plasmid between Streptomyces species in soil
Authors: Bleakley Bruce H. , Crawford Don L.
Published: November 2009

Biparental crosses were established in sterile silt loam between a plasmid-free Streptomyces parvulus strain (recipient) and a recombinant Streptomyces lividans strain (donor) bearing the recombinant, conjugational plasmid pIJ303 which codes for thiostrepton resistance. The crosses were established in autoclaved portions of soil adjusted to approximately 60, 40, and 20% water-holding capacity. The soil was amended with either CaCO3 alone (limed), or CaCO3 along with cottonseed flour, chitin, and cellulose (nutrient amended). After a month or longer incubation at 30 °C, the number of transconjugants in each soil treatment was determined by spread-plating on thiostrepton–agar selective medium. The heterotrophic microbial activity of each soil was also assayed with fluorescein diacetate. Nutrient amendment resulted in two to three times more fluorescein diacetate activity than for the unamended, limed treatments of equivalent moisture content. The nutrient-amended, low moisture treatment resulted in the greatest frequency of plasmid transfer. In comparison, plasmid transfer frequencies for the nutrient-amended, higher moisture treatments and for the limed treatments were approximately 5 to 73 times lower. The results suggest that nutrient-amended, relatively dry soils possess frequent microsites where mycelial growth and conjugationally mediated plasmid exchange between streptomycetes occur readily.Key words: Streptomyces, plasmid, conjugation, soil, gene transfer.
Arthrobacter species as a prey cell reservoir for nonobligate bacterial predators in soil
Authors: Casida Jr. L. E.
Published: November 2009

The possibility was investigated that, in soil, Arthrobacter species might serve as a major reservoir of prey cells for the nonobligate bacterial predators in the soil. Previous evidence had indicated this. Arthrobacter globiformis cells added to soil caused an increase in the total bacterial count and the gram-negative bacteria count of the soil. Copper-resistant bacterial predators, such as Cupriavidus necator, also increased in number, apparently in response to the A. globiformis cells. Other bacterial predators did not respond to A. globiformis. Certain soil bacteria responded specifically and quickly (within 2.5 h) to the A. globiformis cell additions. They had gliding motility and could hydrolyze GELRITE (the solidifying agent for media). Addition of these hydrolyzer bacteria to soil caused marked increases in the total bacteria count, the gram-negative bacteria count, and the bacterial predator counts. These responses mimicked those for A. globiformis soil additions. The results from an alternative method of soil incubation that speeded up the processes, and from other observations, indicated that the large apparent bacterial predator attack on A. globiformis in soil may actually be on other bacteria in soil that respond to A. globiformis in a nonpredatory manner. Therefore, A. globiformis and other Arthrobacter species may not be serving as a major reservoir of prey cells in soil.Key words: predation, predators, prey, soil, Arthrobacter.
Synthesis of a ribosome-bound translatable poly(A)− mRNA during spore germination in Dictyostelium discoideum
Authors: Ramagopal S.
Published: November 2009

A distinct poly(A)− RNA sedimenting around 10–12S was identified during spore germination in Dictyostelium discoideum. Activated spores were labeled with [3H]uracil and the poly(A)− RNA was purified from ribosomal particles for analysis. In the spore swelling stage, 40 to 50% of the newly synthesized poly(A)− RNA was 10–12S RNA. This fraction diminished to one-half or one-fourth depending on the labeling period at the stage of amoeba emergence. The 10–12S RNA was associated with both monosomes and polysomes in vivo. Translation in a wheat germ cell-free system and gel electrophoresis demonstrated that the 10–12S RNA coded for a number of polypeptides, some of which were also represented among the in vitro products of poly(A)+ RNA. However, there were seven unique polypeptides (37.5, 28.2, 27.5, 23, 17.7, 17, and 14.2 kilodaltons) encoded exclusively by 10–12S RNA.Key words: cellular slime mold, RNA synthesis, development, poly(A)− mRNA, in vitro translation.
Effect of protozoan predation on relative abundance of fast- and slow-growing bacteria
Authors: Sinclair James L. , Alexander Martin
Published: November 2009

The survival of six bacterial species that had different growth rates was tested in raw sewage and sewage that was rendered free of protozoa. When test bacteria were added to protozoa-free sewage at densities of approximately 105 to 106 cells/mL, five of the six species did not decline below 105 cells/mL. If protozoa were present, the population sizes of all test species were markedly reduced, but bacterial species able to grow faster in artificial media had the larger number of survivors. When the same bacteria were inoculated into protozoa-free sewage at densities of less than 103 cells/mL, only the three species able to grow quickly in artificial media increased in abundance. When the six species were inoculated at the same densities into sewage containing protozoa, the three slow-growing species were rapidly eliminated, and two of the three fast-growing species survived in detectable numbers. We suggest that in environments with intense protozoan predation, protozoa may alter the composition of the bacterial community by eliminating slow-growing bacteria.Key words: growth rate, predation, protozoa, sewage.